Starting phenix.real_space_refine on Thu Mar 5 19:46:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e51_30989/03_2026/7e51_30989.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e51_30989/03_2026/7e51_30989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e51_30989/03_2026/7e51_30989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e51_30989/03_2026/7e51_30989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e51_30989/03_2026/7e51_30989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e51_30989/03_2026/7e51_30989.map" } resolution = 3.23 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= 0.006 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 16 5.21 5 S 56 5.16 5 C 15608 2.51 5 N 4320 2.21 5 O 5024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 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: 25032 Number of models: 1 Model: "" Number of chains: 16 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} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.46, per 1000 atoms: 0.22 Number of scatterers: 25032 At special positions: 0 Unit cell: (159.43, 159.43, 72.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 8 15.00 Mg 16 11.99 O 5024 8.00 N 4320 7.00 C 15608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 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 37 sheets defined 46.5% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 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 removed outlier: 3.521A pdb=" N VAL A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 98 Processing helix chain 'A' and resid 108 through 124 removed outlier: 4.005A pdb=" N VAL A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 135 removed outlier: 3.537A pdb=" N VAL A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 134 " --> pdb=" O PHE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 194 removed outlier: 3.755A pdb=" N SER A 190 " --> pdb=" O HIS A 186 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 removed outlier: 4.059A pdb=" N ALA A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.613A pdb=" N GLY A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 301 removed outlier: 3.789A pdb=" N ALA A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 326 removed outlier: 3.772A pdb=" N GLU A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.734A 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: 3.935A pdb=" N ASP A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 410 removed outlier: 4.028A 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: 3.502A 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: 3.952A pdb=" N VAL B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 removed outlier: 3.670A pdb=" N VAL B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 195 Processing helix chain 'B' and resid 213 through 229 removed outlier: 3.647A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.711A 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: 3.698A pdb=" N GLU B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.701A pdb=" N ILE B 339 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 354 removed outlier: 3.528A pdb=" N THR B 345 " --> pdb=" O THR B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 380 removed outlier: 3.940A pdb=" N ASP B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 410 removed outlier: 4.023A 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 removed outlier: 3.555A pdb=" N VAL C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 98 removed outlier: 3.792A pdb=" N GLN C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 124 removed outlier: 3.535A pdb=" N ILE C 110 " --> pdb=" O GLY C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 135 Processing helix chain 'C' and resid 173 through 194 removed outlier: 3.606A pdb=" N SER C 190 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 229 removed outlier: 3.556A pdb=" N GLY C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 removed outlier: 3.633A pdb=" N PHE C 248 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.663A 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: 3.886A pdb=" N GLU C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.782A 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: 4.003A pdb=" N ASP C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 410 removed outlier: 3.908A 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: 3.545A 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 removed outlier: 3.565A pdb=" N ILE D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) 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: 3.691A 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: 3.747A pdb=" N GLU D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.717A 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: 4.041A pdb=" N ASP D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 410 removed outlier: 3.899A 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 removed outlier: 3.533A pdb=" N ILE E 110 " --> pdb=" O GLY E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 135 Processing helix chain 'E' and resid 173 through 195 Processing helix chain 'E' and resid 213 through 229 removed outlier: 3.679A 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: 3.703A pdb=" N GLU E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG E 326 " --> pdb=" O GLU E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.717A 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: 3.945A pdb=" N ASP E 375 " --> pdb=" O THR E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 410 removed outlier: 3.901A 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 