Starting phenix.real_space_refine on Tue Nov 19 11:26:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/11_2024/6si7_10206.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/11_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_10206/11_2024/6si7_10206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/11_2024/6si7_10206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/11_2024/6si7_10206.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/11_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.28, 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: 4.54 Conformation dependent library (CDL) restraints added in 2.6 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: 2.33 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: 6.36 Time building geometry restraints manager: 5.29 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: 7.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.440 Set scattering table: 0.000 Process input model: 37.660 Find NCS groups from input model: 0.610 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: