Starting phenix.real_space_refine on Fri Jul 3 20:32:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2g_42911/07_2026/8v2g_42911.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2g_42911/07_2026/8v2g_42911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v2g_42911/07_2026/8v2g_42911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2g_42911/07_2026/8v2g_42911.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2g_42911/07_2026/8v2g_42911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2g_42911/07_2026/8v2g_42911.cif" } resolution = 3.18 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= 1.000 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 Ca 8 9.91 5 K 4 8.98 5 S 124 5.16 5 C 10324 2.51 5 N 2724 2.21 5 O 2979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16163 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2883 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1152 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "B" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2884 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain: "F" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1152 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "C" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2884 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain: "G" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1152 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "D" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2884 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain: "H" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1152 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' K': 4} Chain breaks: 4 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.69, per 1000 atoms: 0.23 Number of scatterers: 16163 At special positions: 0 Unit cell: (143.62, 141.9, 98.04, 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) Ca 8 19.99 K 4 19.00 S 124 16.00 O 2979 8.00 N 2724 7.00 C 10324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 371 " distance=2.04 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 371 " distance=2.04 Simple disulfide: pdb=" SG CYS D 333 " - pdb=" SG CYS D 371 " distance=2.04 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: 1.32 Conformation dependent library (CDL) restraints added in 709.0 milliseconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3824 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 74.5% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 123 through 160 removed outlier: 3.580A pdb=" N SER A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TRP A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 202 removed outlier: 3.846A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.594A pdb=" N LEU A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 268 through 278 removed outlier: 3.503A pdb=" N ARG A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 298 through 310 removed outlier: 3.626A pdb=" N VAL A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 335 removed outlier: 3.617A pdb=" N ILE A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 369 through 396 removed outlier: 4.645A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU A 389 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 439 removed outlier: 3.661A pdb=" N LYS A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 430 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 478 removed outlier: 4.056A pdb=" N VAL A 449 " --> pdb=" O ASP A 445 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG A 450 " --> pdb=" O HIS A 446 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 17 Processing helix chain 'E' and resid 28 through 38 removed outlier: 3.551A pdb=" N SER E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.811A pdb=" N VAL E 55 " --> pdb=" O MET E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.667A pdb=" N ILE E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 138 through 147 removed outlier: 4.184A pdb=" N VAL E 142 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET E 144 " --> pdb=" O GLU E 140 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET E 145 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA E 147 " --> pdb=" O GLN E 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 158 removed outlier: 3.556A pdb=" N SER B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TRP B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 201 removed outlier: 3.849A pdb=" N LEU B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 212 through 226 Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'B' and resid 260 through 267 Processing helix chain 'B' and resid 268 through 278 removed outlier: 3.521A pdb=" N ARG B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 298 through 310 removed outlier: 3.823A pdb=" N VAL B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 335 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 369 through 396 removed outlier: 4.755A pdb=" N ALA