removed outlier: 3.560A pdb=" N ILE F 110 " --> pdb=" O GLY F 106 " (cutoff:3.500A) 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: 3.698A 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: 3.751A pdb=" N GLU F 322 " --> pdb=" O GLU F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.683A 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: 3.981A pdb=" N ASP F 375 " --> pdb=" O THR F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 410 removed outlier: 3.897A 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 removed outlier: 3.557A pdb=" N ILE G 110 " --> pdb=" O GLY G 106 " (cutoff:3.500A) 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: 3.737A 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: 3.926A pdb=" N GLU G 322 " --> pdb=" O GLU G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 339 removed outlier: 3.677A 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: 4.004A pdb=" N ASP G 375 " --> pdb=" O THR G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 410 removed outlier: 3.909A 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 125 removed outlier: 3.561A pdb=" N ILE H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) 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: 3.692A 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: 3.744A pdb=" N GLU H 322 " --> pdb=" O GLU H 318 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG H 326 " --> pdb=" O GLU H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 339 removed outlier: 3.688A 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: 3.949A pdb=" N ASP H 375 " --> pdb=" O THR H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 410 removed outlier: 3.920A 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: 5.983A pdb=" N VAL A 143 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR A 359 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LYS A 386 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 6.673A 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: 5.586A pdb=" N ASN A 147 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL A 166 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 167 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU A 238 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.106A 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: 3.619A pdb=" N THR A 249 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 13 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: 5.944A pdb=" N VAL B 143 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR B 359 " --> pdb=" O GLN B 384 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS B 386 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 6.628A 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: 5.539A pdb=" N ASN B 147 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL B 166 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 149 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 167 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU B 238 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER B 281 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL B 280 " --> pdb=" O GLN B 306 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL B 308 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 282 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 248 through 249 removed outlier: 3.627A pdb=" N THR B 249 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 13 removed outlier: 3.588A pdb=" N ARG C 8 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'C' and resid 331 through 332 removed outlier: 6.994A pdb=" N VAL C 280 " --> pdb=" O GLN C 306 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL C 308 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE C 282 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU C 238 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 282 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU C 240 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 167 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 149 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL C 166 " --> pdb=" O ASN C 147 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASN C 147 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE C 361 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 254 through 256 Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 13 Processing sheet with id=AB7, first strand: chain 'D' and resid 140 through 141 Processing sheet with id=AB8, first strand: chain 'D' and resid 306 through 308 removed outlier: 7.016A pdb=" N VAL D 280 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL D 308 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE D 282 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU D 238 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE D 282 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU D 240 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE D 164 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE D 361 " --> pdb=" O LYS D 386 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.820A pdb=" N THR D 249 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 4 through 13 Processing sheet with id=AC2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AC3, first strand: chain 'E' and resid 143 through 144 removed outlier: 5.933A pdb=" N VAL E 143 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE E 361 " --> pdb=" O LYS E 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 146 through 150 removed outlier: 7.007A pdb=" N PHE E 164 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU E 238 