Starting phenix.real_space_refine on Sat May 17 20:27:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2g_42911/05_2025/8v2g_42911.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2g_42911/05_2025/8v2g_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_42911/05_2025/8v2g_42911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2g_42911/05_2025/8v2g_42911.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2g_42911/05_2025/8v2g_42911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2g_42911/05_2025/8v2g_42911.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 10.94, per 1000 atoms: 0.68 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: 4.08 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.38 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: 5.08 Time building geometry restraints manager: 4.79 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: 18.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.350 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 35.710 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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:3.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (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 TRP 0.008 0.001 TRP B 432 HIS 0.004 0.001 HIS B 337 PHE 0.017 0.001 PHE F 141 TYR 0.009 0.001 TYR D 120 ARG 0.006 0.001 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.13758 ( 1078) hydrogen bonds : angle 4.33598 ( 3147) SS BOND : bond 0.00471 ( 4) SS BOND : angle 1.13910 ( 8) covalent geometry : bond 0.00295 (16427) covalent geometry : angle 0.50554 (22174) *********************** 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 : 1.843 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: 0.3264 time to fit residues: 119.9060 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 : 1.768 ------------------------------------------------------------------------------- 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 168 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 0.0670 chunk 116 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3683 r_free = 0.3683 target = 0.120938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.093901 restraints weight = 29263.850| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.39 r_work: 0.2971 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.0650 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= 0.120 Angle : 0.450 6.204 22182 Z= 0.247 Chirality : 0.037 0.185 2564 Planarity : 0.003 0.035 2783 Dihedral : 5.134 62.412 2227 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 1.43 % Allowed : 10.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.20), residues: 2012 helix: 2.48 (0.14), residues: 1408 sheet: 1.15 (0.69), residues: 40 loop : -1.31 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 432 HIS 0.003 0.001 HIS B 190 PHE 0.012 0.001 PHE A 357 TYR 0.015 0.001 TYR G 99 ARG 0.004 0.000 ARG G 90 Details of bonding type rmsd hydrogen bonds : bond 0.05573 ( 1078) hydrogen bonds : angle 3.51489 ( 3147) SS BOND : bond 0.00375 ( 4) SS BOND : angle 0.84867 ( 8) covalent geometry : bond 0.00246 (16427) covalent geometry : angle 0.44986 (22174) *********************** 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 296 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 271 time to evaluate : 1.872 Fit side-chains REVERT: E 85 ILE cc_start: 0.8597 (pt) cc_final: 0.8347 (pt) REVERT: F 111 ASN cc_start: 0.8810 (m110) cc_final: 0.8548 (m110) REVERT: G 48 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7832 (pp) REVERT: G 86 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7947 (mtm110) outliers start: 25 outliers final: 18 residues processed: 280 average time/residue: 0.3042 time to fit residues: 121.6392 Evaluate side-chains 269 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 250 time to evaluate : 1.758 ------------------------------------------------------------------------------- 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 177 optimal weight: 0.6980 chunk 72 optimal weight: 0.0010 chunk 104 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 54 optimal weight: 0.0060 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 ASN H 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.122491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.095797 restraints weight = 29327.316| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.45 r_work: 0.2998 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16431 Z= 0.103 Angle : 0.417 6.341 22182 Z= 0.227 Chirality : 0.036 0.183 2564 Planarity : 0.003 0.031 2783 Dihedral : 4.450 50.890 2209 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.49 % Favored : 97.47 % Rotamer: Outliers : 1.54 % Allowed : 11.21 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.20), residues: 2012 helix: 2.59 (0.14), residues: 1408 sheet: 0.14 (0.70), residues: 46 loop : -1.22 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 328 HIS 0.004 0.001 HIS G 107 PHE 0.010 0.001 PHE A 357 TYR 0.008 0.001 TYR D 120 ARG 0.004 0.000 ARG E 74 Details of bonding type rmsd hydrogen bonds : bond 0.04694 ( 1078) hydrogen bonds : angle 3.32377 ( 3147) SS BOND : bond 0.00324 ( 4) SS BOND : angle 0.72415 ( 8) covalent geometry : bond 0.00205 (16427) covalent geometry : angle 0.41638 (22174) *********************** 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 295 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 1.788 Fit side-chains REVERT: E 85 ILE cc_start: 0.8500 (pt) cc_final: 0.8282 (pt) REVERT: G 86 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.7937 (mtm110) REVERT: H 8 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7871 (pm20) outliers start: 27 outliers final: 17 residues processed: 278 