Starting phenix.real_space_refine on Sun Jan 26 11:54:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e4x_30988/01_2025/7e4x_30988.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e4x_30988/01_2025/7e4x_30988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e4x_30988/01_2025/7e4x_30988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e4x_30988/01_2025/7e4x_30988.map" model { file = "/net/cci-nas-00/data/ceres_data/7e4x_30988/01_2025/7e4x_30988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e4x_30988/01_2025/7e4x_30988.cif" } resolution = 3.08 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= 0.000 sd= 0.007 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 56 5.16 5 C 15584 2.51 5 N 4320 2.21 5 O 4976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24936 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "B" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "C" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "D" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "E" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "F" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "G" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "H" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Time building chain proxies: 14.63, per 1000 atoms: 0.59 Number of scatterers: 24936 At special positions: 0 Unit cell: (159.43, 160.5, 71.69, 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 56 16.00 O 4976 8.00 N 4320 7.00 C 15584 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: 6.83 Conformation dependent library (CDL) restraints added in 3.3 seconds 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 38 sheets defined 46.5% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 63 through 73 Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 85 through 98 Processing helix chain 'A' and resid 108 through 124 removed outlier: 3.984A pdb=" N VAL A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 135 removed outlier: 3.504A pdb=" N VAL A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 134 " --> pdb=" O PHE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 194 removed outlier: 3.847A pdb=" N SER A 190 " --> pdb=" O HIS A 186 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 removed outlier: 4.039A pdb=" N ALA A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.637A pdb=" N GLY A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 301 removed outlier: 3.940A pdb=" N ALA A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 326 removed outlier: 3.725A pdb=" N GLU A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.700A pdb=" N ILE A 339 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 354 Processing helix chain 'A' and resid 371 through 380 removed outlier: 3.902A pdb=" N ASP A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 410 removed outlier: 4.006A pdb=" N TYR A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.507A pdb=" N GLY B 59 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 73 Processing helix chain 'B' and resid 73 through 79 Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 108 through 122 removed outlier: 3.904A pdb=" N VAL B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 removed outlier: 3.627A pdb=" N VAL B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 195 removed outlier: 3.529A pdb=" N LYS B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 229 removed outlier: 3.539A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 246 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 290 through 302 Processing helix chain 'B' and resid 316 through 326 removed outlier: 3.725A pdb=" N GLU B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.693A pdb=" N ILE B 339 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 354 Processing helix chain 'B' and resid 371 through 380 removed outlier: 3.895A pdb=" N ASP B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 410 removed outlier: 3.967A pdb=" N TYR B 399 " --> pdb=" O ARG B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 85 through 98 removed outlier: 3.630A pdb=" N GLN C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 124 Processing helix chain 'C' and resid 128 through 135 Processing helix chain 'C' and resid 173 through 194 removed outlier: 3.608A pdb=" N SER C 190 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 229 removed outlier: 3.597A pdb=" N GLY C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 removed outlier: 3.651A pdb=" N PHE C 248 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.624A pdb=" N ALA C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 302 Processing helix chain 'C' and resid 316 through 326 removed outlier: 3.905A pdb=" N GLU C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.875A pdb=" N ILE C 339 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 371 through 380 removed outlier: 3.937A pdb=" N ASP C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 410 removed outlier: 3.845A pdb=" N TYR C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 413 No H-bonds generated for 'chain 'C' and resid 411 through 413' Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.530A pdb=" N GLY D 59 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 73 through 79 Processing helix chain 'D' and resid 85 through 98 Processing helix chain 'D' and resid 106 through 125 Processing helix chain 'D' and resid 128 through 135 Processing helix chain 'D' and resid 173 through 195 Processing helix chain 'D' and resid 213 through 229 removed outlier: 3.724A pdb=" N GLY D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 246 Processing helix chain 'D' and resid 262 through 277 Processing helix chain 'D' and resid 290 through 302 Processing helix chain 'D' and resid 316 through 326 removed outlier: 3.786A pdb=" N GLU D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.679A pdb=" N ILE D 339 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 354 Processing helix chain 'D' and resid 371 through 380 removed outlier: 3.945A pdb=" N ASP D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 410 removed outlier: 3.890A pdb=" N TYR D 399 " --> pdb=" O ARG D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 413 No H-bonds generated for 'chain 'D' and resid 411 through 413' Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 73 through 79 Processing helix chain 'E' and resid 85 through 98 Processing helix chain 'E' and resid 106 through 125 Processing helix chain 'E' and resid 128 through 135 Processing helix chain 'E' and resid 173 through 195 removed outlier: 3.542A pdb=" N GLU E 195 " --> pdb=" O VAL E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 229 removed outlier: 3.722A pdb=" N GLY E 229 " --> pdb=" O ILE E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 246 Processing helix chain 'E' and resid 262 through 277 Processing helix chain 'E' and resid 290 through 302 Processing helix chain 'E' and resid 316 through 326 removed outlier: 3.786A pdb=" N GLU E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG E 326 " --> pdb=" O GLU E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.657A pdb=" N ILE E 339 " --> pdb=" O VAL E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 354 Processing helix chain 'E' and resid 371 through 380 removed outlier: 3.917A pdb=" N ASP E 375 " --> pdb=" O THR E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 410 removed outlier: 3.882A pdb=" N TYR E 399 " --> pdb=" O ARG E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 413 No H-bonds generated for 'chain 'E' and resid 411 through 413' Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 63 through 73 Processing helix chain 'F' and resid 73 through 79 Processing helix chain 'F' and resid 85 through 98 Processing helix chain 'F' and resid 106 through 125 Processing helix chain 'F' and resid 128 through 135 Processing helix chain 'F' and resid 173 through 195 Processing helix chain 'F' and resid 213 through 229 removed outlier: 3.696A pdb=" N GLY F 229 " --> pdb=" O ILE F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 246 Processing helix chain 'F' and resid 262 through 277 Processing helix chain 'F' and resid 290 through 302 Processing helix chain 'F' and resid 316 through 326 removed outlier: 3.809A pdb=" N GLU F 322 " --> pdb=" O GLU F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.660A pdb=" N ILE F 339 " --> pdb=" O VAL F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 354 Processing helix chain 'F' and resid 371 through 380 removed outlier: 3.929A pdb=" N ASP F 375 " --> pdb=" O THR F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 410 removed outlier: 3.883A pdb=" N TYR F 399 " --> pdb=" O ARG F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 413 No H-bonds generated for 'chain 'F' and resid 411 through 413' Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 63 through 73 Processing helix chain 'G' and resid 73 through 79 Processing helix chain 'G' and resid 85 through 98 Processing helix chain 'G' and resid 106 through 125 Processing helix chain 'G' and resid 128 through 135 Processing helix chain 'G' and resid 173 through 195 Processing helix chain 'G' and resid 213 through 229 removed outlier: 3.714A pdb=" N GLY G 229 " --> pdb=" O ILE G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 246 Processing helix chain 'G' and resid 262 through 277 Processing helix chain 'G' and resid 290 through 302 Processing helix chain 'G' and resid 316 through 326 removed outlier: 4.014A pdb=" N GLU G 322 " --> pdb=" O GLU G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 339 removed outlier: 3.664A pdb=" N ILE G 339 " --> pdb=" O VAL G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 354 Processing helix chain 'G' and resid 371 through 380 removed outlier: 3.927A pdb=" N ASP G 375 " --> pdb=" O THR G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 410 removed outlier: 3.891A pdb=" N TYR G 399 " --> pdb=" O ARG G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 413 No H-bonds generated for 'chain 'G' and resid 411 through 413' Processing helix chain 'H' and resid 56 through 61 Processing helix chain 'H' and resid 63 through 73 Processing helix chain 'H' and resid 73 through 79 Processing helix chain 'H' and resid 85 through 98 