Starting phenix.real_space_refine on Thu Mar 5 19:14:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e4x_30988/03_2026/7e4x_30988.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e4x_30988/03_2026/7e4x_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_30988/03_2026/7e4x_30988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e4x_30988/03_2026/7e4x_30988.map" model { file = "/net/cci-nas-00/data/ceres_data/7e4x_30988/03_2026/7e4x_30988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e4x_30988/03_2026/7e4x_30988.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.20, per 1000 atoms: 0.21 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: 2.14 Conformation dependent library (CDL) restraints added in 1.1 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: 0.80 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: 4.38 Time building geometry restraints manager: 2.78 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: 0.01 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: 1.900 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.950 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- 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= 0.259 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (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 ARG 0.008 0.001 ARG A 34 TYR 0.010 0.002 TYR B 415 PHE 0.011 0.002 PHE A 247 TRP 0.005 0.001 TRP F 294 HIS 0.008 0.001 HIS H 363 Details of bonding type rmsd covalent geometry : bond 0.00595 (25336) covalent geometry : angle 0.61129 (34464) hydrogen bonds : bond 0.16456 ( 1247) hydrogen bonds : angle 6.49158 ( 3486) *********************** 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 : 0.989 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: 0.1741 time to fit residues: 99.0423 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 : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110557 restraints weight = 34798.419| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.02 r_work: 0.3128 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1125 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= 0.174 Angle : 0.559 6.089 34464 Z= 0.295 Chirality : 0.042 0.177 3992 Planarity : 0.004 0.039 4616 Dihedral : 4.708 22.551 3632 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.63 % Allowed : 8.08 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3368 helix: 0.54 (0.13), residues: 1408 sheet: -2.14 (0.21), residues: 536 loop : -2.49 (0.14), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.028 0.001 TYR A 357 PHE 0.024 0.002 PHE C 247 TRP 0.006 0.001 TRP F 294 HIS 0.007 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00404 (25336) covalent geometry : angle 0.55852 (34464) hydrogen bonds : bond 0.03907 ( 1247) hydrogen bonds : angle 4.73490 ( 3486) *********************** 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 281 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 240 time to evaluate : 0.776 Fit side-chains REVERT: B 119 LYS cc_start: 0.8683 (mttt) cc_final: 0.8476 (mttt) REVERT: B 288 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6903 (tm-30) REVERT: B 294 TRP cc_start: 0.7528 (m100) cc_final: 0.6871 (m100) REVERT: C 294 TRP cc_start: 0.7693 (m100) cc_final: 0.7152 (m100) REVERT: D 294 TRP cc_start: 0.7737 (m100) cc_final: 0.6929 (m100) REVERT: E 68 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8771 (tp-100) REVERT: E 294 TRP cc_start: 0.7724 (m100) cc_final: 0.6828 (m100) REVERT: G 294 TRP cc_start: 0.7738 (m100) cc_final: 0.7112 (m100) REVERT: G 326 ARG cc_start: 0.7429 (mtp180) cc_final: 0.7158 (mtp-110) REVERT: G 419 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8591 (mp) REVERT: H 68 GLN cc_start: 0.8685 (tp40) cc_final: 0.8343 (tp-100) REVERT: H 294 TRP cc_start: 0.7704 (m100) cc_final: 0.7040 (m100) outliers start: 41 outliers final: 17 residues processed: 267 average time/residue: 0.1543 time to fit residues: 66.9872 Evaluate side-chains 238 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 B residue 28 ILE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 297 LEU 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 F residue 314 VAL 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 317 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 148 optimal weight: 0.0970 chunk 323 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 312 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 292 optimal weight: 1.9990 chunk 237 optimal weight: 0.6980 chunk 210 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 D 147 ASN E 86 GLN E 147 ASN F 147 ASN F 150 ASN G 147 ASN G 150 ASN H 147 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112892 restraints weight = 34504.449| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.02 r_work: 0.3170 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25336 Z= 0.114 Angle : 0.493 5.930 34464 Z= 0.260 Chirality : 0.041 0.187 3992 Planarity : 0.003 0.032 4616 Dihedral : 4.373 23.116 3632 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.23 % Allowed : 10.23 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.14), residues: 3368 helix: 1.46 (0.13), residues: 1400 sheet: -1.82 (0.22), residues: 528 loop : -2.18 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.022 0.001 TYR C 357 PHE 0.017 0.001 PHE C 247 TRP 0.009 0.001 TRP F 294 HIS 0.001 0.000 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00261 (25336) covalent geometry : angle 0.49348 (34464) hydrogen bonds : bond 0.03064 ( 1247) hydrogen bonds : angle 4.31950 ( 3486) *********************** 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 282 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 0.616 Fit side-chains REVERT: B 288 GLU cc_start: 0.7339 (tm-30) cc_final: 0.6801 (tm-30) REVERT: B 294 TRP cc_start: 0.7589 (m100) cc_final: 0.6943 (m100) REVERT: C 290 ASP cc_start: 0.7661 (t0) cc_final: 0.7274 (t0) REVERT: C 294 TRP cc_start: 0.7656 (m100) cc_final: 0.7119 (m100) REVERT: D 294 TRP cc_start: 0.7683 (m100) cc_final: 0.6773 (m100) REVERT: E 294 TRP cc_start: 0.7700 (m100) cc_final: 0.6820 (m100) REVERT: G 294 TRP cc_start: 0.7752 (m100) cc_final: 0.7095 (m100) REVERT: H 68 GLN cc_start: 0.8695 (tp40) cc_final: 0.8389 (tp-100) REVERT: H 290 ASP cc_start: 0.7673 (t0) cc_final: 0.7297 (t0) REVERT: H 294 TRP cc_start: 0.7629 (m100) cc_final: 0.6914 (m100) outliers start: 31 outliers final: 17 residues processed: 267 average time/residue: 0.1514 time to fit residues: 66.8537 Evaluate side-chains 238 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 B residue 28 ILE Chi-restraints excluded: chain B residue 297 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 86 GLN Chi-restraints excluded: chain E residue 297 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 8.9990 chunk 146 optimal weight: 0.0060 chunk 187 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 326 optimal weight: 8.9990 chunk 181 optimal weight: 0.5980 chunk 206 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 0.0040 chunk 253 optimal weight: 0.8980 chunk 317 optimal weight: 3.9990 overall best weight: 0.7010 ------------------------------------------------------------------------------- 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 68 GLN D 147 ASN E 68 GLN E 86 GLN E 147 ASN E 150 ASN F 68 GLN F 147 ASN F 150 ASN G 68 GLN G 147 ASN G 150 ASN H 147 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.145191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117808 restraints weight = 34009.092| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.05 r_work: 0.3229 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25336 Z= 0.100 Angle : 0.480 5.863 34464 Z= 0.252 Chirality : 0.040 0.168 3992 Planarity : 0.003 0.031 4616 Dihedral : 4.233 23.227 3632 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.47 % Allowed : 10.95 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.15), residues: 3368 helix: 1.78 (0.14), residues: 1416 sheet: -1.56 (0.22), residues: 528 loop : -2.07 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 87 TYR 0.022 0.001 TYR B 357 PHE 0.014 0.001 PHE A 247 TRP 0.015 0.001 TRP A 294 HIS 0.001 0.000 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00225 (25336) covalent geometry : angle 0.48050 (34464) hydrogen bonds : bond 0.02781 ( 1247) hydrogen bonds : angle 4.16568 ( 3486) *********************** 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 282 