B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU B 389 " --> pdb=" O GLY B 385 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 440 removed outlier: 3.734A pdb=" N LYS B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 478 removed outlier: 4.006A pdb=" N VAL B 449 " --> pdb=" O ASP B 445 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 450 " --> pdb=" O HIS B 446 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 28 through 39 Processing helix chain 'F' and resid 44 through 56 removed outlier: 3.750A pdb=" N ILE F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL F 55 " --> pdb=" O MET F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 76 Processing helix chain 'F' and resid 80 through 93 removed outlier: 3.682A pdb=" N ILE F 85 " --> pdb=" O SER F 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'F' and resid 138 through 144 removed outlier: 4.056A pdb=" N VAL F 142 " --> pdb=" O TYR F 138 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 138 through 144' Processing helix chain 'C' and resid 123 through 157 removed outlier: 3.586A pdb=" N SER C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY C 146 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 202 removed outlier: 3.762A pdb=" N ILE C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 256 through 258 No H-bonds generated for 'chain 'C' and resid 256 through 258' Processing helix chain 'C' and resid 260 through 266 Processing helix chain 'C' and resid 267 through 278 removed outlier: 4.210A pdb=" N ALA C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 293 Processing helix chain 'C' and resid 298 through 310 removed outlier: 3.560A pdb=" N VAL C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 335 Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'C' and resid 369 through 396 removed outlier: 4.646A pdb=" N ALA C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU C 389 " --> pdb=" O GLY C 385 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 440 removed outlier: 3.653A pdb=" N LYS C 418 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 478 removed outlier: 3.990A pdb=" N VAL C 449 " --> pdb=" O ASP C 445 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG C 450 " --> pdb=" O HIS C 446 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 18 removed outlier: 3.566A pdb=" N LEU G 18 " --> pdb=" O GLU G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 39 Processing helix chain 'G' and resid 44 through 56 removed outlier: 3.853A pdb=" N VAL G 55 " --> pdb=" O MET G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 77 removed outlier: 4.125A pdb=" N LYS G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 92 removed outlier: 4.193A pdb=" N ILE G 85 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG G 86 " --> pdb=" O GLU G 82 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 138 through 147 removed outlier: 3.593A pdb=" N VAL G 142 " --> pdb=" O TYR G 138 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA G 147 " --> pdb=" O GLN G 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 160 removed outlier: 3.573A pdb=" N SER D 136 " --> pdb=" O ARG D 132 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU D 140 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 146 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP D 158 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 202 removed outlier: 3.849A pdb=" N LEU D 169 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 212 through 226 Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 260 through 267 Processing helix chain 'D' and resid 268 through 278 removed outlier: 3.541A pdb=" N ARG D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 298 through 310 removed outlier: 3.704A pdb=" N VAL D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 335 removed outlier: 3.603A pdb=" N ILE D 324 " --> pdb=" O ILE D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 Processing helix chain 'D' and resid 369 through 396 removed outlier: 4.784A pdb=" N ALA D 388 " --> pdb=" O ALA D 384 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU D 389 " --> pdb=" O GLY D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 440 removed outlier: 3.634A pdb=" N LYS D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN D 426 " --> pdb=" O ASN D 422 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 478 removed outlier: 3.661A pdb=" N VAL D 449 " --> pdb=" O ASP D 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.526A pdb=" N ILE H 9 " --> pdb=" O THR H 5 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU H 11 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 39 Processing helix chain 'H' and resid 44 through 56 removed outlier: 3.813A pdb=" N VAL H 55 " --> pdb=" O MET H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 76 Processing helix chain 'H' and resid 80 through 93 removed outlier: 3.814A pdb=" N ILE H 85 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE H 89 " --> pdb=" O ILE H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 112 Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 140 through 146 removed outlier: 4.117A pdb=" N MET H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 241 Processing sheet with id=AA2, first strand: chain 'E' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'B' and resid 235 through 241 Processing sheet with id=AA4, first strand: chain 'F' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'C' and resid 235 through 241 Processing sheet with id=AA6, first strand: chain 'G' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'D' and resid 235 through 241 Processing sheet with id=AA8, first strand: chain 'H' and resid 100 through 101 1078 hydrogen bonds defined for protein. 