Starting phenix.real_space_refine on Sat Sep 28 12:36:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/09_2024/6si7_10206.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/09_2024/6si7_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/09_2024/6si7_10206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/09_2024/6si7_10206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/09_2024/6si7_10206.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/09_2024/6si7_10206.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: "K" 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: C, B, E, D, G, F, I, H, J, M, L, O, N, Q, P, R Time building chain proxies: 6.26, per 1000 atoms: 0.32 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: 4.79 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.21 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: 6.19 Time building geometry restraints manager: 5.59 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: 0.00 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 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 1.000 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 38.010 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.870 ------------------------------------------------------------------------------- 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= 0.291 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 : 12.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP J 77 HIS 0.001 0.000 HIS Q 26 PHE 0.012 0.002 PHE C 21 TYR 0.011 0.001 TYR O 143 ARG 0.003 0.000 ARG Q 83 *********************** 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 fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 2.282 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: 0.7913 (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: 0.7930 (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: 0.3410 time to fit residues: 262.3224 Evaluate side-chains 336 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.8980 chunk 184 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 0.1980 chunk 141 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 156 GLN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 ASN J 153 GLN J 156 GLN ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 11 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** O 88 ASN O 133 ASN O 156 GLN ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 GLN Q 133 ASN Q 153 GLN Q 156 GLN ** I 11 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: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19845 Z= 0.232 Angle : 0.577 8.713 26919 Z= 0.312 Chirality : 0.043 0.150 3024 Planarity : 0.005 0.060 3546 Dihedral : 5.241 21.679 2700 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.78 % Allowed : 13.84 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.15), residues: 2448 helix: -2.84 (0.13), residues: 702 sheet: -2.26 (0.21), residues: 594 loop : -1.82 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 77 HIS 0.001 0.000 HIS R 26 PHE 0.017 0.001 PHE K 191 TYR 0.023 0.001 TYR R 21 ARG 0.006 0.000 ARG J 142 *********************** 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 467 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 408 time to evaluate : 2.072 Fit side-chains REVERT: P 122 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7720 (ptt) REVERT: P 164 VAL cc_start: 0.8661 (t) cc_final: 0.8415 (t) REVERT: P 217 MET cc_start: 0.8041 (tpp) cc_final: 0.7511 (tpt) REVERT: J 35 PHE cc_start: 0.8563 (m-80) cc_final: 0.8309 (m-80) REVERT: J 42 GLN cc_start: 0.7944 (tp40) cc_final: 0.7692 (tt0) REVERT: J 82 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7315 (tm-30) REVERT: J 131 GLU cc_start: 0.6631 (tp30) cc_final: 0.6340 (tp30) REVERT: J 256 MET cc_start: 0.6602 (mtt) cc_final: 0.6327 (mtp) REVERT: K 42 GLN cc_start: 0.7931 (tp40) cc_final: 0.7724 (tt0) REVERT: K 131 GLU cc_start: 0.6651 (tp30) cc_final: 0.6403 (tp30) REVERT: K 183 SER cc_start: 0.8952 (m) cc_final: 0.8752 (p) REVERT: K 256 MET cc_start: 0.6652 (mtt) cc_final: 0.6325 (mtp) REVERT: D 29 GLN cc_start: 0.8893 (pt0) cc_final: 0.8652 (pt0) REVERT: D 33 LYS cc_start: 0.7894 (mppt) cc_final: 0.7657 (mmtm) REVERT: L 226 PHE cc_start: 0.8791 (m-10) cc_final: 0.8523 (m-10) REVERT: L 256 MET cc_start: 0.6497 (mtt) cc_final: 0.6208 (mtp) REVERT: E 32 TYR cc_start: 0.8311 (m-80) cc_final: 0.8045 (m-80) REVERT: M 217 MET cc_start: 0.7891 (tpp) cc_final: 0.7688 (tpp) REVERT: M 256 MET cc_start: 0.6622 (mtt) cc_final: 0.6310 (mtp) REVERT: N 33 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8441 (mtmt) REVERT: N 82 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7125 (tm-30) REVERT: N 143 TYR cc_start: 0.7823 (t80) cc_final: 0.7586 (t80) REVERT: N 256 MET cc_start: 0.6496 (mtt) cc_final: 0.6241 (mtp) REVERT: O 200 LEU cc_start: 0.7734 (tt) cc_final: 0.7345 (tp) REVERT: O 256 MET cc_start: 0.6636 (mtt) cc_final: 0.6327 (mtp) REVERT: H 29 GLN cc_start: 0.8490 (pt0) cc_final: 0.8122 (pt0) REVERT: Q 217 MET cc_start: 0.7967 (tpp) cc_final: 0.7469 (tpt) REVERT: Q 256 MET cc_start: 0.6738 (mtt) cc_final: 0.6486 (mtp) REVERT: R 82 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7138 (tm-30) REVERT: R 165 ASN cc_start: 0.7538 (t0) cc_final: 0.7325 (t0) REVERT: R 170 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7111 (mt-10) REVERT: R 200 LEU cc_start: 0.7793 (tt) cc_final: 0.7537 (tp) REVERT: R 217 MET cc_start: 0.8264 (tpt) cc_final: 0.7834 (tpt) REVERT: R 256 MET cc_start: 0.6675 (mtt) cc_final: 0.6348 (mtp) outliers start: 59 outliers final: 22 residues processed: 438 average time/residue: 0.3106 time to fit residues: 206.7380 Evaluate side-chains 359 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 336 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 122 MET 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 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 65 THR Chi-restraints excluded: chain M residue 69 VAL 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 122 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 221 optimal weight: 0.7980 chunk 238 optimal weight: 0.9990 chunk 196 optimal weight: 0.5980 chunk 219 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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 K 153 GLN K 247 ASN L 240 GLN L 247 ASN ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 GLN ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 19845 Z= 0.230 Angle : 0.553 7.856 26919 Z= 0.295 Chirality : 0.042 0.210 3024 Planarity : 0.005 0.054 3546 Dihedral : 4.978 19.953 2700 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.81 % Allowed : 16.01 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.15), residues: 2448 helix: -1.53 (0.16), residues: 702 sheet: -2.32 (0.20), residues: 594 loop : -1.41 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 77 HIS 0.001 0.000 HIS K 26 PHE 0.011 0.001 PHE J 144 TYR 0.019 0.001 TYR I 32 ARG 0.003 0.000 ARG L 17 *********************** 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 481 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 400 time to evaluate : 2.286 Fit side-chains revert: symmetry clash REVERT: P 164 VAL cc_start: 0.8723 (t) cc_final: 0.8452 (t) REVERT: P 217 MET cc_start: 0.7930 (tpp) cc_final: 0.7694 (tpt) REVERT: J 35 PHE cc_start: 0.8592 (m-80) cc_final: 0.8313 (m-80) REVERT: J 49 LYS cc_start: 0.9176 (mttm) cc_final: 0.8901 (mttp) REVERT: J 131 GLU cc_start: 0.6743 (tp30) cc_final: 0.6503 (tp30) REVERT: J 200 LEU cc_start: 0.8059 (tt) cc_final: 0.7671 (tp) REVERT: J 256 MET cc_start: 0.6725 (mtt) cc_final: 0.6403 (mtp) REVERT: K 82 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7182 (tm-30) REVERT: K 131 GLU cc_start: 0.6779 (tp30) cc_final: 0.6542 (tp30) REVERT: K 201 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6433 (pt0) REVERT: K 256 MET cc_start: 0.6683 (mtt) cc_final: 0.6354 (mtp) REVERT: D 33 LYS cc_start: 0.8025 (mppt) cc_final: 0.7778 (mmtm) REVERT: L 82 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7193 (tm-30) REVERT: L 200 LEU cc_start: 0.8073 (tt) cc_final: 0.7828 (tp) REVERT: L 226 PHE cc_start: 0.8771 (m-10) cc_final: 0.8540 (m-10) REVERT: L 256 MET cc_start: 0.6495 (mtt) cc_final: 0.6221 (mtp) REVERT: E 32 TYR cc_start: 0.8392 (m-80) cc_final: 0.8088 (m-80) REVERT: M 82 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7163 (tm-30) REVERT: M 170 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7137 (mt-10) REVERT: M 217 MET cc_start: 0.7950 (tpp) cc_final: 0.7335 (tpt) REVERT: M 256 MET cc_start: 0.6676 (mtt) cc_final: 0.6372 (mtp) REVERT: N 82 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7069 (tm-30) REVERT: N 143 TYR cc_start: 0.7985 (t80) cc_final: 0.7779 (t80) REVERT: N 217 MET cc_start: 0.7870 (tpp) cc_final: 0.7450 (tpt) REVERT: N 256 MET cc_start: 0.6513 (mtt) cc_final: 0.6307 (mtp) REVERT: O 82 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7153 (tm-30) REVERT: O 200 LEU cc_start: 0.8128 (tt) cc_final: 0.7855 (tp) REVERT: O 201 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6295 (pt0) REVERT: O 256 MET cc_start: 0.6727 (mtt) cc_final: 0.6435 (mtp) REVERT: H 29 GLN cc_start: 0.8551 (pt0) cc_final: 0.8275 (pt0) REVERT: Q 217 MET cc_start: 0.7950 (tpp) cc_final: 0.7115 (tpt) REVERT: Q 256 MET cc_start: 0.6722 (mtt) cc_final: 0.6402 (mtp) REVERT: R 82 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7206 (tm-30) REVERT: R 165 ASN cc_start: 0.7441 (t0) cc_final: 0.7173 (t0) REVERT: R 200 LEU cc_start: 0.8014 (tt) cc_final: 0.7604 (tp) REVERT: R 217 MET cc_start: 0.8309 (tpt) cc_final: 0.7790 (tpt) REVERT: R 256 MET cc_start: 0.6670 (mtt) cc_final: 0.6336 (mtp) outliers start: 81 outliers final: 44 residues processed: 442 average time/residue: 0.3207 time to fit residues: 213.2249 Evaluate side-chains 403 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 357 time to evaluate : 2.165 ------------------------------------------------------------------------------- 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 114 GLN Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 153 GLN Chi-restraints excluded: chain P residue 183 SER 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 117 THR Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain K residue 201 GLU 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 114 GLN 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 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 177 THR 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 218 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** ** 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** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 240 GLN H 6 GLN ** H 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19845 Z= 0.254 Angle : 0.545 8.376 26919 Z= 0.290 Chirality : 0.042 0.169 3024 Planarity : 0.005 0.054 3546 Dihedral : 4.885 20.276 2700 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.24 % Allowed : 16.81 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.16), residues: 2448 helix: -0.93 (0.17), residues: 747 sheet: -2.41 (0.19), residues: 594 loop : -1.32 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 237 HIS 0.001 0.000 HIS N 26 PHE 0.024 0.002 PHE M 191 TYR 0.019 0.001 TYR H 32 ARG 0.004 0.000 ARG J 142 *********************** 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 485 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 395 time to evaluate : 2.215 Fit side-chains revert: symmetry clash REVERT: P 124 GLU cc_start: 0.7341 (tp30) cc_final: 0.7049 (tp30) REVERT: P 164 VAL cc_start: 0.8731 (t) cc_final: 0.8497 (t) REVERT: P 217 MET cc_start: 0.7952 (tpp) cc_final: 0.7153 (tpt) REVERT: B 2 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7749 (m) REVERT: J 35 PHE cc_start: 0.8594 (m-80) cc_final: 0.8298 (m-80) REVERT: J 49 LYS cc_start: 0.9174 (mttm) cc_final: 0.8930 (mttp) REVERT: J 200 LEU cc_start: 0.8222 (tt) cc_final: 0.7929 (tp) REVERT: J 256 MET cc_start: 0.6744 (mtt) cc_final: 0.6426 (mtp) REVERT: K 35 PHE cc_start: 0.8549 (m-80) cc_final: 0.8316 (m-80) REVERT: K 256 MET cc_start: 0.6728 (mtt) cc_final: 0.6399 (mtp) REVERT: D 33 LYS cc_start: 0.8024 (mppt) cc_final: 0.7793 (mmtm) REVERT: L 82 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7115 (tm-30) REVERT: L 256 MET cc_start: 0.6668 (mtt) cc_final: 0.6356 (mtp) REVERT: E 32 TYR cc_start: 0.8418 (m-80) cc_final: 0.8078 (m-80) REVERT: M 82 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7179 (tm-30) REVERT: M 131 GLU cc_start: 0.6951 (tp30) cc_final: 0.6739 (tp30) REVERT: M 217 MET cc_start: 0.7866 (tpp) cc_final: 0.7233 (tpt) REVERT: M 256 MET cc_start: 0.6752 (mtt) cc_final: 0.6435 (mtp) REVERT: N 82 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7077 (tm-30) REVERT: N 210 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7624 (tt0) REVERT: N 217 MET cc_start: 0.7829 (tpp) cc_final: 0.7151 (tpt) REVERT: N 256 MET cc_start: 0.6625 (mtt) cc_final: 0.6384 (mtp) REVERT: G 29 GLN cc_start: 0.9131 (pt0) cc_final: 0.8707 (pt0) REVERT: O 82 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7115 (tm-30) REVERT: O 256 MET cc_start: 0.6758 (mtt) cc_final: 0.6436 (mtp) REVERT: H 29 GLN cc_start: 0.8483 (pt0) cc_final: 0.8278 (pt0) REVERT: Q 124 GLU cc_start: 0.7112 (tp30) cc_final: 0.6839 (tp30) REVERT: Q 256 MET cc_start: 0.6790 (mtt) cc_final: 0.6474 (mtp) REVERT: R 200 LEU cc_start: 0.8211 (tt) cc_final: 0.7962 (tp) REVERT: R 217 MET cc_start: 0.8270 (tpt) cc_final: 0.7920 (tpt) REVERT: R 234 ARG cc_start: 0.6441 (tpp80) cc_final: 0.6230 (tpp80) REVERT: R 256 MET cc_start: 0.6587 (mtt) cc_final: 0.6221 (mtp) outliers start: 90 outliers final: 60 residues processed: 448 average time/residue: 0.3342 time to fit residues: 221.9748 Evaluate side-chains 430 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 369 time to evaluate : 2.035 ------------------------------------------------------------------------------- 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 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 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 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 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 126 SER Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain E residue 3 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 190 VAL Chi-restraints excluded: chain F residue 6 GLN 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 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 153 GLN 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 69 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 200 optimal weight: 0.4980 chunk 162 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 210 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 B 9 ASN B 11 ASN B 27 GLN ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN H 6 GLN H 27 GLN ** R 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19845 Z= 0.299 Angle : 0.569 8.390 26919 Z= 0.301 Chirality : 0.042 0.200 3024 Planarity : 0.005 0.054 3546 Dihedral : 4.910 19.806 2700 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.38 % Allowed : 18.08 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.16), residues: 2448 helix: -0.59 (0.18), residues: 747 sheet: -2.45 (0.18), residues: 594 loop : -1.18 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 237 HIS 0.001 0.000 HIS K 26 PHE 0.026 0.002 PHE N 191 TYR 0.020 0.001 TYR H 32 ARG 0.006 0.000 ARG N 142 *********************** 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 513 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 420 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 210 GLU cc_start: 0.8050 (tt0) cc_final: 0.7766 (tt0) REVERT: B 33 LYS cc_start: 0.7971 (mppt) cc_final: 0.7691 (mmtm) REVERT: J 35 PHE cc_start: 0.8636 (m-80) cc_final: 0.8371 (m-80) REVERT: J 49 LYS cc_start: 0.9186 (mttm) cc_final: 0.8916 (mttp) REVERT: J 143 TYR cc_start: 0.7515 (t80) cc_final: 0.7309 (t80) REVERT: J 170 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6930 (mt-10) REVERT: J 256 MET cc_start: 0.6809 (mtt) cc_final: 0.6455 (mtp) REVERT: K 82 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7322 (tm-30) REVERT: K 256 MET cc_start: 0.6890 (mtt) cc_final: 0.6540 (mtp) REVERT: L 256 MET cc_start: 0.6644 (mtt) cc_final: 0.6319 (mtp) REVERT: E 32 TYR cc_start: 0.8421 (m-80) cc_final: 0.8032 (m-80) REVERT: M 67 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8046 (mtp) REVERT: M 82 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7219 (tm-30) REVERT: M 256 MET cc_start: 0.6700 (mtt) cc_final: 0.6407 (mtp) REVERT: N 82 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7099 (tm-30) REVERT: N 210 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7611 (tt0) REVERT: N 256 MET cc_start: 0.6779 (mtt) cc_final: 0.6505 (mtp) REVERT: O 82 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7197 (tm-30) REVERT: O 144 PHE cc_start: 0.8167 (t80) cc_final: 0.7916 (t80) REVERT: O 256 MET cc_start: 0.6808 (mtt) cc_final: 0.6490 (mtp) REVERT: Q 124 GLU cc_start: 0.7096 (tp30) cc_final: 0.6808 (tp30) REVERT: Q 127 ILE cc_start: 0.8890 (mt) cc_final: 0.8687 (mt) REVERT: Q 199 LEU cc_start: 0.8456 (tt) cc_final: 0.8234 (tt) REVERT: Q 201 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6514 (pt0) REVERT: Q 217 MET cc_start: 0.8334 (tpt) cc_final: 0.8085 (tpt) REVERT: Q 256 MET cc_start: 0.6817 (mtt) cc_final: 0.6455 (mtp) REVERT: I 8 ARG cc_start: 0.7806 (mpt-90) cc_final: 0.7572 (mpt-90) REVERT: R 170 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7256 (mt-10) REVERT: R 200 LEU cc_start: 0.8427 (tt) cc_final: 0.8208 (tp) REVERT: R 201 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6368 (pt0) REVERT: R 217 MET cc_start: 0.8286 (tpt) cc_final: 0.7909 (tpt) REVERT: R 256 MET cc_start: 0.6728 (mtt) cc_final: 0.6298 (mtp) outliers start: 93 outliers final: 71 residues processed: 473 average time/residue: 0.3268 time to fit residues: 228.3503 Evaluate side-chains 458 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 384 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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 190 VAL Chi-restraints excluded: chain P residue 200 LEU 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 139 VAL 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 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 139 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 65 THR Chi-restraints excluded: chain M residue 67 MET Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 117 THR 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 F residue 6 GLN 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 139 VAL Chi-restraints excluded: chain N residue 183 SER 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 213 MET Chi-restraints excluded: chain Q residue 34 ILE 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 Q residue 201 GLU 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 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 79 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 235 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 ASN ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN H 6 GLN ** R 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19845 Z= 0.244 Angle : 0.554 7.145 26919 Z= 0.295 Chirality : 0.042 0.170 3024 Planarity : 0.005 0.053 3546 Dihedral : 4.908 18.732 2700 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.43 % Allowed : 20.01 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.17), residues: 2448 helix: -0.36 (0.18), residues: 747 sheet: -2.42 (0.19), residues: 594 loop : -1.11 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 237 HIS 0.001 0.000 HIS N 26 PHE 0.025 0.002 PHE L 191 TYR 0.020 0.001 TYR H 32 ARG 0.005 0.000 ARG O 142 *********************** 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 495 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 401 time to evaluate : 2.185 Fit side-chains revert: symmetry clash REVERT: P 17 ARG cc_start: 0.7403 (mmm-85) cc_final: 0.7146 (mmt-90) REVERT: P 164 VAL cc_start: 0.8734 (t) cc_final: 0.8517 (t) REVERT: P 210 GLU cc_start: 0.8063 (tt0) cc_final: 0.7823 (tt0) REVERT: P 217 MET cc_start: 0.8301 (tpt) cc_final: 0.8090 (tpt) REVERT: B 33 LYS cc_start: 0.7955 (mppt) cc_final: 0.7705 (mmtm) REVERT: J 35 PHE cc_start: 0.8606 (m-80) cc_final: 0.8344 (m-80) REVERT: J 49 LYS cc_start: 0.9182 (mttm) cc_final: 0.8935 (mttp) REVERT: J 170 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6812 (mt-10) REVERT: J 200 LEU cc_start: 0.8441 (tt) cc_final: 0.8027 (tp) REVERT: J 256 MET cc_start: 0.6814 (mtt) cc_final: 0.6461 (mtp) REVERT: K 82 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7269 (tm-30) REVERT: K 256 MET cc_start: 0.6899 (mtt) cc_final: 0.6533 (mtp) REVERT: L 256 MET cc_start: 0.6770 (mtt) cc_final: 0.6468 (mtp) REVERT: E 29 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8537 (pt0) REVERT: E 32 TYR cc_start: 0.8393 (m-80) cc_final: 0.8122 (m-80) REVERT: M 256 MET cc_start: 0.6742 (mtt) cc_final: 0.6472 (mtp) REVERT: N 82 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7091 (tm-30) REVERT: N 217 MET cc_start: 0.8315 (tpt) cc_final: 0.8069 (tpt) REVERT: N 256 MET cc_start: 0.6774 (mtt) cc_final: 0.6509 (mtp) REVERT: G 29 GLN cc_start: 0.9166 (pt0) cc_final: 0.8851 (pt0) REVERT: O 256 MET cc_start: 0.6795 (mtt) cc_final: 0.6450 (mtp) REVERT: Q 124 GLU cc_start: 0.7087 (tp30) cc_final: 0.6793 (tp30) REVERT: Q 217 MET cc_start: 0.8313 (tpt) cc_final: 0.7945 (tpt) REVERT: Q 256 MET cc_start: 0.6831 (mtt) cc_final: 0.6475 (mtp) REVERT: R 62 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7718 (mm110) REVERT: R 170 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7183 (mt-10) REVERT: R 200 LEU cc_start: 0.8314 (tt) cc_final: 0.8020 (tp) REVERT: R 217 MET cc_start: 0.8246 (tpt) cc_final: 0.7816 (tpt) REVERT: R 256 MET cc_start: 0.6718 (mtt) cc_final: 0.6306 (mtp) outliers start: 94 outliers final: 71 residues processed: 450 average time/residue: 0.3364 time to fit residues: 223.3518 Evaluate side-chains 446 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 373 time to evaluate : 2.341 ------------------------------------------------------------------------------- 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 126 SER 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 200 LEU 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 132 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain C residue 6 GLN 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 190 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 177 THR 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 E residue 29 GLN 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 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 139 VAL Chi-restraints excluded: chain N residue 183 SER 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 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 I residue 3 MET 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 183 SER Chi-restraints excluded: chain R residue 190 VAL 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 226 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 142 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 160 ASN ** J 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19845 Z= 0.239 Angle : 0.562 11.214 26919 Z= 0.298 Chirality : 0.043 0.242 3024 Planarity : 0.005 0.054 3546 Dihedral : 4.902 18.788 2700 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.47 % Allowed : 20.15 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.17), residues: 2448 helix: -0.18 (0.19), residues: 729 sheet: -2.40 (0.19), residues: 594 loop : -1.00 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 237 HIS 0.001 0.000 HIS K 26 PHE 0.036 0.002 PHE O 144 TYR 0.022 0.001 TYR H 32 ARG 0.007 0.000 ARG Q 142 *********************** 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 494 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 399 time to evaluate : 2.220 Fit side-chains revert: symmetry clash REVERT: P 17 ARG cc_start: 0.7437 (mmm-85) cc_final: 0.7214 (mmt-90) REVERT: P 164 VAL cc_start: 0.8739 (t) cc_final: 0.8526 (t) REVERT: P 210 GLU cc_start: 0.8016 (tt0) cc_final: 0.7736 (tt0) REVERT: P 217 MET cc_start: 0.8259 (tpt) cc_final: 0.7960 (tpt) REVERT: B 33 LYS cc_start: 0.7948 (mppt) cc_final: 0.7710 (mmtm) REVERT: J 35 PHE cc_start: 0.8612 (m-80) cc_final: 0.8352 (m-80) REVERT: J 49 LYS cc_start: 0.9190 (mttm) cc_final: 0.8953 (mttp) REVERT: J 200 LEU cc_start: 0.8545 (tt) cc_final: 0.8115 (tp) REVERT: J 256 MET cc_start: 0.6826 (mtt) cc_final: 0.6472 (mtp) REVERT: K 82 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7252 (tm-30) REVERT: K 256 MET cc_start: 0.6881 (mtt) cc_final: 0.6532 (mtp) REVERT: L 256 MET cc_start: 0.6818 (mtt) cc_final: 0.6548 (mtp) REVERT: E 32 TYR cc_start: 0.8386 (m-80) cc_final: 0.8174 (m-80) REVERT: M 67 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8226 (mtp) REVERT: M 82 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7192 (tm-30) REVERT: M 256 MET cc_start: 0.6764 (mtt) cc_final: 0.6470 (mtp) REVERT: N 82 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7097 (tm-30) REVERT: N 217 MET cc_start: 0.8232 (tpt) cc_final: 0.7927 (tpt) REVERT: N 256 MET cc_start: 0.6765 (mtt) cc_final: 0.6501 (mtp) REVERT: G 29 GLN cc_start: 0.9181 (pt0) cc_final: 0.8754 (pt0) REVERT: O 201 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6431 (pt0) REVERT: O 256 MET cc_start: 0.6832 (mtt) cc_final: 0.6493 (mtp) REVERT: Q 124 GLU cc_start: 0.7109 (tp30) cc_final: 0.6792 (tp30) REVERT: Q 217 MET cc_start: 