Processing helix chain 'H' and resid 106 through 126 Processing helix chain 'H' and resid 128 through 135 Processing helix chain 'H' and resid 173 through 195 Processing helix chain 'H' and resid 213 through 229 removed outlier: 3.693A pdb=" N GLY H 229 " --> pdb=" O ILE H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 246 Processing helix chain 'H' and resid 262 through 277 Processing helix chain 'H' and resid 290 through 302 Processing helix chain 'H' and resid 316 through 326 removed outlier: 3.778A pdb=" N GLU H 322 " --> pdb=" O GLU H 318 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG H 326 " --> pdb=" O GLU H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 339 removed outlier: 3.651A pdb=" N ILE H 339 " --> pdb=" O VAL H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 354 Processing helix chain 'H' and resid 371 through 380 removed outlier: 3.905A pdb=" N ASP H 375 " --> pdb=" O THR H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 410 removed outlier: 3.877A pdb=" N TYR H 399 " --> pdb=" O ARG H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 413 No H-bonds generated for 'chain 'H' and resid 411 through 413' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 144 removed outlier: 5.942A pdb=" N VAL A 143 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR A 359 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LYS A 386 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A 361 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 150 removed outlier: 5.478A pdb=" N ASN A 147 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 166 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 167 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU A 238 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER A 281 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 249 removed outlier: 3.531A pdb=" N PHE A 256 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 13 removed outlier: 3.522A pdb=" N GLN B 6 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 144 removed outlier: 5.964A pdb=" N VAL B 143 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR B 359 " --> pdb=" O GLN B 384 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS B 386 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE B 361 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 150 removed outlier: 7.173A pdb=" N PHE B 164 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 167 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU B 238 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 282 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 240 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 248 through 249 Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 6 removed outlier: 6.805A pdb=" N ALA C 26 " --> pdb=" O GLU C 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 13 Processing sheet with id=AB4, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'C' and resid 331 through 332 removed outlier: 7.793A pdb=" N LEU C 238 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 282 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C 240 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 167 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE C 164 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 361 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 254 through 256 Processing sheet with id=AB7, first strand: chain 'D' and resid 4 through 13 Processing sheet with id=AB8, first strand: chain 'D' and resid 140 through 141 Processing sheet with id=AB9, first strand: chain 'D' and resid 143 through 144 removed outlier: 5.956A pdb=" N VAL D 143 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 361 " --> pdb=" O LYS D 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 146 through 150 removed outlier: 7.013A pdb=" N PHE D 164 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU D 238 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE D 282 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU D 240 " --> pdb=" O ILE D 282 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 248 through 249 Processing sheet with id=AC3, first strand: chain 'E' and resid 4 through 13 Processing sheet with id=AC4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AC5, first strand: chain 'E' and resid 306 through 308 removed outlier: 7.746A pdb=" N LEU E 238 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE E 282 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU E 240 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE E 164 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE E 361 " --> pdb=" O LYS E 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 248 through 249 Processing sheet with id=AC7, first strand: chain 'F' and resid 4 through 13 Processing sheet with id=AC8, first strand: chain 'F' and resid 140 through 141 Processing sheet with id=AC9, first strand: chain 'F' and resid 143 through 144 removed outlier: 5.958A pdb=" N VAL F 143 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE F 361 " --> pdb=" O LYS F 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 