3147 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: 2.56 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5232 1.34 - 1.46: 3703 1.46 - 1.58: 7276 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 16427 Sorted by residual: bond pdb=" C ILE C 261 " pdb=" N PRO C 262 " ideal model delta sigma weight residual 1.337 1.347 -0.011 9.80e-03 1.04e+04 1.23e+00 bond pdb=" CB ASN H 53 " pdb=" CG ASN H 53 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.12e+00 bond pdb=" C ILE A 261 " pdb=" N PRO A 262 " ideal model delta sigma weight residual 1.337 1.347 -0.010 9.80e-03 1.04e+04 1.06e+00 bond pdb=" CB GLU E 7 " pdb=" CG GLU E 7 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.89e-01 bond pdb=" CB GLU F 114 " pdb=" CG GLU F 114 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.84e-01 ... (remaining 16422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 21784 1.53 - 3.07: 324 3.07 - 4.60: 41 4.60 - 6.14: 18 6.14 - 7.67: 7 Bond angle restraints: 22174 Sorted by residual: angle pdb=" N SER B 245 " pdb=" CA SER B 245 " pdb=" C SER B 245 " ideal model delta sigma weight residual 114.56 110.43 4.13 1.27e+00 6.20e-01 1.06e+01 angle pdb=" N SER D 245 " pdb=" CA SER D 245 " pdb=" C SER D 245 " ideal model delta sigma weight residual 114.56 110.52 4.04 1.27e+00 6.20e-01 1.01e+01 angle pdb=" N SER C 245 " pdb=" CA SER C 245 " pdb=" C SER C 245 " ideal model delta sigma weight residual 114.56 110.54 4.02 1.27e+00 6.20e-01 1.00e+01 angle pdb=" N SER A 245 " pdb=" CA SER A 245 " pdb=" C SER A 245 " ideal model delta sigma weight residual 114.56 110.59 3.97 1.27e+00 6.20e-01 9.79e+00 angle pdb=" N VAL G 55 " pdb=" CA VAL G 55 " pdb=" C VAL G 55 " ideal model delta sigma weight residual 113.39 108.85 4.54 1.47e+00 4.63e-01 9.55e+00 ... (remaining 22169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 8690 17.81 - 35.61: 946 35.61 - 53.42: 183 53.42 - 71.22: 68 71.22 - 89.03: 5 Dihedral angle restraints: 9892 sinusoidal: 3988 harmonic: 5904 Sorted by residual: dihedral pdb=" CA ASP A 200 " pdb=" CB ASP A 200 " pdb=" CG ASP A 200 " pdb=" OD1 ASP A 200 " ideal model delta sinusoidal sigma weight residual -30.00 -86.60 56.60 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP A 445 " pdb=" CB ASP A 445 " pdb=" CG ASP A 445 " pdb=" OD1 ASP A 445 " ideal model delta sinusoidal sigma weight residual -30.00 -86.34 56.34 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU G 6 " pdb=" CG GLU G 6 " pdb=" CD GLU G 6 " pdb=" OE1 GLU G 6 " ideal model delta sinusoidal sigma weight residual 0.00 -89.03 89.03 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 9889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1800 0.036 - 0.071: 620 0.071 - 0.107: 113 0.107 - 0.142: 26 0.142 - 0.178: 5 Chirality restraints: 2564 Sorted by residual: chirality pdb=" CA ASP H 24 " pdb=" N ASP H 24 " pdb=" C ASP H 24 " pdb=" CB ASP H 24 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" CB THR C 379 " pdb=" CA THR C 379 " pdb=" OG1 THR C 379 " pdb=" CG2 THR C 379 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CB THR D 379 " pdb=" CA THR D 379 " pdb=" OG1 THR D 379 " pdb=" CG2 THR D 379 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 2561 not shown) Planarity restraints: 2783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 261 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO C 262 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 262 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 262 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 261 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO D 262 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 262 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 262 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 261 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO A 262 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " 0.021 5.00e-02 4.00e+02 ... (remaining 2780 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.76: 2739 2.76 - 3.35: 18766 3.35 - 3.95: 28784 3.95 - 4.54: 40003 4.54 - 5.14: 59595 Nonbonded interactions: 149887 Sorted by model distance: nonbonded pdb=" O ARG G 106 " pdb=" OG1 THR G 110 " model vdw 2.165 3.040 nonbonded pdb=" N GLU E 7 " pdb=" OE1 GLU E 7 " model vdw 2.194 3.120 nonbonded pdb=" OG1 THR G 28 " pdb=" OE1 GLU G 31 " model vdw 2.207 