average time/residue: 0.3035 time to fit residues: 120.8922 Evaluate side-chains 270 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 252 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain E residue 91 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 142 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 343 THR 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 343 THR Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 141 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 10 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 0.0470 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.121255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094828 restraints weight = 29583.521| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.62 r_work: 0.2970 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.0972 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= 0.120 Angle : 0.443 6.512 22182 Z= 0.238 Chirality : 0.037 0.183 2564 Planarity : 0.003 0.030 2783 Dihedral : 4.059 53.242 2201 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 2.17 % Allowed : 11.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 2012 helix: 2.54 (0.14), residues: 1408 sheet: -0.26 (0.67), residues: 48 loop : -1.23 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 158 HIS 0.004 0.001 HIS B 190 PHE 0.012 0.001 PHE C 357 TYR 0.009 0.001 TYR D 120 ARG 0.005 0.000 ARG G 126 Details of bonding type rmsd hydrogen bonds : bond 0.05231 ( 1078) hydrogen bonds : angle 3.30474 ( 3147) SS BOND : bond 0.00313 ( 4) SS BOND : angle 0.66917 ( 8) covalent geometry : bond 0.00265 (16427) covalent geometry : angle 0.44294 (22174) *********************** 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 298 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 260 time to evaluate : 2.106 Fit side-chains REVERT: E 85 ILE cc_start: 0.8515 (pt) cc_final: 0.8307 (pt) REVERT: G 86 ARG cc_start: 0.8319 (ttm-80) cc_final: 0.8002 (mtm110) outliers start: 38 outliers final: 26 residues processed: 274 average time/residue: 0.3452 time to fit residues: 135.8325 Evaluate side-chains 276 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 2.015 ------------------------------------------------------------------------------- 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 E residue 91 VAL 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 91 VAL Chi-restraints excluded: chain F residue 109 MET 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 47 GLU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 85 ILE 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 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 83 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 179 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 158 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.121825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.094923 restraints weight = 29572.204| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.44 r_work: 0.2986 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1074 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= 0.108 Angle : 0.427 6.988 22182 Z= 0.231 Chirality : 0.036 0.181 2564 Planarity : 0.003 0.030 2783 Dihedral : 3.850 54.230 2199 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.49 % Favored : 97.47 % Rotamer: Outliers : 2.12 % Allowed : 11.67 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.20), residues: 2012 helix: 2.59 (0.14), residues: 1408 sheet: -0.19 (0.66), residues: 48 loop : -1.22 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 328 HIS 0.003 0.001 HIS B 190 PHE 0.011 0.001 PHE C 357 TYR 0.008 0.001 TYR D 120 ARG 0.007 0.000 ARG G 126 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 1078) hydrogen bonds : angle 3.26257 ( 3147) SS BOND : bond 0.00292 ( 4) SS BOND : angle 0.60857 ( 8) covalent geometry : bond 0.00225 (16427) covalent geometry : angle 0.42727 (22174) *********************** 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 : 1.911 Fit side-chains REVERT: E 85 ILE cc_start: 0.8502 (pt) cc_final: 0.8298 (pt) REVERT: E 109 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8127 (mtp) REVERT: G 86 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.7996 (mtm110) outliers start: 37 outliers final: 30 residues processed: 279 average time/residue: 0.3080 time to fit residues: 123.0097 Evaluate side-chains 287 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 256 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 100 ILE 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 109 MET 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 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 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 Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 99 optimal weight: 0.0470 chunk 158 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.121709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.094794 restraints weight = 29341.191| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.43 r_work: 0.2984 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1138 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 : 0.442 7.226 22182 Z= 0.235 Chirality : 0.036 0.180 2564 Planarity : 0.003 0.029 2783 Dihedral : 3.858 55.048 2199 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 2.35 % Allowed : 12.