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 0.847 Fit side-chains REVERT: A 204 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7806 (mm-30) REVERT: A 294 TRP cc_start: 0.7715 (m-10) cc_final: 0.7255 (m-10) REVERT: B 288 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6851 (tm-30) REVERT: B 294 TRP cc_start: 0.7587 (m100) cc_final: 0.6945 (m100) REVERT: C 290 ASP cc_start: 0.7547 (t0) cc_final: 0.7152 (t0) REVERT: C 294 TRP cc_start: 0.7628 (m100) cc_final: 0.7114 (m100) REVERT: D 290 ASP cc_start: 0.7590 (t0) cc_final: 0.7127 (t0) REVERT: D 294 TRP cc_start: 0.7647 (m100) cc_final: 0.6744 (m100) REVERT: E 68 GLN cc_start: 0.8747 (tp40) cc_final: 0.8398 (tp-100) REVERT: E 294 TRP cc_start: 0.7683 (m100) cc_final: 0.6832 (m100) REVERT: F 266 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6840 (mmm) REVERT: G 294 TRP cc_start: 0.7727 (m100) cc_final: 0.7114 (m100) REVERT: H 68 GLN cc_start: 0.8671 (tp40) cc_final: 0.8345 (tp-100) REVERT: H 290 ASP cc_start: 0.7591 (t0) cc_final: 0.7180 (t0) REVERT: H 294 TRP cc_start: 0.7594 (m100) cc_final: 0.6865 (m100) outliers start: 37 outliers final: 15 residues processed: 268 average time/residue: 0.1496 time to fit residues: 66.3618 Evaluate side-chains 235 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 81 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 D residue 297 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 25 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 132 optimal weight: 0.0060 chunk 209 optimal weight: 5.9990 chunk 312 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 297 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN D 186 HIS E 147 ASN E 186 HIS F 147 ASN F 150 ASN F 186 HIS G 147 ASN G 150 ASN G 186 HIS H 147 ASN H 186 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111208 restraints weight = 34474.934| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.05 r_work: 0.3154 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 25336 Z= 0.312 Angle : 0.624 6.452 34464 Z= 0.332 Chirality : 0.047 0.158 3992 Planarity : 0.005 0.045 4616 Dihedral : 4.576 19.436 3632 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 1.59 % Allowed : 12.74 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3368 helix: 1.14 (0.13), residues: 1408 sheet: -1.60 (0.22), residues: 528 loop : -2.04 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.023 0.002 TYR E 357 PHE 0.014 0.002 PHE C 130 TRP 0.017 0.001 TRP F 294 HIS 0.010 0.001 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00749 (25336) covalent geometry : angle 0.62405 (34464) hydrogen bonds : bond 0.04287 ( 1247) hydrogen bonds : angle 4.49916 ( 3486) *********************** 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 268 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 0.842 Fit side-chains REVERT: A 68 GLN cc_start: 0.9027 (tp40) cc_final: 0.8689 (tp-100) REVERT: A 294 TRP cc_start: 0.7674 (m100) cc_final: 0.7418 (m-10) REVERT: B 288 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7050 (tm-30) REVERT: B 294 TRP cc_start: 0.7517 (m100) cc_final: 0.6853 (m100) REVERT: C 68 GLN cc_start: 0.8969 (tp40) cc_final: 0.8689 (tp-100) REVERT: C 294 TRP cc_start: 0.7729 (m100) cc_final: 0.7205 (m100) REVERT: D 294 TRP cc_start: 0.7652 (m100) cc_final: 0.6794 (m100) REVERT: E 68 GLN cc_start: 0.8983 (tp40) cc_final: 0.8714 (tp-100) REVERT: E 294 TRP cc_start: 0.7729 (m100) cc_final: 0.6918 (m100) REVERT: F 266 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6597 (mmm) REVERT: G 294 TRP cc_start: 0.7757 (m100) cc_final: 0.7117 (m100) REVERT: H 68 GLN cc_start: 0.8790 (tp40) cc_final: 0.8456 (tp-100) REVERT: H 294 TRP cc_start: 0.7647 (m100) cc_final: 0.6936 (m100) outliers start: 40 outliers final: 32 residues processed: 248 average time/residue: 0.1468 time to fit residues: 60.0582 Evaluate side-chains 244 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 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 C residue 28 ILE 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 C residue 314 VAL 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 266 MET 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 G residue 314 VAL 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 314 VAL 