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE E 282 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU E 240 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL E 280 " --> pdb=" O GLN E 306 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL E 308 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE E 282 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 248 through 249 removed outlier: 3.581A pdb=" N THR E 249 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 4 through 13 Processing sheet with id=AC7, first strand: chain 'F' and resid 140 through 141 Processing sheet with id=AC8, first strand: chain 'F' and resid 143 through 144 removed outlier: 5.966A pdb=" N VAL F 143 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE F 361 " --> pdb=" O LYS F 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 146 through 150 removed outlier: 7.042A pdb=" N PHE F 164 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N VAL F 280 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU F 238 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE F 282 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU F 240 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL F 280 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL F 308 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE F 282 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 248 through 249 removed outlier: 3.736A pdb=" N THR F 249 " --> pdb=" O GLY F 253 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 4 through 13 Processing sheet with id=AD3, first strand: chain 'G' and resid 140 through 141 Processing sheet with id=AD4, first strand: chain 'G' and resid 143 through 144 removed outlier: 5.896A pdb=" N VAL G 143 " --> pdb=" O ILE G 385 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE G 361 " --> pdb=" O LYS G 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G' and resid 146 through 150 removed outlier: 6.970A pdb=" N PHE G 164 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU G 238 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE G 282 " --> pdb=" O LEU G 238 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU G 240 " --> pdb=" O ILE G 282 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL G 280 " --> pdb=" O GLN G 306 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL G 308 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE G 282 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 248 through 249 removed outlier: 4.371A pdb=" N THR G 249 " --> pdb=" O GLY G 253 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY G 253 " --> pdb=" O THR G 249 " (cutoff:3.500A) 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 306 through 308 removed outlier: 7.806A pdb=" N LEU H 238 " --> pdb=" O VAL H 280 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE H 282 " --> pdb=" O LEU H 238 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU H 240 " --> pdb=" O ILE H 282 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N PHE H 164 " --> pdb=" O ILE H 148 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE H 361 " --> pdb=" O LYS H 386 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 248 through 249 removed outlier: 3.876A pdb=" N THR H 249 " --> pdb=" O GLY H 253 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE H 256 " --> pdb=" O THR H 259 " (cutoff:3.500A) 1215 hydrogen bonds defined for protein. 3411 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: 4.27 Time building geometry restraints manager: 2.35 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: 8750 1.34 - 1.45: 2681 1.45 - 1.57: 13857 1.57 - 1.69: 8 1.69 - 1.81: 112 Bond restraints: 25408 Sorted by residual: bond pdb=" N GLU E 45 " pdb=" CA GLU E 45 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" N GLU E 47 " pdb=" CA GLU E 47 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.32e-02 5.74e+03 9.64e+00 bond pdb=" N THR G 43 " pdb=" CA THR G 43 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.83e+00 bond pdb=" N GLY D 40 " pdb=" CA GLY D 40 " ideal model delta sigma weight residual 1.448 1.476 -0.028 1.04e-02 9.25e+03 7.13e+00 bond pdb=" N THR H 43 " pdb=" CA THR H 43 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.27e-02 6.20e+03 6.92e+00 ... (remaining 25403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 33621 1.79 - 3.58: 798 3.58 - 5.37: 124 5.37 - 7.16: 15 7.16 - 8.95: 10 Bond angle restraints: 34568 Sorted by residual: angle pdb=" C2 PEP C 501 " pdb=" C1 PEP C 501 " pdb=" O2' PEP C 501 " ideal model delta sigma weight residual 113.54 120.43 -6.89 1.21e+00 6.82e-01 3.24e+01 angle pdb=" C2 PEP E 501 " pdb=" C1 PEP E 501 " pdb=" O2' PEP E 501 " ideal model delta sigma weight residual 113.54 120.42 -6.88 1.21e+00 6.82e-01 3.23e+01 angle pdb=" C2 PEP G 501 " pdb=" C1 PEP G 501 " pdb=" O2' PEP G 501 " ideal model delta sigma weight residual 113.54 120.37 -6.83 1.21e+00 6.82e-01 3.18e+01 angle pdb=" C2 PEP A 501 " pdb=" C1 PEP A 501 " pdb=" O2' PEP A 501 " ideal model delta sigma weight residual 113.54 120.31 -6.77 1.21e+00 6.82e-01 3.13e+01 angle pdb=" C1 PEP H 501 " pdb=" C2 PEP H 501 " pdb=" O2 PEP H 501 " ideal model delta sigma weight residual 111.24 120.19 -8.95 1.68e+00 3.56e-01 2.85e+01 ... (remaining 34563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 13815 17.89 - 35.78: 1086 35.78 - 53.66: 132 53.66 - 71.55: 57 71.55 - 89.44: 38 Dihedral angle restraints: 15128 sinusoidal: 5680 harmonic: 9448 Sorted by residual: dihedral pdb=" CA ARG D 392 " pdb=" C ARG D 392 " pdb=" N SER D 393 " pdb=" CA SER D 393 " ideal model delta harmonic sigma weight residual -180.00 -159.01 -20.99 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ARG F 392 " pdb=" C ARG F 392 " pdb=" N SER F 393 " pdb=" CA SER F 393 " ideal model delta harmonic sigma weight residual 180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ARG E 392 " pdb=" C ARG E 392 " pdb=" N SER E 393 " pdb=" CA SER E 393 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 15125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3065 0.051 - 0.103: 808 0.103 - 0.154: 111 0.154 - 0.206: 6 0.206 - 0.257: 2 Chirality restraints: 3992 Sorted by residual: chirality pdb=" CA GLU E 45 " pdb=" N GLU E 45 " pdb=" C GLU E 45 " pdb=" CB GLU E 45 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL B 328 " pdb=" N VAL B 328 " pdb=" C VAL B 328 " pdb=" CB VAL B 328 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB VAL A 305 " pdb=" CA VAL A 305 " pdb=" CG1 VAL A 305 " pdb=" CG2 VAL A 305 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3989 not shown) Planarity restraints: 4632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 47 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C GLU E 47 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU E 47 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA E 48 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 328 " 0.011 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C VAL B 328 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL B 328 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 329 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 189 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C LYS B 189 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS B 189 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 190 " -0.014 2.00e-02 2.50e+03 ... (remaining 4629 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 383 2.62 - 3.19: 22985 3.19 - 3.76: 38630 3.76 - 4.33: 55540 4.33 - 4.90: 92117 Nonbonded interactions: 209655 Sorted by model distance: nonbonded pdb=" OE2 GLU B 283 " pdb="MG MG B 503 " model vdw 2.055 2.170 nonbonded pdb=" O2P PEP F 501 " pdb="MG MG F 502 " model vdw 2.069 2.170 nonbonded pdb=" OG SER H 42 " pdb="MG MG H 502 " model vdw 2.069 2.170 nonbonded pdb=" O2P PEP D 501 " pdb="MG MG D 502 " model vdw 2.074 2.170 nonbonded pdb=" O2P PEP E 501 " pdb="MG MG E 502 " model vdw 2.077 2.170 ... (remaining 209650 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.260 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.005 0.058 25408 Z= 0.232 Angle : 0.689 8.951 34568 Z= 0.403 Chirality : 0.045 0.257 3992 Planarity : 0.004 0.052 4632 Dihedral : 14.036 89.439 9128 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.09 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.14 (0.12), residues: 3368 helix: -1.02 (0.12), residues: 1368 sheet: -2.52 (0.20), residues: 536 loop : -2.92 (0.13), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 34 TYR 0.009 0.001 TYR C 132 PHE 0.015 0.002 PHE B 247 TRP 0.008 0.001 TRP C 294 HIS 0.007 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00508 (25408) covalent geometry : angle 0.68931 (34568) hydrogen bonds : bond 0.16917 ( 1215) hydrogen bonds : angle 6.66319 ( 3411) *********************** 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 360 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7960 (pm20) cc_final: 0.7592 (pm20) REVERT: B 65 LYS cc_start: 0.8844 (ptpt) cc_final: 0.8498 (ptmt) REVERT: C 47 GLU cc_start: 0.7782 (pm20) cc_final: 0.7572 (pm20) REVERT: C 264 ASP cc_start: 0.7355 (m-30) cc_final: 0.7126 (p0) REVERT: C 288 GLU cc_start: 0.7331 (pm20) cc_final: 0.6973 (pp20) REVERT: D 119 LYS cc_start: 0.8236 (mtpt) cc_final: 0.7856 (mttp) REVERT: E 288 GLU cc_start: 0.7353 (pm20) cc_final: 0.7048 (pp20) REVERT: G 145 MET cc_start: 0.8833 (mmm) cc_final: 0.8608 (mmt) REVERT: G 321 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6883 (mm-30) REVERT: H 288 GLU cc_start: 0.7223 (pm20) cc_final: 0.6884 (pp20) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.1936 time to fit residues: 105.0221 Evaluate side-chains 216 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 363 HIS E 6 GLN F 6 GLN G 6 GLN G 363 HIS H 6 GLN H 363 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.131636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103422 restraints weight = 38168.264| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.28 r_work: 0.3150 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 25408 Z= 0.156 Angle : 0.553 7.066 34568 Z= 0.292 Chirality : 0.042 0.154 3992 Planarity : 0.004 0.035 4632 Dihedral : 5.378 71.228 3664 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.00 % Allowed : 7.76 % Favored : 91.24 % 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: -1.56 (0.14), residues: 3368 helix: 0.69 (0.13), residues: 1416 sheet: -2.29 (0.20), residues: 544 loop : -2.33 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 392 TYR 0.019 0.001 TYR C 357 PHE 0.021 0.002 PHE D 32 TRP 0.006 0.001 TRP A 294 HIS 0.006 0.001 HIS G 363 Details of bonding type rmsd covalent geometry : bond 0.00364 (25408) covalent geometry : angle 0.55304 (34568) hydrogen bonds : bond 0.03703 ( 1215) hydrogen bonds : angle 4.76584 ( 3411) *********************** 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 272 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8483 (pm20) cc_final: 0.8025 (pm20) REVERT: A 282 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8634 (pt) REVERT: B 65 LYS cc_start: 0.8804 (ptpt) cc_final: 0.8587 (ptmt) REVERT: D 119 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7781 (mttp) REVERT: D 264 ASP cc_start: 0.7755 (m-30) cc_final: 0.7198 (p0) REVERT: E 264 ASP cc_start: 0.7763 (m-30) cc_final: 0.7277 (p0) REVERT: E 288 GLU cc_start: 0.7675 (pm20) cc_final: 