0.8327 (tpt) cc_final: 0.7780 (tpt) REVERT: Q 256 MET cc_start: 0.6832 (mtt) cc_final: 0.6504 (mtp) REVERT: R 170 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7137 (mt-10) REVERT: R 200 LEU cc_start: 0.8496 (tt) cc_final: 0.8264 (tp) REVERT: R 256 MET cc_start: 0.6703 (mtt) cc_final: 0.6288 (mtp) outliers start: 95 outliers final: 74 residues processed: 450 average time/residue: 0.3569 time to fit residues: 235.1630 Evaluate side-chains 461 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 385 time to evaluate : 2.145 ------------------------------------------------------------------------------- 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 126 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 139 VAL 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 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 C residue 6 GLN 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 190 VAL Chi-restraints excluded: chain L residue 36 VAL 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 177 THR 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 65 THR Chi-restraints excluded: chain M residue 67 MET 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 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 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 132 SER Chi-restraints excluded: chain O residue 183 SER 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 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 Chi-restraints excluded: chain R residue 207 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 115 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN K 156 GLN M 62 GLN G 24 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19845 Z= 0.266 Angle : 0.578 9.993 26919 Z= 0.306 Chirality : 0.043 0.225 3024 Planarity : 0.005 0.057 3546 Dihedral : 4.977 19.146 2700 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.57 % Allowed : 20.72 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.17), residues: 2448 helix: -0.07 (0.19), residues: 729 sheet: -2.39 (0.19), residues: 594 loop : -0.94 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 77 HIS 0.001 0.000 HIS R 26 PHE 0.032 0.002 PHE O 144 TYR 0.023 0.001 TYR H 32 ARG 0.005 0.000 ARG M 17 *********************** 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 500 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 403 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 17 ARG cc_start: 0.7481 (mmm-85) cc_final: 0.7250 (mmt-90) REVERT: P 67 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7936 (ttm) REVERT: P 124 GLU cc_start: 0.7355 (tp30) cc_final: 0.7015 (tp30) REVERT: P 164 VAL cc_start: 0.8760 (t) cc_final: 0.8544 (t) REVERT: P 210 GLU cc_start: 0.8034 (tt0) cc_final: 0.7733 (tt0) REVERT: P 217 MET cc_start: 0.8278 (tpt) cc_final: 0.7773 (tpt) REVERT: B 33 LYS cc_start: 0.7960 (mppt) cc_final: 0.7727 (mmtm) REVERT: J 35 PHE cc_start: 0.8653 (m-80) cc_final: 0.8404 (m-80) REVERT: J 49 LYS cc_start: 0.9164 (mttm) cc_final: 0.8921 (mttp) REVERT: J 256 MET cc_start: 0.6861 (mtt) cc_final: 0.6491 (mtp) REVERT: K 82 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7222 (tm-30) REVERT: K 256 MET cc_start: 0.6968 (mtt) cc_final: 0.6623 (mtp) REVERT: L 256 MET cc_start: 0.6860 (mtt) cc_final: 0.6578 (mtp) REVERT: E 32 TYR cc_start: 0.8396 (m-80) cc_final: 0.8195 (m-80) REVERT: M 67 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8227 (mtp) REVERT: M 256 MET cc_start: 0.6767 (mtt) cc_final: 0.6482 (mtp) REVERT: N 82 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7116 (tm-30) REVERT: N 217 MET cc_start: 0.8105 (tpt) cc_final: 0.7791 (tpt) REVERT: N 256 MET cc_start: 0.6725 (mtt) cc_final: 0.6402 (mtp) REVERT: O 256 MET cc_start: 0.6857 (mtt) cc_final: 0.6509 (mtp) REVERT: H 6 GLN cc_start: 0.7131 (mp10) cc_final: 0.6927 (mp10) REVERT: Q 124 GLU cc_start: 0.7205 (tp30) cc_final: 0.6863 (tp30) REVERT: Q 217 MET cc_start: 0.8321 (tpt) cc_final: 0.7774 (tpt) REVERT: Q 256 MET cc_start: 0.6847 (mtt) cc_final: 0.6513 (mtp) REVERT: R 170 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7144 (mt-10) REVERT: R 185 GLU cc_start: 0.7372 (tt0) cc_final: 0.7169 (tt0) REVERT: R 187 GLN cc_start: 0.7643 (mt0) cc_final: 0.7426 (mt0) REVERT: R 217 MET cc_start: 0.7437 (mmm) cc_final: 0.7113 (tpp) REVERT: R 256 MET cc_start: 0.6701 (mtt) cc_final: 0.6280 (mtp) outliers start: 97 outliers final: 82 residues processed: 455 average time/residue: 0.3422 time to fit residues: 229.5601 Evaluate side-chains 466 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 382 time to evaluate : 2.189 ------------------------------------------------------------------------------- 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 67 MET 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 126 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 139 VAL 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 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 C residue 6 GLN 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 190 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 132 SER 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 