3.040 nonbonded pdb=" O HOH B 502 " pdb=" O HOH C 501 " model vdw 2.270 3.040 nonbonded pdb=" O HOH C 502 " pdb=" O HOH D 501 " model vdw 2.270 3.040 ... (remaining 149882 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 118 through 478) selection = (chain 'B' and (resid 118 through 435 or (resid 436 and (name N or name CA or na \ me C or name CB or name CG or name CD or name CE or name NZ )) or resid 437 thro \ ugh 478)) selection = (chain 'C' and (resid 118 through 435 or (resid 436 and (name N or name CA or na \ me C or name CB or name CG or name CD or name CE or name NZ )) or resid 437 thro \ ugh 478)) selection = (chain 'D' and (resid 118 through 435 or (resid 436 and (name N or name CA or na \ me C or name CB or name CG or name CD or name CE or name NZ )) or resid 437 thro \ ugh 478)) } ncs_group { reference = 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: 8.670 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.240 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 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 : 0.003 0.039 16431 Z= 0.137 Angle : 0.506 7.675 22182 Z= 0.280 Chirality : 0.037 0.178 2564 Planarity : 0.003 0.037 2783 Dihedral : 15.723 89.031 6056 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 1.26 % Allowed : 10.47 % Favored : 88.27 % 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: 1.91 (0.20), residues: 2012 helix: 2.23 (0.14), residues: 1440 sheet: -0.05 (0.81), residues: 48 loop : -1.44 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 86 TYR 0.009 0.001 TYR D 120 PHE 0.017 0.001 PHE F 141 TRP 0.008 0.001 TRP B 432 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (16427) covalent geometry : angle 0.50554 / 0.28 (22174) SS BOND : bond 0.00471 / 0.22 ( 4) SS BOND : angle 1.13910 / 0.59 ( 8) hydrogen bonds : bond 0.13758 / 9.28 ( 1078) hydrogen bonds : angle 4.33598 / 3.06 ( 3147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 0.574 Fit side-chains REVERT: E 85 ILE cc_start: 0.8870 (pt) cc_final: 0.8595 (pt) REVERT: F 111 ASN cc_start: 0.8812 (m110) cc_final: 0.8491 (m110) REVERT: F 143 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8440 (tm-30) outliers start: 22 outliers final: 20 residues processed: 260 average time/residue: 0.1383 time to fit residues: 51.5904 Evaluate side-chains 268 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 247 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 143 GLN Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 ASN E 111 ASN F 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.121073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.094189 restraints weight = 29391.360| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.41 r_work: 0.2972 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16431 Z= 0.119 Angle : 0.451 6.218 22182 Z= 0.246 Chirality : 0.037 0.194 2564 Planarity : 0.003 0.036 2783 Dihedral : 5.143 62.075 2227 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 1.49 % Allowed : 10.18 % Favored : 88.33 % 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: 2.18 (0.20), residues: 2012 helix: 2.48 (0.14), residues: 1408 sheet: 1.17 (0.68), residues: 40 loop : -1.34 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 90 TYR 0.016 0.001 TYR G 99 PHE 0.012 0.001 PHE A 357 TRP 0.007 0.001 TRP B 432 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (16427) covalent geometry : angle 0.45055 / 0.25 (22174) SS BOND : bond 0.00388 / 0.18 ( 4) SS BOND : angle 0.88482 / 0.44 ( 8) hydrogen bonds : bond 0.05571 / 3.74 ( 1078) hydrogen bonds : angle 3.51041 / 2.48 ( 3147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 0.616 Fit side-chains REVERT: E 85 ILE cc_start: 0.8589 (pt) cc_final: 0.8335 (pt) REVERT: F 111 ASN cc_start: 0.8796 (m110) cc_final: 0.8577 (m110) REVERT: G 48 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7835 (pp) REVERT: G 86 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.7971 (mtm110) outliers start: 26 outliers final: 18 residues processed: 276 average time/residue: 0.1355 time to fit residues: 53.8987 Evaluate side-chains 267 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 248 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 141 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 173 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 422 ASN C 409 ASN H 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.118272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.084185 restraints weight = 29733.500| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.76 r_work: 0.2977 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16431 Z= 0.173 Angle : 0.506 7.070 22182 Z= 0.272 Chirality : 0.039 0.188 2564 Planarity : 0.003 0.036 2783 Dihedral : 4.866 51.983 2209 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 2.63 % Allowed : 10.47 % Favored : 86.90 % 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: 1.94 (0.20), residues: 2012 helix: 2.30 (0.14), residues: 1408 sheet: -0.57 (0.67), residues: 48 loop : -1.31 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 