Starting phenix.real_space_refine on Tue Mar 3 17:45:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dhi_30681/03_2026/7dhi_30681.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dhi_30681/03_2026/7dhi_30681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dhi_30681/03_2026/7dhi_30681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dhi_30681/03_2026/7dhi_30681.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dhi_30681/03_2026/7dhi_30681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dhi_30681/03_2026/7dhi_30681.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4990 2.51 5 N 1341 2.21 5 O 1420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7799 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1692 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain breaks: 4 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 9, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2497 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 7, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "G" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 377 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 952 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2262 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 5, 'PHE:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'68H': 1} Classifications: {'undetermined': 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} Time building chain proxies: 1.74, per 1000 atoms: 0.22 Number of scatterers: 7799 At special positions: 0 Unit cell: (91.26, 95.316, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1420 8.00 N 1341 7.00 C 4990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 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: 0.64 Conformation dependent library (CDL) restraints added in 303.6 milliseconds 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 11 sheets defined 38.4% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.576A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.627A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.578A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.869A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.685A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.815A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 370 removed outlier: 3.543A pdb=" N GLU A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 370' Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.641A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 removed outlier: 3.559A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 12 through 22 removed outlier: 3.989A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.759A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.633A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.899A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.178A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 40 removed outlier: 3.520A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 51 removed outlier: 3.923A pdb=" N PHE R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 59 removed outlier: 3.601A pdb=" N ILE R 55 " --> pdb=" O ASN R 51 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA R 57 " --> pdb=" O LEU R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 79 removed outlier: 3.960A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL R 77 " --> pdb=" O THR R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 86 removed outlier: 3.574A pdb=" N VAL R 86 " --> pdb=" O MET R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 105 through 137 removed outlier: 3.500A pdb=" N SER R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 141 removed outlier: 3.992A pdb=" N TYR R 141 " --> pdb=" O PRO R 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 138 through 141' Processing helix chain 'R' and resid 149 through 161 removed outlier: 3.974A pdb=" N ILE R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 201 through 208 Processing helix chain 'R' and resid 208 through 220 removed outlier: 3.577A pdb=" N TYR R 219 " --> pdb=" O MET R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 237 removed outlier: 4.083A pdb=" N ARG R 228 " --> pdb=" O GLN R 224 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 274 removed outlier: 