Starting phenix.real_space_refine on Thu Jul 2 07:55:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dhi_30681/07_2026/7dhi_30681.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dhi_30681/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7dhi_30681/07_2026/7dhi_30681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dhi_30681/07_2026/7dhi_30681.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7dhi_30681/07_2026/7dhi_30681.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dhi_30681/07_2026/7dhi_30681.cif" model { file = "/net/cci-nas-00/data/ceres_data/7dhi_30681/07_2026/7dhi_30681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dhi_30681/07_2026/7dhi_30681.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.37, per 1000 atoms: 0.18 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: 0.51 Conformation dependent library (CDL) restraints added in 545.6 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: 0.23 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: 1.09 Time building geometry restraints manager: 0.68 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: 4150 16.97 - 33.95: 421 33.95 - 50.92: 70 50.92 - 67.90: 13 67.90 - 84.87: 9 Dihedral angle restraints: 4663 sinusoidal: 1700 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 4660 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 14.447 84.870 2737 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/Z covalent geometry : bond 0.00386 / 0.18 ( 7960) covalent geometry : angle 0.76167 / 0.42 (10826) SS BOND : bond 0.00394 / 0.19 ( 2) SS BOND : angle 0.81758 / 0.40 ( 4) hydrogen bonds : bond 0.31203 / 20.85 ( 287) hydrogen bonds : angle 10.52564 / 7.05 ( 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 : 0.248 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: 0.0895 time to fit residues: 23.2696 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 : 0.212 ------------------------------------------------------------------------------- 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... 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 = 0.3663 r_free = 0.3663 target = 0.140679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107849 restraints weight = 10505.002| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.29 r_work: 0.3088 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7962 Z= 0.126 Angle : 0.545 5.564 10830 Z= 0.299 Chirality : 0.043 0.137 1255 Planarity : 0.004 0.047 1367 Dihedral : 6.192 84.692 1096 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.63 % Allowed : 15.04 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.23), residues: 999 helix: -2.47 (0.22), residues: 367 sheet: -1.70 (0.34), residues: 212 loop : -2.62 (0.26), residues: 420 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/Z covalent geometry : bond 0.00283 / 0.13 ( 7960) covalent geometry : angle 0.54508 / 0.30 (10826) SS BOND : bond 0.00139 / 0.07 ( 2) SS BOND : angle 0.79621 / 0.43 ( 4) hydrogen bonds : bond 0.04194 / 2.83 ( 287) hydrogen bonds : angle 5.22907 / 3.45 ( 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 182 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.178 Fit side-chains REVERT: A 20 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7519 (mtm-85) REVERT: N 87 LYS cc_start: 0.8539 (ttmt) cc_final: 0.7941 (mmtp) REVERT: R 64 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8066 (pp) outliers start: 13 outliers final: 10 residues processed: 179 average time/residue: 0.0848 time to fit residues: 19.7529 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 : 0.493 ------------------------------------------------------------------------------- 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: 5.9990 chunk 40 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3592 r_free = 0.3592 target = 0.136450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102347 restraints weight = 10386.168| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.32 r_work: 0.2968 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2095 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= 0.271 Angle : 0.630 6.803 10830 Z= 0.340 Chirality : 0.046 0.151 1255 Planarity : 0.004 0.043 1367 Dihedral : 6.546 87.486 1096 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.76 % Allowed : 18.80 % Favored : 77.44 % 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: -2.90 (0.24), residues: 999 helix: -1.24 (0.27), residues: 352 sheet: -1.65 (0.34), residues: 215 loop : -2.58 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 228 TYR 0.024 0.002 TYR B 59 PHE 0.019 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/Z covalent geometry : bond 0.00638 / 0.27 ( 7960) covalent geometry : angle 0.63007 / 0.34 (10826) SS BOND : bond 0.00331 / 0.16 ( 2) SS BOND : angle 1.18219 / 0.65 ( 4) hydrogen bonds : bond 