0.7340 (pp20) REVERT: F 119 LYS cc_start: 0.8304 (mtpt) cc_final: 0.7758 (mttp) REVERT: F 264 ASP cc_start: 0.7836 (m-30) cc_final: 0.7315 (p0) REVERT: G 119 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7817 (mttp) REVERT: G 256 PHE cc_start: 0.6349 (t80) cc_final: 0.6143 (t80) REVERT: G 264 ASP cc_start: 0.7969 (m-30) cc_final: 0.7433 (p0) REVERT: G 322 GLU cc_start: 0.7909 (tt0) cc_final: 0.7179 (tp30) REVERT: G 351 LEU cc_start: 0.8776 (mp) cc_final: 0.8547 (mp) REVERT: H 261 ARG cc_start: 0.7046 (ptp-170) cc_final: 0.6810 (ptp-170) REVERT: H 264 ASP cc_start: 0.7782 (m-30) cc_final: 0.7189 (p0) REVERT: H 288 GLU cc_start: 0.7784 (pm20) cc_final: 0.6918 (pp20) outliers start: 25 outliers final: 10 residues processed: 268 average time/residue: 0.1606 time to fit residues: 68.1177 Evaluate side-chains 221 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 210 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 75 optimal weight: 0.9980 chunk 195 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 230 optimal weight: 0.0570 chunk 150 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 328 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 253 optimal weight: 0.8980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.129238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102226 restraints weight = 38475.833| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.18 r_work: 0.3148 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25408 Z= 0.106 Angle : 0.493 6.806 34568 Z= 0.259 Chirality : 0.040 0.146 3992 Planarity : 0.004 0.058 4632 Dihedral : 5.194 73.573 3664 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.76 % Allowed : 10.07 % Favored : 89.17 % 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: -0.78 (0.14), residues: 3368 helix: 1.51 (0.14), residues: 1416 sheet: -1.95 (0.21), residues: 544 loop : -2.08 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 10 TYR 0.023 0.001 TYR G 357 PHE 0.023 0.002 PHE G 32 TRP 0.004 0.001 TRP B 294 HIS 0.004 0.000 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00244 (25408) covalent geometry : angle 0.49261 (34568) hydrogen bonds : bond 0.03003 ( 1215) hydrogen bonds : angle 4.39426 ( 3411) *********************** 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 234 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 282 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8620 (pt) REVERT: A 301 ILE cc_start: 0.8154 (pt) cc_final: 0.7771 (mt) REVERT: C 47 GLU cc_start: 0.8438 (pm20) cc_final: 0.8047 (pm20) REVERT: D 119 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7771 (mttp) REVERT: D 264 ASP cc_start: 0.7725 (m-30) cc_final: 0.7199 (p0) REVERT: D 351 LEU cc_start: 0.8657 (mp) cc_final: 0.8385 (mp) REVERT: E 256 PHE cc_start: 0.5781 (t80) cc_final: 0.5525 (t80) REVERT: E 264 ASP cc_start: 0.7727 (m-30) cc_final: 0.7323 (p0) REVERT: E 288 GLU cc_start: 0.7531 (pm20) cc_final: 0.7299 (pp20) REVERT: E 351 LEU cc_start: 0.8638 (mp) cc_final: 0.8392 (mp) REVERT: F 119 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7751 (mttp) REVERT: F 264 ASP cc_start: 0.7774 (m-30) cc_final: 0.7338 (p0) REVERT: G 119 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7780 (mttp) REVERT: G 256 PHE cc_start: 0.6357 (t80) cc_final: 0.6098 (t80) REVERT: G 264 ASP cc_start: 0.8087 (m-30) cc_final: 0.7542 (p0) REVERT: G 322 GLU cc_start: 0.7862 (tt0) cc_final: 0.7172 (tp30) REVERT: G 351 LEU cc_start: 0.8768 (mp) cc_final: 0.8525 (mp) REVERT: H 261 ARG cc_start: 0.7146 (ptp-170) cc_final: 0.6897 (ptp-170) REVERT: H 264 ASP cc_start: 0.7774 (m-30) cc_final: 0.7265 (p0) REVERT: H 282 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8611 (pt) REVERT: H 351 LEU cc_start: 0.8644 (mp) cc_final: 0.8376 (mp) outliers start: 19 outliers final: 13 residues processed: 228 average time/residue: 0.1690 time to fit residues: 61.5034 Evaluate side-chains 211 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 282 ILE 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 259 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 7 optimal weight: 0.0050 chunk 210 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 284 optimal weight: 0.9980 chunk 272 optimal weight: 5.9990 overall best weight: 1.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.101969 restraints weight = 38137.787| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.29 r_work: 0.3136 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25408 Z= 0.182 Angle : 0.525 6.342 34568 Z= 0.276 Chirality : 0.042 0.141 3992 Planarity : 0.004 0.033 4632 Dihedral : 5.241 76.046 3664 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.23 % Allowed : 11.15 % Favored : 87.62 % 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: -0.58 (0.14), residues: 3368 helix: 1.61 (0.14), residues: 1424 sheet: -1.81 (0.21), residues: 544 loop : -1.93 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 326 TYR 0.021 0.002 TYR F 357 PHE 0.022 0.002 PHE C 32 TRP 0.006 0.001 TRP B 294 HIS 0.007 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00441 (25408) covalent geometry : angle 0.52462 (34568) hydrogen bonds : bond 0.03364 ( 1215) hydrogen bonds : angle 4.34674 ( 3411) *********************** 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 221 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8530 (pm20) cc_final: 0.8098 (pm20) REVERT: A 301 ILE cc_start: 0.8074 (pt) cc_final: 0.7628 (mt) REVERT: B 194 LYS cc_start: 0.8920 (tmmt) cc_final: 0.8718 (ttpt) REVERT: C 351 LEU cc_start: 0.8622 (mp) cc_final: 0.8353 (mp) REVERT: D 119 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7796 (mttp) REVERT: D 264 ASP cc_start: 0.7727 (m-30) cc_final: 