Starting phenix.real_space_refine on Wed Feb 4 05:55:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jeq_61421/02_2026/9jeq_61421.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jeq_61421/02_2026/9jeq_61421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jeq_61421/02_2026/9jeq_61421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jeq_61421/02_2026/9jeq_61421.map" model { file = "/net/cci-nas-00/data/ceres_data/9jeq_61421/02_2026/9jeq_61421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jeq_61421/02_2026/9jeq_61421.cif" } resolution = 3.05 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= 0.022 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 60 5.16 5 C 5665 2.51 5 N 1515 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8890 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2592 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 440 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1807 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2290 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 9, 'TRANS': 273} Chain breaks: 1 Chain: "S" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1753 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.67, per 1000 atoms: 0.19 Number of scatterers: 8890 At special positions: 0 Unit cell: (89.856, 118.976, 127.296, 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 60 16.00 O 1650 8.00 N 1515 7.00 C 5665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 188 " distance=2.02 Simple disulfide: pdb=" SG CYS R 384 " - pdb=" SG CYS R 388 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 328.0 milliseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 37.6% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.585A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.582A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.695A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.262A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 256 removed outlier: 3.792A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.527A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.825A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 348 removed outlier: 3.824A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'R' and resid 33 through 62 Processing helix chain 'R' and resid 67 through 97 Proline residue: R 89 - end of helix Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 105 through 138 removed outlier: 4.032A pdb=" N LEU R 109 " --> pdb=" O GLY R 105 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL R 136 " --> pdb=" O ARG R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 146 removed outlier: 3.729A pdb=" N TYR R 142 " --> pdb=" O ARG R 138 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG R 143 " --> pdb=" O ALA R 139 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA R 144 " --> pdb=" O VAL R 140 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN R 145 " --> pdb=" O SER R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 179 removed outlier: 4.284A pdb=" N ALA R 152 " --> pdb=" O ASP R 148 " (cutoff:3.500A) Proline residue: R 169 - end of helix removed outlier: 3.925A pdb=" N GLU R 175 " --> pdb=" O ILE R 171 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 207 removed outlier: 3.834A pdb=" N THR R 204 " --> pdb=" O ILE R 200 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 235 Processing helix chain 'R' and resid 348 through 384 removed outlier: 3.521A pdb=" N VAL R 364 " --> pdb=" O LEU R 360 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE R 367 " --> pdb=" O ILE R 363 " (cutoff:3.500A) Proline residue: R 373 - end of helix removed outlier: 3.755A pdb=" N ILE R 379 " --> pdb=" O THR R 375 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA R 382 " --> pdb=" O MET R 378 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA R 383 " --> pdb=" O ILE R 379 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 412 removed outlier: 3.807A pdb=" N TRP R 402 " --> pdb=" O PHE R 398 " (cutoff:3.500A) Proline residue: R 409 - end of helix Processing helix chain 'R' and resid 417 through 424 removed outlier: 3.566A pdb=" N ARG R 421 " --> pdb=" O HIS R 417 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR R 424 " --> pdb=" O ARG R 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.847A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.718A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.547A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.631A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.736A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.732A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.908A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 