74 TYR 0.011 0.001 TYR A 268 PHE 0.015 0.002 PHE A 357 TRP 0.009 0.001 TRP C 158 HIS 0.006 0.001 HIS C 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (16427) covalent geometry : angle 0.50599 / 0.27 (22174) SS BOND : bond 0.00420 / 0.20 ( 4) SS BOND : angle 0.99469 / 0.50 ( 8) hydrogen bonds : bond 0.06783 / 4.56 ( 1078) hydrogen bonds : angle 3.52938 / 2.51 ( 3147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 0.621 Fit side-chains REVERT: F 111 ASN cc_start: 0.8874 (m110) cc_final: 0.8620 (m110) REVERT: C 396 ARG cc_start: 0.8410 (ttm110) cc_final: 0.8146 (mtm-85) REVERT: G 38 SER cc_start: 0.8633 (t) cc_final: 0.8422 (t) REVERT: G 86 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.8056 (mtm110) REVERT: G 99 TYR cc_start: 0.7665 (m-80) cc_final: 0.7429 (m-80) REVERT: H 90 ARG cc_start: 0.8343 (mtm-85) cc_final: 0.8073 (mtt-85) outliers start: 46 outliers final: 37 residues processed: 276 average time/residue: 0.1417 time to fit residues: 56.1059 Evaluate side-chains 283 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 7 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 199 optimal weight: 0.8980 chunk 190 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.119148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.086408 restraints weight = 29496.653| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.81 r_work: 0.2965 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16431 Z= 0.141 Angle : 0.467 6.925 22182 Z= 0.253 Chirality : 0.038 0.187 2564 Planarity : 0.003 0.035 2783 Dihedral : 4.877 53.102 2209 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.82 % Rotamer: Outliers : 2.69 % Allowed : 11.04 % Favored : 86.27 % 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: 1.99 (0.20), residues: 2012 helix: 2.35 (0.14), residues: 1408 sheet: -0.60 (0.65), residues: 48 loop : -1.32 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 471 TYR 0.009 0.001 TYR D 120 PHE 0.015 0.001 PHE C 357 TRP 0.008 0.001 TRP C 158 HIS 0.004 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (16427) covalent geometry : angle 0.46675 / 0.25 (22174) SS BOND : bond 0.00345 / 0.16 ( 4) SS BOND : angle 0.79236 / 0.38 ( 8) hydrogen bonds : bond 0.06108 / 4.10 ( 1078) hydrogen bonds : angle 3.43667 / 2.45 ( 3147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 0.434 Fit side-chains REVERT: F 111 ASN cc_start: 0.8854 (m110) cc_final: 0.8554 (m110) REVERT: G 86 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8093 (mtm110) REVERT: G 99 TYR cc_start: 0.7765 (m-80) cc_final: 0.7526 (m-80) REVERT: H 8 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7958 (pm20) outliers start: 47 outliers final: 36 residues processed: 280 average time/residue: 0.1337 time to fit residues: 53.4389 Evaluate side-chains 288 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 468 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 91 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 190 optimal weight: 0.0770 chunk 43 optimal weight: 0.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.120294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.094075 restraints weight = 29644.143| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.53 r_work: 0.2965 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16431 Z= 0.119 Angle : 0.442 6.582 22182 Z= 0.241 Chirality : 0.037 0.185 2564 Planarity : 0.003 0.033 2783 Dihedral : 4.844 55.153 2209 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 2.12 % Allowed : 12.13 % Favored : 85.76 % 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: 2.09 (0.20), residues: 2012 helix: 2.43 (0.14), residues: 1408 sheet: -0.54 (0.64), residues: 48 loop : -1.29 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 126 TYR 0.008 0.001 TYR D 120 PHE 0.013 0.001 PHE A 357 TRP 0.007 0.001 TRP B 328 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (16427) covalent geometry : angle 0.44150 / 0.24 (22174) SS BOND : bond 0.00315 / 0.15 ( 4) SS BOND : angle 0.63004 / 0.30 ( 8) hydrogen bonds : bond 0.05522 / 3.71 ( 1078) hydrogen bonds : angle 3.36140 / 2.40 ( 3147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 0.609 Fit side-chains REVERT: E 109 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8289 (mtp) REVERT: F 111 ASN cc_start: 0.8798 (m110) cc_final: 0.8573 (m110) REVERT: G 99 TYR cc_start: 0.7740 (m-80) cc_final: 0.7476 (m-80) REVERT: H 8 GLN cc_start: 0.8282 (pm20) cc_final: 0.8075 (pm20) outliers start: 37 outliers final: 28 residues processed: 280 average time/residue: 0.1320 time to fit residues: 53.6742 Evaluate side-chains 281 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 252 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 141 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 185 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 409 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.120862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094666 restraints weight = 29629.515| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.47 