0.7307 (p0) REVERT: E 256 PHE cc_start: 0.5725 (t80) cc_final: 0.5446 (t80) REVERT: E 264 ASP cc_start: 0.7842 (m-30) cc_final: 0.7432 (p0) REVERT: E 282 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8874 (pt) REVERT: F 145 MET cc_start: 0.9354 (mmm) cc_final: 0.9012 (mmm) REVERT: F 264 ASP cc_start: 0.7882 (m-30) cc_final: 0.7360 (p0) REVERT: G 119 LYS cc_start: 0.8315 (mtpt) cc_final: 0.7792 (mttp) REVERT: G 264 ASP cc_start: 0.8054 (m-30) cc_final: 0.7504 (p0) REVERT: G 322 GLU cc_start: 0.7960 (tt0) cc_final: 0.7212 (tp30) REVERT: H 264 ASP cc_start: 0.7882 (m-30) cc_final: 0.7354 (p0) REVERT: H 282 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8634 (pt) outliers start: 31 outliers final: 19 residues processed: 214 average time/residue: 0.1626 time to fit residues: 55.6754 Evaluate side-chains 201 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 91 optimal weight: 3.9990 chunk 287 optimal weight: 0.5980 chunk 137 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 233 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.101953 restraints weight = 38019.306| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.28 r_work: 0.3147 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25408 Z= 0.169 Angle : 0.514 6.143 34568 Z= 0.270 Chirality : 0.041 0.155 3992 Planarity : 0.004 0.033 4632 Dihedral : 5.259 78.621 3664 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 1.67 % Allowed : 11.70 % Favored : 86.62 % 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: -0.37 (0.15), residues: 3368 helix: 1.76 (0.14), residues: 1424 sheet: -1.64 (0.21), residues: 544 loop : -1.82 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 52 TYR 0.027 0.002 TYR G 357 PHE 0.024 0.002 PHE H 256 TRP 0.005 0.001 TRP B 294 HIS 0.005 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00409 (25408) covalent geometry : angle 0.51359 (34568) hydrogen bonds : bond 0.03224 ( 1215) hydrogen bonds : angle 4.28090 ( 3411) *********************** 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 223 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8609 (pm20) cc_final: 0.8115 (pm20) REVERT: A 282 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8651 (pt) REVERT: A 301 ILE cc_start: 0.7979 (pt) cc_final: 0.7561 (mt) REVERT: C 47 GLU cc_start: 0.8402 (pm20) cc_final: 0.7919 (pt0) REVERT: C 351 LEU cc_start: 0.8633 (mp) cc_final: 0.8367 (mp) REVERT: D 119 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7798 (mttp) REVERT: D 264 ASP cc_start: 0.7751 (m-30) cc_final: 0.7352 (p0) REVERT: E 256 PHE cc_start: 0.5796 (t80) cc_final: 0.5538 (t80) REVERT: E 264 ASP cc_start: 0.7796 (m-30) cc_final: 0.7400 (p0) REVERT: F 119 LYS cc_start: 0.8333 (mtpt) cc_final: 0.7795 (mttp) REVERT: F 264 ASP cc_start: 0.7923 (m-30) cc_final: 0.7362 (p0) REVERT: G 119 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7789 (mttp) REVERT: G 264 ASP cc_start: 0.8078 (m-30) cc_final: 0.7504 (p0) REVERT: G 322 GLU cc_start: 0.7994 (tt0) cc_final: 0.7253 (tp30) REVERT: H 145 MET cc_start: 0.9468 (mmm) cc_final: 0.9220 (mmt) REVERT: H 282 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8655 (pt) outliers start: 42 outliers final: 22 residues processed: 214 average time/residue: 0.1702 time to fit residues: 58.4508 Evaluate side-chains 194 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 63 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 270 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.102116 restraints weight = 38012.644| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.27 r_work: 0.3139 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25408 Z= 0.159 Angle : 0.508 6.116 34568 Z= 0.267 Chirality : 0.041 0.149 3992 Planarity : 0.004 0.033 4632 Dihedral : 5.237 80.648 3664 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 1.59 % Allowed : 12.66 % Favored : 85.75 % 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: -0.26 (0.15), residues: 3368 helix: 1.81 (0.14), residues: 1440 sheet: -1.53 (0.21), residues: 544 loop : -1.79 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 131 TYR 0.021 0.002 TYR E 357 PHE 0.023 0.002 PHE C 32 TRP 0.004 0.000 TRP B 294 HIS 0.003 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00383 (25408) covalent geometry : angle 0.50824 (34568) hydrogen bonds : bond 0.03130 ( 1215) hydrogen bonds : angle 4.22001 ( 3411) *********************** 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 223 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.826 Fit side-chains REVERT: A 47 GLU cc_start: 0.8607 (pm20) cc_final: 0.8102 (pm20) REVERT: A 301 ILE cc_start: 0.7902 (pt) cc_final: 0.7486 (mt) REVERT: B 146 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.9058 (mtt) REVERT: C 119 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7751 (mttp) REVERT: D 119 LYS cc_start: 0.8333 (mtpt) cc_final: 0.7796 (mttp) REVERT: D 264 ASP cc_start: 0.7795 (m-30) cc_final: 0.7399 (p0) REVERT: E 256 PHE cc_start: 0.5783 (t80) cc_final: 0.5576 (t80) REVERT: E 264 ASP cc_start: 0.7868 (m-30) cc_final: 0.7460 (p0) REVERT: F 119 LYS cc_start: 0.8335 (mtpt) cc_final: 0.7798 (mttp) REVERT: F 264 ASP cc_start: 0.8039 (m-30) cc_final: 0.7471 (p0) REVERT: G 119 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7861 (mttp) REVERT: G 145 MET cc_start: 0.9356 (mmm) cc_final: 0.9041 (mmm) REVERT: G 252 THR cc_start: 0.6901 (OUTLIER) cc_final: 0.6672 (t) REVERT: G 264 ASP cc_start: 0.8064 (m-30) cc_final: 0.7504 (p0) REVERT: G 322 GLU cc_start: 0.7992 (tt0) cc_final: 0.7324 (tp30) REVERT: H 145 MET cc_start: 0.9460 (mmm) cc_final: 0.9248 (mmt) REVERT: H 282 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8657 (pt) outliers