Starting phenix.real_space_refine on Sat Jun 14 01:12:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dlx_46992/06_2025/9dlx_46992_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dlx_46992/06_2025/9dlx_46992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dlx_46992/06_2025/9dlx_46992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dlx_46992/06_2025/9dlx_46992.map" model { file = "/net/cci-nas-00/data/ceres_data/9dlx_46992/06_2025/9dlx_46992_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dlx_46992/06_2025/9dlx_46992_neut.cif" } resolution = 2.91 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 80 5.16 5 C 9881 2.51 5 N 2660 2.21 5 O 2922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15551 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3246 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 26, 'TRANS': 378} Chain breaks: 1 Chain: "B" Number of atoms: 3063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3063 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 17, 'TRANS': 365} Chain breaks: 1 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: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 824 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain breaks: 1 Chain: "H" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 252 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain breaks: 1 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: 10.35, per 1000 atoms: 0.67 Number of scatterers: 15551 At special positions: 0 Unit cell: (96.32, 132.44, 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 80 16.00 P 6 15.00 Mg 2 11.99 O 2922 8.00 N 2660 7.00 C 9881 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: 3.68 Conformation dependent library (CDL) restraints added in 2.1 seconds 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3642 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 22 sheets defined 41.8% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 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: 3.542A pdb=" N MET A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 134 removed outlier: 3.758A pdb=" N ARG A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 152 removed outlier: 3.928A pdb=" N LEU A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 187 through 190 removed outlier: 4.032A pdb=" N ILE A 190 " --> pdb=" O GLY A 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 196 through 212 removed outlier: 3.715A pdb=" N ILE A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.752A pdb=" N SER A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 removed outlier: 3.648A pdb=" N GLU A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 4.078A pdb=" N TRP A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.531A pdb=" N GLY A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.680A pdb=" N ALA A 288 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 306 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 311 through 318 removed outlier: 3.811A pdb=" N LYS A 317 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 318 " --> pdb=" O PRO A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.789A pdb=" N THR A 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 3.693A 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 331 through 355 Processing helix chain 'A' and resid 375 through 386 Processing helix chain 'A' and resid 387 through 393 removed outlier: 4.076A pdb=" N TYR A 391 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.606A 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 81 through 93 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.740A pdb=" N ARG B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.583A pdb=" N GLN B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 removed outlier: 3.976A pdb=" N LEU B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.786A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.537A pdb=" N GLU B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 267 removed outlier: 4.076A pdb=" N PHE B 266 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 272 removed outlier: 3.545A pdb=" N ASN B 272 " --> pdb=" O HIS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 288 Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 293 through 300 removed outlier: 3.542A pdb=" N PHE B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 removed outlier: 3.669A pdb=" N THR B 308 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET B 309 " --> pdb=" O GLY B 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 305 through 309' Processing helix chain 'B' and resid 312 through 329 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.931A pdb=" N SER B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 340' Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 365 Processing helix chain 'B' and resid 374 through 380 Processing helix chain 'B' and resid 381 through 389 removed outlier: 3.971A pdb=" N ARG B 384 " --> pdb=" O LYS B 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 364 removed outlier: 3.620A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 