Starting phenix.real_space_refine on Wed Mar 4 04:14:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rgp_24453/03_2026/7rgp_24453_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rgp_24453/03_2026/7rgp_24453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rgp_24453/03_2026/7rgp_24453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rgp_24453/03_2026/7rgp_24453.map" model { file = "/net/cci-nas-00/data/ceres_data/7rgp_24453/03_2026/7rgp_24453_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rgp_24453/03_2026/7rgp_24453_neut.cif" } resolution = 2.9 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= 0.004 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 65 5.16 5 C 6884 2.51 5 N 1853 2.21 5 O 1993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10795 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1773 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 209} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "N" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 240 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2999 Classifications: {'peptide': 378} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 39} Link IDs: {'PTRANS': 14, 'TRANS': 363} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 5, 'GLU:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 109 Time building chain proxies: 2.50, per 1000 atoms: 0.23 Number of scatterers: 10795 At special positions: 0 Unit cell: (163.904, 123.136, 105.664, 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 65 16.00 O 1993 8.00 N 1853 7.00 C 6884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.02 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: 0.78 Conformation dependent library (CDL) restraints added in 496.9 milliseconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 17 sheets defined 34.2% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 15 through 39 removed outlier: 3.929A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.599A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.781A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.544A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 371 through 390 removed outlier: 4.199A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 33 through 37 removed outlier: 4.281A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.670A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.870A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.501A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.827A 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: 3.840A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'R' and resid 31 through 52 Processing helix chain 'R' and resid 90 through 95 removed outlier: 3.970A pdb=" N SER R 93 " --> pdb=" O PRO R 90 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL R 95 " --> pdb=" O ALA R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 160 removed outlier: 4.098A pdb=" N TYR R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER R 157 " --> pdb=" O ALA R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 166 removed outlier: 3.623A pdb=" N ILE R 165 " --> pdb=" O ILE R 161 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU R 166 " --> pdb=" O ALA R 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 161 through 166' Processing helix chain 'R' and resid 174 through 206 removed outlier: 3.867A pdb=" N SER R 193 " --> pdb=" O LEU R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 243 removed outlier: 4.077A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 257 Processing helix chain 'R' and resid 261 through 292 removed outlier: 3.727A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix removed outlier: 3.691A pdb=" N LYS R 288 " --> pdb=" O TRP R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 336 removed outlier: 4.984A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 4.028A pdb=" N ALA R 316 " --> pdb=" O PRO R 312 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE R 330 " --> pdb=" O ARG R 326 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER R 333 " --> pdb=" O CYS R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 356 removed outlier: 4.310A pdb=" N LEU R 354 " --> pdb=" O ALA R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 361 Processing helix chain 'R' and resid 362 through 368 removed outlier: 3.591A pdb=" N ILE R 366 " --> pdb=" O HIS R 363 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA R 368 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 393 removed outlier: 4.236A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU R 388 " --> pdb=" O LEU R 384 