146 through 150 removed outlier: 7.010A pdb=" N PHE F 164 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU F 238 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE F 282 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU F 240 " --> pdb=" O ILE F 282 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 248 through 249 Processing sheet with id=AD3, first strand: chain 'G' and resid 4 through 13 Processing sheet with id=AD4, first strand: chain 'G' and resid 140 through 141 Processing sheet with id=AD5, first strand: chain 'G' and resid 331 through 332 removed outlier: 7.746A pdb=" N LEU G 238 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE G 282 " --> pdb=" O LEU G 238 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU G 240 " --> pdb=" O ILE G 282 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE G 164 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE G 361 " --> pdb=" O LYS G 386 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 248 through 249 Processing sheet with id=AD7, first strand: chain 'H' and resid 4 through 13 Processing sheet with id=AD8, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AD9, first strand: chain 'H' and resid 143 through 144 removed outlier: 5.933A pdb=" N VAL H 143 " --> pdb=" O ILE H 385 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE H 361 " --> pdb=" O LYS H 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'H' and resid 146 through 150 removed outlier: 6.888A pdb=" N PHE H 164 " --> pdb=" O ILE H 148 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU H 238 " --> pdb=" O VAL H 280 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE H 282 " --> pdb=" O LEU H 238 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU H 240 " --> pdb=" O ILE H 282 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 248 through 249 removed outlier: 3.830A pdb=" N PHE H 256 " --> pdb=" O THR H 259 " (cutoff:3.500A) 1247 hydrogen bonds defined for protein. 3486 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: 10.00 Time building geometry restraints manager: 7.48 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: 8762 1.34 - 1.45: 2923 1.45 - 1.57: 13539 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 25336 Sorted by residual: bond pdb=" N ASP D 418 " pdb=" CA ASP D 418 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.23e-02 6.61e+03 1.11e+01 bond pdb=" N ASP B 418 " pdb=" CA ASP B 418 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.23e-02 6.61e+03 1.05e+01 bond pdb=" N ASP G 418 " pdb=" CA ASP G 418 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.49e+00 bond pdb=" N ARG E 8 " pdb=" CA ARG E 8 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.22e-02 6.72e+03 8.53e+00 bond pdb=" N VAL E 7 " pdb=" CA VAL E 7 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.79e+00 ... (remaining 25331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 33229 1.45 - 2.90: 1071 2.90 - 4.36: 140 4.36 - 5.81: 23 5.81 - 7.26: 1 Bond angle restraints: 34464 Sorted by residual: angle pdb=" CA GLY D 417 " pdb=" C GLY D 417 " pdb=" O GLY D 417 " ideal model delta sigma weight residual 120.91 116.90 4.01 8.70e-01 1.32e+00 2.12e+01 angle pdb=" CA GLY G 417 " pdb=" C GLY G 417 " pdb=" O GLY G 417 " ideal model delta sigma weight residual 120.89 117.09 3.80 9.20e-01 1.18e+00 1.71e+01 angle pdb=" N LEU D 419 " pdb=" CA LEU D 419 " pdb=" C LEU D 419 " ideal model delta sigma weight residual 112.72 108.10 4.62 1.14e+00 7.69e-01 1.64e+01 angle pdb=" N LEU G 419 " pdb=" CA LEU G 419 " pdb=" C LEU G 419 " ideal model delta sigma weight residual 112.72 108.18 4.54 1.14e+00 7.69e-01 1.59e+01 angle pdb=" O GLY G 417 " pdb=" C GLY G 417 " pdb=" N ASP G 418 " ideal model delta sigma weight residual 122.99 126.39 -3.40 8.60e-01 1.35e+00 1.56e+01 ... (remaining 34459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 13806 17.39 - 34.79: 1076 34.79 - 52.18: 134 52.18 - 69.58: 41 69.58 - 86.97: 39 Dihedral angle restraints: 15096 sinusoidal: 5648 harmonic: 9448 Sorted by residual: dihedral pdb=" C ASP G 418 " pdb=" N ASP G 418 " pdb=" CA ASP G 418 " pdb=" CB ASP G 418 " ideal model delta harmonic sigma weight residual -122.60 -133.26 10.66 0 2.50e+00 1.60e-01 1.82e+01 dihedral pdb=" C ASP D 418 " pdb=" N ASP D 418 " pdb=" CA ASP D 418 " pdb=" CB ASP D 418 " ideal model delta harmonic sigma weight residual -122.60 -133.12 10.52 0 2.50e+00 1.60e-01 1.77e+01 dihedral pdb=" N ASP G 418 " pdb=" C ASP G 418 " pdb=" CA ASP G 418 " pdb=" CB ASP G 418 " ideal model delta harmonic sigma weight residual 122.80 133.16 -10.36 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 15093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3506 0.070 - 0.139: 477 0.139 - 0.209: 6 0.209 - 0.279: 0 0.279 - 0.348: 3 Chirality restraints: 3992 Sorted by residual: chirality pdb=" CA ASP G 418 " pdb=" N ASP G 418 " pdb=" C ASP G 418 " pdb=" CB ASP G 418 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA ASP D 418 " pdb=" N ASP D 418 " pdb=" C ASP D 418 " pdb=" CB ASP D 418 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ASP B 418 " pdb=" N ASP B 418 " pdb=" C ASP B 418 " pdb=" CB ASP