25 removed outlier: 4.058A pdb=" N GLU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.624A 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: 3.812A pdb=" N GLY D 50 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 70 removed outlier: 3.697A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 80 removed outlier: 4.299A pdb=" N LEU D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 84 removed outlier: 3.508A pdb=" N LEU D 84 " --> pdb=" O GLY D 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 81 through 84' Processing helix chain 'D' and resid 107 through 114 removed outlier: 3.501A pdb=" N HIS D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 121 Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 171 through 187 removed outlier: 3.748A pdb=" N VAL D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 176 " --> pdb=" O ASP D 172 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU D 187 " --> pdb=" O GLN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 245 Processing helix chain 'D' and resid 246 through 279 removed outlier: 3.620A pdb=" N HIS D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 53 removed outlier: 4.732A pdb=" N LYS E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 83 removed outlier: 4.259A pdb=" N THR E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 100 removed outlier: 4.062A pdb=" N ILE E 100 " --> pdb=" O TYR E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 149 removed outlier: 3.977A pdb=" N GLU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL E 148 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE E 149 " --> pdb=" O CYS E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.962A pdb=" N ASN E 170 " --> pdb=" O GLN E 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 20 removed outlier: 3.622A pdb=" N TYR F 8 " --> pdb=" O THR F 4 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA F 18 " --> pdb=" O ALA F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 43 through 47 removed outlier: 3.822A pdb=" N LEU F 46 " --> pdb=" O SER F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 97 removed outlier: 3.778A pdb=" N MET F 96 " --> pdb=" O ARG F 92 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 167 removed outlier: 4.648A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE F 164 " --> pdb=" O VAL F 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 60 Processing helix chain 'G' and resid 68 through 85 removed outlier: 3.750A pdb=" N LYS G 72 " --> pdb=" O SER G 68 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER G 85 " --> pdb=" O LYS G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 96 removed outlier: 3.570A pdb=" N ALA G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 114 removed outlier: 3.536A pdb=" N PHE G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 134 removed outlier: 4.088A pdb=" N VAL G 124 " --> pdb=" O ASN G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 146 Processing helix chain 'H' and resid 465 through 479 removed outlier: 4.200A pdb=" N GLU H 469 " --> pdb=" O GLY H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 485 Processing helix chain 'I' and resid 462 through 482 removed outlier: 3.921A pdb=" N ALA I 466 " --> pdb=" O GLY I 462 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS I 476 " --> pdb=" O GLN I 472 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA I 477 " --> pdb=" O LYS I 473 " (cutoff:3.500A) removed outlier: 3.830A 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: 3.875A pdb=" N THR A 113 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE A 110 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA A 142 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 112 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 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: 3.561A 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: 6.197A pdb=" N THR A 166 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER A 322 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE A 168 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 7.108A 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: 4.007A pdb=" N THR B 110 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN B 13 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY B 135 " --> pdb=" O CYS B 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 74 through 75 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: 6.766A pdb=" N ILE B 301 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 242 through 245 Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.563A pdb=" N VAL C 32 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU C 47 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE C 34 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 55 through 60 Processing sheet with id=AB6, first strand: chain 'C' and resid 99 through 104 removed outlier: 6.483A pdb=" N GLY C 114 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL C 102 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA C 112 