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 2 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 326 optimal weight: 8.9990 chunk 202 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 258 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 chunk 328 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 147 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 = 0.3677 r_free = 0.3677 target = 0.141593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113409 restraints weight = 34378.095| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.02 r_work: 0.3168 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25336 Z= 0.114 Angle : 0.493 5.989 34464 Z= 0.260 Chirality : 0.040 0.176 3992 Planarity : 0.003 0.033 4616 Dihedral : 4.313 22.784 3632 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.35 % Allowed : 14.01 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.15), residues: 3368 helix: 1.77 (0.14), residues: 1416 sheet: -1.38 (0.22), residues: 528 loop : -1.91 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 131 TYR 0.024 0.001 TYR G 357 PHE 0.016 0.001 PHE A 247 TRP 0.011 0.001 TRP F 294 HIS 0.002 0.000 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00261 (25336) covalent geometry : angle 0.49315 (34464) hydrogen bonds : bond 0.02887 ( 1247) hydrogen bonds : angle 4.16004 ( 3486) *********************** 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 267 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.919 Fit side-chains REVERT: A 68 GLN cc_start: 0.9012 (tp40) cc_final: 0.8670 (tp-100) REVERT: A 204 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7779 (mm-30) REVERT: B 288 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7002 (tm-30) REVERT: B 294 TRP cc_start: 0.7532 (m100) cc_final: 0.6916 (m100) REVERT: C 68 GLN cc_start: 0.8868 (tp40) cc_final: 0.8577 (tp-100) REVERT: C 294 TRP cc_start: 0.7658 (m100) cc_final: 0.7166 (m100) REVERT: C 372 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8061 (tmm) REVERT: D 68 GLN cc_start: 0.8915 (tp40) cc_final: 0.8621 (tp-100) REVERT: D 294 TRP cc_start: 0.7627 (m100) cc_final: 0.6815 (m100) REVERT: E 68 GLN cc_start: 0.8912 (tp40) cc_final: 0.8613 (tp-100) REVERT: E 294 TRP cc_start: 0.7657 (m100) cc_final: 0.6846 (m100) REVERT: F 68 GLN cc_start: 0.8911 (tp40) cc_final: 0.8617 (tp-100) REVERT: F 266 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6810 (mmm) REVERT: G 288 GLU cc_start: 0.8366 (pm20) cc_final: 0.7595 (pm20) REVERT: G 294 TRP cc_start: 0.7675 (m100) cc_final: 0.7046 (m100) REVERT: H 68 GLN cc_start: 0.8688 (tp40) cc_final: 0.8342 (tp-100) REVERT: H 290 ASP cc_start: 0.7698 (t0) cc_final: 0.7334 (t0) REVERT: H 294 TRP cc_start: 0.7553 (m100) cc_final: 0.6908 (m100) outliers start: 34 outliers final: 26 residues processed: 251 average time/residue: 0.1396 time to fit residues: 58.1659 Evaluate side-chains 245 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 332 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 28 ILE 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 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 147 ASN Chi-restraints excluded: chain F residue 266 MET 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 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 326 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 271 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 173 optimal weight: 0.4980 chunk 136 optimal weight: 5.9990 chunk 237 optimal weight: 0.0980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 D 147 ASN E 147 ASN F 150 ASN G 68 GLN G 150 ASN H 147 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112252 restraints weight = 34524.637| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.03 r_work: 0.3157 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25336 Z= 0.156 Angle : 0.513 6.105 34464 Z= 0.271 Chirality : 0.041 0.165 3992 Planarity : 0.004 0.032 4616 Dihedral : 4.280 21.748 3632 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.47 % Allowed : 14.65 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 3368 helix: 1.80 (0.13), residues: 1416 sheet: -1.29 (0.23), residues: 528 loop : -1.85 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.026 