0.04633 / 3.14 ( 287) hydrogen bonds : angle 4.86292 / 3.23 ( 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 187 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 343 ASP cc_start: 0.8831 (m-30) cc_final: 0.8583 (m-30) REVERT: B 118 ASP cc_start: 0.8733 (p0) cc_final: 0.8496 (p0) REVERT: B 234 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8266 (t80) REVERT: B 308 LEU cc_start: 0.8735 (pp) cc_final: 0.8488 (pt) REVERT: N 18 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7696 (tt) REVERT: N 87 LYS cc_start: 0.8592 (ttmt) cc_final: 0.7995 (mmtp) REVERT: R 30 GLU cc_start: 0.6601 (tp30) cc_final: 0.6327 (tp30) REVERT: R 64 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8218 (pp) REVERT: R 224 GLN cc_start: 0.8421 (mt0) cc_final: 0.7854 (tm-30) outliers start: 30 outliers final: 18 residues processed: 178 average time/residue: 0.0746 time to fit residues: 17.5547 Evaluate side-chains 172 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 85 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3638 r_free = 0.3638 target = 0.138784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106594 restraints weight = 10600.256| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.19 r_work: 0.2947 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2242 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= 0.140 Angle : 0.527 5.781 10830 Z= 0.287 Chirality : 0.043 0.144 1255 Planarity : 0.003 0.041 1367 Dihedral : 6.166 87.567 1096 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.51 % Allowed : 20.93 % 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: -2.38 (0.25), residues: 999 helix: -0.64 (0.28), residues: 355 sheet: -1.49 (0.34), residues: 214 loop : -2.38 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.015 0.001 TYR B 59 PHE 0.013 0.001 PHE N 68 TRP 0.011 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 7960) covalent geometry : angle 0.52675 / 0.29 (10826) SS BOND : bond 0.00209 / 0.11 ( 2) SS BOND : angle 0.80617 / 0.44 ( 4) hydrogen bonds : bond 0.03507 / 2.39 ( 287) hydrogen bonds : angle 4.42549 / 2.95 ( 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 189 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.264 Fit side-chains REVERT: A 336 ARG cc_start: 0.8315 (ptm-80) cc_final: 0.7992 (ttt180) REVERT: A 343 ASP cc_start: 0.8770 (m-30) cc_final: 0.8531 (m-30) REVERT: B 105 TYR cc_start: 0.9269 (OUTLIER) cc_final: 0.8910 (t80) REVERT: B 234 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8312 (t80) REVERT: N 87 LYS cc_start: 0.8542 (ttmt) cc_final: 0.7964 (mmtp) REVERT: R 30 GLU cc_start: 0.6725 (tp30) cc_final: 0.6418 (tp30) REVERT: R 40 MET cc_start: 0.8384 (mtm) cc_final: 0.7828 (mtt) REVERT: R 64 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8196 (pp) outliers start: 28 outliers final: 20 residues processed: 180 average time/residue: 0.0709 time to fit residues: 17.1028 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 : 0.264 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain G residue 38 MET 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 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: 0.7980 chunk 5 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 58 optimal weight: 0.0050 chunk 43 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3695 r_free = 0.3695 target = 0.143276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110964 restraints weight = 10625.000| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.22 r_work: 0.3008 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2460 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= 0.088 Angle : 0.485 7.274 10830 Z= 0.262 Chirality : 0.042 0.138 1255 Planarity : 0.003 0.044 1367 Dihedral : 5.637 81.917 1096 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.88 % Allowed : 22.06 % Favored : 75.06 % 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: -1.92 (0.26), residues: 999 helix: -0.12 (0.29), residues: 352 sheet: -1.29 (0.34), residues: 213 loop : -2.21 (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 0.003 0.000 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 ( 7960) covalent geometry : angle 0.48458 / 0.26 (10826) SS BOND : bond 0.00137 / 0.07 ( 2) SS BOND : angle 0.56388 / 0.31 ( 4) hydrogen bonds : bond 0.02818 / 1.93 ( 287) hydrogen bonds : angle 4.10802 / 2.74 ( 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 188 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.214 Fit side-chains REVERT: A 336 ARG cc_start: 0.8291 (ptm-80) cc_final: 0.8020 (ttt180) REVERT: A 344 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8987 (mm-30) REVERT: B 105 TYR cc_start: 0.9257 (OUTLIER) cc_final: 0.8804 (t80) REVERT: B 264 TYR cc_start: 0.9287 (m-80) cc_final: 0.8830 (m-80) REVERT: N 87 LYS cc_start: 0.8438 (ttmt) cc_final: 0.7806 (mmtp) REVERT: N 117 TYR cc_start: 0.8847 (m-80) cc_final: 0.8594 (m-80) REVERT: R 40 MET cc_start: 0.8183 (mtm) cc_final: 0.7606 (mtt) REVERT: R 64 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8074 (pp) outliers start: 23 outliers final: 15 residues processed: 179 average time/residue: 0.0803 time to fit residues: 18.9321 Evaluate side-chains 171 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 183 ASN 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: 3.9990 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 0.0870 chunk 87 optimal weight: 8.9990 overall best weight: 2.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 313 ASN R 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.137353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104579 restraints weight = 10502.499| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.18 r_work: 0.2903 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 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 : 0.006 0.054 7962 Z= 0.236 Angle : 0.592 7.168 10830 Z= 0.319 Chirality : 0.046 0.152 1255 Planarity : 0.004 0.042 1367 Dihedral : 5.900 75.331 1096 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.89 % Allowed : 21.05 % 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: -1.94 (0.26), residues: 999 helix: -0.19 (0.29), residues: 355 sheet: -1.26 (0.35), residues: 217 loop : -2.20 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.015 0.002 TYR B 85 PHE 0.013 0.002 PHE N 68 TRP 0.010 0.002 TRP R 109 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 ( 7960) covalent geometry : angle 0.59223 / 0.32 (10826) SS BOND : bond 0.00323 / 0.16 ( 2) SS BOND : angle 1.04207 / 0.59 ( 4) hydrogen bonds : bond 0.03909 / 2.69 ( 287) hydrogen bonds : angle 4.35799 / 2.93 ( 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 191 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.271 Fit side-chains REVERT: A 336 ARG cc_start: 0.8316 (ptm-80) cc_final: 0.7977 (ttt-90) REVERT: A 343 ASP cc_start: 0.8813 (m-30) cc_final: 0.8532 (m-30) REVERT: B 19 ARG cc_start: 0.7565 (ttm-80) cc_final: 0.7266 (ttp-110) REVERT: B 105 TYR cc_start: 0.9289 (OUTLIER) cc_final: 0.8925 (t80) REVERT: B 118 ASP cc_start: 0.8776 (p0) cc_final: 0.8547 (p0) REVERT: B 234 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8373 (t80) REVERT: B 274 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9145 (p) REVERT: N 87 LYS cc_start: 0.8590 (ttmt) cc_final: 0.7953 (mmtp) REVERT: R 64 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8300 (pp) outliers start: 39 outliers final: 28 residues processed: 180 average time/residue: 0.0801 time to fit residues: 19.0717 Evaluate side-chains 179 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 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 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 N residue 83 MET Chi-restraints excluded: chain R residue 39 VAL 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 242 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 7.9990 chunk 17 optimal weight: 0.0670 chunk 88 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3683 r_free = 0.3683 target = 0.142121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109654 restraints weight = 10638.350| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.22 r_work: 0.2980 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2596 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= 0.096 Angle : 0.504 9.622 10830 Z= 0.270 Chirality : 0.042 0.140 1255 Planarity : 0.003 0.043 1367 Dihedral : 5.468 78.399 1096 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.26 % Allowed : 22.18 % Favored : 74.56 % 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: -1.58 (0.26), residues: 999 helix: 0.15 (0.30), residues: 353 sheet: -1.04 (0.35), residues: 213 loop : -2.03 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.008 0.001 TYR R 174 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/Z covalent geometry : bond 0.00216 / 0.10 ( 7960) covalent geometry : angle 0.50398 / 0.27 (10826) SS BOND : bond 0.00159 / 0.08 ( 2) SS BOND : angle 0.54639 / 0.30 ( 4) hydrogen bonds : bond 0.02910 / 1.99 ( 287) hydrogen bonds : angle 4.09975 / 2.76 ( 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 185 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.242 Fit side-chains REVERT: A 46 LEU cc_start: 0.8790 (tp) cc_final: 0.8571 (tt) REVERT: A 336 ARG cc_start: 0.8338 (ptm-80) cc_final: 0.8076 (ttt180) REVERT: A 344 GLU cc_start: 0.9287 (mm-30) cc_final: 0.9016 (mm-30) REVERT: B 19 ARG cc_start: 0.7566 (ttm-80) cc_final: 0.7310 (ttp-110) REVERT: B 61 MET cc_start: 0.8867 (ppp) cc_final: 0.8463 (ptm) REVERT: B 105 TYR cc_start: 0.9222 (OUTLIER) cc_final: 0.8754 (t80) REVERT: B 118 ASP cc_start: 0.8679 (p0) cc_final: 0.8430 (p0) REVERT: B 264 TYR cc_start: 0.9290 (m-80) cc_final: 0.9028 (m-80) REVERT: B 274 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.9084 (p) REVERT: N 87 LYS cc_start: 0.8517 (ttmt) cc_final: 0.7896 (mmtp) REVERT: R 30 GLU cc_start: 0.6765 (tp30) cc_final: 0.6529 (tp30) REVERT: R 40 MET cc_start: 0.8058 (mtm) cc_final: 0.7424 (mtt) REVERT: R 64 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8167 (pp) outliers start: 26 outliers final: 20 residues processed: 178 average time/residue: 0.0789 time to fit residues: 18.5838 Evaluate side-chains 173 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 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 255 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 34 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 190 CYS Chi-restraints excluded: chain R residue 197 GLN 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: 0.6980 chunk 15 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106608 restraints weight = 10629.248| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.24 r_work: 0.2953 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2606 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= 0.146 Angle : 0.535 9.154 10830 Z= 0.286 Chirality : 0.043 0.145 1255 Planarity : 0.003 0.043 1367 Dihedral : 5.442 74.946 1096 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.88 % Allowed : 21.68 % Favored : 74.44 % 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: -1.49 (0.26), residues: 999 helix: 0.21 (0.29), residues: 356 sheet: -1.00 (0.35), residues: 213 loop : -1.97 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.010 0.001 TYR N 60 PHE 0.012 0.001 PHE N 68 TRP 0.008 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 7960) covalent geometry : angle 0.53512 / 0.29 (10826) SS BOND : bond 0.00254 / 0.13 ( 2) SS BOND : angle 0.73902 / 0.42 ( 4) hydrogen bonds : bond 0.03289 / 2.26 ( 287) hydrogen bonds : angle 4.13868 / 2.78 ( 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 185 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.280 Fit side-chains REVERT: A 20 ARG cc_start: 0.7722 (mtm-85) cc_final: 0.7271 (mtm-85) REVERT: A 343 ASP cc_start: 0.8790 (m-30) cc_final: 0.8526 (m-30) REVERT: B 19 ARG cc_start: 0.7593 (ttm-80) cc_final: 0.7338 (ttp-110) REVERT: B 105 TYR cc_start: 0.9260 (OUTLIER) cc_final: 0.8879 (t80) REVERT: B 118 ASP cc_start: 0.8667 (p0) cc_final: 0.8424 (p0) REVERT: B 234 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8424 (t80) REVERT: B 264 TYR cc_start: 0.9326 (m-80) cc_final: 0.9031 (m-80) REVERT: B 274 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9135 (p) REVERT: G 42 GLU cc_start: 0.8806 (tp30) cc_final: 0.8588 (tp30) REVERT: N 87 LYS cc_start: 0.8514 (ttmt) cc_final: 0.7887 (mmtp) REVERT: N 118 ARG cc_start: 0.8601 (mtm-85) cc_final: 0.8398 (mtm-85) REVERT: R 30 GLU cc_start: 0.6795 (tp30) cc_final: 0.6365 (tp30) REVERT: R 64 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8221 (pp) outliers start: 31 outliers final: 21 residues processed: 177 average time/residue: 0.0814 time to fit residues: 18.9295 Evaluate side-chains 175 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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 34 VAL Chi-restraints excluded: chain R residue 39 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 197 GLN 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: 0.9980 chunk 25 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3671 r_free = 0.3671 target = 0.141236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108617 restraints weight = 10586.485| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.22 r_work: 0.2979 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2690 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= 0.106 Angle : 0.504 6.441 10830 Z= 0.271 Chirality : 0.042 0.142 1255 Planarity : 0.003 0.043 1367 Dihedral : 5.214 75.994 1096 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.26 % Allowed : 22.43 % 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: -1.32 (0.26), residues: 999 helix: 0.38 (0.30), residues: 353 sheet: -0.95 (0.35), residues: 214 loop : -1.86 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.011 0.001 TYR N 60 PHE 0.010 0.001 PHE N 68 TRP 0.009 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7960) covalent geometry : angle 0.50406 / 0.27 (10826) SS BOND : bond 0.00205 / 0.10 ( 2) SS BOND : angle 0.58219 / 0.33 ( 4) hydrogen bonds : bond 0.02925 / 2.02 ( 287) hydrogen bonds : angle 4.05528 / 2.73 ( 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 180 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 336 ARG cc_start: 0.8310 (ptm-80) cc_final: 0.8083 (ttt180) REVERT: A 344 GLU cc_start: 0.9286 (mm-30) cc_final: 0.9035 (mm-30) REVERT: B 19 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7314 (ttp-110) REVERT: B 59 