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR R 391 " --> pdb=" O GLU R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 403 Processing helix chain 'R' and resid 406 through 421 removed outlier: 3.692A pdb=" N GLU R 418 " --> pdb=" O ARG R 414 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG R 421 " --> pdb=" O TRP R 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.442A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.458A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.066A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.618A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.571A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 4.400A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.840A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.540A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.270A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.270A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.983A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 182 through 183 removed outlier: 6.429A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.602A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 83 through 84 476 hydrogen bonds defined for protein. 1317 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: 1.76 Time building geometry restraints manager: 1.07 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: 3393 1.34 - 1.46: 2264 1.46 - 1.58: 5292 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 11039 Sorted by residual: bond pdb=" N VAL R 259 " pdb=" CA VAL R 259 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.66e+00 bond pdb=" N GLU R 262 " pdb=" CA GLU R 262 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.17e-02 7.31e+03 7.75e+00 bond pdb=" N VAL R 319 " pdb=" CA VAL R 319 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.26e-02 6.30e+03 7.65e+00 bond pdb=" N ILE A 26 " pdb=" CA ILE A 26 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.41e+00 bond pdb=" N ARG G 62 " pdb=" CA ARG G 62 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 6.82e+00 ... (remaining 11034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 14308 2.00 - 4.01: 584 4.01 - 6.01: 66 6.01 - 8.01: 15 8.01 - 10.02: 10 Bond angle restraints: 14983 Sorted by residual: angle pdb=" N GLU A 15 " pdb=" CA GLU A 15 " pdb=" C GLU A 15 " ideal model delta sigma weight residual 114.12 105.96 8.16 1.39e+00 5.18e-01 3.44e+01 angle pdb=" N GLN A 384 " pdb=" CA GLN A 384 " pdb=" C GLN A 384 " ideal model delta sigma weight residual 111.36 106.30 5.06 1.09e+00 8.42e-01 2.16e+01 angle pdb=" C GLN A 384 " pdb=" CA GLN A 384 " pdb=" CB GLN A 384 " ideal model delta sigma weight residual 110.85 117.46 -6.61 1.70e+00 3.46e-01 1.51e+01 angle pdb=" C VAL A 20 " pdb=" N GLU A 21 " pdb=" CA GLU A 21 " ideal model delta sigma weight residual 120.29 115.41 4.88 1.42e+00 4.96e-01 1.18e+01 angle pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " pdb=" CG TYR R 148 " ideal model delta sigma weight residual 113.90 119.99 -6.09 1.80e+00 3.09e-01 1.14e+01 ... (remaining 14978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5860 17.99 - 35.99: 527 35.99 - 53.98: 88 53.98 - 71.98: 15 71.98 - 89.97: 15 Dihedral angle restraints: 6505 sinusoidal: 2496 harmonic: 4009 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -3.12 -82.88 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -166.54 80.54 1 1.00e+01 1.00e-02 8.02e+01 dihedral pdb=" CA PHE A 222 " pdb=" C PHE A 222 " pdb=" N ASP A 223 " pdb=" CA ASP A 223 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 6502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1321 0.063 - 0.125: 305 0.125 - 0.188: 37 0.188 - 0.250: 2 0.250 - 0.312: 3 Chirality restraints: 1668 Sorted by residual: chirality pdb=" CB VAL R 259 " pdb=" CA VAL R 259 " pdb=" CG1 VAL R 259 " pdb=" CG2 VAL R 259 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA GLU A 15 " pdb=" N GLU A 15 " pdb=" C GLU A 15 " pdb=" CB GLU A 15 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE A 244 " pdb=" CA ILE A 244 " pdb=" CG1 ILE A 244 " pdb=" CG2 ILE A 244 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1665 not shown) Planarity restraints: 1900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 243 " -0.041 2.00e-02 2.50e+03 3.53e-02 3.12e+01 pdb=" CG TRP R 243 " 0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP R 243 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP R 243 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP R 243 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP R 243 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 243 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 