B 418 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 3989 not shown) Planarity restraints: 4616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 75 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO C 76 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 75 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO A 76 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 75 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO E 76 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 76 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 76 " 0.028 5.00e-02 4.00e+02 ... (remaining 4613 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2577 2.74 - 3.28: 25365 3.28 - 3.82: 41571 3.82 - 4.36: 51080 4.36 - 4.90: 89231 Nonbonded interactions: 209824 Sorted by model distance: nonbonded pdb=" OD2 ASP C 90 " pdb=" OG1 THR C 343 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR F 245 " pdb=" OE1 GLU F 288 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR G 245 " pdb=" OE1 GLU G 288 " model vdw 2.209 3.040 nonbonded pdb=" OE2 GLU H 73 " pdb=" NH2 ARG H 104 " model vdw 2.210 3.120 nonbonded pdb=" OG1 THR C 245 " pdb=" OE1 GLU C 288 " model vdw 2.219 3.040 ... (remaining 209819 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: 0.04 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 56.420 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.400 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: 0.030 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 25336 Z= 0.397 Angle : 0.611 7.260 34464 Z= 0.354 Chirality : 0.045 0.348 3992 Planarity : 0.004 0.054 4616 Dihedral : 13.516 86.971 9096 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.89 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % 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: -3.25 (0.12), residues: 3368 helix: -1.03 (0.12), residues: 1360 sheet: -2.54 (0.20), residues: 536 loop : -3.07 (0.13), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 294 HIS 0.008 0.001 HIS H 363 PHE 0.011 0.002 PHE A 247 TYR 0.010 0.002 TYR B 415 ARG 0.008 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 2.750 Fit side-chains REVERT: B 288 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6720 (tm-30) REVERT: B 294 TRP cc_start: 0.7491 (m100) cc_final: 0.6873 (m100) REVERT: C 294 TRP cc_start: 0.7481 (m100) cc_final: 0.6899 (m100) REVERT: D 294 TRP cc_start: 0.7517 (m100) cc_final: 0.6956 (m100) REVERT: E 247 PHE cc_start: 0.8046 (p90) cc_final: 0.7473 (p90) REVERT: E 294 TRP cc_start: 0.7558 (m100) cc_final: 0.7037 (m100) REVERT: E 414 ARG cc_start: 0.8086 (mmt-90) cc_final: 0.7885 (tpp80) REVERT: F 294 TRP cc_start: 0.7476 (m100) cc_final: 0.7239 (m100) REVERT: G 294 TRP cc_start: 0.7527 (m100) cc_final: 0.6924 (m100) REVERT: H 294 TRP cc_start: 0.7662 (m100) cc_final: 0.7007 (m100) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.4203 time to fit residues: 237.3106 Evaluate side-chains 231 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 263 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 305 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 64 GLN A 147 ASN A 186 HIS A 363 HIS B 147 ASN B 306 GLN B 363 HIS C 186 HIS ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 147 ASN D 363 HIS E 6 GLN E 147 ASN E 363 HIS F 6 GLN F 147 ASN F 363 HIS G 6 GLN G 147 ASN G 150 ASN G 363 HIS H 6 GLN H 68 GLN H 147 ASN H 363 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112191 restraints weight = 34348.977| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.01 r_work: 0.3154 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25336 Z= 0.189 Angle : 0.531 5.937 34464 Z= 0.281 Chirality : 0.041 0.179 3992 Planarity : 0.004 0.036 4616 Dihedral : 4.605 23.570 3632 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.43 % Allowed : 7.48 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.58 (0.14), residues: 3368 helix: 0.73 (0.13), residues: 1408 sheet: -2.11 (0.21), residues: 536 loop : -2.48 (0.14), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 294 HIS 0.006 0.001 HIS F 363 PHE 0.025 0.002 PHE C 247 TYR 0.029 0.001 TYR A 357 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 2.638 Fit side-chains REVERT: A 328 VAL cc_start: 0.6382 (OUTLIER) cc_final: 0.6151 (p) REVERT: B 82 ASN cc_start: 0.8181 (t0) cc_final: 0.7915 (t0) REVERT: B 288 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6738 (tm-30) REVERT: B 294 TRP cc_start: 0.7488 (m100) cc_final: 0.6841 (m100) REVERT: C 294 TRP cc_start: 0.7658 (m100) cc_final: 0.7192 (m100) REVERT: D 294 TRP cc_start: 0.7746 (m100) cc_final: 0.6873 (m100) REVERT: E 294 TRP cc_start: 0.7752 (m100) cc_final: 0.6892 (m100) REVERT: F 247 PHE cc_start: 0.7765 (p90) cc_final: 0.7441 (p90) REVERT: G 247 PHE cc_start: 0.7732 (p90) cc_final: 0.7528 (p90) REVERT: G 294 TRP cc_start: 0.7729 (m100) cc_final: 0.7115 (m100) REVERT: G 326 ARG cc_start: 0.7375 (mtp180) cc_final: 0.7114 (mtp-110) REVERT: G 419 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8557 (mp) REVERT: H 294 TRP cc_start: 0.7720 (m100) cc_final: 0.7086 (m100) outliers start: 36 outliers final: 15 residues