start: 40 outliers final: 28 residues processed: 214 average time/residue: 0.1668 time to fit residues: 56.7356 Evaluate side-chains 199 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 266 MET Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 396 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 74 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 289 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 177 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 329 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.124887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.096696 restraints weight = 38708.249| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.25 r_work: 0.3059 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.065 25408 Z= 0.414 Angle : 0.704 6.944 34568 Z= 0.374 Chirality : 0.050 0.181 3992 Planarity : 0.006 0.052 4632 Dihedral : 5.807 86.707 3664 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 2.11 % Allowed : 13.85 % Favored : 84.04 % 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: -0.88 (0.14), residues: 3368 helix: 1.11 (0.13), residues: 1416 sheet: -1.46 (0.23), residues: 472 loop : -2.00 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 10 TYR 0.032 0.003 TYR G 357 PHE 0.025 0.003 PHE D 269 TRP 0.008 0.001 TRP F 291 HIS 0.008 0.002 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00998 (25408) covalent geometry : angle 0.70425 (34568) hydrogen bonds : bond 0.04781 ( 1215) hydrogen bonds : angle 4.78173 ( 3411) *********************** 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 211 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 158 time to evaluate : 1.013 Fit side-chains REVERT: C 47 GLU cc_start: 0.8562 (pm20) cc_final: 0.8206 (pm20) REVERT: C 119 LYS cc_start: 0.8424 (mtpt) cc_final: 0.7886 (mttp) REVERT: D 119 LYS cc_start: 0.8384 (mtpt) cc_final: 0.7956 (mttp) REVERT: D 146 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.9077 (mtt) REVERT: E 145 MET cc_start: 0.9400 (mmm) cc_final: 0.9120 (mmt) REVERT: E 146 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.9028 (mtt) REVERT: F 145 MET cc_start: 0.9387 (mmm) cc_final: 0.9088 (mmt) REVERT: F 146 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8961 (mtt) REVERT: G 119 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7901 (mttp) REVERT: G 322 GLU cc_start: 0.8066 (tt0) cc_final: 0.7291 (tp30) outliers start: 53 outliers final: 34 residues processed: 192 average time/residue: 0.1656 time to fit residues: 50.7564 Evaluate side-chains 193 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 396 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 82 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 0.0010 chunk 81 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.128294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101490 restraints weight = 38232.224| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.17 r_work: 0.3120 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25408 Z= 0.103 Angle : 0.500 5.970 34568 Z= 0.262 Chirality : 0.040 0.154 3992 Planarity : 0.004 0.033 4632 Dihedral : 5.381 85.807 3664 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.12 % Rotamer: Outliers : 1.35 % Allowed : 14.69 % Favored : 83.96 % 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: -0.12 (0.15), residues: 3368 helix: 1.92 (0.14), residues: 1440 sheet: -1.19 (0.23), residues: 472 loop : -1.82 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 10 TYR 0.027 0.002 TYR B 357 PHE 0.027 0.002 PHE D 269 TRP 0.004 0.001 TRP C 294 HIS 0.003 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00242 (25408) covalent geometry : angle 0.50029 (34568) hydrogen bonds : bond 0.02757 ( 1215) hydrogen bonds : angle 4.19764 ( 3411) *********************** 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 207 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.954 Fit side-chains REVERT: A 47 GLU cc_start: 0.8469 (pm20) cc_final: 0.8027 (pt0) REVERT: B 146 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.8913 (mtt) REVERT: C 47 GLU cc_start: 0.8412 (pm20) cc_final: 0.8013 (pm20) REVERT: C 119 LYS cc_start: 0.8296 (mtpt) cc_final: 0.7792 (mttp) REVERT: C 146 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8963 (mtt) REVERT: C 351 LEU cc_start: 0.8703 (mp) cc_final: 0.8469 (mp) REVERT: D 119 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7757 (mttp) REVERT: F 119 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7724 (mttp) REVERT: G 119 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7696 (mttp) REVERT: G 252 THR cc_start: 0.6752 (OUTLIER) cc_final: 0.6513 (t) REVERT: G 322 GLU cc_start: 0.7973 (tt0) cc_final: 0.7326 (tp30) REVERT: G 351 LEU cc_start: 0.8811 (mp) cc_final: 0.8596 (mp) outliers start: 34 outliers final: 26 residues processed: 199 average time/residue: 0.1744 time to fit residues: 55.1815 Evaluate side-chains 192 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 266 MET Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 258 optimal weight: 0.0770 chunk 159 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 220 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102117 restraints weight = 38296.392| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.17 r_work: 0.3137 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25408 Z= 0.099 Angle : 0.477 5.858 34568 Z= 0.250 Chirality : 0.040 0.155 3992 Planarity : 0.003 0.032 4632 Dihedral : 5.088 84.293 3664 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 1.51 % Allowed : 14.45 % Favored : 84.04 % 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: 0.22 (0.15), residues: 3368 helix: 2.24 (0.14), residues: 1440 