243 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 243 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP R 243 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO B 236 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 222 " -0.020 2.00e-02 2.50e+03 2.16e-02 8.17e+00 pdb=" CG PHE A 222 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 222 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 222 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 222 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 222 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 222 " -0.001 2.00e-02 2.50e+03 ... (remaining 1897 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 394 2.70 - 3.25: 11237 3.25 - 3.80: 17630 3.80 - 4.35: 23004 4.35 - 4.90: 37596 Nonbonded interactions: 89861 Sorted by model distance: nonbonded pdb=" O ASP B 76 " pdb=" OD1 ASP B 76 " model vdw 2.145 3.040 nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.201 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.203 3.040 nonbonded pdb=" O TRP R 203 " pdb=" OG1 THR R 207 " model vdw 2.205 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.205 3.040 ... (remaining 89856 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.750 Find NCS groups from input model: 0.050 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 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 : 0.006 0.085 11047 Z= 0.297 Angle : 0.925 10.017 14999 Z= 0.514 Chirality : 0.053 0.312 1668 Planarity : 0.006 0.074 1900 Dihedral : 14.391 89.971 3897 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.88 % Allowed : 1.14 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.81 (0.22), residues: 1346 helix: -1.79 (0.22), residues: 437 sheet: -1.71 (0.27), residues: 331 loop : -1.84 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 314 TYR 0.031 0.002 TYR R 148 PHE 0.048 0.003 PHE A 222 TRP 0.092 0.004 TRP R 243 HIS 0.008 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00638 (11039) covalent geometry : angle 0.92464 (14983) SS BOND : bond 0.00483 ( 8) SS BOND : angle 1.23622 ( 16) hydrogen bonds : bond 0.16248 ( 472) hydrogen bonds : angle 7.57857 ( 1317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 0.412 Fit side-chains REVERT: A 229 ASP cc_start: 0.6787 (p0) cc_final: 0.6395 (p0) REVERT: A 293 LYS cc_start: 0.8029 (mptt) cc_final: 0.7737 (mmtt) outliers start: 10 outliers final: 0 residues processed: 223 average time/residue: 0.5883 time to fit residues: 140.5902 Evaluate side-chains 138 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 390 GLN B 17 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 ASN R 394 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.156361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.129968 restraints weight = 20468.025| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.23 r_work: 0.3818 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11047 Z= 0.148 Angle : 0.707 9.576 14999 Z= 0.365 Chirality : 0.045 0.171 1668 Planarity : 0.006 0.071 1900 Dihedral : 6.027 71.434 1508 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.81 % Allowed : 14.69 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.22 (0.22), residues: 1346 helix: -1.21 (0.22), residues: 447 sheet: -1.35 (0.28), residues: 326 loop : -1.60 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 67 TYR 0.034 0.001 TYR R 148 PHE 0.026 0.002 PHE E 200 TRP 0.040 0.002 TRP R 243 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00336 (11039) covalent geometry : angle 0.70648 (14983) SS BOND : bond 0.00414 ( 8) SS BOND : angle 1.05179 ( 16) hydrogen bonds : bond 0.04454 ( 472) hydrogen bonds : angle 5.85312 ( 1317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.437 Fit side-chains REVERT: A 229 ASP cc_start: 0.7608 (p0) cc_final: 0.7096 (p0) REVERT: A 293 LYS cc_start: 0.8205 (mptt) cc_final: 0.8004 (mtpt) REVERT: N 106 ASP cc_start: 0.5082 (t70) cc_final: 0.4680 (t70) REVERT: R 36 VAL cc_start: 0.6042 (p) cc_final: 0.5702 (p) REVERT: R 40 ARG cc_start: 0.5369 (mpt-90) cc_final: 0.5046 (mmt-90) REVERT: R 243 TRP cc_start: 0.6682 (m100) cc_final: 0.6153 (m100) outliers start: 32 outliers final: 8 residues processed: 213 average time/residue: 0.5538 time to fit residues: 127.2960 Evaluate side-chains 167 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain N residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 100 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.155884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.129400 restraints weight = 20577.831| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.39 