processed: 275 average time/residue: 0.3589 time to fit residues: 158.2987 Evaluate side-chains 241 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 277 optimal weight: 9.9990 chunk 281 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 309 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 147 ASN B 147 ASN B 150 ASN B 306 GLN C 150 ASN C 363 HIS D 147 ASN E 86 GLN E 147 ASN F 147 ASN F 150 ASN G 147 ASN G 150 ASN H 68 GLN H 147 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111117 restraints weight = 34393.824| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.00 r_work: 0.3139 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25336 Z= 0.262 Angle : 0.524 6.125 34464 Z= 0.277 Chirality : 0.042 0.176 3992 Planarity : 0.004 0.035 4616 Dihedral : 4.464 21.968 3632 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.51 % Allowed : 10.03 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.06 (0.14), residues: 3368 helix: 1.19 (0.13), residues: 1408 sheet: -1.87 (0.22), residues: 528 loop : -2.23 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 294 HIS 0.007 0.001 HIS C 363 PHE 0.015 0.002 PHE A 247 TYR 0.023 0.002 TYR B 357 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 2.661 Fit side-chains REVERT: A 294 TRP cc_start: 0.7842 (m100) cc_final: 0.7597 (m-10) REVERT: A 328 VAL cc_start: 0.6350 (OUTLIER) cc_final: 0.5954 (p) REVERT: B 288 GLU cc_start: 0.7423 (tm-30) cc_final: 0.6900 (tm-30) REVERT: B 294 TRP cc_start: 0.7522 (m100) cc_final: 0.6822 (m100) REVERT: C 294 TRP cc_start: 0.7692 (m100) cc_final: 0.7188 (m100) REVERT: D 294 TRP cc_start: 0.7752 (m100) cc_final: 0.6849 (m100) REVERT: E 68 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8530 (tp-100) REVERT: E 294 TRP cc_start: 0.7701 (m100) cc_final: 0.6832 (m100) REVERT: F 294 TRP cc_start: 0.7775 (m100) cc_final: 0.7546 (m100) REVERT: G 294 TRP cc_start: 0.7755 (m100) cc_final: 0.7159 (m100) REVERT: H 68 GLN cc_start: 0.8811 (tp40) cc_final: 0.8524 (tp-100) REVERT: H 294 TRP cc_start: 0.7662 (m100) cc_final: 0.6903 (m100) outliers start: 38 outliers final: 20 residues processed: 254 average time/residue: 0.3474 time to fit residues: 144.3267 Evaluate side-chains 239 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 218 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 304 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 297 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 270 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 146 optimal weight: 0.0040 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 147 ASN B 150 ASN C 68 GLN D 147 ASN E 86 GLN E 147 ASN F 68 GLN F 147 ASN F 150 ASN G 147 ASN G 150 ASN H 147 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.142853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115025 restraints weight = 34367.369| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.07 r_work: 0.3205 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25336 Z= 0.214 Angle : 0.505 6.027 34464 Z= 0.267 Chirality : 0.041 0.178 3992 Planarity : 0.004 0.032 4616 Dihedral : 4.356 22.375 3632 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.43 % Allowed : 11.03 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.14), residues: 3368 helix: 1.61 (0.13), residues: 1400 sheet: -1.67 (0.22), residues: 528 loop : -2.07 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 294 HIS 0.002 0.001 HIS B 363 PHE 0.014 0.001 PHE A 247 TYR 0.022 0.002 TYR B 357 ARG 0.005 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 2.690 Fit side-chains REVERT: A 294 TRP cc_start: 0.7790 (m100) cc_final: 0.7478 (m-10) REVERT: A 328 VAL cc_start: 0.6156 (OUTLIER) cc_final: 0.5845 (p) REVERT: B 82 ASN cc_start: 0.8240 (t0) cc_final: 0.7996 (t0) REVERT: B 288 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6881 (tm-30) REVERT: B 294 TRP cc_start: 0.7459 (m100) cc_final: 0.6833 (m100) REVERT: C 294 TRP cc_start: 0.7686 (m100) cc_final: 0.7207 (m100) REVERT: D 294 TRP cc_start: 0.7642 (m100) cc_final: 0.6774 (m100) REVERT: E 68 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8587 (tp-100) REVERT: E 294 TRP cc_start: 0.7686 (m100) cc_final: 0.6826 (m100) REVERT: F 294 TRP cc_start: 0.7686 (m100) cc_final: 0.7463 (m100) REVERT: G 294 TRP cc_start: 0.7702 (m100) cc_final: 0.7088 (m100) REVERT: H 68 GLN cc_start: 0.8802 (tp40) cc_final: 0.8591 (tp-100) REVERT: H 290 ASP cc_start: 0.7645 (t0) cc_final: 0.7243 (t0) REVERT: H 294 TRP cc_start: 0.7616 (m100) cc_final: 0.6878 (m100) outliers start: 36 outliers final: 17 residues processed: 266 average time/residue: 0.3373 time to fit residues: 148.7468 Evaluate side-chains 245 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 115 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 305 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 249 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 302 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 147 ASN B 150 ASN C 150 ASN D 147 ASN D 186 HIS E 147 ASN E 150 ASN E 186 HIS F 147 ASN F 150 ASN G 68 GLN G 147 ASN G 150 ASN G 186 HIS H 147 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113245 restraints