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.901A pdb=" N GLY C 160 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU C 148 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA C 158 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TRP C 150 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU C 156 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYS C 166 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU C 197 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C 168 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.815A pdb=" N GLY C 209 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 249 through 254 removed outlier: 6.995A pdb=" N LEU C 271 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 327 through 332 removed outlier: 3.720A 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 removed outlier: 3.782A pdb=" N VAL D 93 " --> pdb=" O ILE D 59 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 142 through 144 Processing sheet with id=AC4, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.932A pdb=" N LYS F 60 " --> pdb=" O ALA F 75 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 1863 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: 4.52 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4825 1.34 - 1.46: 2819 1.46 - 1.57: 8100 1.57 - 1.69: 12 1.69 - 1.81: 129 Bond restraints: 15885 Sorted by residual: bond pdb=" CA ASN C 38 " pdb=" CB ASN C 38 " ideal model delta sigma weight residual 1.530 1.585 -0.054 1.50e-02 4.44e+03 1.30e+01 bond pdb=" C ARG F 6 " pdb=" N PRO F 7 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.23e-02 6.61e+03 5.21e+00 bond pdb=" CB ASN E 153 " pdb=" CG ASN E 153 " ideal model delta sigma weight residual 1.516 1.568 -0.052 2.50e-02 1.60e+03 4.38e+00 bond pdb=" CA ASP E 12 " pdb=" CB ASP E 12 " ideal model delta sigma weight residual 1.528 1.582 -0.054 2.61e-02 1.47e+03 4.27e+00 bond pdb=" CB ASN E 86 " pdb=" CG ASN E 86 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.73e+00 ... (remaining 15880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 21240 3.43 - 6.86: 209 6.86 - 10.29: 26 10.29 - 13.72: 2 13.72 - 17.15: 1 Bond angle restraints: 21478 Sorted by residual: angle pdb=" CB GLU H 485 " pdb=" CG GLU H 485 " pdb=" CD GLU H 485 " ideal model delta sigma weight residual 112.60 121.99 -9.39 1.70e+00 3.46e-01 3.05e+01 angle pdb=" C SER G 118 " pdb=" N ASP G 119 " pdb=" CA ASP G 119 " ideal model delta sigma weight residual 121.54 131.79 -10.25 1.91e+00 2.74e-01 2.88e+01 angle pdb=" C SER C 236 " pdb=" N VAL C 237 " pdb=" CA VAL C 237 " ideal model delta sigma weight residual 121.97 131.22 -9.25 1.80e+00 3.09e-01 2.64e+01 angle pdb=" CA LEU B 64 " pdb=" CB LEU B 64 " pdb=" CG LEU B 64 " ideal model delta sigma weight residual 116.30 133.45 -17.15 3.50e+00 8.16e-02 2.40e+01 angle pdb=" C LYS G 60 " pdb=" N ASN G 61 " pdb=" CA ASN G 61 " ideal model delta sigma weight residual 121.80 133.31 -11.51 2.44e+00 1.68e-01 2.23e+01 ... (remaining 21473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 8663 17.23 - 34.45: 777 34.45 - 51.68: 155 51.68 - 68.90: 20 68.90 - 86.13: 10 Dihedral angle restraints: 9625 sinusoidal: 3993 harmonic: 5632 Sorted by residual: dihedral pdb=" CA GLU H 483 " pdb=" C GLU H 483 " pdb=" N ASP H 484 " pdb=" CA ASP H 484 " ideal model delta harmonic sigma weight residual 180.00 148.82 31.18 0 5.00e+00 4.00e-02 3.89e+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 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA SER D 235 " pdb=" C SER D 235 " pdb=" N ALA D 236 " pdb=" CA ALA D 236 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 9622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 2272 0.129 - 0.258: 83 0.258 - 0.387: 3 0.387 - 0.516: 0 0.516 - 0.644: 1 Chirality restraints: 2359 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 2.00 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CB VAL B 385 " pdb=" CA VAL B 385 " pdb=" CG1 VAL B 385 " pdb=" CG2 VAL B 385 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.89e+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 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 2356 not shown) Planarity restraints: 2755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 131 " 0.031 2.00e-02 2.50e+03 2.63e-02 1.73e+01 pdb=" CG TRP C 131 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP C 131 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 131 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 131 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 131 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 131 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 131 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 131 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 131 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 241 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ILE D 241 " 0.058 2.00e-02 2.50e+03 pdb=" O ILE D 241 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN D 242 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 228 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO D 229 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 229 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 229 " 0.041 5.00e-02 4.00e+02 ... (remaining 2752 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 138 2.66 - 3.22: 12576 3.22 - 3.78: 22190 3.78 - 4.34: 31267 4.34 - 4.90: 52346 Nonbonded interactions: 118517 Sorted by model distance: nonbonded pdb=" O2G ATP B 500 " pdb="MG MG B 501 " model vdw 2.096 2.170 nonbonded pdb=" O2B ATP A 500 " pdb="MG MG A 501 " model vdw 2.108 2.170 nonbonded pdb=" O1G ATP A 500 " pdb="MG MG A 501 " model vdw 2.109 2.170 nonbonded pdb=" O1B ATP B 500 " pdb="MG MG B 501 " model vdw 2.111 2.170 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.307 3.040 ... (remaining 118512 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 Found NCS groups: ncs_group { reference = chain 'H' selection = (chain 'I' and (resid 461 through 483 or resid 492 or resid 494 through 501)) } 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: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 36.910 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 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 0.057 15885 Z= 0.240 Angle : 0.869 17.148 21478 Z= 0.486 Chirality : 0.057 0.644 2359 Planarity : 0.007 0.075 2755 Dihedral : 13.625 86.129 5983 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -2.34 (0.17), residues: 1908 helix: -2.47 (0.13), residues: 695 sheet: 0.33 (0.27), residues: 385 loop : -1.50 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP C 131 HIS 0.005 0.001 HIS D 254 PHE 0.046 0.002 PHE F 90 TYR 0.022 0.002 TYR D 250 ARG 0.018 0.001 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.16261 ( 669) hydrogen bonds : angle 6.28231 ( 1863) covalent geometry : bond 0.00485 (15885) covalent geometry : angle 0.86894 (21478) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.662 Fit side-chains REVERT: C 9 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8560 (mt-10) REVERT: E 10 ASP cc_start: 0.8732 (t0) cc_final: 0.8452 (t0) REVERT: E 43 ASP cc_start: 0.8795 (m-30) cc_final: 0.8460 (m-30) REVERT: E 57 ASN cc_start: 0.9260 (m-40) cc_final: 0.9024 (m-40) REVERT: E 85 CYS cc_start: 0.8904 (m) cc_final: 0.8658 (m) REVERT: E 150 ASP cc_start: 0.8924 (t0) cc_final: 0.8438 (t0) REVERT: E 153 ASN cc_start: 0.9248 (t0) cc_final: 0.8995 (t0) REVERT: E 172 SER cc_start: 0.9141 (p) cc_final: 0.8937 (p) REVERT: F 80 ASP cc_start: 0.8251 (m-30) cc_final: 0.7944 (m-30) REVERT: G 51 MET cc_start: 0.8652 (mmm) cc_final: 0.8349 (mmt) REVERT: G 151 VAL cc_start: 0.9402 (p) cc_final: 0.9171 (m) REVERT: H 469 GLU cc_start: 0.8639 (pm20) cc_final: 0.8371 (pm20) outliers start: 0 outliers final: 2 residues processed: 146 average time/residue: 1.4083 time to fit residues: 225.7057 Evaluate side-chains 127 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 99 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 GLN E 102 ASN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 GLN G 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.056538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.039012 restraints weight = 45998.957| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 3.29 r_work: 0.2453 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 15885 Z= 0.291 Angle : 0.605 8.906 21478 Z= 0.329 Chirality : 0.046 0.159 2359 Planarity : 0.005 0.051 2755 Dihedral : 5.884 58.418 2169 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.67 % Favored : 96.23 % Rotamer: Outliers : 1.12 % Allowed : 5.06 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.45 (0.19), residues: 1908 helix: 0.36 (0.19), residues: 698 sheet: 0.38 (0.27), residues: 384 loop : -1.16 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 131 HIS 0.007 0.001 HIS F 129 PHE 0.033 0.002 PHE F 90 TYR 0.019 0.001 TYR D 250 ARG 0.007 0.000 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.06513 ( 669) hydrogen bonds : angle 4.24536 ( 1863) covalent geometry : bond 0.00699 (15885) covalent geometry : angle 0.60515 (21478) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.709 Fit side-chains REVERT: A 327 MET cc_start: 0.9376 (mmm) cc_final: 0.9030 (mmp) REVERT: A 372 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8631 (mtt) REVERT: C 9 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8701 (mt-10) REVERT: D 207 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9238 (tm) REVERT: E 10 ASP cc_start: 0.8798 (t0) cc_final: 0.8440 (t0) REVERT: E 43 ASP cc_start: 0.8858 (m-30) cc_final: 0.8567 (m-30) REVERT: E 97 THR cc_start: 0.9396 (OUTLIER) cc_final: 0.9189 (t) REVERT: E 150 ASP cc_start: 0.9101 (t0) cc_final: 0.8614 (t0) REVERT: E 153 ASN cc_start: 0.9353 (t0) cc_final: 0.9067 (t0) REVERT: G 51 MET cc_start: 0.8691 (mmm) cc_final: 0.8292 (mmt) REVERT: G 119 ASP cc_start: 0.8724 (p0) cc_final: 0.8339 (p0) REVERT: H 469 GLU cc_start: 0.8605 (pm20) cc_final: 0.8300 (pm20) REVERT: I 472 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8621 (tm-30) outliers start: 19 outliers final: 4 residues processed: 134 average time/residue: 1.3867 time to fit residues: 