r_work: 0.3791 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11047 Z= 0.144 Angle : 0.670 9.883 14999 Z= 0.345 Chirality : 0.044 0.252 1668 Planarity : 0.005 0.070 1900 Dihedral : 5.732 71.157 1508 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.40 % Allowed : 19.17 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.88 (0.23), residues: 1346 helix: -0.77 (0.24), residues: 439 sheet: -1.25 (0.27), residues: 336 loop : -1.47 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 148 TYR 0.034 0.002 TYR R 148 PHE 0.023 0.002 PHE E 200 TRP 0.028 0.002 TRP R 243 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00328 (11039) covalent geometry : angle 0.66944 (14983) SS BOND : bond 0.00387 ( 8) SS BOND : angle 0.82710 ( 16) hydrogen bonds : bond 0.04146 ( 472) hydrogen bonds : angle 5.52145 ( 1317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: B 12 GLU cc_start: 0.7850 (tp30) cc_final: 0.7648 (tp30) REVERT: B 101 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8016 (mmm) REVERT: B 138 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: N 106 ASP cc_start: 0.5421 (t70) cc_final: 0.5079 (t70) REVERT: R 40 ARG cc_start: 0.5393 (mpt-90) cc_final: 0.5013 (mpt-90) REVERT: R 177 ASN cc_start: 0.7479 (t0) cc_final: 0.7038 (t160) REVERT: R 243 TRP cc_start: 0.6655 (m100) cc_final: 0.6277 (m100) REVERT: R 267 ARG cc_start: 0.6104 (mtm-85) cc_final: 0.5844 (mtp85) outliers start: 50 outliers final: 14 residues processed: 206 average time/residue: 0.5518 time to fit residues: 122.7552 Evaluate side-chains 161 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 154 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 42 optimal weight: 0.1980 chunk 12 optimal weight: 0.0170 chunk 99 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN E 174 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.158191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.131612 restraints weight = 20613.000| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.25 r_work: 0.3838 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11047 Z= 0.119 Angle : 0.634 9.943 14999 Z= 0.325 Chirality : 0.043 0.262 1668 Planarity : 0.005 0.069 1900 Dihedral : 5.396 72.429 1508 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.40 % Allowed : 22.78 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.59 (0.23), residues: 1346 helix: -0.44 (0.25), residues: 440 sheet: -1.06 (0.28), residues: 336 loop : -1.41 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 317 TYR 0.033 0.001 TYR R 148 PHE 0.019 0.001 PHE E 200 TRP 0.020 0.002 TRP R 243 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00263 (11039) covalent geometry : angle 0.63363 (14983) SS BOND : bond 0.00269 ( 8) SS BOND : angle 0.72933 ( 16) hydrogen bonds : bond 0.03829 ( 472) hydrogen bonds : angle 5.26810 ( 1317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: A 215 ASP cc_start: 0.6872 (t0) cc_final: 0.6650 (t0) REVERT: A 229 ASP cc_start: 0.7619 (p0) cc_final: 0.7142 (p0) REVERT: A 265 ARG cc_start: 0.7393 (mtp85) cc_final: 0.7073 (mtt180) REVERT: B 138 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: B 214 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6712 (ptt-90) REVERT: E 57 THR cc_start: 0.7335 (m) cc_final: 0.6771 (m) REVERT: E 143 VAL cc_start: 0.7728 (m) cc_final: 0.7521 (p) REVERT: E 234 GLU cc_start: 0.4624 (OUTLIER) cc_final: 0.4308 (mm-30) REVERT: G 24 ASN cc_start: 0.7622 (p0) cc_final: 0.7174 (m-40) REVERT: G 59 ASN cc_start: 0.6428 (t0) cc_final: 0.5332 (t0) REVERT: G 63 GLU cc_start: 0.2858 (OUTLIER) cc_final: 0.2362 (tp30) REVERT: R 40 ARG cc_start: 0.5616 (mpt-90) cc_final: 0.5185 (mpt-90) REVERT: R 156 PHE cc_start: 0.7347 (t80) cc_final: 0.6961 (t80) REVERT: R 177 ASN cc_start: 0.7319 (t0) cc_final: 0.6740 (t0) REVERT: R 243 TRP cc_start: 0.6457 (m100) cc_final: 0.6179 (m100) REVERT: R 267 ARG cc_start: 0.6067 (mtm-85) cc_final: 0.5664 (mmm160) REVERT: R 348 ARG cc_start: 0.6712 (tmt170) cc_final: 0.6177 (tmt170) outliers start: 50 outliers final: 13 residues processed: 212 average time/residue: 0.5432 time to fit residues: 124.4468 Evaluate side-chains 173 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 80 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 0.0770 chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 29 optimal weight: 0.0060 chunk 25 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN R 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.157801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.131539 restraints weight = 20455.253| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.35 r_work: 0.3817 