3.718A pdb=" N THR R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 292 removed outlier: 3.751A pdb=" N MET R 279 " --> pdb=" O LEU R 275 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR R 283 " --> pdb=" O MET R 279 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.013A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 314 Processing helix chain 'R' and resid 317 through 326 removed outlier: 3.523A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix removed outlier: 3.536A pdb=" N TYR R 326 " --> pdb=" O ASN R 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 317 through 326' Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.650A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 245 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.650A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 245 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.672A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.673A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.848A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.677A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.872A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.766A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.888A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.569A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 5.662A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 831 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: 1.08 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2504 1.34 - 1.46: 1921 1.46 - 1.58: 3468 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 7960 Sorted by residual: bond pdb=" CA THR A 263 " pdb=" CB THR A 263 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.69e-02 3.50e+03 1.68e+00 bond pdb=" C VAL R 87 " pdb=" N PRO R 88 " ideal model delta sigma weight residual 1.336 1.351 -0.016 1.23e-02 6.61e+03 1.64e+00 bond pdb=" N ARG R 239 " pdb=" CA ARG R 239 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.77e-02 3.19e+03 1.52e+00 bond pdb=" CB PRO R 211 " pdb=" CG PRO R 211 " ideal model delta sigma weight residual 1.492 1.431 0.061 5.00e-02 4.00e+02 1.48e+00 bond pdb=" N THR A 263 " pdb=" CA THR A 263 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.47e+00 ... (remaining 7955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 10442 1.75 - 3.51: 317 3.51 - 5.26: 45 5.26 - 7.01: 16 7.01 - 8.76: 6 Bond angle restraints: 10826 Sorted by residual: angle pdb=" N VAL R 31 " pdb=" CA VAL R 31 " pdb=" C VAL R 31 " ideal model delta sigma weight residual 113.53 109.05 4.48 9.80e-01 1.04e+00 2.09e+01 angle pdb=" C GLN A 262 " pdb=" N THR A 263 " pdb=" CA THR A 263 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" C ASP N 109 " pdb=" N VAL N 110 " pdb=" CA VAL N 110 " ideal model delta sigma weight residual 121.97 129.33 -7.36 1.80e+00 3.09e-01 1.67e+01 angle pdb=" C GLY R 238 " pdb=" N ARG R 239 " pdb=" CA ARG R 239 " ideal model delta sigma weight residual 125.66 133.15 -7.49 1.85e+00 2.92e-01 1.64e+01 angle pdb=" C HIS R 241 " pdb=" N VAL R 242 " pdb=" CA VAL R 242 " ideal model delta sigma weight residual 121.70 128.26 -6.56 1.80e+00 3.09e-01 1.33e+01 ... (remaining 10821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 4152 16.97 - 33.95: 421 33.95 - 50.92: 74 50.92 - 67.90: 13 67.90 - 84.87: 9 Dihedral angle restraints: 4669 sinusoidal: 1706 harmonic: 2963 Sorted by residual: dihedral pdb=" CA HIS R 178 " pdb=" C HIS R 178 " pdb=" N GLN R 179 " pdb=" CA GLN R 179 " ideal model delta harmonic sigma weight residual -180.00 -147.15 -32.85 0 5.00e+00 4.00e-02 4.32e+01 dihedral pdb=" CA GLY R 238 " pdb=" C GLY R 238 " pdb=" N ARG R 239 " pdb=" CA ARG R 239 " ideal model delta harmonic sigma weight residual -180.00 -152.41 -27.59 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA THR R 177 " pdb=" C THR R 177 " pdb=" N HIS R 178 " pdb=" CA HIS R 178 " ideal model delta harmonic sigma weight residual 180.00 -152.95 -27.05 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 4666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 878 0.049 - 0.097: 292 0.097 - 0.146: 76 0.146 - 0.195: 8 0.195 - 0.244: 1 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA THR A 263 " pdb=" N THR A 263 " pdb=" C THR A 263 " pdb=" CB THR A 263 