205.6277 Evaluate side-chains 127 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain G residue 120 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 108 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN C 33 HIS C 54 HIS C 316 ASN D 252 HIS ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN G 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.058031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.040393 restraints weight = 45801.682| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 3.36 r_work: 0.2488 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15885 Z= 0.133 Angle : 0.494 7.865 21478 Z= 0.267 Chirality : 0.043 0.146 2359 Planarity : 0.004 0.054 2755 Dihedral : 5.293 58.413 2165 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.99 % Favored : 96.91 % Rotamer: Outliers : 1.24 % Allowed : 6.53 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.17 (0.19), residues: 1908 helix: 1.24 (0.20), residues: 696 sheet: 0.38 (0.27), residues: 391 loop : -0.98 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 131 HIS 0.003 0.001 HIS F 129 PHE 0.019 0.001 PHE F 90 TYR 0.014 0.001 TYR D 250 ARG 0.005 0.000 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 669) hydrogen bonds : angle 3.89249 ( 1863) covalent geometry : bond 0.00309 (15885) covalent geometry : angle 0.49403 (21478) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.801 Fit side-chains revert: symmetry clash REVERT: C 9 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8711 (mt-10) REVERT: D 207 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9292 (tm) REVERT: E 10 ASP cc_start: 0.8849 (t0) cc_final: 0.8369 (t0) REVERT: E 12 ASP cc_start: 0.9116 (p0) cc_final: 0.8885 (p0) REVERT: E 39 THR cc_start: 0.9460 (m) cc_final: 0.9091 (t) REVERT: E 43 ASP cc_start: 0.8807 (m-30) cc_final: 0.8604 (m-30) REVERT: E 150 ASP cc_start: 0.9166 (t0) cc_final: 0.8584 (t0) REVERT: E 153 ASN cc_start: 0.9402 (t0) cc_final: 0.9142 (t0) REVERT: G 51 MET cc_start: 0.8644 (mmm) cc_final: 0.8412 (mmm) REVERT: G 119 ASP cc_start: 0.8847 (p0) cc_final: 0.8411 (p0) REVERT: H 469 GLU cc_start: 0.8617 (pm20) cc_final: 0.8299 (pm20) REVERT: I 472 GLN cc_start: 0.8960 (tm-30) cc_final: 0.8726 (tm-30) outliers start: 21 outliers final: 7 residues processed: 129 average time/residue: 1.3687 time to fit residues: 195.0183 Evaluate side-chains 126 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain I residue 475 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 173 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN E 102 ASN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN G 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.040087 restraints weight = 46097.780| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 3.38 r_work: 0.2466 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15885 Z= 0.160 Angle : 0.497 7.771 21478 Z= 0.267 Chirality : 0.043 0.151 2359 Planarity : 0.004 0.048 2755 Dihedral : 5.038 56.693 2165 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.59 % Rotamer: Outliers : 1.35 % Allowed : 7.59 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.42 (0.20), residues: 1908 helix: 1.55 (0.21), residues: 702 sheet: 0.44 (0.27), residues: 391 loop : -0.92 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 131 HIS 0.005 0.001 HIS F 129 PHE 0.019 0.001 PHE F 90 TYR 0.016 0.001 TYR D 250 ARG 0.003 0.000 ARG F 105 Details of bonding type rmsd hydrogen bonds : bond 0.04926 ( 669) hydrogen bonds : angle 3.83334 ( 1863) covalent geometry : bond 0.00381 (15885) covalent geometry : angle 0.49653 (21478) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.634 Fit side-chains revert: symmetry clash REVERT: A 372 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8060 (mmm) REVERT: C 1 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8398 (mtt) REVERT: C 9 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8658 (mt-10) REVERT: C 225 ASP cc_start: 0.8739 (t0) cc_final: 0.8264 (t0) REVERT: D 207 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9290 (tm) REVERT: E 10 ASP cc_start: 0.8800 (t0) cc_final: 0.8334 (t0) REVERT: E 39 THR cc_start: 0.9446 (m) cc_final: 0.9092 (t) REVERT: E 150 ASP cc_start: 0.9128 (t0) cc_final: 0.8523 (t0) REVERT: E 153 ASN cc_start: 0.9432 (t0) cc_final: 0.9153 (t0) REVERT: G 51 MET cc_start: 0.8700 (mmm) cc_final: 0.8469 (mmm) REVERT: G 119 ASP cc_start: 0.8928 (p0) cc_final: 0.8478 (p0) REVERT: H 469 GLU cc_start: 0.8599 (pm20) cc_final: 0.8255 (pm20) REVERT: H 471 MET cc_start: 0.9042 (mmm) cc_final: 0.8262 (mmm) REVERT: I 472 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8736 (tm-30) outliers start: 23 outliers final: 5 residues processed: 132 average time/residue: 1.5249 time to fit residues: 221.1923 Evaluate side-chains 130 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain D residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 70 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN G 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.056694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.039201 restraints weight = 46953.661| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 3.39 r_work: 0.2440 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15885 Z= 0.218 Angle : 0.539 7.659 21478 Z= 0.289 Chirality : 0.045 0.155 2359 Planarity : 0.004 0.055 2755 Dihedral : 5.047 53.754 2165 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.38 % Rotamer: Outliers : 1.06 % Allowed : 9.06 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.51 (0.20), residues: 1908 helix: 1.67 (0.21), residues: 701 sheet: 0.43 (0.27), residues: 393 loop : -0.88 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 131 HIS 0.006 0.001 HIS D 254 PHE 0.017 0.001 PHE F 90 TYR 0.018 0.001 TYR D 250 ARG 0.005 0.000 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.05496 ( 669) hydrogen bonds : angle 3.91282 ( 1863) covalent geometry : bond 0.00528 (15885) covalent geometry : angle 0.53919 (21478) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.9034 (mmp) REVERT: B 56 MET cc_start: 0.8543 (tpp) cc_final: 0.8282 (mmm) REVERT: C 1 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8359 (mtt) REVERT: C 9 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8691 (mt-10) REVERT: D 207 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9315 (tm) REVERT: E 10 ASP cc_start: 0.8829 (t0) cc_final: 0.8325 (t0) REVERT: E 12 ASP cc_start: 0.9149 (p0) cc_final: 0.8945 (p0) REVERT: E 39 THR cc_start: 0.9468 (m) cc_final: 0.9138 (t) REVERT: E 150 ASP cc_start: 0.9138 (t0) cc_final: 0.8607 (t0) REVERT: E 153 ASN cc_start: 0.9492 (t0) cc_final: 0.9246 (t0) REVERT: G 51 MET cc_start: 0.8801 (mmm) cc_final: 0.8513 (mmt) REVERT: G 64 ILE cc_start: 0.9335 (pt) cc_final: 0.8874 (mm) REVERT: G 119 ASP cc_start: 0.9005 (p0) cc_final: 0.8597 (p0) REVERT: H 469 GLU cc_start: 0.8615 (pm20) cc_final: 0.8252 (pm20) REVERT: I 472 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8786 (tm-30) outliers start: 18 outliers final: 7 residues processed: 132 average time/residue: 1.3338 time to fit residues: 194.2470 Evaluate side-chains 132 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain H residue 472 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 155 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 chunk 140 optimal weight: 7.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 365 GLN E 102 ASN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN G 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.056124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.038386 restraints weight = 46627.474| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 3.38 r_work: 0.2418 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 15885 Z= 0.271 Angle : 0.577 7.772 21478 Z= 0.308 Chirality : 0.046 0.162 2359 Planarity : 0.004 0.047 2755 Dihedral : 5.141 52.332 2165 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 1.24 % Allowed : 10.00 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.47 (0.20), residues: 1908 helix: 1.65 (0.20), residues: 701 sheet: 0.36 (0.27), residues: 393 loop : -0.89 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 131 HIS 0.006 0.001 HIS F 129 PHE 0.017 0.002 PHE C 254 TYR 0.020 0.001 TYR D 250 ARG 0.004 0.000 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.06033 ( 669) hydrogen bonds : angle 4.03099 ( 1863) covalent geometry : bond 0.00658 (15885) covalent geometry : angle 0.57666 (21478) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.9020 (mmp) REVERT: C 9 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8715 (mt-10) REVERT: D 207 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9313 (tm) REVERT: E 10 ASP cc_start: 0.8838 (t0) cc_final: 0.8304 (t0) REVERT: E 12 ASP cc_start: 0.9133 (p0) cc_final: 0.8917 (p0) REVERT: E 39 THR cc_start: 0.9492 (m) cc_final: 0.9194 (t) REVERT: E 150 ASP cc_start: 0.9192 (t0) cc_final: 0.8611 (t0) REVERT: E 153 ASN cc_start: 0.9547 (t0) cc_final: 0.9309 (t0) REVERT: G 51 MET cc_start: 0.8822 (mmm) cc_final: 0.8573 (mmt) REVERT: G 64 ILE cc_start: 0.9413 (pt) cc_final: 0.8934 (mm) REVERT: H 469 GLU cc_start: 0.8629 (pm20) cc_final: 0.8261 (pm20) REVERT: H 471 MET cc_start: 0.9080 (mmm) cc_final: 0.8352 (mmm) REVERT: I 472 GLN cc_start: 0.8960 (tm-30) cc_final: 0.8744 (tm-30) outliers start: 21 outliers final: 9 residues processed: 129 average time/residue: 1.3835 time to fit residues: 197.1850 Evaluate side-chains 131 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 472 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 185 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 133 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN G 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.057573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.040190 restraints weight = 46577.027| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 3.38 r_work: 0.2472 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15885 Z= 0.128 Angle : 0.515 10.102 21478 Z= 0.273 Chirality : 0.043 0.178 2359 Planarity : 0.004 0.060 2755 Dihedral : 4.881 54.343 2165 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.86 % Rotamer: Outliers : 0.88 % Allowed : 11.18 