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11047 Z= 0.128 Angle : 0.651 10.294 14999 Z= 0.330 Chirality : 0.044 0.358 1668 Planarity : 0.005 0.069 1900 Dihedral : 5.285 71.628 1508 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.93 % Allowed : 24.36 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.23), residues: 1346 helix: -0.22 (0.25), residues: 439 sheet: -0.94 (0.28), residues: 335 loop : -1.34 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 317 TYR 0.031 0.001 TYR R 148 PHE 0.022 0.001 PHE P 22 TRP 0.020 0.002 TRP R 297 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00292 (11039) covalent geometry : angle 0.65091 (14983) SS BOND : bond 0.00272 ( 8) SS BOND : angle 0.67824 ( 16) hydrogen bonds : bond 0.03799 ( 472) hydrogen bonds : angle 5.15117 ( 1317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 177 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: A 215 ASP cc_start: 0.6750 (t0) cc_final: 0.6529 (t0) REVERT: A 229 ASP cc_start: 0.7306 (p0) cc_final: 0.6837 (p0) REVERT: A 265 ARG cc_start: 0.7328 (mtp85) cc_final: 0.6896 (mmm-85) REVERT: A 372 ILE cc_start: 0.8782 (mp) cc_final: 0.8451 (mm) REVERT: A 389 ARG cc_start: 0.7499 (ttt-90) cc_final: 0.7271 (ttt90) REVERT: B 138 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: E 206 ARG cc_start: 0.7072 (tmm-80) cc_final: 0.6801 (tmm-80) REVERT: E 234 GLU cc_start: 0.4512 (OUTLIER) cc_final: 0.4074 (mm-30) REVERT: G 24 ASN cc_start: 0.7556 (p0) cc_final: 0.7250 (m-40) REVERT: G 63 GLU cc_start: 0.3202 (OUTLIER) cc_final: 0.2747 (tp30) REVERT: R 140 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.6064 (pm20) REVERT: R 226 CYS cc_start: 0.7284 (OUTLIER) cc_final: 0.5939 (m) REVERT: R 243 TRP cc_start: 0.6410 (m100) cc_final: 0.6007 (m100) REVERT: R 267 ARG cc_start: 0.5881 (mtm-85) cc_final: 0.5615 (mmm160) REVERT: R 308 ILE cc_start: 0.7444 (tt) cc_final: 0.7122 (mp) REVERT: R 348 ARG cc_start: 0.6746 (tmt170) cc_final: 0.6446 (tmt170) outliers start: 56 outliers final: 20 residues processed: 214 average time/residue: 0.5278 time to fit residues: 122.1196 Evaluate side-chains 180 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 140 GLN Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 226 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 46 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 chunk 60 optimal weight: 0.0970 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 24 optimal weight: 0.2980 chunk 71 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 230 ASN E 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.157091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.130429 restraints weight = 20629.396| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.26 r_work: 0.3825 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11047 Z= 0.141 Angle : 0.670 10.792 14999 Z= 0.337 Chirality : 0.044 0.247 1668 Planarity : 0.005 0.069 1900 Dihedral : 5.292 69.365 1508 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.19 % Allowed : 25.59 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.38 (0.23), residues: 1346 helix: -0.16 (0.25), residues: 441 sheet: -0.90 (0.28), residues: 331 loop : -1.41 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.030 0.001 TYR R 148 PHE 0.018 0.001 PHE E 200 TRP 0.029 0.002 TRP R 297 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00324 (11039) covalent geometry : angle 0.66953 (14983) SS BOND : bond 0.00255 ( 8) SS BOND : angle 0.75807 ( 16) hydrogen bonds : bond 0.03846 ( 472) hydrogen bonds : angle 5.12737 ( 1317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: A 215 ASP cc_start: 0.6869 (t0) cc_final: 0.6651 (t0) REVERT: A 229 ASP cc_start: 0.7483 (p0) cc_final: 0.7016 (p0) REVERT: A 265 ARG cc_start: 0.7468 (mtp85) cc_final: 0.7224 (mtt180) REVERT: A 356 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7000 (mtm180) REVERT: A 389 ARG cc_start: 0.7625 (ttt-90) cc_final: 0.7407 (ttt90) REVERT: B 138 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: E 78 THR cc_start: 0.6850 (m) cc_final: 0.6612 (m) REVERT: E 113 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7261 (mm-40) REVERT: E 234 GLU cc_start: 0.4662 (OUTLIER) cc_final: 0.4160 (mm-30) REVERT: G 24 ASN cc_start: 0.7493 (p0) cc_final: 0.7237 (m-40) REVERT: G 63 GLU cc_start: 0.2763 (OUTLIER) cc_final: 0.2411 (tp30) REVERT: R 140 GLN cc_start: 0.6465 (OUTLIER) cc_final: 0.6050 (pm20) REVERT: R 142 LEU cc_start: 0.6807 (tm) cc_final: 0.6199 (pp) REVERT: R 156 PHE cc_start: 0.7398 (t80) cc_final: 0.7016 (t80) REVERT: R 226 CYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6045 (m) REVERT: R 243 TRP cc_start: 0.6503 (m100) cc_final: 0.6097 (m100) REVERT: R 267 ARG cc_start: 0.6081 (mtm-85) cc_final: 0.5670 (mmm160) REVERT: R 308 ILE cc_start: 0.7447 (tt) cc_final: 0.7149 (mp) outliers start: 59 outliers final: 26 residues processed: 202 average time/residue: 0.5521 time to fit residues: 120.4731 Evaluate side-chains 174 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 140 GLN Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 413 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN E 174 GLN R 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.157724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.131696 restraints weight = 20574.665| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.35 r_work: 0.3815 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11047 Z= 0.129 Angle : 0.662 10.647 14999 Z= 0.334 Chirality : 0.043 0.280 1668 Planarity : 0.005 0.069 1900 Dihedral : 5.206 67.649 1508 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.93 % Allowed : 26.82 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.27 (0.23), residues: 1346 helix: -0.09 (0.25), residues: 445 sheet: -0.74 (0.28), residues: 322 loop : -1.41 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 40 TYR 0.028 0.001 TYR R 148 PHE 0.024 0.001 PHE P 22 TRP 0.029 0.002 TRP R 297 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00296 (11039) covalent geometry : angle 0.66214 (14983) SS BOND : bond 0.00267 ( 8) SS BOND : angle 0.74261 ( 16) hydrogen bonds : bond 0.03753 ( 472) hydrogen bonds : angle 5.03742 ( 1317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 158 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: A 43 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8198 (pp) REVERT: A 208 PHE cc_start: 0.4702 (m-10) cc_final: 0.4245 (m-80) REVERT: A 215 ASP cc_start: 0.6692 (t0) cc_final: 0.6449 (t0) REVERT: A 229 ASP cc_start: 0.7249 (p0) cc_final: 0.6770 (p0) REVERT: A 293 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7739 (mttt) REVERT: A 389 ARG cc_start: 0.7476 (ttt-90) cc_final: 0.7241 (ttt90) REVERT: B 12 GLU cc_start: 0.7955 (tp30) cc_final: 0.7680 (tp30) REVERT: B 17 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7305 (pm20) REVERT: B 138 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: B 262 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7298 (mmp) REVERT: G 24 ASN cc_start: 0.7591 (p0) cc_final: 0.7336 (m-40) REVERT: G 63 GLU cc_start: 0.2910 (OUTLIER) cc_final: 0.2576 (tp30) REVERT: P 16 LYS cc_start: 0.7368 (tptt) cc_final: 0.6935 (mmtm) REVERT: R 40 ARG cc_start: 0.5716 (mmt-90) cc_final: 0.5387 (mpt-90) REVERT: R 140 GLN cc_start: 0.6342 (OUTLIER) cc_final: 0.5940 (pm20) REVERT: R 142 LEU cc_start: 0.6797 (tm) cc_final: 0.6177 (pp) REVERT: R 156 PHE cc_start: 0.7346 (t80) cc_final: 0.6953 (t80) REVERT: R 226 CYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6003 (m) REVERT: R 243 TRP cc_start: 0.6489 (m100) cc_final: 0.5982 (m100) REVERT: R 308 ILE cc_start: 0.7371 (tt) cc_final: 0.6932 (mt) REVERT: R 348 ARG cc_start: 0.6717 (tmt170) cc_final: 0.6504 (tmt170) REVERT: R 413 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7409 (t80) outliers start: 56 outliers final: 24 residues processed: 194 average time/residue: 0.5241 time to fit residues: 110.1453 Evaluate side-chains 175 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 140 GLN Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 413 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 9 GLN E 174 GLN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.157556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.131465 restraints weight = 20524.149| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.32 r_work: 0.3811 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11047 Z= 0.135 Angle : 0.678 9.979 14999 Z= 0.341 Chirality : 0.043 0.267 1668 Planarity : 0.005 0.068 1900 Dihedral : 5.172 65.101 1508 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.01 % Allowed : 27.35 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.27 (0.23), residues: 1346 helix: -0.07 (0.25), residues: 445 sheet: -0.70 (0.28), residues: 335 loop : -1.46 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 40 TYR 0.028 0.001 TYR R 148 PHE 0.016 0.001 PHE N 108 TRP 0.022 0.002 TRP R 120 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00310 (11039) covalent geometry : angle 0.67837 (14983) SS BOND : bond 0.00277 ( 8) SS BOND : angle 0.79193 ( 16) hydrogen bonds : bond 0.03752 ( 472) hydrogen bonds : angle 5.00017 ( 1317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 148 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: A 208 PHE cc_start: 0.4652 (m-10) cc_final: 0.4219 (m-80) REVERT: A 293 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7797 (mtmt) REVERT: A 389 ARG cc_start: 0.7471 (ttt-90) cc_final: 0.7239 (ttt90) REVERT: B 12 GLU cc_start: 0.7913 (tp30) cc_final: 0.7653 (tp30) REVERT: B 17 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7297 (pm20) REVERT: B 61 MET cc_start: 0.6969 (pp-130) cc_final: 0.6710 (ppp) REVERT: B 138 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6600 (mp0) REVERT: B 214 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6520 (ptp-170) REVERT: E 113 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7096 (mm-40) REVERT: G 24 ASN cc_start: 0.7577 (p0) cc_final: 0.7346 (m-40) REVERT: G 63 GLU cc_start: 0.2909 (OUTLIER) cc_final: 0.2660 (tp30) REVERT: N 1 GLN cc_start: 0.6582 (pt0) cc_final: 0.6233 (tt0) REVERT: R 140 GLN cc_start: 0.6196 (OUTLIER) cc_final: 0.5805 (pm20) REVERT: R 156 PHE cc_start: 0.7331 (t80) cc_final: 0.6956 (t80) REVERT: R 226 CYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6132 (m) REVERT: R 243 TRP cc_start: 0.6503 (m100) cc_final: 0.5927 (m100) REVERT: R 308 ILE cc_start: 0.7328 (tt) cc_final: 0.6927 (mt) REVERT: R 348 ARG cc_start: 0.6736 (tmt170) cc_final: 0.6510 (tmt170) REVERT: R 413 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7430 (t80) outliers start: 57 outliers final: 29 residues processed: 183 average time/residue: 0.5325 time to fit residues: 105.4471 Evaluate side-chains 176 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 140 GLN Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 413 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 57 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 118 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN E 174 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.157913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.131604 restraints weight = 20558.136| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.22 r_work: 0.3838 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11047 Z= 0.126 Angle : 0.678 13.612 14999 Z= 0.338 Chirality : 0.043 0.250 1668 Planarity : 0.005 0.069 1900 Dihedral : 5.051 62.708 1508 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.61 % Allowed : 29.02 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.23), residues: 1346 helix: 0.02 (0.25), residues: 447 sheet: -0.63 (0.28), residues: 334 loop : -1.48 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 206 TYR 0.027 0.001 TYR R 148 PHE 0.030 0.001 PHE P 22 TRP 0.031 0.002 TRP R 297 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00288 (11039) covalent geometry : angle 0.67821 (14983) SS BOND : bond 0.00261 ( 8) SS BOND : angle 0.75042 ( 16) hydrogen bonds : bond 0.03668 ( 472) hydrogen bonds : angle 4.92977 ( 1317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: A 208 PHE cc_start: 0.4757 (m-10) cc_final: 0.4317 (m-80) REVERT: A 293 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7763 (mtmm) REVERT: A 389 ARG cc_start: 0.7541 (ttt-90) cc_final: 0.7294 (ttt90) REVERT: B 12 GLU cc_start: 0.7999 (tp30) cc_final: 0.7753 (tp30) REVERT: B 17 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7330 (pm20) REVERT: B 138 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: B 214 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6630 (ptp-170) REVERT: E 113 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7256 (mm-40) REVERT: E 117 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7880 (tm) REVERT: G 24 ASN cc_start: 0.7590 (p0) cc_final: 0.7379 (m-40) REVERT: G 53 PRO cc_start: 0.5736 (Cg_endo) cc_final: 0.5510 (Cg_exo) REVERT: G 63 GLU cc_start: 0.2610 (OUTLIER) cc_final: 0.2388 (tp30) REVERT: N 1 GLN cc_start: 0.6656 (pt0) cc_final: 0.6273 (tt0) REVERT: P 16 LYS cc_start: 0.7389 (tptt) cc_final: 0.6921 (mmtm) REVERT: R 140 GLN cc_start: 0.6078 (OUTLIER) cc_final: 0.5592 (pm20) REVERT: R 142 LEU cc_start: 0.6903 (tm) cc_final: 0.6273 (pp) REVERT: R 156 PHE cc_start: 0.7341 (t80) cc_final: 0.6998 (t80) REVERT: R 226 CYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6180 (m) REVERT: R 228 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6037 (tm) REVERT: R 243 TRP cc_start: 0.6442 (m100) cc_final: 0.6012 (m100) REVERT: R 308 ILE cc_start: 0.7210 (tt) cc_final: 0.6896 (mt) REVERT: R 348 ARG cc_start: 0.6757 (tmt170) cc_final: 0.6537 (tmt170) REVERT: R 413 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7389 (t80) outliers start: 41 outliers final: 23 residues processed: 182 average time/residue: 0.5337 time to fit residues: 105.0257 Evaluate side-chains 175 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 140 GLN Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 413 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 0.0270 chunk 106 optimal weight: 0.3980 chunk 79 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN E 174 GLN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.157731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.132054 restraints weight = 20485.209| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.31 r_work: 0.3841 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11047 Z= 0.132 Angle : 0.695 13.206 14999 Z= 0.346 Chirality : 0.043 0.239 1668 Planarity : 0.005 0.068 1900 Dihedral : 5.026 59.062 1508 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.13 % Allowed : 28.76 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.15 (0.23), residues: 1346 helix: 0.10 (0.25), residues: 446 sheet: -0.63 (0.27), residues: 340 loop : -1.47 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 317 TYR 0.025 0.001 TYR R 148 PHE 0.015 0.001 PHE N 108 TRP 0.027 0.002 TRP R 297 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00307 (11039) covalent geometry : angle 0.69521 (14983) SS BOND : bond 0.00248 ( 8) SS BOND : angle 0.70972 ( 16) hydrogen bonds : bond 0.03673 ( 472) hydrogen bonds : angle 4.91055 ( 1317) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: A 208 PHE cc_start: 0.4736 (m-10) cc_final: 0.4305 (m-80) REVERT: A 274 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8127 (tttm) REVERT: A 293 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7690 (mtmm) REVERT: A 389 ARG cc_start: 0.7568 (ttt-90) cc_final: 0.7306 (ttt90) REVERT: B 12 GLU cc_start: 0.7973 (tp30) cc_final: 0.7724 (tp30) REVERT: B 17 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7326 (pm20) REVERT: B 138 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: B 214 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6682 (ptp-170) REVERT: E 113 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7220 (mm-40) REVERT: E 117 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7856 (tm) REVERT: E 162 LEU cc_start: 0.7212 (tt) cc_final: 0.7002 (tt) REVERT: G 24 ASN cc_start: 0.7590 (p0) cc_final: 0.7387 (m-40) REVERT: G 53 PRO cc_start: 0.5825 (Cg_endo) cc_final: 0.5620 (Cg_exo) REVERT: P 16 LYS cc_start: 0.7404 (tptt) cc_final: 0.6932 (mmtm) REVERT: R 140 GLN cc_start: 0.6038 (OUTLIER) cc_final: 0.5579 (pm20) REVERT: R 156 PHE cc_start: 0.7312 (t80) cc_final: 0.6958 (t80) REVERT: R 177 ASN cc_start: 0.7456 (t0) cc_final: 0.7128 (t160) REVERT: R 226 CYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6168 (m) REVERT: R 228 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6010 (tm) REVERT: R 243 TRP cc_start: 0.6459 (m100) cc_final: 0.5943 (m100) REVERT: R 308 ILE cc_start: 0.7294 (tt) cc_final: 0.6946 (mt) REVERT: R 348 ARG cc_start: 0.6729 (tmt170) cc_final: 0.6248 (tmt170) REVERT: R 413 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7383 (t80) outliers start: 47 outliers final: 26 residues processed: 181 average time/residue: 0.5479 time to fit residues: 107.1883 Evaluate side-chains 180 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 140 GLN Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 413 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 17 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 72 optimal weight: 0.1980 chunk 6 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 27 optimal weight: 0.0980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN E 174 GLN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.157887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.131856 restraints weight = 20444.664| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.38 r_work: 0.3817 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11047 Z= 0.137 Angle : 0.695 12.940 14999 Z= 0.346 Chirality : 0.043 0.238 1668 Planarity : 0.005 0.068 1900 Dihedral : 5.017 54.533 1508 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.61 % Allowed : 29.46 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.12 (0.23), residues: 1346 helix: 0.11 (0.25), residues: 446 sheet: -0.61 (0.27), residues: 340 loop : -1.44 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 317 TYR 0.024 0.001 TYR R 148 PHE 0.032 0.001 PHE P 22 TRP 0.025 0.002 TRP R 297 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00319 (11039) covalent geometry : angle 0.69545 (14983) SS BOND : bond 0.00274 ( 8) SS BOND : angle 0.73603 ( 16) hydrogen bonds : bond 0.03732 ( 472) hydrogen bonds : angle 4.92968 ( 1317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4596.99 seconds wall clock time: 78 minutes 51.68 seconds (4731.68 seconds total)