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.20), residues: 2012 helix: 2.59 (0.14), residues: 1408 sheet: -0.20 (0.66), residues: 48 loop : -1.21 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 328 HIS 0.003 0.001 HIS B 190 PHE 0.011 0.001 PHE A 357 TYR 0.008 0.001 TYR D 120 ARG 0.007 0.000 ARG G 126 Details of bonding type rmsd hydrogen bonds : bond 0.04909 ( 1078) hydrogen bonds : angle 3.24795 ( 3147) SS BOND : bond 0.00284 ( 4) SS BOND : angle 0.56229 ( 8) covalent geometry : bond 0.00238 (16427) covalent geometry : angle 0.44180 (22174) *********************** 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 304 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 263 time to evaluate : 1.774 Fit side-chains REVERT: E 109 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8117 (mtp) REVERT: G 48 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7784 (pp) REVERT: G 86 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8139 (mtm110) outliers start: 41 outliers final: 32 residues processed: 281 average time/residue: 0.2981 time to fit residues: 120.7549 Evaluate side-chains 289 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 393 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 404 GLU 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 109 MET Chi-restraints excluded: chain F residue 122 ASP 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 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 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 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 168 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 154 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.120627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.086580 restraints weight = 29552.658| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.78 r_work: 0.3022 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1095 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= 0.123 Angle : 0.459 7.108 22182 Z= 0.244 Chirality : 0.037 0.180 2564 Planarity : 0.003 0.030 2783 Dihedral : 3.791 55.821 2197 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 2.35 % Allowed : 12.13 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.20), residues: 2012 helix: 2.56 (0.14), residues: 1408 sheet: -0.34 (0.65), residues: 48 loop : -1.22 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 158 HIS 0.004 0.001 HIS B 190 PHE 0.012 0.001 PHE C 357 TYR 0.008 0.001 TYR A 268 ARG 0.007 0.000 ARG G 126 Details of bonding type rmsd hydrogen bonds : bond 0.05376 ( 1078) hydrogen bonds : angle 3.28328 ( 3147) SS BOND : bond 0.00301 ( 4) SS BOND : angle 0.60081 ( 8) covalent geometry : bond 0.00274 (16427) covalent geometry : angle 0.45889 (22174) *********************** 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 307 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 1.823 Fit side-chains REVERT: E 109 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8065 (mtp) REVERT: E 145 MET cc_start: 0.6922 (mmp) cc_final: 0.6476 (ttt) REVERT: G 48 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7715 (pp) REVERT: G 90 ARG cc_start: 0.8336 (ttm170) cc_final: 0.8125 (mtm180) outliers start: 41 outliers final: 34 residues processed: 284 average time/residue: 0.3138 time to fit residues: 127.8568 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 : 1.770 ------------------------------------------------------------------------------- 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 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 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 109 MET Chi-restraints excluded: chain F residue 122 ASP 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 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 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 Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 37 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 166 optimal weight: 0.0980 chunk 145 optimal weight: 0.0370 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 0.0270 chunk 185 optimal weight: 0.5980 chunk 181 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.123180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.091758 restraints weight = 29314.482| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.84 r_work: 0.3045 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16431 Z= 0.101 Angle : 0.437 7.932 22182 Z= 0.232 Chirality : 0.036 0.179 2564 Planarity : 0.003 0.030 2783 Dihedral : 3.604 55.927 2197 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 1.77 % Allowed : 12.93 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.20), residues: 2012 helix: 2.62 (0.14), residues: 1415 sheet: -0.15 (0.67), residues: 48 loop : -1.12 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 328 HIS 0.002 0.001 HIS A 408 PHE 0.010 0.001 PHE A 357 TYR 0.007 0.001 TYR D 120 ARG 0.007 0.000 ARG G 126 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 1078) hydrogen bonds : angle 3.20436 ( 3147) SS BOND : bond 0.00266 ( 4) SS BOND : angle 0.53209 ( 8) covalent geometry : bond 0.00204 (16427) covalent geometry : angle 0.43664 (22174) *********************** 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 299 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 268 time to evaluate : 2.149 Fit side-chains REVERT: E 116 LEU cc_start: 0.6999 (mt) cc_final: 0.6680 (tp) REVERT: E 145 MET cc_start: 0.6912 (mmp) cc_final: 0.6381 (ttt) REVERT: G 90 ARG cc_start: 0.8377 (ttm170) cc_final: 0.8134 (mtm110) outliers start: 31 outliers final: 24 residues processed: 281 average time/residue: 0.3027 time to fit residues: 122.2965 Evaluate side-chains 283 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 259 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 404 GLU 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 343 THR 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 109 MET Chi-restraints excluded: chain F residue 122 ASP 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 89 PHE 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 141 PHE Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 125 