207 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 67 MET 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 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 183 SER 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 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 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 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 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 157 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.6980 chunk 204 optimal weight: 4.9990 chunk 218 optimal weight: 0.7980 chunk 131 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 217 optimal weight: 0.4980 chunk 143 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN K 160 ASN E 29 GLN M 62 GLN G 24 ASN ** H 6 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3890 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= 0.231 Angle : 0.578 10.978 26919 Z= 0.304 Chirality : 0.043 0.306 3024 Planarity : 0.005 0.056 3546 Dihedral : 4.953 18.904 2700 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.28 % Allowed : 21.19 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.17), residues: 2448 helix: -0.04 (0.19), residues: 729 sheet: -2.36 (0.19), residues: 594 loop : -0.95 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 237 HIS 0.001 0.000 HIS P 255 PHE 0.028 0.001 PHE O 144 TYR 0.022 0.001 TYR H 32 ARG 0.008 0.000 ARG N 17 *********************** 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 488 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 397 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 67 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7835 (ttm) REVERT: P 124 GLU cc_start: 0.7324 (tp30) cc_final: 0.7003 (tp30) REVERT: P 217 MET cc_start: 0.8263 (tpt) cc_final: 0.7722 (tpt) REVERT: B 33 LYS cc_start: 0.7923 (mppt) cc_final: 0.7677 (mmtm) REVERT: J 35 PHE cc_start: 0.8607 (m-80) cc_final: 0.8392 (m-80) REVERT: J 49 LYS cc_start: 0.9152 (mttm) cc_final: 0.8915 (mttp) REVERT: J 217 MET cc_start: 0.8202 (tpt) cc_final: 0.7842 (tpt) REVERT: J 256 MET cc_start: 0.6843 (mtt) cc_final: 0.6492 (mtp) REVERT: C 8 ARG cc_start: 0.7590 (mpt-90) cc_final: 0.6829 (mpt-90) REVERT: K 82 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7248 (tm-30) REVERT: K 142 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7549 (ttt180) REVERT: K 256 MET cc_start: 0.6956 (mtt) cc_final: 0.6607 (mtp) REVERT: L 142 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7509 (ttm-80) REVERT: L 256 MET cc_start: 0.6849 (mtt) cc_final: 0.6578 (mtp) REVERT: M 256 MET cc_start: 0.6762 (mtt) cc_final: 0.6469 (mtp) REVERT: F 8 ARG cc_start: 0.7656 (mpt-90) cc_final: 0.6759 (mpt-90) REVERT: N 67 MET cc_start: 0.8268 (ttm) cc_final: 0.7641 (ttm) REVERT: N 82 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7064 (tm-30) REVERT: N 217 MET cc_start: 0.8111 (tpt) cc_final: 0.7531 (tpt) REVERT: N 256 MET cc_start: 0.6707 (mtt) cc_final: 0.6458 (mtp) REVERT: G 29 GLN cc_start: 0.9181 (pt0) cc_final: 0.8719 (pt0) REVERT: O 256 MET cc_start: 0.6839 (mtt) cc_final: 0.6517 (mtp) REVERT: Q 124 GLU cc_start: 0.7183 (tp30) cc_final: 0.6853 (tp30) REVERT: Q 256 MET cc_start: 0.6948 (mtt) cc_final: 0.6638 (mtp) REVERT: I 32 TYR cc_start: 0.8356 (m-80) cc_final: 0.8101 (m-80) REVERT: R 170 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7049 (mt-10) REVERT: R 200 LEU cc_start: 0.8635 (tt) cc_final: 0.8300 (tp) REVERT: R 217 MET cc_start: 0.7460 (mmm) cc_final: 0.7128 (tpp) REVERT: R 256 MET cc_start: 0.6685 (mtt) cc_final: 0.6269 (mtp) outliers start: 91 outliers final: 83 residues processed: 450 average time/residue: 0.3505 time to fit residues: 234.4807 Evaluate side-chains 468 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 384 time to evaluate : 2.125 ------------------------------------------------------------------------------- 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 67 MET 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 126 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 139 VAL 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 J residue 204 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 6 GLN 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 190 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 139 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 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 117 THR 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 70 THR 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 183 SER 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 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 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 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 157 ILE 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 230 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 242 optimal weight: 8.9990 chunk 222 optimal weight: 0.0670 chunk 192 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 GLN Q 156 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19845 Z= 0.222 Angle : 0.584 9.349 26919 Z= 0.306 Chirality : 0.043 0.316 