0.002 TYR G 357 PHE 0.013 0.001 PHE A 247 TRP 0.023 0.001 TRP A 294 HIS 0.004 0.001 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00374 (25336) covalent geometry : angle 0.51278 (34464) hydrogen bonds : bond 0.03129 ( 1247) hydrogen bonds : angle 4.15855 ( 3486) *********************** 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 265 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.801 Fit side-chains REVERT: A 68 GLN cc_start: 0.9009 (tp40) cc_final: 0.8653 (tp-100) REVERT: A 204 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7617 (mm-30) REVERT: A 294 TRP cc_start: 0.7756 (m-10) cc_final: 0.7061 (m-10) REVERT: B 288 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7028 (tm-30) REVERT: B 294 TRP cc_start: 0.7550 (m100) cc_final: 0.6912 (m100) REVERT: C 68 GLN cc_start: 0.8864 (tp40) cc_final: 0.8561 (tp-100) REVERT: C 294 TRP cc_start: 0.7658 (m100) cc_final: 0.7156 (m100) REVERT: C 372 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8041 (tmm) REVERT: D 68 GLN cc_start: 0.8911 (tp40) cc_final: 0.8608 (tp-100) REVERT: D 294 TRP cc_start: 0.7619 (m100) cc_final: 0.6798 (m100) REVERT: E 68 GLN cc_start: 0.8929 (tp40) cc_final: 0.8625 (tp-100) REVERT: E 294 TRP cc_start: 0.7671 (m100) cc_final: 0.6920 (m100) REVERT: F 68 GLN cc_start: 0.8909 (tp40) cc_final: 0.8632 (tp-100) REVERT: G 288 GLU cc_start: 0.8471 (pm20) cc_final: 0.7734 (pm20) REVERT: G 294 TRP cc_start: 0.7689 (m100) cc_final: 0.7066 (m100) REVERT: H 68 GLN cc_start: 0.8691 (tp40) cc_final: 0.8343 (tp-100) REVERT: H 294 TRP cc_start: 0.7588 (m100) cc_final: 0.6974 (m100) outliers start: 37 outliers final: 31 residues processed: 248 average time/residue: 0.1388 time to fit residues: 57.5056 Evaluate side-chains 252 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 28 ILE 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 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 147 ASN 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 211 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 240 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 145 optimal weight: 0.1980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN C 150 ASN F 147 ASN F 150 ASN G 68 GLN G 147 ASN G 150 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.142034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.113795 restraints weight = 34204.964| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.04 r_work: 0.3178 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25336 Z= 0.105 Angle : 0.483 5.956 34464 Z= 0.255 Chirality : 0.040 0.166 3992 Planarity : 0.003 0.031 4616 Dihedral : 4.188 22.588 3632 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.71 % Allowed : 14.69 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 3368 helix: 1.99 (0.14), residues: 1432 sheet: -1.35 (0.22), residues: 544 loop : -1.67 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 395 TYR 0.019 0.001 TYR C 357 PHE 0.015 0.001 PHE A 247 TRP 0.014 0.001 TRP A 294 HIS 0.002 0.000 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00242 (25336) covalent geometry : angle 0.48331 (34464) hydrogen bonds : bond 0.02700 ( 1247) hydrogen bonds : angle 4.03562 ( 3486) *********************** 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 267 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 1.669 Fit side-chains REVERT: A 68 GLN cc_start: 0.8954 (tp40) cc_final: 0.8603 (tp-100) REVERT: A 204 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7639 (mm-30) REVERT: A 294 TRP cc_start: 0.7813 (m-10) cc_final: 0.7224 (m-10) REVERT: B 288 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6972 (tm-30) REVERT: B 294 TRP cc_start: 0.7575 (m100) cc_final: 0.6862 (m100) REVERT: C 68 GLN cc_start: 0.8843 (tp40) cc_final: 0.8515 (tp-100) REVERT: C 290 ASP cc_start: 0.7680 (t0) cc_final: 0.7305 (t0) REVERT: C 294 TRP cc_start: 0.7650 (m100) cc_final: 0.7132 (m100) REVERT: C 372 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8063 (tmm) REVERT: D 68 GLN cc_start: 0.8889 (tp40) cc_final: 0.8588 (tp-100) REVERT: D 294 TRP cc_start: 0.7578 (m100) cc_final: 0.6817 (m100) REVERT: E 68 GLN cc_start: 0.8809 (tp40) cc_final: 0.8484 (tp-100) REVERT: E 294 TRP cc_start: 0.7704 (m100) cc_final: 0.6939 (m100) REVERT: F 68 GLN cc_start: 0.8889 (tp40) cc_final: 0.8593 (tp-100) REVERT: G 68 GLN cc_start: 0.8882 (tp40) cc_final: 0.8622 (tp-100) REVERT: G 288 GLU cc_start: 0.8418 (pm20) cc_final: 0.7688 (pm20) REVERT: G 294 TRP cc_start: 0.7709 (m100) cc_final: 0.7087 (m100) REVERT: H 68 GLN cc_start: 0.8691 (tp40) cc_final: 0.8350 (tp-100) REVERT: H 290 ASP cc_start: 0.7695 (t0) cc_final: 0.7344 (t0) REVERT: H 294 TRP cc_start: 0.7591 (m100) cc_final: 0.6927 (m100) outliers start: 43 outliers final: 28 residues processed: 250 average time/residue: 0.1600 time to fit residues: 66.5317 Evaluate side-chains 244 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 28 ILE 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 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 341 THR 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 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 117 optimal weight: 0.1980 chunk 175 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 165 optimal weight: 0.6980 chunk 238 optimal weight: 3.9990 chunk 317 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 D 147 ASN E 147 ASN F 147 ASN F 150 ASN G 147 ASN G 150 ASN H 147 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.113753 restraints weight = 34345.247| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.03 r_work: 0.3173 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25336 Z= 0.119 Angle : 0.490 6.182 34464 Z= 0.257 Chirality : 0.040 0.165 3992 Planarity : 0.003 0.031 4616 Dihedral : 4.130 22.132 3632 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.67 % Allowed : 14.93 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3368 helix: 2.08 (0.14), residues: 1432 sheet: -1.24 (0.23), residues: 544 loop : -1.61 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 395 TYR 0.015 0.001 TYR H 357 PHE 0.014 0.001 PHE A 247 TRP 0.012 0.001 TRP A 294 HIS 0.002 0.000 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00281 (25336) covalent geometry : angle 0.48990 (34464) hydrogen bonds : bond 0.02765 ( 1247) hydrogen bonds : angle 4.00455 ( 3486) *********************** REFINEMENT MACRO_CYCLE 9 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: 42 poor density : 226 time to evaluate : 0.798 Fit side-chains REVERT: A 68 GLN cc_start: 0.8963 (tp40) cc_final: 0.8620 (tp-100) REVERT: A 204 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7667 (mm-30) REVERT: A 294 TRP cc_start: 0.7808 (m-10) cc_final: 0.7209 (m-10) REVERT: B 288 GLU cc_start: 0.7479 (tm-30) cc_final: 0.6992 (tm-30) REVERT: B 294 TRP cc_start: 0.7526 (m100) cc_final: 0.6858 (m100) REVERT: C 68 GLN cc_start: 0.8841 (tp40) cc_final: 0.8509 (tp-100) REVERT: C 290 ASP cc_start: 0.7689 (t0) cc_final: 0.7320 (t0) REVERT: C 294 TRP cc_start: 0.7664 (m100) cc_final: 0.7142 (m100) REVERT: C 372 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8062 (tmm) REVERT: D 68 GLN cc_start: 0.8871 (tp40) cc_final: 0.8571 (tp-100) REVERT: D 294 TRP cc_start: 0.7605 (m100) cc_final: 0.6836 (m100) REVERT: E 68 GLN cc_start: 0.8821 (tp40) cc_final: 0.8495 (tp-100) REVERT: E 294 TRP cc_start: 0.7706 (m100) cc_final: 0.6942 (m100) REVERT: F 68 GLN cc_start: 0.8884 (tp40) cc_final: 0.8589 (tp-100) REVERT: G 288 GLU cc_start: 0.8425 (pm20) cc_final: 0.7697 (pm20) REVERT: G 294 TRP cc_start: 0.7694 (m100) cc_final: 0.7042 (m100) REVERT: H 68 GLN cc_start: 0.8690 (tp40) cc_final: 0.8343 (tp-100) REVERT: H 290 ASP cc_start: 0.7700 (t0) cc_final: 0.7347 (t0) REVERT: H 294 TRP cc_start: 0.7593 (m100) cc_final: 0.6926 (m100) outliers start: 42 outliers final: 32 residues processed: 252 average time/residue: 0.1521 time to fit residues: 63.4560 Evaluate side-chains 254 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 28 ILE 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 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 147 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 147 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 231 optimal weight: 8.9990 chunk 198 optimal weight: 7.9990 chunk 266 optimal weight: 0.0870 chunk 270 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 262 optimal weight: 6.9990 chunk 7 optimal weight: 0.0370 chunk 159 optimal weight: 