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.0570 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.122231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.088384 restraints weight = 29470.479| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.77 r_work: 0.3056 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16431 Z= 0.109 Angle : 0.453 7.935 22182 Z= 0.241 Chirality : 0.037 0.179 2564 Planarity : 0.003 0.029 2783 Dihedral : 3.653 56.530 2197 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.07 % Rotamer: Outliers : 1.72 % Allowed : 13.10 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.20), residues: 2012 helix: 2.60 (0.14), residues: 1415 sheet: -0.09 (0.67), residues: 48 loop : -1.11 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 328 HIS 0.003 0.001 HIS B 190 PHE 0.011 0.001 PHE A 357 TYR 0.008 0.001 TYR D 120 ARG 0.007 0.000 ARG G 86 Details of bonding type rmsd hydrogen bonds : bond 0.04689 ( 1078) hydrogen bonds : angle 3.19832 ( 3147) SS BOND : bond 0.00281 ( 4) SS BOND : angle 0.52493 ( 8) covalent geometry : bond 0.00235 (16427) covalent geometry : angle 0.45284 (22174) *********************** 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 289 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 259 time to evaluate : 1.806 Fit side-chains REVERT: E 116 LEU cc_start: 0.6969 (mt) cc_final: 0.6668 (tp) REVERT: E 145 MET cc_start: 0.7002 (mmp) cc_final: 0.6551 (ttt) REVERT: G 90 ARG cc_start: 0.8362 (ttm170) cc_final: 0.8126 (mtm110) REVERT: G 145 MET cc_start: 0.6363 (mmp) cc_final: 0.5780 (mtt) outliers start: 30 outliers final: 28 residues processed: 272 average time/residue: 0.3024 time to fit residues: 118.3960 Evaluate side-chains 285 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 322 LEU Chi-restraints excluded: chain B residue 343 THR 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 109 MET 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 4 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 89 PHE 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 141 PHE Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 140 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.120771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.087236 restraints weight = 29459.108| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.80 r_work: 0.3012 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1258 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= 0.126 Angle : 0.484 8.799 22182 Z= 0.256 Chirality : 0.037 0.178 2564 Planarity : 0.003 0.037 2783 Dihedral : 3.796 56.911 2197 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.22 % Rotamer: Outliers : 2.00 % Allowed : 13.04 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.20), residues: 2012 helix: 2.56 (0.14), residues: 1411 sheet: -0.18 (0.67), residues: 48 loop : -1.16 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 158 HIS 0.004 0.001 HIS B 190 PHE 0.012 0.001 PHE G 141 TYR 0.008 0.001 TYR F 99 ARG 0.009 0.000 ARG G 86 Details of bonding type rmsd hydrogen bonds : bond 0.05317 ( 1078) hydrogen bonds : angle 3.26436 ( 3147) SS BOND : bond 0.00298 ( 4) SS BOND : angle 0.56381 ( 8) covalent geometry : bond 0.00283 (16427) covalent geometry : angle 0.48436 (22174) ********************** 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 296 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 1.779 Fit side-chains REVERT: E 145 MET cc_start: 0.7033 (mmp) cc_final: 0.6598 (ttt) REVERT: G 86 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8620 (ttm-80) REVERT: G 90 ARG cc_start: 0.8414 (ttm170) cc_final: 0.8181 (mtm110) REVERT: H 90 ARG cc_start: 0.8417 (ttm170) cc_final: 0.8209 (ttm-80) outliers start: 35 outliers final: 32 residues processed: 280 average time/residue: 0.3021 time to fit residues: 121.4533 Evaluate side-chains 290 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 258 time to evaluate : 1.761 ------------------------------------------------------------------------------- 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 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 F residue 85 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 122 ASP 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 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 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 141 PHE Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 63 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 145 optimal weight: 0.1980 chunk 168 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.121030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.086987 restraints weight = 29347.690| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.77 r_work: 0.3032 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 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 : 0.003 0.039 16431 Z= 0.122 Angle : 0.475 8.028 22182 Z= 0.252 Chirality : 0.037 0.178 2564 Planarity : 0.003 0.044 2783 Dihedral : 3.801 57.033 2197 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 1.83 % Allowed : 13.22 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.20), residues: 2012 helix: 2.56 (0.14), residues: 1411 sheet: -0.22 (0.66), residues: 48 loop : -1.13 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 158 HIS 0.004 0.001 HIS B 190 PHE 0.012 0.001 PHE C 357 TYR 0.007 0.001 TYR D 120 ARG 0.009 0.000 ARG G 86 Details of bonding type rmsd hydrogen bonds : bond 0.05226 ( 1078) hydrogen bonds : angle 3.26273 ( 3147) SS BOND : bond 0.00294 ( 4) SS BOND : angle 0.57444 ( 8) covalent geometry : bond 0.00269 (16427) covalent geometry : angle 0.47529 (22174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9694.73 seconds wall clock time: 169 minutes 2.21 seconds (10142.21 seconds total)