3024 Planarity : 0.005 0.058 3546 Dihedral : 4.976 18.455 2700 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.10 % Allowed : 21.33 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.17), residues: 2448 helix: -0.00 (0.19), residues: 729 sheet: -2.35 (0.19), residues: 594 loop : -0.94 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 237 HIS 0.001 0.000 HIS P 26 PHE 0.027 0.001 PHE O 144 TYR 0.022 0.001 TYR H 32 ARG 0.006 0.000 ARG I 8 ********************** 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 fitting. rotamer outliers: 87 poor density : 394 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 67 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7687 (ttm) REVERT: P 124 GLU cc_start: 0.7293 (tp30) cc_final: 0.6910 (tp30) REVERT: P 217 MET cc_start: 0.8143 (tpt) cc_final: 0.6938 (tpt) REVERT: B 33 LYS cc_start: 0.7865 (mppt) cc_final: 0.7632 (mmtm) REVERT: J 49 LYS cc_start: 0.9126 (mttm) cc_final: 0.8900 (mttp) REVERT: J 217 MET cc_start: 0.8234 (tpt) cc_final: 0.7840 (tpt) REVERT: J 256 MET cc_start: 0.6866 (mtt) cc_final: 0.6523 (mtp) REVERT: K 82 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7230 (tm-30) REVERT: K 185 GLU cc_start: 0.7150 (pt0) cc_final: 0.6942 (tt0) REVERT: K 256 MET cc_start: 0.6943 (mtt) cc_final: 0.6605 (mtp) REVERT: L 142 ARG cc_start: 0.7651 (ttm-80) cc_final: 0.7398 (ttt180) REVERT: L 256 MET cc_start: 0.6853 (mtt) cc_final: 0.6575 (mtp) REVERT: M 170 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7264 (mt-10) REVERT: M 256 MET cc_start: 0.6731 (mtt) cc_final: 0.6435 (mtp) REVERT: F 8 ARG cc_start: 0.7629 (mpt-90) cc_final: 0.6761 (mpt-90) REVERT: N 67 MET cc_start: 0.8210 (ttm) cc_final: 0.7533 (ttm) REVERT: N 82 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7056 (tm-30) REVERT: N 124 GLU cc_start: 0.7252 (tp30) cc_final: 0.6906 (tp30) REVERT: N 217 MET cc_start: 0.8060 (tpt) cc_final: 0.7501 (tpt) REVERT: N 256 MET cc_start: 0.6726 (mtt) cc_final: 0.6490 (mtp) REVERT: G 29 GLN cc_start: 0.9172 (pt0) cc_final: 0.8674 (pt0) REVERT: O 43 ASP cc_start: 0.8531 (t0) cc_final: 0.8329 (t0) REVERT: O 217 MET cc_start: 0.8234 (tpt) cc_final: 0.7594 (tpt) REVERT: O 256 MET cc_start: 0.6798 (mtt) cc_final: 0.6504 (mtp) REVERT: Q 124 GLU cc_start: 0.7171 (tp30) cc_final: 0.6840 (tp30) REVERT: Q 256 MET cc_start: 0.6966 (mtt) cc_final: 0.6668 (mtp) REVERT: I 8 ARG cc_start: 0.7533 (mpt-90) cc_final: 0.7171 (mpt-90) REVERT: R 200 LEU cc_start: 0.8654 (tt) cc_final: 0.8190 (tp) REVERT: R 217 MET cc_start: 0.7434 (mmm) cc_final: 0.7153 (tpp) REVERT: R 256 MET cc_start: 0.6667 (mtt) cc_final: 0.6260 (mtp) outliers start: 87 outliers final: 80 residues processed: 449 average time/residue: 0.3335 time to fit residues: 223.6923 Evaluate side-chains 457 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 376 time to evaluate : 2.094 ------------------------------------------------------------------------------- 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 67 MET 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 139 VAL 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 J residue 204 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 6 GLN 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 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 139 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 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 70 THR 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 183 SER 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 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 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 157 ILE 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 205 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 177 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 0.0020 chunk 80 optimal weight: 4.9990 chunk 198 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 169 optimal weight: 0.0570 overall best weight: 0.3906 ------------------------------------------------------------------------------- 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** P 62 GLN P 156 GLN ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN F 29 GLN N 55 ASN G 24 ASN O 62 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.161204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.140878 restraints weight = 25284.860| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.69 r_work: 0.3509 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19845 Z= 0.195 Angle : 0.582 10.064 26919 Z= 0.304 Chirality : 0.043 0.263 3024 Planarity : 0.005 0.058 3546 Dihedral : 4.950 18.484 2700 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.53 % Allowed : 22.03 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2448 helix: 0.13 (0.19), residues: 720 sheet: -2.28 (0.20), residues: 594 loop : -0.88 (0.20), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 237 HIS 0.000 0.000 HIS P 26 PHE 0.025 0.001 PHE O 144 TYR 0.024 0.001 TYR H 32 ARG 0.006 0.000 ARG R 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4912.87 seconds wall clock time: 88 minutes 15.79 seconds (5295.79 seconds total)