190 removed outlier: 9.310A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'S' and resid 56 through 60 removed outlier: 5.984A pdb=" N THR S 57 " --> pdb=" O SER S 52 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER S 52 " --> pdb=" O THR S 57 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG S 98 " --> pdb=" O PHE S 110 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.802A pdb=" N VAL S 147 " --> pdb=" O LYS S 244 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.802A pdb=" N VAL S 147 " --> pdb=" O LYS S 244 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN S 231 " --> pdb=" O THR S 238 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 155 through 160 411 hydrogen bonds defined for protein. 1182 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: 1.28 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2595 1.33 - 1.45: 1543 1.45 - 1.57: 4863 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 9086 Sorted by residual: bond pdb=" CA ASP R 148 " pdb=" C ASP R 148 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.23e-02 6.61e+03 4.03e+00 bond pdb=" CA VAL R 389 " pdb=" C VAL R 389 " ideal model delta sigma weight residual 1.524 1.545 -0.021 1.05e-02 9.07e+03 3.96e+00 bond pdb=" CG HSM R 501 " pdb=" ND1 HSM R 501 " ideal model delta sigma weight residual 1.383 1.344 0.039 2.00e-02 2.50e+03 3.83e+00 bond pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " ideal model delta sigma weight residual 1.531 1.560 -0.029 1.51e-02 4.39e+03 3.73e+00 bond pdb=" C ASP B 154 " pdb=" O ASP B 154 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.19e-02 7.06e+03 2.99e+00 ... (remaining 9081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 12057 1.86 - 3.72: 223 3.72 - 5.59: 28 5.59 - 7.45: 6 7.45 - 9.31: 5 Bond angle restraints: 12319 Sorted by residual: angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 111.36 118.41 -7.05 1.09e+00 8.42e-01 4.18e+01 angle pdb=" N GLY R 147 " pdb=" CA GLY R 147 " pdb=" C GLY R 147 " ideal model delta sigma weight residual 115.36 107.45 7.91 1.33e+00 5.65e-01 3.54e+01 angle pdb=" N CYS R 107 " pdb=" CA CYS R 107 " pdb=" C CYS R 107 " ideal model delta sigma weight residual 111.36 117.21 -5.85 1.09e+00 8.42e-01 2.88e+01 angle pdb=" N CYS B 317 " pdb=" CA CYS B 317 " pdb=" C CYS B 317 " ideal model delta sigma weight residual 109.24 117.01 -7.77 1.51e+00 4.39e-01 2.65e+01 angle pdb=" N ALA B 240 " pdb=" CA ALA B 240 " pdb=" C ALA B 240 " ideal model delta sigma weight residual 109.18 116.39 -7.21 1.42e+00 4.96e-01 2.58e+01 ... (remaining 12314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 5067 15.29 - 30.58: 213 30.58 - 45.87: 57 45.87 - 61.16: 8 61.16 - 76.45: 1 Dihedral angle restraints: 5346 sinusoidal: 2048 harmonic: 3298 Sorted by residual: dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 0.00 28.47 -28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" C ASN B 119 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " ideal model delta harmonic sigma weight residual -122.60 -136.69 14.09 0 2.50e+00 1.60e-01 3.18e+01 dihedral pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " ideal model delta harmonic sigma weight residual 122.80 136.30 -13.50 0 2.50e+00 1.60e-01 2.92e+01 ... (remaining 5343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1320 0.102 - 0.205: 59 0.205 - 0.307: 7 0.307 - 0.410: 1 0.410 - 0.512: 1 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" CA ASP B 323 " pdb=" N ASP B 323 " pdb=" C ASP B 323 " pdb=" CB ASP B 323 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA CYS R 107 " pdb=" N CYS R 107 " pdb=" C CYS R 107 " pdb=" CB CYS R 107 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 1385 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.054 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO B 236 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 37 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C LEU A 37 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU A 37 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 38 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 412 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO R 413 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO R 413 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 413 " -0.025 5.00e-02 4.00e+02 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2639 2.82 - 3.34: 7947 3.34 - 3.86: 14734 3.86 - 4.38: 17017 4.38 - 4.90: 29590 Nonbonded interactions: 71927 Sorted by model distance: nonbonded pdb=" O THR R 67 " pdb=" CD2 PHE R 71 " model vdw 2.296 3.340 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.305 3.120 nonbonded pdb=" CE2 PHE R 193 " pdb=" NH1 ARG R 381 " model vdw 2.317 3.420 nonbonded pdb=" O PHE S 29 " pdb=" NH2 ARG S 72 " model vdw 2.317 3.120 nonbonded pdb=" OE1 GLN R 226 " pdb=" NH1 ARG R 230 " model vdw 2.320 3.120 ... (remaining 71922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9088 Z= 0.193 Angle : 0.632 9.312 12323 Z= 0.421 Chirality : 0.048 0.512 1388 Planarity : 0.004 0.083 1557 Dihedral : 9.167 76.451 3214 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.84 % Allowed : 5.76 % Favored : 93.40 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.33 % 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: -1.35 (0.23), residues: 1120 helix: 0.08 (0.26), residues: 380 sheet: -0.61 (0.32), residues: 240 loop : -1.78 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 104 TYR 0.017 0.001 TYR S 235 PHE 0.013 0.001 PHE B 151 TRP 0.004 0.001 TRP R 160 HIS 0.001 0.000 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9086) covalent geometry : angle 0.63125 (12319) SS BOND : bond 0.00877 ( 2) SS BOND : angle 1.57763 ( 4) hydrogen bonds : bond 0.20151 ( 408) hydrogen bonds : angle 6.65017 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 314 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7182 (mm-40) REVERT: B 230 ASN cc_start: 0.6942 (m-40) cc_final: 0.6692 (t0) REVERT: A 38 LEU cc_start: 0.8000 (tp) cc_final: 0.7710 (mp) REVERT: A 261 ASP cc_start: 0.8243 (p0) cc_final: 0.7817 (p0) REVERT: R 350 LEU cc_start: 0.7046 (tm) cc_final: 0.6296 (mt) REVERT: S 189 ILE cc_start: 0.9047 (mp) cc_final: 0.8805 (mm) outliers start: 8 outliers final: 2 residues processed: 320 average time/residue: 0.1138 time to fit residues: 46.9223 Evaluate side-chains 181 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 416 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 125 ASN B 220 GLN B 268 ASN A 204 GLN A 269 ASN A 294 ASN A 333 GLN R 69 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.162157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.114547 restraints weight = 12147.590| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.92 r_work: 0.3285 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.098 9088 Z= 0.471 Angle : 0.910 10.750 12323 Z= 0.491 Chirality : 0.058 0.299 1388 Planarity : 0.007 0.081 1557 Dihedral : 6.195 59.623 1241 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.92 % Allowed : 14.35 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.04 (0.24), residues: 1120 helix: 0.04 (0.24), residues: 404 sheet: -0.59 (0.30), residues: 279 loop : -1.32 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 314 TYR 0.035 0.004 TYR S 50 PHE 0.040 0.004 PHE R 367 TRP 0.034 0.004 TRP S 36 HIS 0.012 0.003 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.01099 ( 9086) covalent geometry : angle 0.90875 (12319) SS BOND : bond 0.00880 ( 2) SS BOND : angle 3.13825 ( 4) hydrogen bonds : bond 0.06241 ( 408) hydrogen bonds : angle 5.24021 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 GLU cc_start: 0.8137 (mp0) cc_final: 0.7879 (mp0) REVERT: B 134 ARG cc_start: 0.7378 (ptt-90) cc_final: 0.7175 (ptt-90) REVERT: B 258 ASP cc_start: 0.7254 (t0) cc_final: 0.6765 (t0) REVERT: B 325 MET cc_start: 0.8560 (tpp) cc_final: 0.8310 (tpp) REVERT: G 50 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6842 (tp) REVERT: A 9 ASP cc_start: 0.8173 (m-30) cc_final: 0.7524 (t0) REVERT: A 269 ASN cc_start: 0.7896 (m110) cc_final: 0.7643 (m110) REVERT: A 305 CYS cc_start: 0.8149 (t) cc_final: 0.7406 (p) REVERT: R 41 MET cc_start: 0.3297 (tpp) cc_final: 0.2900 (mmt) REVERT: R 66 ARG cc_start: 0.5957 (mtt90) cc_final: 0.5517 (ttm110) REVERT: R 102 PHE cc_start: 0.5485 (m-10) cc_final: 0.4662 (m-10) REVERT: R 106 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5260 (tp) REVERT: R 160 TRP cc_start: 0.7326 (OUTLIER) cc_final: 0.7106 (t60) REVERT: R 192 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6620 (t80) REVERT: R 392 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.6003 (t80) REVERT: R 393 TRP cc_start: 0.6516 (m100) cc_final: 0.5836 (m-90) REVERT: S 89 GLU cc_start: 0.8429 (mp0) cc_final: 0.8209 (mp0) REVERT: S 244 LYS cc_start: 0.8062 (tptt) cc_final: 0.7760 (tptt) outliers start: 47 outliers final: 23 residues processed: 205 average time/residue: 0.0891 time to fit residues: 24.4229 Evaluate side-chains 180 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 160 TRP Chi-restraints excluded: chain R residue 192 PHE Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 350 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain R residue 414 LEU Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.0670 chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.168728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.120415 restraints weight = 11860.230| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.02 r_work: 0.3377 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9088 Z= 0.125 Angle : 0.558 6.203 12323 Z= 0.296 Chirality : 0.042 0.261 1388 Planarity : 0.005 0.078 1557 Dihedral : 5.267 58.115 1241 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.72 % Allowed : 17.59 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.24 (0.25), residues: 1120 helix: 0.89 (0.26), residues: 401 sheet: -0.27 (0.31), residues: 276 loop : -0.97 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.014 0.002 TYR S 235 PHE 0.015 0.001 PHE R 367 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9086) covalent geometry : angle 0.55839 (12319) SS BOND : bond 0.00349 ( 2) SS BOND : angle 0.50986 ( 4) hydrogen bonds : bond 0.04142 ( 408) hydrogen bonds : angle 4.46792 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7806 (tp30) cc_final: 0.7590 (tp30) REVERT: B 19 ARG cc_start: 0.8282 (ptp-170) cc_final: 0.7982 (ptt-90) REVERT: B 130 GLU cc_start: 0.8157 (mp0) cc_final: 0.7496 (pm20) REVERT: B 134 ARG cc_start: 0.7438 (ptt-90) cc_final: 0.7231 (ptt-90) REVERT: B 262 MET cc_start: 0.8711 (tpt) cc_final: 0.8311 (mmm) REVERT: A 32 ARG cc_start: 0.7663 (mtp85) cc_final: 0.7364 (mtp85) REVERT: A 305 CYS cc_start: 0.8002 (t) cc_final: 0.7252 (p) REVERT: R 66 ARG cc_start: 0.5895 (mtt90) cc_final: 0.5398 (ttm110) REVERT: R 102 PHE cc_start: 0.5317 (m-10) cc_final: 0.4482 (m-10) REVERT: R 106 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5688 (tp) REVERT: R 160 TRP cc_start: 0.7294 (OUTLIER) cc_final: 0.7051 (t-100) REVERT: R 192 PHE cc_start: 0.7228 (t80) cc_final: 0.6943 (t80) REVERT: R 393 TRP cc_start: 0.6554 (m100) cc_final: 0.5630 (m-90) REVERT: R 401 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5614 (tt) REVERT: S 89 GLU cc_start: 0.8408 (mp0) cc_final: 0.8150 (mp0) outliers start: 26 outliers final: 14 residues processed: 179 average time/residue: 0.0890 time to fit residues: 21.5730 Evaluate side-chains 167 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 160 TRP Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 0.7980 chunk 87 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 88 optimal weight: 0.0870 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN R 70 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 218 ASN R 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.169250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122515 restraints weight = 11886.977| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.96 r_work: 0.3391 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9088 Z= 0.115 Angle : 0.540 7.118 12323 Z= 0.281 Chirality : 0.041 0.198 1388 Planarity : 0.005 0.075 1557 Dihedral : 4.870 58.689 1241 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.93 % Allowed : 17.70 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.07 (0.25), residues: 1120 helix: 1.14 (0.27), residues: 400 sheet: 0.00 (0.31), residues: 271 loop : -0.85 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 27 TYR 0.018 0.001 TYR R 94 PHE 0.011 0.001 PHE R 367 TRP 0.011 0.001 TRP R 160 HIS 0.007 0.001 HIS R 187 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9086) covalent geometry : angle 0.54050 (12319) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.47419 ( 4) hydrogen bonds : bond 0.03663 ( 408) hydrogen bonds : angle 4.17227 ( 1182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7848 (tp30) cc_final: 0.7610 (tp30) REVERT: B 130 GLU cc_start: 0.8136 (mp0) cc_final: 0.7837 (mp0) REVERT: B 134 ARG cc_start: 0.7512 (ptt-90) cc_final: 0.7302 (ptt-90) REVERT: B 262 MET cc_start: 0.8599 (tpt) cc_final: 0.8219 (mmm) REVERT: G 50 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6440 (tp) REVERT: A 32 ARG cc_start: 0.7547 (mtp85) cc_final: 0.7287 (mtp85) REVERT: A 240 MET cc_start: 0.5669 (tpp) cc_final: 0.5300 (tpp) REVERT: A 305 CYS cc_start: 0.8010 (t) cc_final: 0.6997 (p) REVERT: R 41 MET cc_start: 0.3098 (mmt) cc_final: 0.2499 (mmt) REVERT: R 66 ARG cc_start: 0.6033 (mtt90) cc_final: 0.5495 (ttm110) REVERT: R 102 PHE cc_start: 0.5314 (m-10) cc_final: 0.4655 (m-10) REVERT: R 160 TRP cc_start: 0.7347 (OUTLIER) cc_final: 0.7126 (t-100) REVERT: R 192 PHE cc_start: 0.7069 (t80) cc_final: 0.6449 (t80) REVERT: R 393 TRP cc_start: 0.6628 (m100) cc_final: 0.5667 (m-90) REVERT: S 191 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6032 (mtm180) outliers start: 28 outliers final: 18 residues processed: 179 average time/residue: 0.1167 time to fit residues: 27.4598 Evaluate side-chains 178 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 160 TRP Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 414 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 110 ASN B 340 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 404 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.168790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122554 restraints weight = 11915.471| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.91 r_work: 0.3395 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9088 Z= 0.113 Angle : 0.516 6.705 12323 Z= 0.272 Chirality : 0.041 0.207 1388 Planarity : 0.005 0.082 1557 Dihedral : 4.403 54.957 1239 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.14 % Allowed : 17.17 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.30 (0.25), residues: 1120 helix: 1.35 (0.27), residues: 400 sheet: 0.13 (0.31), residues: 272 loop : -0.74 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 27 TYR 0.013 0.001 TYR R 222 PHE 0.011 0.001 PHE R 367 TRP 0.011 0.001 TRP R 160 HIS 0.004 0.001 HIS R 187 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9086) covalent geometry : angle 0.51619 (12319) SS BOND : bond 0.00247 ( 2) SS BOND : angle 0.49636 ( 4) hydrogen bonds : bond 0.03451 ( 408) hydrogen bonds : angle 4.09237 ( 1182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7931 (tp30) cc_final: 0.7690 (tp30) REVERT: B 15 LYS cc_start: 0.7651 (mttp) cc_final: 0.7444 (mptt) REVERT: B 19 ARG cc_start: 0.8013 (ptt-90) cc_final: 0.7693 (ptt-90) REVERT: B 32 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7523 (pp30) REVERT: B 130 GLU cc_start: 0.8165 (mp0) cc_final: 0.7846 (mp0) REVERT: B 134 ARG cc_start: 0.7543 (ptt-90) cc_final: 0.7316 (ptt-90) REVERT: B 262 MET cc_start: 0.8637 (tpt) cc_final: 0.8114 (mmm) REVERT: B 275 SER cc_start: 0.8676 (m) cc_final: 0.8461 (m) REVERT: G 21 MET cc_start: 0.7809 (mmt) cc_final: 0.7553 (mmt) REVERT: G 50 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6228 (tp) REVERT: A 24 ARG cc_start: 0.6804 (mtm-85) cc_final: 0.6603 (ttp-110) REVERT: A 305 CYS cc_start: 0.7782 (t) cc_final: 0.7053 (p) REVERT: R 41 MET cc_start: 0.3246 (mmt) cc_final: 0.2535 (mmt) REVERT: R 66 ARG cc_start: 0.6042 (mtt90) cc_final: 0.5473 (ttm110) REVERT: R 91 TYR cc_start: 0.5242 (t80) cc_final: 0.5038 (t80) REVERT: R 102 PHE cc_start: 0.5418 (m-10) cc_final: 0.4744 (m-10) REVERT: R 192 PHE cc_start: 0.7115 (t80) cc_final: 0.6445 (t80) REVERT: R 393 TRP cc_start: 0.6646 (m100) cc_final: 0.5677 (m-90) REVERT: R 401 LEU cc_start: 0.5871 (OUTLIER) cc_final: 0.5457 (tt) REVERT: S 191 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.6022 (mtm180) outliers start: 30 outliers final: 19 residues processed: 189 average time/residue: 0.1198 time to fit residues: 29.8458 Evaluate side-chains 185 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 414 LEU Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 70 ASN ** R 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.169977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123390 restraints weight = 11967.260| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.94 r_work: 0.3400 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9088 Z= 0.111 Angle : 0.532 12.714 12323 Z= 0.274 Chirality : 0.041 0.214 1388 Planarity : 0.005 0.084 1557 Dihedral : 4.352 56.442 1239 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.72 % Allowed : 18.43 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.32 (0.25), residues: 1120 helix: 1.30 (0.27), residues: 402 sheet: 0.15 (0.31), residues: 271 loop : -0.68 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 27 TYR 0.013 0.001 TYR R 222 PHE 0.021 0.001 PHE R 367 TRP 0.008 0.001 TRP B 82 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9086) covalent geometry : angle 0.53180 (12319) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.45182 ( 4) hydrogen bonds : bond 0.03380 ( 408) hydrogen bonds : angle 4.06210 ( 1182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7928 (tp30) cc_final: 0.7671 (tp30) REVERT: B 19 ARG cc_start: 0.8072 (ptt-90) cc_final: 0.7766 (ptt-90) REVERT: B 59 TYR cc_start: 0.8279 (m-80) cc_final: 0.7980 (m-80) REVERT: B 130 GLU cc_start: 0.8134 (mp0) cc_final: 0.7817 (mp0) REVERT: B 134 ARG cc_start: 0.7546 (ptt-90) cc_final: 0.7313 (ptt-90) REVERT: B 259 GLN cc_start: 0.7019 (tt0) cc_final: 0.6480 (mt0) REVERT: B 262 MET cc_start: 0.8616 (tpt) cc_final: 0.8129 (mmm) REVERT: B 275 SER cc_start: 0.8673 (m) cc_final: 0.8431 (m) REVERT: G 20 LYS cc_start: 0.8649 (tptp) cc_final: 0.8401 (tptp) REVERT: G 21 MET cc_start: 0.7835 (mmt) cc_final: 0.7523 (mmt) REVERT: G 50 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.6040 (tp) REVERT: A 20 ASP cc_start: 0.8099 (m-30) cc_final: 0.7869 (m-30) REVERT: A 24 ARG cc_start: 0.6775 (mtm-85) cc_final: 0.6572 (ttp-110) REVERT: A 240 MET cc_start: 0.5519 (tpp) cc_final: 0.5238 (tpp) REVERT: A 305 CYS cc_start: 0.7835 (t) cc_final: 0.7120 (p) REVERT: R 41 MET cc_start: 0.3332 (mmt) cc_final: 0.2591 (mmt) REVERT: R 66 ARG cc_start: 0.6048 (mtt90) cc_final: 0.5371 (ttm110) REVERT: R 102 PHE cc_start: 0.5411 (m-10) cc_final: 0.4746 (m-10) REVERT: R 192 PHE cc_start: 0.7087 (t80) cc_final: 0.6540 (t80) REVERT: R 393 TRP cc_start: 0.6657 (m100) cc_final: 0.5697 (m-90) REVERT: R 401 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5467 (tt) REVERT: S 191 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.5871 (mtm180) outliers start: 26 outliers final: 19 residues processed: 184 average time/residue: 0.1063 time to fit residues: 25.8190 Evaluate side-chains 176 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 414 LEU Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN R 124 ASN R 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.166529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.119801 restraints weight = 12020.624| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.92 r_work: 0.3354 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9088 Z= 0.158 Angle : 0.555 7.114 12323 Z= 0.293 Chirality : 0.042 0.200 1388 Planarity : 0.005 0.091 1557 Dihedral : 4.552 59.862 1239 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.14 % Allowed : 18.74 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.24 (0.25), residues: 1120 helix: 1.22 (0.27), residues: 403 sheet: 0.09 (0.31), residues: 271 loop : -0.70 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 27 TYR 0.020 0.002 TYR R 91 PHE 0.024 0.002 PHE R 367 TRP 0.012 0.001 TRP R 110 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9086) covalent geometry : angle 0.55517 (12319) SS BOND : bond 0.00323 ( 2) SS BOND : angle 0.55383 ( 4) hydrogen bonds : bond 0.03726 ( 408) hydrogen bonds : angle 4.16045 ( 1182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7910 (tp30) cc_final: 0.7654 (tp30) REVERT: B 19 ARG cc_start: 0.8066 (ptt-90) cc_final: 0.7653 (ptp90) REVERT: B 59 TYR cc_start: 0.8480 (m-80) cc_final: 0.8239 (m-80) REVERT: B 130 GLU cc_start: 0.8206 (mp0) cc_final: 0.7873 (mp0) REVERT: B 262 MET cc_start: 0.8595 (tpt) cc_final: 0.8073 (mmm) REVERT: B 275 SER cc_start: 0.8677 (m) cc_final: 0.8435 (m) REVERT: G 21 MET cc_start: 0.7832 (mmt) cc_final: 0.7527 (mmt) REVERT: G 50 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6353 (tp) REVERT: A 240 MET cc_start: 0.5646 (tpp) cc_final: 0.5363 (tpp) REVERT: A 305 CYS cc_start: 0.7852 (t) cc_final: 0.7118 (p) REVERT: R 41 MET cc_start: 0.3291 (mmt) cc_final: 0.2631 (mmt) REVERT: R 102 PHE cc_start: 0.5351 (m-10) cc_final: 0.4451 (m-10) REVERT: R 106 LEU cc_start: 0.5846 (OUTLIER) cc_final: 0.5417 (tp) REVERT: R 192 PHE cc_start: 0.7134 (t80) cc_final: 0.6432 (t80) REVERT: R 401 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5526 (tp) REVERT: S 191 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6113 (mtm180) outliers start: 30 outliers final: 24 residues processed: 174 average time/residue: 0.1163 time to fit residues: 26.5509 Evaluate side-chains 184 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 414 LEU Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 89 optimal weight: 0.0980 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.169686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121657 restraints weight = 11847.622| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.01 r_work: 0.3393 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9088 Z= 0.109 Angle : 0.523 6.939 12323 Z= 0.275 Chirality : 0.040 0.176 1388 Planarity : 0.005 0.090 1557 Dihedral : 4.358 58.236 1239 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.83 % Allowed : 19.48 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.40 (0.26), residues: 1120 helix: 1.38 (0.27), residues: 402 sheet: 0.19 (0.31), residues: 270 loop : -0.64 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 27 TYR 0.014 0.001 TYR R 91 PHE 0.016 0.001 PHE R 367 TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9086) covalent geometry : angle 0.52301 (12319) SS BOND : bond 0.00239 ( 2) SS BOND : angle 0.27866 ( 4) hydrogen bonds : bond 0.03371 ( 408) hydrogen bonds : angle 4.01877 ( 1182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7937 (tp30) cc_final: 0.7680 (tp30) REVERT: B 19 ARG cc_start: 0.8110 (ptt-90) cc_final: 0.7665 (ptp90) REVERT: B 59 TYR cc_start: 0.8358 (m-80) cc_final: 0.8144 (m-80) REVERT: B 130 GLU cc_start: 0.8198 (mp0) cc_final: 0.7561 (mp0) REVERT: B 259 GLN cc_start: 0.7035 (tt0) cc_final: 0.6478 (mt0) REVERT: B 262 MET cc_start: 0.8618 (tpt) cc_final: 0.8109 (mmm) REVERT: B 275 SER cc_start: 0.8685 (m) cc_final: 0.8433 (m) REVERT: B 331 SER cc_start: 0.8838 (p) cc_final: 0.8518 (p) REVERT: G 20 LYS cc_start: 0.8510 (tptp) cc_final: 0.8077 (tptp) REVERT: G 21 MET cc_start: 0.7823 (mmt) cc_final: 0.7304 (mmt) REVERT: G 50 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.6182 (tp) REVERT: A 20 ASP cc_start: 0.8106 (m-30) cc_final: 0.7891 (m-30) REVERT: A 240 MET cc_start: 0.5622 (tpp) cc_final: 0.5353 (tpp) REVERT: A 305 CYS cc_start: 0.7814 (t) cc_final: 0.7085 (p) REVERT: R 41 MET cc_start: 0.3324 (mmt) cc_final: 0.2650 (mmt) REVERT: R 102 PHE cc_start: 0.5376 (m-10) cc_final: 0.4733 (m-10) REVERT: R 192 PHE cc_start: 0.7112 (t80) cc_final: 0.6466 (t80) REVERT: R 393 TRP cc_start: 0.5990 (m100) cc_final: 0.5164 (m-90) REVERT: R 401 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5418 (tt) REVERT: S 191 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.5985 (mtm180) outliers start: 27 outliers final: 19 residues processed: 183 average time/residue: 0.1125 time to fit residues: 27.0315 Evaluate side-chains 181 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 414 LEU Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 89 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 0.0270 chunk 80 optimal weight: 8.9990 chunk 88 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.170607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122507 restraints weight = 11947.664| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.05 r_work: 0.3405 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 9088 Z= 0.108 Angle : 0.528 7.650 12323 Z= 0.277 Chirality : 0.041 0.192 1388 Planarity : 0.005 0.089 1557 Dihedral : 4.269 55.778 1239 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.51 % Allowed : 19.90 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.42 (0.26), residues: 1120 helix: 1.38 (0.27), residues: 402 sheet: 0.20 (0.31), residues: 270 loop : -0.62 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 27 TYR 0.014 0.001 TYR R 91 PHE 0.016 0.001 PHE R 367 TRP 0.022 0.001 TRP B 339 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9086) covalent geometry : angle 0.52793 (12319) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.34694 ( 4) hydrogen bonds : bond 0.03253 ( 408) hydrogen bonds : angle 4.01840 ( 1182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7942 (tp30) cc_final: 0.7699 (tp30) REVERT: B 19 ARG cc_start: 0.8160 (ptt-90) cc_final: 0.7703 (ptp90) REVERT: B 59 TYR cc_start: 0.8325 (m-80) cc_final: 0.8066 (m-80) REVERT: B 130 GLU cc_start: 0.8183 (mp0) cc_final: 0.7526 (mp0) REVERT: B 259 GLN cc_start: 0.7017 (tt0) cc_final: 0.6453 (mt0) REVERT: B 262 MET cc_start: 0.8647 (tpt) cc_final: 0.8118 (mmm) REVERT: B 275 SER cc_start: 0.8685 (m) cc_final: 0.8422 (m) REVERT: B 331 SER cc_start: 0.8829 (p) cc_final: 0.8530 (p) REVERT: G 20 LYS cc_start: 0.8496 (tptp) cc_final: 0.8062 (tptp) REVERT: G 21 MET cc_start: 0.7840 (mmt) cc_final: 0.7310 (mmt) REVERT: G 50 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6258 (tp) REVERT: A 240 MET cc_start: 0.5538 (tpp) cc_final: 0.5336 (tpp) REVERT: A 305 CYS cc_start: 0.7778 (t) cc_final: 0.7067 (p) REVERT: R 41 MET cc_start: 0.3314 (mmt) cc_final: 0.2687 (mmt) REVERT: R 102 PHE cc_start: 0.5366 (m-10) cc_final: 0.4728 (m-10) REVERT: R 192 PHE cc_start: 0.7112 (t80) cc_final: 0.6434 (t80) REVERT: R 393 TRP cc_start: 0.5984 (m100) cc_final: 0.5190 (m-90) REVERT: R 401 LEU cc_start: 0.5712 (OUTLIER) cc_final: 0.5322 (tt) REVERT: S 191 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6002 (mtm180) outliers start: 24 outliers final: 17 residues processed: 176 average time/residue: 0.1131 time to fit residues: 26.4389 Evaluate side-chains 183 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 414 LEU Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.169590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.121251 restraints weight = 12035.897| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.05 r_work: 0.3381 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9088 Z= 0.136 Angle : 0.557 7.883 12323 Z= 0.290 Chirality : 0.041 0.168 1388 Planarity : 0.005 0.089 1557 Dihedral : 4.328 52.898 1239 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.30 % Allowed : 20.00 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.38 (0.26), residues: 1120 helix: 1.33 (0.27), residues: 402 sheet: 0.19 (0.31), residues: 270 loop : -0.62 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 27 TYR 0.017 0.001 TYR R 91 PHE 0.018 0.001 PHE R 367 TRP 0.029 0.001 TRP B 339 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9086) covalent geometry : angle 0.55744 (12319) SS BOND : bond 0.00270 ( 2) SS BOND : angle 0.38969 ( 4) hydrogen bonds : bond 0.03397 ( 408) hydrogen bonds : angle 4.06755 ( 1182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7950 (tp30) cc_final: 0.7703 (tp30) REVERT: B 19 ARG cc_start: 0.8173 (ptt-90) cc_final: 0.7711 (ptp90) REVERT: B 59 TYR cc_start: 0.8387 (m-80) cc_final: 0.8095 (m-80) REVERT: B 130 GLU cc_start: 0.8251 (mp0) cc_final: 0.7584 (mp0) REVERT: B 259 GLN cc_start: 0.7017 (tt0) cc_final: 0.6429 (mt0) REVERT: B 262 MET cc_start: 0.8645 (tpt) cc_final: 0.8100 (mmm) REVERT: B 275 SER cc_start: 0.8687 (m) cc_final: 0.8422 (m) REVERT: B 331 SER cc_start: 0.8858 (p) cc_final: 0.8562 (p) REVERT: G 20 LYS cc_start: 0.8514 (tptp) cc_final: 0.8074 (tptp) REVERT: G 21 MET cc_start: 0.7846 (mmt) cc_final: 0.7318 (mmt) REVERT: G 50 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6336 (tp) REVERT: A 20 ASP cc_start: 0.8116 (m-30) cc_final: 0.7872 (m-30) REVERT: A 240 MET cc_start: 0.5578 (tpp) cc_final: 0.5339 (tpp) REVERT: A 305 CYS cc_start: 0.7800 (t) cc_final: 0.7109 (p) REVERT: R 41 MET cc_start: 0.3433 (mmt) cc_final: 0.2784 (mmt) REVERT: R 102 PHE cc_start: 0.5450 (m-10) cc_final: 0.4596 (m-10) REVERT: R 192 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6460 (t80) REVERT: R 363 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7483 (mp) REVERT: R 393 TRP cc_start: 0.6103 (m100) cc_final: 0.5274 (m-90) REVERT: R 401 LEU cc_start: 0.5808 (OUTLIER) cc_final: 0.5471 (tt) REVERT: S 191 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6087 (mtm180) REVERT: S 246 GLU cc_start: 0.6031 (pm20) cc_final: 0.5659 (pm20) outliers start: 22 outliers final: 17 residues processed: 174 average time/residue: 0.1097 time to fit residues: 25.2479 Evaluate side-chains 179 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain R residue 192 PHE Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 351 SER Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 414 LEU Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 88 optimal weight: 0.0170 chunk 5 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 0.0040 overall best weight: 0.5230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.171766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125613 restraints weight = 11791.416| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.94 r_work: 0.3427 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 9088 Z= 0.106 Angle : 0.533 7.986 12323 Z= 0.277 Chirality : 0.040 0.149 1388 Planarity : 0.004 0.085 1557 Dihedral : 4.128 49.152 1239 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.20 % Allowed : 19.79 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.51 (0.26), residues: 1120 helix: 1.45 (0.27), residues: 400 sheet: 0.24 (0.31), residues: 282 loop : -0.56 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.012 0.001 TYR R 91 PHE 0.013 0.001 PHE R 367 TRP 0.029 0.001 TRP B 339 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9086) covalent geometry : angle 0.53343 (12319) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.30941 ( 4) hydrogen bonds : bond 0.03155 ( 408) hydrogen bonds : angle 3.95119 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2420.00 seconds wall clock time: 42 minutes 19.56 seconds (2539.56 seconds total)