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.70 (0.20), residues: 1908 helix: 1.86 (0.21), residues: 697 sheet: 0.46 (0.27), residues: 391 loop : -0.76 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.003 0.001 HIS D 254 PHE 0.013 0.001 PHE C 111 TYR 0.014 0.001 TYR D 250 ARG 0.004 0.000 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 669) hydrogen bonds : angle 3.76984 ( 1863) covalent geometry : bond 0.00301 (15885) covalent geometry : angle 0.51525 (21478) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 2.479 Fit side-chains revert: symmetry clash REVERT: C 9 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8706 (mt-10) REVERT: C 225 ASP cc_start: 0.8682 (t0) cc_final: 0.8299 (t0) REVERT: C 368 ARG cc_start: 0.8316 (mpp-170) cc_final: 0.8021 (mmp80) REVERT: D 207 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9313 (tm) REVERT: E 10 ASP cc_start: 0.8817 (t0) cc_final: 0.8266 (t0) REVERT: E 12 ASP cc_start: 0.9103 (p0) cc_final: 0.8858 (p0) REVERT: E 39 THR cc_start: 0.9471 (m) cc_final: 0.9182 (t) REVERT: E 150 ASP cc_start: 0.9175 (t0) cc_final: 0.8597 (t0) REVERT: E 153 ASN cc_start: 0.9585 (t0) cc_final: 0.9347 (t0) REVERT: G 51 MET cc_start: 0.8795 (mmm) cc_final: 0.8528 (mmt) REVERT: G 64 ILE cc_start: 0.9423 (pt) cc_final: 0.8963 (mm) REVERT: G 119 ASP cc_start: 0.8994 (p0) cc_final: 0.8665 (p0) REVERT: H 469 GLU cc_start: 0.8616 (pm20) cc_final: 0.8266 (pm20) REVERT: H 471 MET cc_start: 0.9045 (mmm) cc_final: 0.8213 (mmm) REVERT: I 472 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8743 (tm-30) outliers start: 15 outliers final: 7 residues processed: 129 average time/residue: 1.4608 time to fit residues: 208.4451 Evaluate side-chains 127 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 207 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 185 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 102 ASN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN G 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.055929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.038146 restraints weight = 46591.197| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 3.38 r_work: 0.2408 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 15885 Z= 0.308 Angle : 0.614 10.551 21478 Z= 0.324 Chirality : 0.047 0.161 2359 Planarity : 0.004 0.047 2755 Dihedral : 5.142 51.619 2165 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 1.18 % Allowed : 10.88 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.55 (0.20), residues: 1908 helix: 1.72 (0.20), residues: 695 sheet: 0.40 (0.27), residues: 388 loop : -0.82 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 131 HIS 0.008 0.001 HIS F 129 PHE 0.019 0.002 PHE C 254 TYR 0.021 0.001 TYR D 250 ARG 0.005 0.000 ARG F 105 Details of bonding type rmsd hydrogen bonds : bond 0.06218 ( 669) hydrogen bonds : angle 4.07125 ( 1863) covalent geometry : bond 0.00747 (15885) covalent geometry : angle 0.61391 (21478) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 9 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8725 (mt-10) REVERT: D 207 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9344 (tm) REVERT: E 10 ASP cc_start: 0.8852 (t0) cc_final: 0.8275 (t0) REVERT: E 12 ASP cc_start: 0.9097 (p0) cc_final: 0.8843 (p0) REVERT: E 39 THR cc_start: 0.9489 (m) cc_final: 0.9201 (t) REVERT: E 90 GLN cc_start: 0.9244 (tt0) cc_final: 0.8569 (tm-30) REVERT: E 150 ASP cc_start: 0.9219 (t0) cc_final: 0.8655 (t0) REVERT: G 51 MET cc_start: 0.8837 (mmm) cc_final: 0.8590 (mmt) REVERT: G 64 ILE cc_start: 0.9419 (pt) cc_final: 0.8958 (mm) REVERT: H 469 GLU cc_start: 0.8656 (pm20) cc_final: 0.8284 (pm20) REVERT: I 472 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8663 (tm-30) REVERT: I 476 LYS cc_start: 0.8423 (pmmt) cc_final: 0.8008 (pmtt) outliers start: 20 outliers final: 12 residues processed: 130 average time/residue: 1.4372 time to fit residues: 206.9124 Evaluate side-chains 132 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 472 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN G 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.057107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.039762 restraints weight = 46413.484| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.37 r_work: 0.2457 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15885 Z= 0.146 Angle : 0.539 11.494 21478 Z= 0.284 Chirality : 0.043 0.182 2359 Planarity : 0.004 0.050 2755 Dihedral : 4.941 54.410 2165 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.75 % Rotamer: Outliers : 0.94 % Allowed : 11.53 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.71 (0.20), residues: 1908 helix: 1.86 (0.21), residues: 698 sheet: 0.49 (0.27), residues: 387 loop : -0.74 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.003 0.001 HIS D 254 PHE 0.013 0.001 PHE C 111 TYR 0.015 0.001 TYR D 250 ARG 0.004 0.000 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.04864 ( 669) hydrogen bonds : angle 3.81565 ( 1863) covalent geometry : bond 0.00347 (15885) covalent geometry : angle 0.53926 (21478) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 