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CB THR A 320 " pdb=" CA THR A 320 " pdb=" OG1 THR A 320 " pdb=" CG2 THR A 320 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 1252 not shown) Planarity restraints: 1367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " -0.048 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO R 323 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO N 88 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " -0.040 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO R 211 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " -0.033 5.00e-02 4.00e+02 ... (remaining 1364 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2464 2.82 - 3.34: 6371 3.34 - 3.86: 12353 3.86 - 4.38: 14647 4.38 - 4.90: 25393 Nonbonded interactions: 61228 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.298 3.040 nonbonded pdb=" O ALA R 119 " pdb=" OG1 THR R 123 " model vdw 2.298 3.040 nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.303 3.040 nonbonded pdb=" OG SER R 203 " pdb=" O2 68H R 401 " model vdw 2.306 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.308 3.040 ... (remaining 61223 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.510 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.870 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.004 0.061 7962 Z= 0.181 Angle : 0.762 8.765 10830 Z= 0.424 Chirality : 0.051 0.244 1255 Planarity : 0.006 0.071 1367 Dihedral : 14.529 84.870 2743 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.13 % Allowed : 8.77 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.36 (0.19), residues: 999 helix: -4.75 (0.09), residues: 351 sheet: -2.28 (0.32), residues: 227 loop : -2.99 (0.24), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 72 TYR 0.017 0.001 TYR B 59 PHE 0.017 0.002 PHE B 199 TRP 0.016 0.002 TRP A 234 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7960) covalent geometry : angle 0.76167 (10826) SS BOND : bond 0.00394 ( 2) SS BOND : angle 0.81758 ( 4) hydrogen bonds : bond 0.31203 ( 287) hydrogen bonds : angle 10.52564 ( 831) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.283 Fit side-chains REVERT: A 16 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7775 (tt0) REVERT: A 236 GLN cc_start: 0.8367 (pt0) cc_final: 0.8074 (pt0) REVERT: A 336 ARG cc_start: 0.8162 (ttt-90) cc_final: 0.7849 (ttt180) REVERT: A 343 ASP cc_start: 0.7752 (m-30) cc_final: 0.7545 (m-30) REVERT: B 308 LEU cc_start: 0.8714 (pp) cc_final: 0.8496 (pt) REVERT: N 87 LYS cc_start: 0.8764 (ttmt) cc_final: 0.8286 (mmtp) REVERT: N 118 ARG cc_start: 0.8493 (ttp-170) cc_final: 0.8272 (ttm170) REVERT: N 123 GLN cc_start: 0.8647 (tp40) cc_final: 0.8413 (tp40) REVERT: R 40 MET cc_start: 0.7860 (mtm) cc_final: 0.7501 (mtt) REVERT: R 224 GLN cc_start: 0.7392 (mt0) cc_final: 0.6990 (tm-30) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.0996 time to fit residues: 25.8230 Evaluate side-chains 160 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 213 GLN A 218 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN B 156 GLN B 340 ASN N 3 GLN N 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107798 restraints weight = 10502.672| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.29 r_work: 0.3106 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7962 Z= 0.127 Angle : 0.545 5.542 10830 Z= 0.299 Chirality : 0.043 0.135 1255 Planarity : 0.004 0.047 1367 Dihedral : 6.547 84.605 1102 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.63 % Allowed : 14.91 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.23), residues: 999 helix: -2.46 (0.22), residues: 367 sheet: -1.74 (0.34), residues: 214 loop : -2.61 (0.26), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.012 0.001 TYR B 59 PHE 0.014 0.001 PHE R 289 TRP 0.011 0.001 TRP R 109 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7960) covalent geometry : angle 0.54482 (10826) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.79422 ( 4) hydrogen bonds : bond 0.04263 ( 287) hydrogen bonds : angle 5.24636 ( 831) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.262 Fit side-chains REVERT: A 20 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7525 (mtm-85) REVERT: A 339 TYR cc_start: 0.8887 (m-80) cc_final: 0.8647 (m-80) REVERT: N 87 LYS cc_start: 0.8544 (ttmt) cc_final: 0.7950 (mmtp) REVERT: R 64 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8072 (pp) outliers start: 13 outliers final: 10 residues processed: 180 average time/residue: 0.0971 time to fit residues: 22.7262 Evaluate side-chains 159 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 64 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 239 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.136693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102597 restraints weight = 10376.140| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.31 r_work: 0.2983 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7962 Z= 0.259 Angle : 0.623 6.784 10830 Z= 0.337 Chirality : 0.046 0.150 1255 Planarity : 0.004 0.043 1367 Dihedral : 6.866 87.327 1102 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.51 % Allowed : 18.92 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.24), residues: 999 helix: -1.24 (0.27), residues: 353 sheet: -1.62 (0.34), residues: 215 loop : -2.57 (0.26), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 228 TYR 0.023 0.002 TYR B 59 PHE 0.018 0.002 PHE N 68 TRP 0.011 0.002 TRP N 47 HIS 0.008 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00611 ( 7960) covalent geometry : angle 0.62321 (10826) SS BOND : bond 0.00296 ( 2) SS BOND : angle 1.16998 ( 4) hydrogen bonds : bond 0.04583 ( 287) hydrogen bonds : angle 4.84093 ( 831) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 343 ASP cc_start: 0.8812 (m-30) cc_final: 0.8586 (m-30) REVERT: B 234 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8251 (t80) REVERT: B 308 LEU cc_start: 0.8744 (pp) cc_final: 0.8517 (pt) REVERT: N 18 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7696 (tt) REVERT: N 87 LYS cc_start: 0.8594 (ttmt) cc_final: 0.7996 (mmtp) REVERT: R 30 GLU cc_start: 0.6602 (tp30) cc_final: 0.6325 (tp30) REVERT: R 64 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8251 (pp) REVERT: R 224 GLN cc_start: 0.8411 (mt0) cc_final: 0.7855 (tm-30) outliers start: 28 outliers final: 17 residues processed: 179 average time/residue: 0.0993 time to fit residues: 23.2301 Evaluate side-chains 173 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106870 restraints weight = 10694.953| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.24 r_work: 0.2956 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7962 Z= 0.130 Angle : 0.521 5.697 10830 Z= 0.284 Chirality : 0.043 0.145 1255 Planarity : 0.003 0.041 1367 Dihedral : 6.300 86.881 1102 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.76 % Allowed : 20.05 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.25), residues: 999 helix: -0.64 (0.28), residues: 355 sheet: -1.47 (0.34), residues: 214 loop : -2.37 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.014 0.001 TYR B 59 PHE 0.013 0.001 PHE N 68 TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7960) covalent geometry : angle 0.52056 (10826) SS BOND : bond 0.00199 ( 2) SS BOND : angle 0.76430 ( 4) hydrogen bonds : bond 0.03433 ( 287) hydrogen bonds : angle 4.40130 ( 831) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.265 Fit side-chains REVERT: A 336 ARG cc_start: 0.8311 (ptm-80) cc_final: 0.7994 (ttt180) REVERT: A 343 ASP cc_start: 0.8737 (m-30) cc_final: 0.8479 (m-30) REVERT: B 105 TYR cc_start: 0.9290 (OUTLIER) cc_final: 0.8941 (t80) REVERT: B 234 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8387 (t80) REVERT: B 264 TYR cc_start: 0.9376 (m-80) cc_final: 0.9169 (m-80) REVERT: N 87 LYS cc_start: 0.8548 (ttmt) cc_final: 0.7963 (mmtp) REVERT: R 30 GLU cc_start: 0.6721 (tp30) cc_final: 0.6418 (tp30) REVERT: R 40 MET cc_start: 0.8309 (mtm) cc_final: 0.7713 (mtt) REVERT: R 64 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8187 (pp) outliers start: 30 outliers final: 20 residues processed: 177 average time/residue: 0.0925 time to fit residues: 21.7050 Evaluate side-chains 168 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 24 optimal weight: 0.1980 chunk 74 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110427 restraints weight = 10626.777| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.23 r_work: 0.3012 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7962 Z= 0.091 Angle : 0.487 7.038 10830 Z= 0.263 Chirality : 0.042 0.140 1255 Planarity : 0.003 0.043 1367 Dihedral : 5.696 76.384 1102 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.76 % Allowed : 21.68 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.26), residues: 999 helix: -0.14 (0.29), residues: 352 sheet: -1.30 (0.34), residues: 213 loop : -2.22 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.010 0.001 TYR B 59 PHE 0.009 0.001 PHE N 68 TRP 0.011 0.001 TRP B 99 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 7960) covalent geometry : angle 0.48695 (10826) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.57231 ( 4) hydrogen bonds : bond 0.02863 ( 287) hydrogen bonds : angle 4.12726 ( 831) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.287 Fit side-chains REVERT: A 336 ARG cc_start: 0.8279 (ptm-80) cc_final: 0.7952 (ttt180) REVERT: B 105 TYR cc_start: 0.9253 (OUTLIER) cc_final: 0.8788 (t80) REVERT: B 264 TYR cc_start: 0.9282 (m-80) cc_final: 0.9042 (m-80) REVERT: N 87 LYS cc_start: 0.8467 (ttmt) cc_final: 0.7853 (mmtp) REVERT: R 40 MET cc_start: 0.8085 (mtm) cc_final: 0.7527 (mtt) REVERT: R 64 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8165 (pp) outliers start: 22 outliers final: 17 residues processed: 178 average time/residue: 0.1068 time to fit residues: 24.8165 Evaluate side-chains 174 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 75 GLN B 313 ASN R 322 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102412 restraints weight = 10568.271| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.19 r_work: 0.2890 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 7962 Z= 0.326 Angle : 0.663 7.609 10830 Z= 0.356 Chirality : 0.048 0.167 1255 Planarity : 0.005 0.041 1367 Dihedral : 6.276 71.995 1102 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 5.89 % Allowed : 20.43 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.26), residues: 999 helix: -0.43 (0.28), residues: 355 sheet: -1.30 (0.34), residues: 215 loop : -2.25 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 20 TYR 0.027 0.002 TYR B 59 PHE 0.020 0.002 PHE N 68 TRP 0.012 0.002 TRP N 47 HIS 0.008 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00777 ( 7960) covalent geometry : angle 0.66253 (10826) SS BOND : bond 0.00401 ( 2) SS BOND : angle 1.23876 ( 4) hydrogen bonds : bond 0.04376 ( 287) hydrogen bonds : angle 4.55220 ( 831) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 0.366 Fit side-chains REVERT: A 20 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7435 (mtm-85) REVERT: A 336 ARG cc_start: 0.8344 (ptm-80) cc_final: 0.7981 (ttt-90) REVERT: A 343 ASP cc_start: 0.8792 (m-30) cc_final: 0.8529 (m-30) REVERT: B 19 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.7260 (ttp-110) REVERT: B 59 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8220 (m-80) REVERT: B 105 TYR cc_start: 0.9325 (OUTLIER) cc_final: 0.8972 (t80) REVERT: B 118 ASP cc_start: 0.8792 (p0) cc_final: 0.8582 (p0) REVERT: B 234 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8542 (t80) REVERT: B 274 THR cc_start: 0.9361 (OUTLIER) cc_final: 0.9128 (p) REVERT: B 308 LEU cc_start: 0.8753 (pp) cc_final: 0.8514 (pt) REVERT: N 87 LYS cc_start: 0.8616 (ttmt) cc_final: 0.8016 (mmtp) REVERT: R 30 GLU cc_start: 0.6805 (tp30) cc_final: 0.6301 (tp30) REVERT: R 64 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8285 (pp) REVERT: R 224 GLN cc_start: 0.8355 (mt0) cc_final: 0.7860 (tm-30) outliers start: 47 outliers final: 31 residues processed: 183 average time/residue: 0.1059 time to fit residues: 25.5101 Evaluate side-chains 184 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.107897 restraints weight = 10644.227| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.24 r_work: 0.2992 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7962 Z= 0.104 Angle : 0.510 6.386 10830 Z= 0.277 Chirality : 0.042 0.142 1255 Planarity : 0.003 0.042 1367 Dihedral : 5.601 62.614 1102 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.51 % Allowed : 22.43 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.26), residues: 999 helix: 0.00 (0.29), residues: 356 sheet: -1.11 (0.34), residues: 213 loop : -2.04 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.015 0.001 TYR B 59 PHE 0.012 0.001 PHE N 68 TRP 0.012 0.001 TRP B 99 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7960) covalent geometry : angle 0.50977 (10826) SS BOND : bond 0.00193 ( 2) SS BOND : angle 0.59595 ( 4) hydrogen bonds : bond 0.03006 ( 287) hydrogen bonds : angle 4.17846 ( 831) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.299 Fit side-chains REVERT: A 46 LEU cc_start: 0.8657 (tp) cc_final: 0.8426 (tt) REVERT: A 336 ARG cc_start: 0.8343 (ptm-80) cc_final: 0.8099 (ttt180) REVERT: A 343 ASP cc_start: 0.8728 (m-30) cc_final: 0.8493 (m-30) REVERT: A 344 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9029 (mm-30) REVERT: B 19 ARG cc_start: 0.7608 (ttm-80) cc_final: 0.7343 (ttp-110) REVERT: B 59 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: B 61 MET cc_start: 0.8837 (ppp) cc_final: 0.8456 (ptm) REVERT: B 105 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.8785 (t80) REVERT: B 118 ASP cc_start: 0.8613 (p0) cc_final: 0.8360 (p0) REVERT: B 234 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8497 (t80) REVERT: B 264 TYR cc_start: 0.9295 (m-80) cc_final: 0.9040 (m-80) REVERT: B 274 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.9050 (p) REVERT: N 87 LYS cc_start: 0.8592 (ttmt) cc_final: 0.7979 (mmtp) REVERT: R 30 GLU cc_start: 0.6894 (tp30) cc_final: 0.6411 (tp30) REVERT: R 40 MET cc_start: 0.8040 (mtm) cc_final: 0.7403 (mtt) REVERT: R 64 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8246 (pp) outliers start: 28 outliers final: 18 residues processed: 175 average time/residue: 0.1087 time to fit residues: 24.9009 Evaluate side-chains 174 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 9.9990 chunk 81 optimal weight: 0.1980 chunk 15 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 34 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111394 restraints weight = 10583.736| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.22 r_work: 0.3003 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7962 Z= 0.085 Angle : 0.479 6.432 10830 Z= 0.260 Chirality : 0.042 0.138 1255 Planarity : 0.003 0.044 1367 Dihedral : 4.888 48.985 1102 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.38 % Allowed : 22.31 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.26), residues: 999 helix: 0.29 (0.29), residues: 358 sheet: -0.97 (0.35), residues: 207 loop : -1.91 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.012 0.001 TYR B 59 PHE 0.007 0.001 PHE N 68 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 7960) covalent geometry : angle 0.47944 (10826) SS BOND : bond 0.00156 ( 2) SS BOND : angle 0.47300 ( 4) hydrogen bonds : bond 0.02676 ( 287) hydrogen bonds : angle 3.94841 ( 831) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8196 (mt-10) REVERT: A 20 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.7283 (mtm-85) REVERT: A 220 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.7529 (t-170) REVERT: A 372 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8024 (mp) REVERT: B 19 ARG cc_start: 0.7543 (ttm-80) cc_final: 0.7310 (ttp-110) REVERT: B 105 TYR cc_start: 0.9209 (OUTLIER) cc_final: 0.8690 (t80) REVERT: B 118 ASP cc_start: 0.8571 (p0) cc_final: 0.8320 (p0) REVERT: B 234 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8511 (t80) REVERT: B 274 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9092 (p) REVERT: N 87 LYS cc_start: 0.8466 (ttmt) cc_final: 0.7836 (mmtp) REVERT: N 118 ARG cc_start: 0.8649 (mtm-85) cc_final: 0.8277 (mtm180) REVERT: R 40 MET cc_start: 0.8077 (mtm) cc_final: 0.7487 (mtt) REVERT: R 64 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8055 (pp) outliers start: 27 outliers final: 19 residues processed: 185 average time/residue: 0.1057 time to fit residues: 25.7433 Evaluate side-chains 182 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS N 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.142247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109473 restraints weight = 10549.315| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.26 r_work: 0.2995 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7962 Z= 0.104 Angle : 0.511 9.038 10830 Z= 0.271 Chirality : 0.042 0.137 1255 Planarity : 0.003 0.043 1367 Dihedral : 4.783 45.339 1102 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.13 % Allowed : 23.31 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.26), residues: 999 helix: 0.46 (0.30), residues: 