r_work: 0.2981 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16431 Z= 0.115 Angle : 0.450 7.268 22182 Z= 0.242 Chirality : 0.037 0.182 2564 Planarity : 0.003 0.031 2783 Dihedral : 4.681 59.744 2207 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.78 % Favored : 97.17 % Rotamer: Outliers : 2.23 % Allowed : 12.19 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.20), residues: 2012 helix: 2.47 (0.14), residues: 1411 sheet: -0.42 (0.65), residues: 48 loop : -1.27 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 126 TYR 0.008 0.001 TYR D 120 PHE 0.012 0.001 PHE C 357 TRP 0.007 0.001 TRP B 328 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (16427) covalent geometry : angle 0.44965 / 0.24 (22174) SS BOND : bond 0.00313 / 0.15 ( 4) SS BOND : angle 0.60745 / 0.28 ( 8) hydrogen bonds : bond 0.05176 / 3.48 ( 1078) hydrogen bonds : angle 3.30446 / 2.36 ( 3147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 262 time to evaluate : 0.616 Fit side-chains REVERT: E 109 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8297 (mtp) REVERT: G 82 GLU cc_start: 0.8032 (tp30) cc_final: 0.7731 (mp0) REVERT: G 99 TYR cc_start: 0.7727 (m-80) cc_final: 0.7451 (m-80) outliers start: 39 outliers final: 35 residues processed: 278 average time/residue: 0.1342 time to fit residues: 53.7801 Evaluate side-chains 289 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 253 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 169 optimal weight: 2.9990 chunk 154 optimal weight: 0.0170 chunk 50 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 172 optimal weight: 0.0980 overall best weight: 0.5220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.121909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.088351 restraints weight = 29472.535| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.77 r_work: 0.3054 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16431 Z= 0.106 Angle : 0.435 7.369 22182 Z= 0.234 Chirality : 0.036 0.181 2564 Planarity : 0.003 0.030 2783 Dihedral : 4.199 59.028 2201 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.68 % Favored : 97.27 % Rotamer: Outliers : 2.12 % Allowed : 12.81 % Favored : 85.07 % 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: 2.26 (0.20), residues: 2012 helix: 2.54 (0.14), residues: 1411 sheet: -0.39 (0.65), residues: 48 loop : -1.23 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 126 TYR 0.008 0.001 TYR F 99 PHE 0.010 0.001 PHE C 357 TRP 0.007 0.001 TRP B 328 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (16427) covalent geometry : angle 0.43493 / 0.23 (22174) SS BOND : bond 0.00286 / 0.14 ( 4) SS BOND : angle 0.55180 / 0.25 ( 8) hydrogen bonds : bond 0.04734 / 3.18 ( 1078) hydrogen bonds : angle 3.25813 / 2.33 ( 3147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 0.540 Fit side-chains REVERT: G 48 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7701 (pp) REVERT: G 82 GLU cc_start: 0.8003 (tp30) cc_final: 0.7724 (mp0) REVERT: G 99 TYR cc_start: 0.7633 (m-80) cc_final: 0.7379 (m-80) outliers start: 37 outliers final: 29 residues processed: 284 average time/residue: 0.1328 time to fit residues: 54.5091 Evaluate side-chains 283 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 114 optimal weight: 0.7980 chunk 198 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 172 optimal weight: 0.0570 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.120746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.086846 restraints weight = 29660.200| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.78 r_work: 0.3025 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16431 Z= 0.122 Angle : 0.466 7.869 22182 Z= 0.247 Chirality : 0.037 0.182 2564 Planarity : 0.003 0.032 2783 Dihedral : 3.890 54.520 2197 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 2.06 % Allowed : 13.10 % Favored : 84.84 % 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: 2.20 (0.20), residues: 2012 helix: 2.50 (0.14), residues: 1411 sheet: -0.42 (0.65), residues: 48 loop : -1.24 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 126 TYR 0.007 0.001 TYR D 120 PHE 0.013 0.001 PHE C 357 TRP 0.006 0.001 TRP C 158 HIS 0.003 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (16427) covalent geometry : angle 0.46623 / 0.25 (22174) SS BOND : bond 0.00303 / 0.14 ( 4) SS BOND : angle 0.55207 / 0.26 ( 8) hydrogen bonds : bond 0.05294 / 3.56 ( 1078) hydrogen bonds : angle 3.29031 / 2.35 ( 3147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 0.666 Fit side-chains REVERT: F 105 LEU cc_start: 0.9017 (mt) cc_final: 0.8783 (tt) REVERT: G 48 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7698 (pp) REVERT: G 82 GLU cc_start: 0.8036 (tp30) cc_final: 0.7832 (mp0) REVERT: G 90 ARG cc_start: 0.8311 (mtm180) cc_final: 0.8069 (mtm-85) REVERT: G 99 TYR cc_start: 0.7671 (m-80) cc_final: 0.7434 (m-80) REVERT: G 145 MET cc_start: 0.6476 (mmp) cc_final: 0.6094 (mtt) outliers start: 36 outliers final: 32 residues processed: 275 average time/residue: 0.1371 time to fit residues: 54.3743 Evaluate side-chains 288 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 255 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 93 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 136 optimal weight: 0.4980 chunk 25 optimal weight: 0.4980 chunk 199 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 94 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.121425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.087721 restraints weight = 29474.658| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.77 r_work: 0.3044 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16431 Z= 0.111 Angle : 0.460 8.101 22182 Z= 0.243 Chirality : 0.037 0.181 2564 Planarity : 0.003 0.031 2783 Dihedral : 3.785 54.524 2197 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 2.06 % Allowed : 13.33 % Favored : 84.61 % 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: 2.28 (0.20), residues: 2012 helix: 2.55 (0.14), residues: 1411 sheet: -0.33 (0.66), residues: 48 loop : -1.19 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 126 TYR 0.007 0.001 TYR D 120 PHE 0.011 0.001 PHE D 357 TRP 0.007 0.001 TRP B 432 HIS 0.003 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (16427) covalent geometry : angle 0.46004 / 0.24 (22174) SS BOND : bond 0.00286 / 0.14 ( 4) SS BOND : angle 0.53760 / 0.25 ( 8) hydrogen bonds : bond 0.04925 / 3.32 ( 1078) hydrogen bonds : angle 3.26314 / 2.33 ( 3147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: G 82 GLU cc_start: 0.8078 (tp30) cc_final: 0.7840 (mp0) REVERT: G 99 TYR cc_start: 0.7662 (m-80) cc_final: 0.7432 (m-80) REVERT: G 145 MET cc_start: 0.6552 (mmp) cc_final: 0.5928 (mtt) outliers start: 36 outliers final: 32 residues processed: 280 average time/residue: 0.1399 time to fit residues: 56.5979 Evaluate side-chains 289 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 154 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.121116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.087248 restraints weight = 29578.429| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.78 r_work: 0.3030 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16431 Z= 0.119 Angle : 0.472 8.201 22182 Z= 0.249 Chirality : 0.037 0.181 2564 Planarity : 0.003 0.032 2783 Dihedral : 3.746 54.943 2197 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 2.12 % Allowed : 13.22 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.20), residues: 2012 helix: 2.52 (0.14), residues: 1411 sheet: -0.36 (0.66), residues: 48 loop : -1.16 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 86 TYR 0.007 0.001 TYR D 120 PHE 0.012 0.001 PHE C 357 TRP 0.006 0.001 TRP C 328 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (16427) covalent geometry : angle 0.47237 / 0.25 (22174) SS BOND : bond 0.00291 / 0.14 ( 4) SS BOND : angle 0.54110 / 0.26 ( 8) hydrogen bonds : bond 0.05167 / 3.47 ( 1078) hydrogen bonds : angle 3.28447 / 2.35 ( 3147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 262 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: F 53 ASN cc_start: 0.8665 (p0) cc_final: 0.8422 (p0) REVERT: G 90 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8134 (mtm-85) REVERT: G 99 TYR cc_start: 0.7684 (m-80) cc_final: 0.7452 (m-80) REVERT: G 145 MET cc_start: 0.6449 (mmp) cc_final: 0.5882 (mtt) REVERT: H 90 ARG cc_start: 0.8375 (ttm170) cc_final: 0.8150 (ttm-80) outliers start: 37 outliers final: 36 residues processed: 281 average time/residue: 0.1378 time to fit residues: 56.0991 Evaluate side-chains 296 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 259 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 111 ASN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 122 optimal weight: 0.0370 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 188 optimal weight: 0.0970 chunk 158 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.121142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.094415 restraints weight = 29483.189| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.41 r_work: 0.2978 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 16431 Z= 0.159 Angle : 0.698 59.040 22182 Z= 0.410 Chirality : 0.038 0.536 2564 Planarity : 0.003 0.040 2783 Dihedral : 3.819 54.935 2197 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.77 % Rotamer: Outliers : 2.06 % Allowed : 13.50 % Favored : 84.44 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.26 (0.20), residues: 2012 helix: 2.53 (0.14), residues: 1411 sheet: -0.37 (0.65), residues: 48 loop : -1.17 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 86 TYR 0.008 0.001 TYR D 120 PHE 0.012 0.001 PHE C 357 TRP 0.006 0.001 TRP C 158 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (16427) covalent geometry : angle 0.69768 / 0.41 (22174) SS BOND : bond 0.00298 / 0.14 ( 4) SS BOND : angle 0.50242 / 0.24 ( 8) hydrogen bonds : bond 0.05242 / 3.49 ( 1078) hydrogen bonds : angle 3.30310 / 2.35 ( 3147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4403.91 seconds wall clock time: 76 minutes 3.02 seconds (4563.02 seconds total)