2.623 Fit side-chains REVERT: C 9 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8681 (mt-10) REVERT: C 225 ASP cc_start: 0.8736 (t0) cc_final: 0.8319 (t0) REVERT: C 368 ARG cc_start: 0.8328 (mpp-170) cc_final: 0.8044 (mmp80) REVERT: D 207 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9325 (tm) REVERT: E 10 ASP cc_start: 0.8838 (t0) cc_final: 0.8228 (t0) REVERT: E 12 ASP cc_start: 0.9097 (p0) cc_final: 0.8884 (p0) REVERT: E 39 THR cc_start: 0.9491 (m) cc_final: 0.9218 (t) REVERT: E 90 GLN cc_start: 0.9184 (tt0) cc_final: 0.8491 (tm-30) REVERT: E 150 ASP cc_start: 0.9213 (t0) cc_final: 0.8570 (t0) REVERT: E 154 ASP cc_start: 0.8816 (t0) cc_final: 0.8335 (t0) REVERT: G 51 MET cc_start: 0.8803 (mmm) cc_final: 0.8536 (mmt) REVERT: G 64 ILE cc_start: 0.9445 (pt) cc_final: 0.8965 (mm) REVERT: G 119 ASP cc_start: 0.9002 (p0) cc_final: 0.8619 (p0) REVERT: H 469 GLU cc_start: 0.8644 (pm20) cc_final: 0.8287 (pm20) REVERT: H 471 MET cc_start: 0.9038 (mmm) cc_final: 0.8215 (mmm) REVERT: I 472 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8759 (tm-30) outliers start: 16 outliers final: 9 residues processed: 129 average time/residue: 1.7502 time to fit residues: 250.3220 Evaluate side-chains 128 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 178 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 102 ASN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN G 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.054722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.037388 restraints weight = 47511.734| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 3.36 r_work: 0.2379 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.062 15885 Z= 0.427 Angle : 0.709 12.059 21478 Z= 0.373 Chirality : 0.051 0.176 2359 Planarity : 0.004 0.070 2755 Dihedral : 5.383 47.762 2165 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.19 % Favored : 95.75 % Rotamer: Outliers : 1.12 % Allowed : 11.53 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.37 (0.20), residues: 1908 helix: 1.59 (0.20), residues: 694 sheet: 0.28 (0.27), residues: 388 loop : -0.93 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 131 HIS 0.009 0.002 HIS D 254 PHE 0.022 0.002 PHE C 254 TYR 0.024 0.002 TYR D 250 ARG 0.006 0.001 ARG F 105 Details of bonding type rmsd hydrogen bonds : bond 0.07056 ( 669) hydrogen bonds : angle 4.29620 ( 1863) covalent geometry : bond 0.01038 (15885) covalent geometry : angle 0.70917 (21478) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.852 Fit side-chains REVERT: A 327 MET cc_start: 0.9308 (mmm) cc_final: 0.9053 (mmp) REVERT: C 9 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8662 (mt-10) REVERT: D 207 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9337 (tm) REVERT: E 10 ASP cc_start: 0.8945 (t0) cc_final: 0.8358 (t0) REVERT: E 39 THR cc_start: 0.9497 (m) cc_final: 0.9225 (t) REVERT: E 150 ASP cc_start: 0.9249 (t0) cc_final: 0.8753 (t0) REVERT: E 154 ASP cc_start: 0.8846 (t0) cc_final: 0.8290 (t0) REVERT: G 51 MET cc_start: 0.8825 (mmm) cc_final: 0.8586 (mmt) REVERT: G 64 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9006 (mm) REVERT: G 119 ASP cc_start: 0.9041 (p0) cc_final: 0.8585 (p0) REVERT: H 469 GLU cc_start: 0.8685 (pm20) cc_final: 0.8327 (pm20) REVERT: I 468 MET cc_start: 0.8652 (mtm) cc_final: 0.8265 (mtm) REVERT: I 472 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8622 (tm-30) REVERT: I 476 LYS cc_start: 0.8452 (pmmt) cc_final: 0.7983 (pmtt) outliers start: 19 outliers final: 9 residues processed: 129 average time/residue: 1.5368 time to fit residues: 221.9862 Evaluate side-chains 128 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain G residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 179 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 93 optimal weight: 0.0170 chunk 4 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 0.0770 chunk 71 optimal weight: 0.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN G 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.040314 restraints weight = 46005.916| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 3.36 r_work: 0.2477 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15885 Z= 0.106 Angle : 0.538 12.454 21478 Z= 0.282 Chirality : 0.043 0.185 2359 Planarity : 0.004 0.051 2755 Dihedral : 4.953 54.392 2165 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.67 % Favored : 97.27 % Rotamer: Outliers : 0.76 % Allowed : 11.82 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.68 (0.20), residues: 1908 helix: 1.85 (0.21), residues: 697 sheet: 0.42 (0.27), residues: 390 loop : -0.74 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 221 HIS 0.002 0.000 HIS F 122 PHE 0.014 0.001 PHE F 138 TYR 0.014 0.001 TYR D 128 ARG 0.004 0.000 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 669) hydrogen bonds : angle 3.79447 ( 1863) covalent geometry : bond 0.00228 (15885) covalent geometry : angle 0.53761 (21478) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8667.33 seconds wall clock time: 154 minutes 33.92 seconds (9273.92 seconds total)