0.2980 chunk 264 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.2840 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113597 restraints weight = 34347.994| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.02 r_work: 0.3171 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1979 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= 0.129 Angle : 0.493 6.048 34464 Z= 0.260 Chirality : 0.041 0.162 3992 Planarity : 0.003 0.031 4616 Dihedral : 4.137 22.001 3632 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.47 % Allowed : 15.41 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 3368 helix: 2.12 (0.13), residues: 1432 sheet: -1.20 (0.23), residues: 544 loop : -1.58 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.021 0.001 TYR H 357 PHE 0.013 0.001 PHE A 247 TRP 0.011 0.001 TRP A 294 HIS 0.003 0.000 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00306 (25336) covalent geometry : angle 0.49272 (34464) hydrogen bonds : bond 0.02811 ( 1247) hydrogen bonds : angle 3.99050 ( 3486) ********************** REFINEMENT MACRO_CYCLE 10 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 259 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.895 Fit side-chains REVERT: A 68 GLN cc_start: 0.8966 (tp40) cc_final: 0.8626 (tp-100) REVERT: A 204 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7670 (mm-30) REVERT: A 294 TRP cc_start: 0.7814 (m-10) cc_final: 0.7200 (m-10) REVERT: B 288 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6917 (tm-30) REVERT: B 294 TRP cc_start: 0.7527 (m100) cc_final: 0.6855 (m100) REVERT: C 68 GLN cc_start: 0.8844 (tp40) cc_final: 0.8515 (tp-100) REVERT: C 290 ASP cc_start: 0.7682 (t0) cc_final: 0.7337 (t0) REVERT: C 294 TRP cc_start: 0.7617 (m100) cc_final: 0.7108 (m100) REVERT: C 372 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8056 (tmm) REVERT: D 68 GLN cc_start: 0.8881 (tp40) cc_final: 0.8581 (tp-100) REVERT: D 294 TRP cc_start: 0.7584 (m100) cc_final: 0.6820 (m100) REVERT: E 68 GLN cc_start: 0.8875 (tp40) cc_final: 0.8559 (tp-100) REVERT: E 294 TRP cc_start: 0.7714 (m100) cc_final: 0.7010 (m100) REVERT: F 68 GLN cc_start: 0.8883 (tp40) cc_final: 0.8588 (tp-100) REVERT: G 288 GLU cc_start: 0.8428 (pm20) cc_final: 0.7696 (pm20) REVERT: G 294 TRP cc_start: 0.7646 (m100) cc_final: 0.7060 (m100) REVERT: H 68 GLN cc_start: 0.8692 (tp40) cc_final: 0.8346 (tp-100) REVERT: H 290 ASP cc_start: 0.7708 (t0) cc_final: 0.7355 (t0) REVERT: H 294 TRP cc_start: 0.7592 (m100) cc_final: 0.6925 (m100) outliers start: 37 outliers final: 31 residues processed: 243 average time/residue: 0.1468 time to fit residues: 59.0918 Evaluate side-chains 246 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 28 ILE 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 259 THR 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 297 LEU Chi-restraints excluded: chain F residue 341 THR 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 147 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 171 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 257 optimal weight: 0.1980 chunk 7 optimal weight: 0.0980 chunk 164 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 chunk 305 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113191 restraints weight = 34170.352| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.02 r_work: 0.3173 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25336 Z= 0.133 Angle : 0.773 59.178 34464 Z= 0.450 Chirality : 0.041 0.327 3992 Planarity : 0.003 0.031 4616 Dihedral : 4.168 24.321 3632 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.51 % Allowed : 15.45 % Favored : 83.04 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3368 helix: 2.14 (0.13), residues: 1432 sheet: -1.20 (0.23), residues: 544 loop : -1.57 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.016 0.001 TYR H 357 PHE 0.013 0.001 PHE A 247 TRP 0.010 0.001 TRP A 294 HIS 0.002 0.000 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00287 (25336) covalent geometry : angle 0.77265 (34464) hydrogen bonds : bond 0.02812 ( 1247) hydrogen bonds : angle 3.98586 ( 3486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6279.77 seconds wall clock time: 107 minutes 52.72 seconds (6472.72 seconds total)