sheet: -1.02 (0.23), residues: 472 loop : -1.68 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 10 TYR 0.011 0.001 TYR A 185 PHE 0.028 0.002 PHE D 269 TRP 0.002 0.000 TRP A 291 HIS 0.002 0.000 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00228 (25408) covalent geometry : angle 0.47681 (34568) hydrogen bonds : bond 0.02562 ( 1215) hydrogen bonds : angle 4.01811 ( 3411) *********************** 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 214 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.793 Fit side-chains REVERT: A 47 GLU cc_start: 0.8400 (pm20) cc_final: 0.7997 (pt0) REVERT: A 301 ILE cc_start: 0.7952 (pt) cc_final: 0.7651 (mt) REVERT: A 325 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7602 (mm-30) REVERT: B 146 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8938 (mtt) REVERT: C 47 GLU cc_start: 0.8377 (pm20) cc_final: 0.7915 (pt0) REVERT: C 119 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7799 (mttp) REVERT: C 146 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.8999 (mtt) REVERT: C 351 LEU cc_start: 0.8684 (mp) cc_final: 0.8417 (mp) REVERT: D 146 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8831 (mtt) REVERT: E 264 ASP cc_start: 0.7921 (m-30) cc_final: 0.7504 (p0) REVERT: G 119 LYS cc_start: 0.8296 (mtpt) cc_final: 0.7757 (mttp) REVERT: G 252 THR cc_start: 0.6899 (OUTLIER) cc_final: 0.6687 (t) REVERT: G 322 GLU cc_start: 0.7921 (tt0) cc_final: 0.7387 (tp30) REVERT: G 351 LEU cc_start: 0.8795 (mp) cc_final: 0.8573 (mp) outliers start: 38 outliers final: 25 residues processed: 205 average time/residue: 0.1638 time to fit residues: 53.9600 Evaluate side-chains 198 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 396 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 321 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.130394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.102313 restraints weight = 38151.704| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.29 r_work: 0.3127 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25408 Z= 0.175 Angle : 0.526 6.173 34568 Z= 0.276 Chirality : 0.042 0.151 3992 Planarity : 0.004 0.032 4632 Dihedral : 5.223 83.155 3664 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 1.35 % Allowed : 14.65 % Favored : 84.00 % 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: 0.12 (0.15), residues: 3368 helix: 2.10 (0.14), residues: 1440 sheet: -1.08 (0.23), residues: 480 loop : -1.66 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 10 TYR 0.014 0.001 TYR A 185 PHE 0.029 0.003 PHE D 269 TRP 0.003 0.001 TRP B 294 HIS 0.003 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00424 (25408) covalent geometry : angle 0.52564 (34568) hydrogen bonds : bond 0.03157 ( 1215) hydrogen bonds : angle 4.18291 ( 3411) ********************** 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 203 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8472 (pm20) cc_final: 0.8082 (pt0) REVERT: A 146 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.9007 (mtt) REVERT: A 284 ASP cc_start: 0.8520 (m-30) cc_final: 0.8250 (m-30) REVERT: A 301 ILE cc_start: 0.7956 (pt) cc_final: 0.7582 (mt) REVERT: B 146 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.9093 (mtt) REVERT: B 325 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7740 (mm-30) REVERT: C 47 GLU cc_start: 0.8442 (pm20) cc_final: 0.8018 (pm20) REVERT: C 90 ASP cc_start: 0.7465 (m-30) cc_final: 0.7188 (m-30) REVERT: C 119 LYS cc_start: 0.8370 (mtpt) cc_final: 0.7855 (mttp) REVERT: C 146 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.9265 (mtt) REVERT: D 119 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7783 (mttp) REVERT: D 146 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8954 (mtt) REVERT: E 264 ASP cc_start: 0.8006 (m-30) cc_final: 0.7517 (p0) REVERT: G 119 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7865 (mttp) REVERT: G 252 THR cc_start: 0.6936 (OUTLIER) cc_final: 0.6712 (t) REVERT: G 322 GLU cc_start: 0.8009 (tt0) cc_final: 0.7432 (tp30) REVERT: G 351 LEU cc_start: 0.8795 (mp) cc_final: 0.8563 (mp) outliers start: 34 outliers final: 28 residues processed: 194 average time/residue: 0.1686 time to fit residues: 52.0742 Evaluate side-chains 199 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 396 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 177 optimal weight: 6.9990 chunk 269 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 273 optimal weight: 9.9990 chunk 240 optimal weight: 8.9990 chunk 306 optimal weight: 0.5980 chunk 330 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 327 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 260 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102439 restraints weight = 38196.214| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.16 r_work: 0.3141 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25408 Z= 0.099 Angle : 0.479 6.704 34568 Z= 0.250 Chirality : 0.040 0.152 3992 Planarity : 0.003 0.032 4632 Dihedral : 5.051 79.953 3664 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 1.19 % Allowed : 14.97 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.36 (0.14), residues: 1440 sheet: -0.96 (0.23), residues: 480 loop : -1.62 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 10 TYR 0.011 0.001 TYR A 185 PHE 0.029 0.002 PHE D 269 TRP 0.003 0.001 TRP A 291 HIS 0.002 0.000 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00231 (25408) covalent geometry : angle 0.47948 (34568) hydrogen bonds : bond 0.02502 ( 1215) hydrogen bonds : angle 4.02510 ( 3411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5330.38 seconds wall clock time: 91 minutes 54.53 seconds (5514.53 seconds total)