weight = 34392.491| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.08 r_work: 0.3160 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 25336 Z= 0.351 Angle : 0.555 6.253 34464 Z= 0.294 Chirality : 0.044 0.167 3992 Planarity : 0.004 0.037 4616 Dihedral : 4.450 20.952 3632 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.52 % Favored : 94.45 % Rotamer: Outliers : 1.47 % Allowed : 12.70 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.14), residues: 3368 helix: 1.46 (0.13), residues: 1400 sheet: -1.61 (0.22), residues: 528 loop : -2.02 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 294 HIS 0.006 0.001 HIS A 363 PHE 0.011 0.002 PHE A 247 TYR 0.027 0.002 TYR D 357 ARG 0.004 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 2.664 Fit side-chains REVERT: A 204 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7704 (mm-30) REVERT: A 294 TRP cc_start: 0.7719 (m100) cc_final: 0.7247 (m-10) REVERT: A 328 VAL cc_start: 0.6163 (OUTLIER) cc_final: 0.5933 (p) REVERT: B 82 ASN cc_start: 0.8139 (t0) cc_final: 0.7880 (t0) REVERT: B 288 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7056 (tm-30) REVERT: B 294 TRP cc_start: 0.7502 (m100) cc_final: 0.6842 (m100) REVERT: C 68 GLN cc_start: 0.8971 (tp40) cc_final: 0.8674 (tp-100) REVERT: C 294 TRP cc_start: 0.7715 (m100) cc_final: 0.7195 (m100) REVERT: D 294 TRP cc_start: 0.7714 (m100) cc_final: 0.6830 (m100) REVERT: E 68 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8665 (tp-100) REVERT: E 294 TRP cc_start: 0.7716 (m100) cc_final: 0.6891 (m100) REVERT: F 68 GLN cc_start: 0.8983 (tp40) cc_final: 0.8716 (tp-100) REVERT: F 294 TRP cc_start: 0.7724 (m100) cc_final: 0.7495 (m100) REVERT: G 294 TRP cc_start: 0.7740 (m100) cc_final: 0.7119 (m100) REVERT: H 68 GLN cc_start: 0.8828 (tp40) cc_final: 0.8571 (tp-100) REVERT: H 290 ASP cc_start: 0.7706 (t0) cc_final: 0.7317 (t0) REVERT: H 294 TRP cc_start: 0.7650 (m100) cc_final: 0.6929 (m100) outliers start: 37 outliers final: 30 residues processed: 251 average time/residue: 0.3444 time to fit residues: 142.1841 Evaluate side-chains 247 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 305 optimal weight: 0.8980 chunk 221 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 267 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 196 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 150 ASN C 150 ASN D 147 ASN E 147 ASN E 150 ASN F 147 ASN F 150 ASN G 147 ASN G 150 ASN H 147 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.140393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112282 restraints weight = 34397.880| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.01 r_work: 0.3154 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25336 Z= 0.224 Angle : 0.507 6.051 34464 Z= 0.268 Chirality : 0.041 0.168 3992 Planarity : 0.003 0.033 4616 Dihedral : 4.341 22.081 3632 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.35 % Allowed : 13.61 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.44 (0.15), residues: 3368 helix: 1.68 (0.13), residues: 1416 sheet: -1.45 (0.22), residues: 528 loop : -1.93 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 294 HIS 0.003 0.001 HIS A 363 PHE 0.013 0.001 PHE A 247 TYR 0.023 0.002 TYR G 357 ARG 0.002 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 2.578 Fit side-chains REVERT: A 68 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8565 (tp-100) REVERT: A 204 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7610 (mm-30) REVERT: A 294 TRP cc_start: 0.7839 (m100) cc_final: 0.7505 (m-10) REVERT: B 82 ASN cc_start: 0.8099 (t0) cc_final: 0.7814 (t0) REVERT: B 288 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7006 (tm-30) REVERT: B 294 TRP cc_start: 0.7453 (m100) cc_final: 0.6842 (m100) REVERT: C 68 GLN cc_start: 0.8874 (tp40) cc_final: 0.8558 (tp-100) REVERT: C 294 TRP cc_start: 0.7659 (m100) cc_final: 0.7166 (m100) REVERT: D 294 TRP cc_start: 0.7609 (m100) cc_final: 0.6850 (m100) REVERT: E 68 GLN cc_start: 0.8870 (tp-100) cc_final: 0.8560 (tp-100) REVERT: E 294 TRP cc_start: 0.7675 (m100) cc_final: 0.6916 (m100) REVERT: F 68 GLN cc_start: 0.8917 (tp40) cc_final: 0.8639 (tp-100) REVERT: G 288 GLU cc_start: 0.8453 (pm20) cc_final: 0.7692 (pm20) REVERT: G 294 TRP cc_start: 0.7663 (m100) cc_final: 0.7036 (m100) REVERT: H 68 GLN cc_start: 0.8747 (tp40) cc_final: 0.8505 (tp-100) REVERT: H 290 ASP cc_start: 0.7758 (t0) cc_final: 0.7391 (t0) REVERT: H 294 TRP cc_start: 0.7590 (m100) cc_final: 0.6899 (m100) outliers start: 34 outliers final: 27 residues processed: 252 average time/residue: 0.3490 time to fit residues: 144.5155 Evaluate side-chains 250 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 147 ASN Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 132 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 147 ASN C 150 ASN D 147 ASN E 150 ASN F 147 ASN F 150 ASN F 186 HIS G 150 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111558 restraints weight = 34528.784| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.99 r_work: 0.3149 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25336 Z= 0.292 Angle : 0.529 6.183 34464 Z= 0.280 