353 sheet: -0.91 (0.35), residues: 207 loop : -1.85 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.013 0.001 TYR N 60 PHE 0.013 0.001 PHE A 212 TRP 0.009 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 7960) covalent geometry : angle 0.51075 (10826) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.53615 ( 4) hydrogen bonds : bond 0.02835 ( 287) hydrogen bonds : angle 3.94412 ( 831) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 336 ARG cc_start: 0.8326 (ptm-80) cc_final: 0.8065 (ttt180) REVERT: B 19 ARG cc_start: 0.7563 (ttm-80) cc_final: 0.7320 (ttp-110) REVERT: B 59 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: B 105 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8806 (t80) REVERT: B 118 ASP cc_start: 0.8563 (p0) cc_final: 0.8318 (p0) REVERT: B 234 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8483 (t80) REVERT: B 274 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.9073 (p) REVERT: N 87 LYS cc_start: 0.8558 (ttmt) cc_final: 0.7861 (mmtp) REVERT: R 40 MET cc_start: 0.8192 (mtm) cc_final: 0.7549 (mtt) REVERT: R 64 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8175 (pp) outliers start: 25 outliers final: 19 residues processed: 174 average time/residue: 0.0969 time to fit residues: 22.4045 Evaluate side-chains 178 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS N 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104965 restraints weight = 10602.103| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.25 r_work: 0.2932 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7962 Z= 0.170 Angle : 0.567 11.823 10830 Z= 0.299 Chirality : 0.045 0.223 1255 Planarity : 0.004 0.042 1367 Dihedral : 5.072 48.165 1102 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.13 % Allowed : 23.43 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.26), residues: 999 helix: 0.27 (0.29), residues: 356 sheet: -0.83 (0.36), residues: 214 loop : -1.86 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.021 0.002 TYR B 59 PHE 0.014 0.001 PHE N 68 TRP 0.008 0.001 TRP R 109 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7960) covalent geometry : angle 0.56721 (10826) SS BOND : bond 0.00289 ( 2) SS BOND : angle 0.79324 ( 4) hydrogen bonds : bond 0.03460 ( 287) hydrogen bonds : angle 4.13483 ( 831) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7359 (mtm-85) REVERT: A 336 ARG cc_start: 0.8345 (ptm-80) cc_final: 0.8054 (ttt180) REVERT: A 343 ASP cc_start: 0.8838 (m-30) cc_final: 0.8545 (m-30) REVERT: B 19 ARG cc_start: 0.7582 (ttm-80) cc_final: 0.7316 (ttp-110) REVERT: B 59 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.8166 (m-80) REVERT: B 105 TYR cc_start: 0.9284 (OUTLIER) cc_final: 0.8901 (t80) REVERT: B 234 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8414 (t80) REVERT: B 274 THR cc_start: 0.9352 (OUTLIER) cc_final: 0.9119 (p) REVERT: N 87 LYS cc_start: 0.8581 (ttmt) cc_final: 0.7869 (mmtp) REVERT: N 118 ARG cc_start: 0.8569 (mtm-85) cc_final: 0.7930 (mtt180) REVERT: R 64 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8212 (pp) outliers start: 25 outliers final: 19 residues processed: 173 average time/residue: 0.0962 time to fit residues: 21.8672 Evaluate side-chains 177 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108477 restraints weight = 10495.695| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.24 r_work: 0.2980 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7962 Z= 0.107 Angle : 0.540 14.488 10830 Z= 0.279 Chirality : 0.043 0.219 1255 Planarity : 0.003 0.042 1367 Dihedral : 4.796 46.809 1102 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.26 % Allowed : 22.68 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.26), residues: 999 helix: 0.45 (0.29), residues: 353 sheet: -0.72 (0.36), residues: 213 loop : -1.83 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.013 0.001 TYR B 59 PHE 0.011 0.001 PHE N 68 TRP 0.010 0.001 TRP A 234 HIS 0.010 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7960) covalent geometry : angle 0.53984 (10826) SS BOND : bond 0.00211 ( 2) SS BOND : angle 0.57666 ( 4) hydrogen bonds : bond 0.02965 ( 287) hydrogen bonds : angle 4.02820 ( 831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2229.98 seconds wall clock time: 38 minutes 43.96 seconds (2323.96 seconds total)