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: B 61 MET cc_start: 0.8899 (ppp) cc_final: 0.8518 (ptm) REVERT: B 105 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.8727 (t80) REVERT: B 118 ASP cc_start: 0.8659 (p0) cc_final: 0.8437 (p0) REVERT: B 234 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8394 (t80) REVERT: B 264 TYR cc_start: 0.9290 (m-80) cc_final: 0.8841 (m-80) REVERT: B 274 THR cc_start: 0.9337 (OUTLIER) cc_final: 0.9103 (p) REVERT: N 87 LYS cc_start: 0.8485 (ttmt) cc_final: 0.7837 (mmtp) REVERT: N 118 ARG cc_start: 0.8494 (mtm-85) cc_final: 0.7818 (mtt180) REVERT: R 40 MET cc_start: 0.8106 (mtm) cc_final: 0.7530 (mtt) REVERT: R 64 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8134 (pp) REVERT: R 234 ASP cc_start: 0.8272 (m-30) cc_final: 0.7891 (t0) outliers start: 26 outliers final: 20 residues processed: 175 average time/residue: 0.0767 time to fit residues: 17.7620 Evaluate side-chains 175 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 112 VAL 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 34 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.141203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108441 restraints weight = 10565.701| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.23 r_work: 0.2983 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7962 Z= 0.109 Angle : 0.503 7.010 10830 Z= 0.271 Chirality : 0.042 0.142 1255 Planarity : 0.003 0.044 1367 Dihedral : 5.084 76.014 1096 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.38 % Allowed : 22.56 % 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: -1.21 (0.26), residues: 999 helix: 0.50 (0.30), residues: 353 sheet: -0.90 (0.35), residues: 214 loop : -1.82 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.012 0.001 TYR N 60 PHE 0.010 0.001 PHE N 68 TRP 0.009 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 7960) covalent geometry : angle 0.50339 / 0.27 (10826) SS BOND : bond 0.00211 / 0.11 ( 2) SS BOND : angle 0.58425 / 0.33 ( 4) hydrogen bonds : bond 0.02952 / 2.03 ( 287) hydrogen bonds : angle 4.02398 / 2.70 ( 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: 27 poor density : 153 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8193 (mt-10) REVERT: A 20 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.7322 (mtm-85) REVERT: A 336 ARG cc_start: 0.8318 (ptm-80) cc_final: 0.8050 (ttt180) REVERT: B 19 ARG cc_start: 0.7580 (ttm-80) cc_final: 0.7339 (ttp-110) REVERT: B 59 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: B 61 MET cc_start: 0.8878 (ppp) cc_final: 0.8484 (ptm) REVERT: B 105 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8819 (t80) REVERT: B 118 ASP cc_start: 0.8631 (p0) cc_final: 0.8394 (p0) REVERT: B 234 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8332 (t80) REVERT: B 264 TYR cc_start: 0.9282 (m-80) cc_final: 0.8800 (m-80) REVERT: B 274 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9088 (p) REVERT: N 87 LYS cc_start: 0.8576 (ttmt) cc_final: 0.7888 (mmtp) REVERT: N 118 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.7894 (mtt180) REVERT: R 40 MET cc_start: 0.8095 (mtm) cc_final: 0.7521 (mtt) REVERT: R 64 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8209 (pp) REVERT: R 234 ASP cc_start: 0.8290 (m-30) cc_final: 0.7933 (t0) outliers start: 27 outliers final: 22 residues processed: 174 average time/residue: 0.0732 time to fit residues: 16.9788 Evaluate side-chains 179 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 319 THR 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 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 34 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 76 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106090 restraints weight = 10521.608| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.28 r_work: 0.2985 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2754 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= 0.118 Angle : 0.505 6.856 10830 Z= 0.272 Chirality : 0.043 0.143 1255 Planarity : 0.003 0.043 1367 Dihedral : 5.057 74.773 1096 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.38 % Allowed : 22.43 % Favored : 74.19 % 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: -1.18 (0.26), residues: 999 helix: 0.55 (0.30), residues: 352 sheet: -0.88 (0.35), residues: 214 loop : -1.85 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.012 0.001 TYR N 60 PHE 0.010 0.001 PHE N 68 TRP 0.009 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 7960) covalent geometry : angle 0.50448 / 0.27 (10826) SS BOND : bond 0.00238 / 0.12 ( 2) SS BOND : angle 0.61177 / 0.34 ( 4) hydrogen bonds : bond 0.02999 / 2.07 ( 287) hydrogen bonds : angle 4.03295 / 2.70 ( 831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1736.88 seconds wall clock time: 30 minutes 20.10 seconds (1820.10 seconds total)