Chirality : 0.043 0.363 3992 Planarity : 0.004 0.033 4616 Dihedral : 4.349 21.377 3632 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.67 % Allowed : 14.01 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.15), residues: 3368 helix: 1.70 (0.13), residues: 1400 sheet: -1.35 (0.23), residues: 528 loop : -1.86 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 294 HIS 0.005 0.001 HIS A 363 PHE 0.012 0.002 PHE A 247 TYR 0.026 0.002 TYR D 357 ARG 0.004 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 2.613 Fit side-chains REVERT: A 68 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8569 (tp-100) REVERT: A 204 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7629 (mm-30) REVERT: A 294 TRP cc_start: 0.7718 (m100) cc_final: 0.6856 (m100) REVERT: B 82 ASN cc_start: 0.8147 (t0) cc_final: 0.7813 (t0) REVERT: B 288 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7055 (tm-30) REVERT: B 294 TRP cc_start: 0.7468 (m100) cc_final: 0.6838 (m100) REVERT: C 68 GLN cc_start: 0.8868 (tp40) cc_final: 0.8544 (tp-100) REVERT: C 294 TRP cc_start: 0.7681 (m100) cc_final: 0.7172 (m100) REVERT: C 372 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8119 (tmm) REVERT: D 294 TRP cc_start: 0.7617 (m100) cc_final: 0.6846 (m100) REVERT: E 68 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8598 (tp-100) REVERT: E 294 TRP cc_start: 0.7686 (m100) cc_final: 0.6917 (m100) REVERT: F 68 GLN cc_start: 0.8919 (tp40) cc_final: 0.8639 (tp-100) REVERT: G 68 GLN cc_start: 0.8918 (tp40) cc_final: 0.8650 (tp-100) REVERT: G 288 GLU cc_start: 0.8469 (pm20) cc_final: 0.7711 (pm20) REVERT: G 294 TRP cc_start: 0.7692 (m100) cc_final: 0.7072 (m100) REVERT: H 68 GLN cc_start: 0.8750 (tp40) cc_final: 0.8500 (tp-100) REVERT: H 294 TRP cc_start: 0.7634 (m100) cc_final: 0.6938 (m100) outliers start: 42 outliers final: 32 residues processed: 248 average time/residue: 0.3460 time to fit residues: 141.5658 Evaluate side-chains 250 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 39 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 279 optimal weight: 0.6980 chunk 120 optimal weight: 0.0770 chunk 15 optimal weight: 9.9990 chunk 193 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 150 ASN C 150 ASN E 147 ASN E 150 ASN F 147 ASN F 150 ASN G 147 ASN G 150 ASN H 147 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114556 restraints weight = 34216.470| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.03 r_work: 0.3185 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25336 Z= 0.146 Angle : 0.479 5.879 34464 Z= 0.253 Chirality : 0.040 0.284 3992 Planarity : 0.003 0.032 4616 Dihedral : 4.181 22.940 3632 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.43 % Allowed : 14.73 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.15), residues: 3368 helix: 1.98 (0.14), residues: 1432 sheet: -1.37 (0.22), residues: 544 loop : -1.70 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 294 HIS 0.002 0.000 HIS B 353 PHE 0.015 0.001 PHE A 247 TYR 0.020 0.001 TYR D 357 ARG 0.001 0.000 ARG F 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 2.697 Fit side-chains REVERT: A 68 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8524 (tp-100) REVERT: A 204 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7664 (mm-30) REVERT: A 294 TRP cc_start: 0.7688 (m100) cc_final: 0.7460 (m-10) REVERT: B 288 GLU cc_start: 0.7447 (tm-30) cc_final: 0.6940 (tm-30) REVERT: B 294 TRP cc_start: 0.7548 (m100) cc_final: 0.6806 (m100) REVERT: C 68 GLN cc_start: 0.8824 (tp40) cc_final: 0.8478 (tp-100) REVERT: C 290 ASP cc_start: 0.7686 (t0) cc_final: 0.7307 (t0) REVERT: C 294 TRP cc_start: 0.7657 (m100) cc_final: 0.7135 (m100) REVERT: C 372 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8066 (tmm) REVERT: D 294 TRP cc_start: 0.7584 (m100) cc_final: 0.6833 (m100) REVERT: E 68 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8407 (tp-100) REVERT: E 294 TRP cc_start: 0.7695 (m100) cc_final: 0.6922 (m100) REVERT: F 68 GLN cc_start: 0.8864 (tp40) cc_final: 0.8568 (tp-100) REVERT: G 288 GLU cc_start: 0.8390 (pm20) cc_final: 0.7648 (pm20) REVERT: G 294 TRP cc_start: 0.7653 (m100) cc_final: 0.7027 (m100) REVERT: H 68 GLN cc_start: 0.8769 (tp40) cc_final: 0.8543 (tp-100) REVERT: H 290 ASP cc_start: 0.7687 (t0) cc_final: 0.7307 (t0) REVERT: H 294 TRP cc_start: 0.7585 (m100) cc_final: 0.6878 (m100) outliers start: 36 outliers final: 23 residues processed: 265 average time/residue: 0.3505 time to fit residues: 151.8912 Evaluate side-chains 248 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 199 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 229 optimal weight: 0.6980 chunk 334 optimal weight: 0.7980 chunk 210 optimal weight: 5.9990 chunk 213 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 147 ASN B 150 ASN D 147 ASN E 147 ASN E 150 ASN F 147 ASN F 150 ASN G 147 ASN G 150 ASN H 147 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113452 restraints weight = 34555.946| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.03 r_work: 0.3168 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1892 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: