Starting phenix.real_space_refine on Fri Jun 13 23:44:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dlz_46993/06_2025/9dlz_46993_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dlz_46993/06_2025/9dlz_46993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dlz_46993/06_2025/9dlz_46993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dlz_46993/06_2025/9dlz_46993.map" model { file = "/net/cci-nas-00/data/ceres_data/9dlz_46993/06_2025/9dlz_46993_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dlz_46993/06_2025/9dlz_46993_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 78 5.16 5 C 9819 2.51 5 N 2646 2.21 5 O 2904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15455 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3235 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 26, 'TRANS': 377} Chain breaks: 1 Chain: "B" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2919 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain breaks: 2 Chain: "C" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2736 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 334} Chain breaks: 1 Chain: "D" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2301 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain: "E" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1422 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 12, 'TRANS': 162} Chain: "F" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1371 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain: "G" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1094 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 140} Chain: "H" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "I" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 272 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.27, per 1000 atoms: 0.60 Number of scatterers: 15455 At special positions: 0 Unit cell: (98.04, 137.6, 147.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 6 15.00 Mg 2 11.99 O 2904 8.00 N 2646 7.00 C 9819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.30 Conformation dependent library (CDL) restraints added in 1.8 seconds 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 23 sheets defined 42.4% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 85 through 99 removed outlier: 3.514A pdb=" N MET A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 134 removed outlier: 3.553A pdb=" N ARG A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 129 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 196 through 212 removed outlier: 3.563A pdb=" N ILE A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.582A pdb=" N THR A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 248 through 253 removed outlier: 4.215A pdb=" N TRP A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.630A pdb=" N GLY A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.630A pdb=" N ALA A 288 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 306 removed outlier: 3.528A pdb=" N VAL A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 removed outlier: 6.414A pdb=" N ASP A 310 " --> pdb=" O CYS A 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'A' and resid 311 through 318 removed outlier: 3.718A pdb=" N LYS A 317 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A 318 " --> pdb=" O PRO A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.797A pdb=" N THR A 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 327 " --> pdb=" O GLY A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 327' Processing helix chain 'A' and resid 330 through 354 Processing helix chain 'A' and resid 375 through 385 Processing helix chain 'A' and resid 387 through 393 removed outlier: 4.010A pdb=" N TYR A 391 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A 392 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.744A pdb=" N ARG B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.838A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.577A pdb=" N THR B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 262 through 266 removed outlier: 3.878A pdb=" N LEU B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.574A pdb=" N LEU B 270 " --> pdb=" O GLN B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 288 removed outlier: 3.538A pdb=" N ALA B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 312 through 328 removed outlier: 4.246A pdb=" N ARG B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 352 through 366 removed outlier: 3.595A pdb=" N MET B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.758A pdb=" N PHE B 371 " --> pdb=" O LYS B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 382 Processing helix chain 'B' and resid 384 through 390 Processing helix chain 'C' and resid 357 through 364 removed outlier: 3.707A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 25 removed outlier: 3.847A pdb=" N GLU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY D 25 " --> pdb=" O ASN D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.929A pdb=" N GLY D 50 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 70 removed outlier: 3.573A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 81 removed outlier: 4.131A pdb=" N LEU D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 114 Processing helix chain 'D' and resid 115 through 135 removed outlier: 4.786A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 187 removed outlier: 3.529A pdb=" N GLU D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 191 removed outlier: 3.851A pdb=" N ALA D 191 " --> pdb=" O GLY D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 188 through 191' Processing helix chain 'D' and resid 228 through 233 Processing helix chain 'D' and resid 233 through 279 removed outlier: 4.506A pdb=" N ASP D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASP D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 53 removed outlier: 4.764A pdb=" N LYS E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 83 removed outlier: 4.216A pdb=" N THR E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 100 removed outlier: 4.175A pdb=" N ILE E 100 " --> pdb=" O TYR E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 149 removed outlier: 3.785A pdb=" N GLU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE E 149 " --> pdb=" O CYS E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.857A pdb=" N ASN E 170 " --> pdb=" O GLN E 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 20 Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 80 through 97 removed outlier: 3.829A pdb=" N ARG F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 102 removed outlier: 4.030A pdb=" N PHE F 101 " --> pdb=" O ARG F 97 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 102' Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 167 removed outlier: 4.712A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE F 164 " --> pdb=" O VAL F 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 39 through 48 Processing helix chain 'G' and resid 51 through 59 removed outlier: 3.523A pdb=" N LEU G 55 " --> pdb=" O MET G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 85 removed outlier: 3.614A pdb=" N LYS G 72 " --> pdb=" O SER G 68 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU G 80 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER G 85 " --> pdb=" O LYS G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 99 through 114 Processing helix chain 'G' and resid 119 through 132 removed outlier: 4.214A pdb=" N ALA G 123 " --> pdb=" O ASP G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.992A pdb=" N ILE G 141 " --> pdb=" O GLY G 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 482 removed outlier: 4.103A pdb=" N ALA I 466 " --> pdb=" O GLY I 462 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS I 476 " --> pdb=" O GLN I 472 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA I 477 " --> pdb=" O LYS I 473 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP I 482 " --> pdb=" O ILE I 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.941A pdb=" N THR A 113 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE A 110 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA A 142 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 112 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 185 removed outlier: 3.647A pdb=" N LYS A 191 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.239A pdb=" N THR A 166 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER A 322 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE A 168 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 319 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 254 through 259 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 33 removed outlier: 3.551A pdb=" N LYS B 19 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 12 " --> pdb=" O LYS B 19 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 21 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR B 110 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ASN B 13 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR B 137 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 56 through 58 removed outlier: 3.698A pdb=" N MET B 56 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 36 " --> pdb=" O ASN B 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 74 through 75 removed outlier: 3.530A pdb=" N GLU B 75 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB2, first strand: chain 'B' and resid 173 through 174 removed outlier: 6.277A pdb=" N VAL B 155 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N SER B 304 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL B 157 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE B 301 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 244 through 245 Processing sheet with id=AB4, first strand: chain 'C' and resid 22 through 25 removed outlier: 3.613A pdb=" N ILE C 34 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N HIS C 46 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LYS C 36 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYS C 44 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASN C 38 " --> pdb=" O TRP C 42 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TRP C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 55 through 60 removed outlier: 3.972A pdb=" N ALA C 76 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 101 through 104 removed outlier: 3.738A pdb=" N PHE C 101 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 145 through 150 removed outlier: 3.727A pdb=" N SER C 161 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS C 166 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU C 197 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 168 " --> pdb=" O MET C 195 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN C 193 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 209 through 211 removed outlier: 4.060A pdb=" N GLY C 209 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 249 through 254 removed outlier: 3.668A pdb=" N SER C 284 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASN C 273 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N PHE C 282 " --> pdb=" O ASN C 273 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 327 through 332 removed outlier: 3.733A pdb=" N GLN C 329 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 33 through 36 Processing sheet with id=AC3, first strand: chain 'D' and resid 142 through 144 removed outlier: 3.724A pdb=" N THR D 151 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AC5, first strand: chain 'F' and resid 51 through 54 666 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.45 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2817 1.32 - 1.45: 3975 1.45 - 1.57: 8862 1.57 - 1.69: 13 1.69 - 1.82: 124 Bond restraints: 15791 Sorted by residual: bond pdb=" CA ASP E 12 " pdb=" CB ASP E 12 " ideal model delta sigma weight residual 1.535 1.632 -0.098 3.03e-02 1.09e+03 1.04e+01 bond pdb=" C ARG F 6 " pdb=" N PRO F 7 " ideal model delta sigma weight residual 1.336 1.363 -0.028 1.23e-02 6.61e+03 5.13e+00 bond pdb=" C ALA B 261 " pdb=" N PRO B 262 " ideal model delta sigma weight residual 1.334 1.351 -0.018 8.40e-03 1.42e+04 4.53e+00 bond pdb=" CB ASN E 86 " pdb=" CG ASN E 86 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.42e+00 bond pdb=" CA VAL C 335 " pdb=" CB VAL C 335 " ideal model delta sigma weight residual 1.540 1.569 -0.028 1.36e-02 5.41e+03 4.36e+00 ... (remaining 15786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 20633 2.28 - 4.56: 599 4.56 - 6.85: 93 6.85 - 9.13: 24 9.13 - 11.41: 7 Bond angle restraints: 21356 Sorted by residual: angle pdb=" CA VAL C 335 " pdb=" CB VAL C 335 " pdb=" CG1 VAL C 335 " ideal model delta sigma weight residual 110.40 120.37 -9.97 1.70e+00 3.46e-01 3.44e+01 angle pdb=" CA MET B 365 " pdb=" CB MET B 365 " pdb=" CG MET B 365 " ideal model delta sigma weight residual 114.10 125.51 -11.41 2.00e+00 2.50e-01 3.25e+01 angle pdb=" N VAL B 241 " pdb=" CA VAL B 241 " pdb=" C VAL B 241 " ideal model delta sigma weight residual 110.74 115.63 -4.89 9.10e-01 1.21e+00 2.89e+01 angle pdb=" C ILE D 244 " pdb=" N HIS D 245 " pdb=" CA HIS D 245 " ideal model delta sigma weight residual 122.38 112.89 9.49 1.81e+00 3.05e-01 2.75e+01 angle pdb=" C SER C 64 " pdb=" N ASP C 65 " pdb=" CA ASP C 65 " ideal model delta sigma weight residual 122.82 130.07 -7.25 1.42e+00 4.96e-01 2.61e+01 ... (remaining 21351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 8562 17.12 - 34.24: 806 34.24 - 51.37: 158 51.37 - 68.49: 17 68.49 - 85.61: 12 Dihedral angle restraints: 9555 sinusoidal: 3962 harmonic: 5593 Sorted by residual: dihedral pdb=" CA THR D 246 " pdb=" C THR D 246 " pdb=" N PHE D 247 " pdb=" CA PHE D 247 " ideal model delta harmonic sigma weight residual -180.00 -139.25 -40.75 0 5.00e+00 4.00e-02 6.64e+01 dihedral pdb=" CA ALA D 236 " pdb=" C ALA D 236 " pdb=" N ARG D 237 " pdb=" CA ARG D 237 " ideal model delta harmonic sigma weight residual -180.00 -150.57 -29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA MET B 365 " pdb=" C MET B 365 " pdb=" N LYS B 366 " pdb=" CA LYS B 366 " ideal model delta harmonic sigma weight residual -180.00 -150.86 -29.14 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 9552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2194 0.117 - 0.234: 132 0.234 - 0.351: 9 0.351 - 0.468: 2 0.468 - 0.585: 1 Chirality restraints: 2338 Sorted by residual: chirality pdb=" CB ILE E 16 " pdb=" CA ILE E 16 " pdb=" CG1 ILE E 16 " pdb=" CG2 ILE E 16 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" CB THR G 146 " pdb=" CA THR G 146 " pdb=" OG1 THR G 146 " pdb=" CG2 THR G 146 " both_signs ideal model delta sigma weight residual False 2.55 2.10 0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" CB VAL A 311 " pdb=" CA VAL A 311 " pdb=" CG1 VAL A 311 " pdb=" CG2 VAL A 311 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 2335 not shown) Planarity restraints: 2745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 242 " 0.021 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C ASN D 242 " -0.075 2.00e-02 2.50e+03 pdb=" O ASN D 242 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU D 243 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 244 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ILE D 244 " 0.066 2.00e-02 2.50e+03 pdb=" O ILE D 244 " -0.024 2.00e-02 2.50e+03 pdb=" N HIS D 245 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 243 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C LEU D 243 " 0.062 2.00e-02 2.50e+03 pdb=" O LEU D 243 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE D 244 " -0.021 2.00e-02 2.50e+03 ... (remaining 2742 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 150 2.65 - 3.21: 12569 3.21 - 3.78: 22418 3.78 - 4.34: 30885 4.34 - 4.90: 51455 Nonbonded interactions: 117477 Sorted by model distance: nonbonded pdb=" O2B ATP A 500 " pdb="MG MG A 501 " model vdw 2.091 2.170 nonbonded pdb=" O1G ATP A 500 " pdb="MG MG A 501 " model vdw 2.107 2.170 nonbonded pdb=" O3B ATP B 500 " pdb="MG MG B 501 " model vdw 2.114 2.170 nonbonded pdb=" O2G ATP B 500 " pdb="MG MG B 501 " model vdw 2.134 2.170 nonbonded pdb=" O1A ATP B 500 " pdb="MG MG B 501 " model vdw 2.146 2.170 ... (remaining 117472 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: 3.230 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.380 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 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 : 0.005 0.098 15791 Z= 0.252 Angle : 0.941 11.410 21356 Z= 0.538 Chirality : 0.061 0.585 2338 Planarity : 0.009 0.081 2745 Dihedral : 13.731 85.608 5943 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.53 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.16), residues: 1899 helix: -2.93 (0.13), residues: 702 sheet: 0.33 (0.26), residues: 374 loop : -1.62 (0.19), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 131 HIS 0.007 0.001 HIS B 165 PHE 0.047 0.003 PHE G 114 TYR 0.026 0.002 TYR E 4 ARG 0.006 0.001 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.20973 ( 662) hydrogen bonds : angle 7.46866 ( 1851) covalent geometry : bond 0.00503 (15791) covalent geometry : angle 0.94080 (21356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.846 Fit side-chains revert: symmetry clash REVERT: B 345 GLU cc_start: 0.8714 (tp30) cc_final: 0.8036 (mm-30) REVERT: C 352 MET cc_start: 0.8460 (tmm) cc_final: 0.8078 (tmm) REVERT: E 150 ASP cc_start: 0.9321 (t70) cc_final: 0.8875 (t0) REVERT: G 51 MET cc_start: 0.7119 (ppp) cc_final: 0.6683 (ppp) REVERT: G 115 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8087 (tm-30) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2769 time to fit residues: 57.0228 Evaluate side-chains 102 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 205 GLN A 411 ASN B 149 GLN C 30 HIS D 44 HIS D 68 GLN D 197 GLN ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.056577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.040133 restraints weight = 59215.855| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.23 r_work: 0.2545 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15791 Z= 0.195 Angle : 0.566 6.895 21356 Z= 0.312 Chirality : 0.044 0.167 2338 Planarity : 0.005 0.049 2745 Dihedral : 6.065 78.796 2156 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.63 % Favored : 97.10 % Rotamer: Outliers : 0.36 % Allowed : 4.92 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 1899 helix: -0.24 (0.19), residues: 701 sheet: 0.35 (0.27), residues: 383 loop : -1.23 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 372 HIS 0.005 0.001 HIS F 129 PHE 0.021 0.002 PHE F 102 TYR 0.018 0.001 TYR D 250 ARG 0.008 0.000 ARG E 166 Details of bonding type rmsd hydrogen bonds : bond 0.06171 ( 662) hydrogen bonds : angle 4.66783 ( 1851) covalent geometry : bond 0.00448 (15791) covalent geometry : angle 0.56593 (21356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 1.773 Fit side-chains revert: symmetry clash REVERT: B 74 MET cc_start: 0.5855 (ppp) cc_final: 0.5606 (tmm) REVERT: B 221 CYS cc_start: 0.9060 (m) cc_final: 0.8775 (m) REVERT: B 345 GLU cc_start: 0.8852 (tp30) cc_final: 0.8304 (mm-30) REVERT: C 352 MET cc_start: 0.8647 (tmm) cc_final: 0.8435 (tmm) REVERT: E 39 THR cc_start: 0.9486 (m) cc_final: 0.9130 (t) REVERT: E 90 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8439 (tm-30) REVERT: E 126 ASP cc_start: 0.8863 (m-30) cc_final: 0.8535 (m-30) REVERT: E 150 ASP cc_start: 0.9305 (t70) cc_final: 0.9036 (t0) REVERT: G 48 GLN cc_start: 0.8962 (pp30) cc_final: 0.8604 (pp30) REVERT: G 50 ASN cc_start: 0.7487 (t0) cc_final: 0.6892 (t0) REVERT: G 51 MET cc_start: 0.6956 (ppp) cc_final: 0.6502 (ppp) REVERT: G 115 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8035 (tm-30) REVERT: I 469 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8694 (tm-30) outliers start: 6 outliers final: 2 residues processed: 108 average time/residue: 0.2605 time to fit residues: 43.6197 Evaluate side-chains 97 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain E residue 148 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 182 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** 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 = 0.3208 r_free = 0.3208 target = 0.056546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.040173 restraints weight = 59546.069| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.30 r_work: 0.2554 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15791 Z= 0.148 Angle : 0.500 6.461 21356 Z= 0.273 Chirality : 0.043 0.150 2338 Planarity : 0.004 0.041 2745 Dihedral : 5.357 59.329 2156 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.95 % Favored : 96.84 % Rotamer: Outliers : 0.59 % Allowed : 6.82 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1899 helix: 0.81 (0.20), residues: 704 sheet: 0.48 (0.27), residues: 385 loop : -1.01 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 372 HIS 0.004 0.001 HIS F 129 PHE 0.017 0.001 PHE F 102 TYR 0.014 0.001 TYR D 43 ARG 0.006 0.000 ARG E 166 Details of bonding type rmsd hydrogen bonds : bond 0.05261 ( 662) hydrogen bonds : angle 4.28704 ( 1851) covalent geometry : bond 0.00341 (15791) covalent geometry : angle 0.50018 (21356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.845 Fit side-chains REVERT: B 215 MET cc_start: 0.8866 (tpp) cc_final: 0.8512 (tpt) REVERT: B 345 GLU cc_start: 0.8849 (tp30) cc_final: 0.8207 (mm-30) REVERT: B 373 MET cc_start: 0.7913 (mmm) cc_final: 0.7542 (mmm) REVERT: C 254 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8552 (m-10) REVERT: C 352 MET cc_start: 0.8693 (tmm) cc_final: 0.8457 (tmm) REVERT: E 39 THR cc_start: 0.9498 (m) cc_final: 0.9174 (t) REVERT: E 90 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8304 (tm-30) REVERT: G 48 GLN cc_start: 0.8895 (pp30) cc_final: 0.8608 (pp30) REVERT: G 50 ASN cc_start: 0.7400 (t0) cc_final: 0.6696 (t0) REVERT: G 51 MET cc_start: 0.7143 (ppp) cc_final: 0.6708 (ppp) REVERT: I 469 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8692 (tm-30) outliers start: 10 outliers final: 5 residues processed: 103 average time/residue: 0.2648 time to fit residues: 42.4321 Evaluate side-chains 98 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain E residue 148 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 58 optimal weight: 0.4980 chunk 120 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.056085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.039807 restraints weight = 59887.715| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 3.28 r_work: 0.2540 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15791 Z= 0.166 Angle : 0.498 5.769 21356 Z= 0.272 Chirality : 0.043 0.150 2338 Planarity : 0.004 0.041 2745 Dihedral : 5.185 53.203 2156 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.00 % Favored : 96.79 % Rotamer: Outliers : 0.77 % Allowed : 8.54 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1899 helix: 1.27 (0.20), residues: 704 sheet: 0.42 (0.27), residues: 391 loop : -0.84 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 372 HIS 0.005 0.001 HIS F 129 PHE 0.016 0.001 PHE F 102 TYR 0.016 0.001 TYR D 250 ARG 0.005 0.000 ARG E 166 Details of bonding type rmsd hydrogen bonds : bond 0.05213 ( 662) hydrogen bonds : angle 4.21007 ( 1851) covalent geometry : bond 0.00389 (15791) covalent geometry : angle 0.49826 (21356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.763 Fit side-chains REVERT: B 74 MET cc_start: 0.5316 (tmm) cc_final: 0.4823 (tpt) REVERT: B 345 GLU cc_start: 0.8849 (tp30) cc_final: 0.8230 (mm-30) REVERT: B 373 MET cc_start: 0.7983 (mmm) cc_final: 0.7674 (mmm) REVERT: C 254 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8598 (m-10) REVERT: C 352 MET cc_start: 0.8783 (tmm) cc_final: 0.8513 (tmm) REVERT: E 39 THR cc_start: 0.9512 (m) cc_final: 0.9209 (t) REVERT: E 90 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8454 (tm-30) REVERT: G 48 GLN cc_start: 0.8950 (pp30) cc_final: 0.8725 (pp30) REVERT: G 50 ASN cc_start: 0.7400 (t0) cc_final: 0.6719 (t0) REVERT: G 51 MET cc_start: 0.7297 (ppp) cc_final: 0.6780 (ppp) REVERT: I 469 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8706 (tm-30) outliers start: 13 outliers final: 11 residues processed: 110 average time/residue: 0.2441 time to fit residues: 42.2449 Evaluate side-chains 107 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain H residue 499 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 79 optimal weight: 10.0000 chunk 9 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 96 GLN ** 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 = 0.3204 r_free = 0.3204 target = 0.056503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.040212 restraints weight = 60002.098| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.18 r_work: 0.2551 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15791 Z= 0.145 Angle : 0.483 6.172 21356 Z= 0.262 Chirality : 0.043 0.151 2338 Planarity : 0.003 0.043 2745 Dihedral : 5.036 48.429 2156 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.05 % Favored : 96.74 % Rotamer: Outliers : 1.25 % Allowed : 9.43 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1899 helix: 1.49 (0.20), residues: 706 sheet: 0.42 (0.27), residues: 391 loop : -0.73 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 131 HIS 0.004 0.001 HIS F 129 PHE 0.013 0.001 PHE F 102 TYR 0.015 0.001 TYR D 250 ARG 0.004 0.000 ARG E 166 Details of bonding type rmsd hydrogen bonds : bond 0.04881 ( 662) hydrogen bonds : angle 4.08608 ( 1851) covalent geometry : bond 0.00337 (15791) covalent geometry : angle 0.48254 (21356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 2.144 Fit side-chains revert: symmetry clash REVERT: B 345 GLU cc_start: 0.8833 (tp30) cc_final: 0.8175 (mm-30) REVERT: B 365 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8035 (tmm) REVERT: B 373 MET cc_start: 0.7935 (mmm) cc_final: 0.7620 (mmm) REVERT: C 254 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8635 (m-10) REVERT: C 352 MET cc_start: 0.8761 (tmm) cc_final: 0.8506 (tmm) REVERT: E 39 THR cc_start: 0.9511 (m) cc_final: 0.9235 (t) REVERT: E 90 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8399 (tm-30) REVERT: G 50 ASN cc_start: 0.7435 (t0) cc_final: 0.6889 (t0) REVERT: G 51 MET cc_start: 0.7399 (ppp) cc_final: 0.6856 (ppp) REVERT: I 469 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8734 (tm-30) outliers start: 21 outliers final: 14 residues processed: 115 average time/residue: 0.2687 time to fit residues: 48.6878 Evaluate side-chains 109 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 499 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 58 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** 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 = 0.3197 r_free = 0.3197 target = 0.056263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.039984 restraints weight = 59913.489| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 3.23 r_work: 0.2540 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15791 Z= 0.153 Angle : 0.487 6.194 21356 Z= 0.263 Chirality : 0.043 0.153 2338 Planarity : 0.003 0.043 2745 Dihedral : 4.988 47.404 2156 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.05 % Favored : 96.74 % Rotamer: Outliers : 1.07 % Allowed : 10.20 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1899 helix: 1.63 (0.20), residues: 706 sheet: 0.39 (0.27), residues: 390 loop : -0.68 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 131 HIS 0.004 0.001 HIS F 129 PHE 0.034 0.001 PHE G 11 TYR 0.019 0.001 TYR B 137 ARG 0.004 0.000 ARG G 47 Details of bonding type rmsd hydrogen bonds : bond 0.04908 ( 662) hydrogen bonds : angle 4.05041 ( 1851) covalent geometry : bond 0.00358 (15791) covalent geometry : angle 0.48735 (21356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 1.958 Fit side-chains REVERT: B 215 MET cc_start: 0.8857 (tpp) cc_final: 0.8541 (tpt) REVERT: B 345 GLU cc_start: 0.8817 (tp30) cc_final: 0.8159 (mm-30) REVERT: B 365 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8088 (tmm) REVERT: B 373 MET cc_start: 0.7906 (mmm) cc_final: 0.7625 (mmm) REVERT: C 254 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8769 (m-10) REVERT: C 352 MET cc_start: 0.8766 (tmm) cc_final: 0.8508 (tmm) REVERT: E 39 THR cc_start: 0.9513 (m) cc_final: 0.9254 (t) REVERT: G 50 ASN cc_start: 0.7534 (t0) cc_final: 0.6935 (t0) REVERT: G 51 MET cc_start: 0.7501 (ppp) cc_final: 0.7021 (ppp) REVERT: H 499 TRP cc_start: 0.8522 (OUTLIER) cc_final: 0.7625 (t60) REVERT: I 469 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8753 (tm-30) outliers start: 18 outliers final: 12 residues processed: 108 average time/residue: 0.2453 time to fit residues: 42.7696 Evaluate side-chains 106 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 499 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 93 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.038429 restraints weight = 60330.889| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 3.25 r_work: 0.2485 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 15791 Z= 0.277 Angle : 0.592 9.695 21356 Z= 0.317 Chirality : 0.046 0.158 2338 Planarity : 0.004 0.046 2745 Dihedral : 5.253 46.840 2156 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.21 % Favored : 95.68 % Rotamer: Outliers : 1.13 % Allowed : 10.74 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1899 helix: 1.50 (0.20), residues: 705 sheet: 0.34 (0.27), residues: 379 loop : -0.80 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 131 HIS 0.007 0.001 HIS F 129 PHE 0.030 0.002 PHE G 11 TYR 0.026 0.002 TYR B 137 ARG 0.005 0.000 ARG G 47 Details of bonding type rmsd hydrogen bonds : bond 0.06102 ( 662) hydrogen bonds : angle 4.37019 ( 1851) covalent geometry : bond 0.00662 (15791) covalent geometry : angle 0.59235 (21356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.777 Fit side-chains REVERT: B 345 GLU cc_start: 0.8835 (tp30) cc_final: 0.8159 (mm-30) REVERT: B 365 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7885 (tmm) REVERT: B 373 MET cc_start: 0.7945 (mmm) cc_final: 0.7702 (mmm) REVERT: C 254 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8888 (m-10) REVERT: C 352 MET cc_start: 0.8838 (tmm) cc_final: 0.8515 (tmm) REVERT: E 39 THR cc_start: 0.9555 (m) cc_final: 0.9309 (t) REVERT: G 50 ASN cc_start: 0.7541 (t0) cc_final: 0.7193 (t0) REVERT: G 51 MET cc_start: 0.7461 (ppp) cc_final: 0.7058 (ppp) REVERT: H 499 TRP cc_start: 0.8595 (OUTLIER) cc_final: 0.7832 (t60) REVERT: I 469 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8789 (tm-30) outliers start: 19 outliers final: 14 residues processed: 109 average time/residue: 0.2220 time to fit residues: 39.3904 Evaluate side-chains 107 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 340 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 499 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 184 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.040189 restraints weight = 59472.131| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.21 r_work: 0.2549 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15791 Z= 0.123 Angle : 0.493 7.818 21356 Z= 0.265 Chirality : 0.043 0.153 2338 Planarity : 0.003 0.045 2745 Dihedral : 5.007 49.803 2156 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.69 % Favored : 97.21 % Rotamer: Outliers : 1.01 % Allowed : 11.21 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1899 helix: 1.70 (0.20), residues: 707 sheet: 0.35 (0.27), residues: 389 loop : -0.64 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 131 HIS 0.003 0.000 HIS D 245 PHE 0.031 0.001 PHE G 11 TYR 0.025 0.001 TYR G 19 ARG 0.017 0.000 ARG G 47 Details of bonding type rmsd hydrogen bonds : bond 0.04668 ( 662) hydrogen bonds : angle 4.01068 ( 1851) covalent geometry : bond 0.00281 (15791) covalent geometry : angle 0.49281 (21356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 2.498 Fit side-chains REVERT: B 215 MET cc_start: 0.8876 (tpp) cc_final: 0.8601 (tpt) REVERT: B 345 GLU cc_start: 0.8793 (tp30) cc_final: 0.8123 (mm-30) REVERT: B 373 MET cc_start: 0.7939 (mmm) cc_final: 0.7708 (mmm) REVERT: C 254 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8808 (m-10) REVERT: C 352 MET cc_start: 0.8763 (tmm) cc_final: 0.8514 (tmm) REVERT: E 39 THR cc_start: 0.9513 (m) cc_final: 0.9277 (t) REVERT: G 50 ASN cc_start: 0.7483 (t0) cc_final: 0.7236 (t0) REVERT: G 51 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6921 (ppp) REVERT: H 499 TRP cc_start: 0.8468 (OUTLIER) cc_final: 0.7790 (t60) REVERT: I 469 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8780 (tm-30) outliers start: 17 outliers final: 10 residues processed: 112 average time/residue: 0.3094 time to fit residues: 56.5910 Evaluate side-chains 106 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 499 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 12 optimal weight: 0.3980 chunk 74 optimal weight: 0.4980 chunk 13 optimal weight: 0.2980 chunk 113 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 HIS ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.058632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.042076 restraints weight = 60349.431| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.43 r_work: 0.2594 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15791 Z= 0.097 Angle : 0.479 8.608 21356 Z= 0.256 Chirality : 0.042 0.152 2338 Planarity : 0.003 0.044 2745 Dihedral : 4.771 51.483 2156 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.16 % Favored : 96.74 % Rotamer: Outliers : 1.01 % Allowed : 11.33 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1899 helix: 1.88 (0.20), residues: 708 sheet: 0.41 (0.27), residues: 390 loop : -0.52 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 131 HIS 0.003 0.000 HIS D 245 PHE 0.030 0.001 PHE G 11 TYR 0.022 0.001 TYR B 137 ARG 0.012 0.000 ARG G 47 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 662) hydrogen bonds : angle 3.81657 ( 1851) covalent geometry : bond 0.00210 (15791) covalent geometry : angle 0.47887 (21356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 1.756 Fit side-chains REVERT: B 74 MET cc_start: 0.5829 (tpp) cc_final: 0.4679 (tpp) REVERT: B 215 MET cc_start: 0.8832 (tpp) cc_final: 0.8551 (tpt) REVERT: B 345 GLU cc_start: 0.8809 (tp30) cc_final: 0.8182 (mm-30) REVERT: B 373 MET cc_start: 0.7885 (mmm) cc_final: 0.7621 (mmm) REVERT: C 254 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8714 (m-10) REVERT: C 352 MET cc_start: 0.8816 (tmm) cc_final: 0.8477 (tmm) REVERT: D 130 GLN cc_start: 0.9041 (tp40) cc_final: 0.8806 (tp40) REVERT: E 39 THR cc_start: 0.9513 (m) cc_final: 0.9279 (t) REVERT: E 85 CYS cc_start: 0.8898 (m) cc_final: 0.8399 (p) REVERT: G 48 GLN cc_start: 0.8122 (pp30) cc_final: 0.7824 (pp30) REVERT: G 50 ASN cc_start: 0.7392 (t0) cc_final: 0.7086 (t0) REVERT: G 51 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6863 (ppp) REVERT: H 499 TRP cc_start: 0.8329 (OUTLIER) cc_final: 0.7871 (t60) REVERT: I 469 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8779 (tm-30) outliers start: 17 outliers final: 11 residues processed: 115 average time/residue: 0.2502 time to fit residues: 46.0332 Evaluate side-chains 108 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 499 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 173 optimal weight: 0.2980 chunk 145 optimal weight: 0.6980 chunk 167 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 HIS ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.056225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.040026 restraints weight = 59751.014| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.21 r_work: 0.2544 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15791 Z= 0.160 Angle : 0.518 8.851 21356 Z= 0.277 Chirality : 0.043 0.154 2338 Planarity : 0.004 0.045 2745 Dihedral : 4.906 48.349 2156 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 1.01 % Allowed : 11.57 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1899 helix: 1.89 (0.20), residues: 708 sheet: 0.38 (0.27), residues: 387 loop : -0.57 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 131 HIS 0.005 0.001 HIS F 129 PHE 0.028 0.001 PHE G 11 TYR 0.029 0.001 TYR B 137 ARG 0.018 0.000 ARG G 47 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 662) hydrogen bonds : angle 3.96476 ( 1851) covalent geometry : bond 0.00382 (15791) covalent geometry : angle 0.51832 (21356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.746 Fit side-chains REVERT: B 215 MET cc_start: 0.8874 (tpp) cc_final: 0.8574 (tpt) REVERT: B 345 GLU cc_start: 0.8742 (tp30) cc_final: 0.8173 (mm-30) REVERT: B 373 MET cc_start: 0.7936 (mmm) cc_final: 0.7708 (mmm) REVERT: C 254 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8844 (m-10) REVERT: C 352 MET cc_start: 0.8765 (tmm) cc_final: 0.8518 (tmm) REVERT: D 130 GLN cc_start: 0.9072 (tp40) cc_final: 0.8837 (tp40) REVERT: E 39 THR cc_start: 0.9522 (m) cc_final: 0.9313 (t) REVERT: G 50 ASN cc_start: 0.7449 (t0) cc_final: 0.7132 (t0) REVERT: G 51 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7005 (ppp) REVERT: H 499 TRP cc_start: 0.8320 (OUTLIER) cc_final: 0.8039 (t60) REVERT: I 469 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8818 (tm-30) outliers start: 17 outliers final: 13 residues processed: 111 average time/residue: 0.2224 time to fit residues: 40.1945 Evaluate side-chains 111 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 340 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 499 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 184 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** 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 = 0.3225 r_free = 0.3225 target = 0.057177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.040918 restraints weight = 59299.521| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.32 r_work: 0.2582 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15791 Z= 0.113 Angle : 0.496 8.997 21356 Z= 0.263 Chirality : 0.042 0.152 2338 Planarity : 0.003 0.045 2745 Dihedral : 4.819 50.364 2156 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 0.95 % Allowed : 11.57 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1899 helix: 1.94 (0.20), residues: 708 sheet: 0.39 (0.27), residues: 385 loop : -0.50 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 372 HIS 0.003 0.000 HIS D 245 PHE 0.028 0.001 PHE G 11 TYR 0.013 0.001 TYR D 250 ARG 0.007 0.000 ARG G 47 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 662) hydrogen bonds : angle 3.85825 ( 1851) covalent geometry : bond 0.00261 (15791) covalent geometry : angle 0.49593 (21356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6836.37 seconds wall clock time: 119 minutes 58.88 seconds (7198.88 seconds total)