Starting phenix.real_space_refine on Thu Sep 18 09:12:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dlx_46992/09_2025/9dlx_46992_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dlx_46992/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dlx_46992/09_2025/9dlx_46992_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dlx_46992/09_2025/9dlx_46992_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dlx_46992/09_2025/9dlx_46992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dlx_46992/09_2025/9dlx_46992.map" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.49, per 1000 atoms: 0.22 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: 1.16 Conformation dependent library (CDL) restraints added in 595.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.51 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: 1.98 Time building geometry restraints manager: 1.60 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: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.500 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:8.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.020 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.018 0.001 ARG C 368 TYR 0.022 0.002 TYR D 250 PHE 0.046 0.002 PHE F 90 TRP 0.070 0.002 TRP C 131 HIS 0.005 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00485 (15885) covalent geometry : angle 0.86894 (21478) hydrogen bonds : bond 0.16261 ( 669) hydrogen bonds : angle 6.28231 ( 1863) *********************** 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 : 0.702 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: 0.7390 time to fit residues: 118.1288 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 : 0.670 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN C 54 HIS C 316 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.059095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.041494 restraints weight = 45410.021| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 3.38 r_work: 0.2531 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15885 Z= 0.126 Angle : 0.502 8.980 21478 Z= 0.272 Chirality : 0.043 0.164 2359 Planarity : 0.004 0.052 2755 Dihedral : 5.616 60.593 2169 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.83 % Favored : 97.06 % Rotamer: Outliers : 0.82 % Allowed : 4.65 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.19), residues: 1908 helix: 0.22 (0.19), residues: 694 sheet: 0.48 (0.28), residues: 385 loop : -1.08 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 368 TYR 0.014 0.001 TYR D 250 PHE 0.022 0.001 PHE F 90 TRP 0.030 0.001 TRP C 131 HIS 0.003 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00286 (15885) covalent geometry : angle 0.50236 (21478) hydrogen bonds : bond 0.04797 ( 669) hydrogen bonds : angle 4.07393 ( 1863) *********************** 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 139 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.701 Fit side-chains REVERT: C 9 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8658 (mt-10) REVERT: D 207 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9249 (tm) REVERT: E 10 ASP cc_start: 0.8784 (t0) cc_final: 0.8408 (t0) REVERT: E 43 ASP cc_start: 0.8864 (m-30) cc_final: 0.8573 (m-30) REVERT: E 57 ASN cc_start: 0.9313 (m-40) cc_final: 0.9067 (m-40) REVERT: E 97 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.9158 (t) REVERT: E 150 ASP cc_start: 0.9041 (t0) cc_final: 0.8514 (t0) REVERT: E 153 ASN cc_start: 0.9316 (t0) cc_final: 0.9008 (t0) REVERT: E 172 SER cc_start: 0.9189 (p) cc_final: 0.8984 (p) REVERT: G 51 MET cc_start: 0.8657 (mmm) cc_final: 0.8274 (mmt) REVERT: H 469 GLU cc_start: 0.8619 (pm20) cc_final: 0.8318 (pm20) REVERT: H 471 MET cc_start: 0.9118 (mmm) cc_final: 0.8451 (mmm) outliers start: 14 outliers final: 5 residues processed: 129 average time/residue: 0.7492 time to fit residues: 105.6015 Evaluate side-chains 128 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 9 MET 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 179 optimal weight: 0.4980 chunk 153 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.057470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.039809 restraints weight = 46253.920| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 3.36 r_work: 0.2470 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 15885 Z= 0.200 Angle : 0.535 7.561 21478 Z= 0.287 Chirality : 0.044 0.138 2359 Planarity : 0.004 0.049 2755 Dihedral : 5.253 57.514 2165 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.65 % Rotamer: Outliers : 1.47 % Allowed : 6.00 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.19), residues: 1908 helix: 1.26 (0.20), residues: 697 sheet: 0.50 (0.27), residues: 387 loop : -0.96 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 368 TYR 0.017 0.001 TYR D 250 PHE 0.027 0.002 PHE F 90 TRP 0.033 0.001 TRP C 131 HIS 0.007 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00481 (15885) covalent geometry : angle 0.53456 (21478) hydrogen bonds : bond 0.05466 ( 669) hydrogen bonds : angle 3.92740 ( 1863) *********************** 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 150 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: C 9 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8708 (mt-10) REVERT: D 207 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9282 (tm) REVERT: E 10 ASP cc_start: 0.8850 (t0) cc_final: 0.8390 (t0) REVERT: E 39 THR cc_start: 0.9451 (m) cc_final: 0.9092 (t) REVERT: E 43 ASP cc_start: 0.8837 (m-30) cc_final: 0.8590 (m-30) REVERT: E 150 ASP cc_start: 0.9152 (t0) cc_final: 0.8567 (t0) REVERT: E 153 ASN cc_start: 0.9379 (t0) cc_final: 0.9116 (t0) REVERT: G 51 MET cc_start: 0.8698 (mmm) cc_final: 0.8477 (mmm) REVERT: G 119 ASP cc_start: 0.8850 (p0) cc_final: 0.8499 (p0) REVERT: H 469 GLU cc_start: 0.8644 (pm20) cc_final: 0.8306 (pm20) REVERT: I 472 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8647 (tm-30) outliers start: 25 outliers final: 6 residues processed: 132 average time/residue: 0.7153 time to fit residues: 103.2806 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 : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR 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 99 ASP Chi-restraints excluded: chain G residue 120 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 122 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 150 optimal weight: 0.0070 chunk 44 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 = 0.3160 r_free = 0.3160 target = 0.058803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.041334 restraints weight = 46080.884| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.39 r_work: 0.2512 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15885 Z= 0.104 Angle : 0.469 7.660 21478 Z= 0.252 Chirality : 0.042 0.151 2359 Planarity : 0.003 0.046 2755 Dihedral : 4.938 58.519 2165 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.41 % Favored : 97.48 % Rotamer: Outliers : 0.82 % Allowed : 7.65 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.20), residues: 1908 helix: 1.64 (0.21), residues: 696 sheet: 0.60 (0.28), residues: 385 loop : -0.85 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 277 TYR 0.013 0.001 TYR D 250 PHE 0.016 0.001 PHE F 90 TRP 0.020 0.001 TRP C 131 HIS 0.003 0.000 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00233 (15885) covalent geometry : angle 0.46917 (21478) hydrogen bonds : bond 0.04287 ( 669) hydrogen bonds : angle 3.71278 ( 1863) *********************** 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 139 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: C 9 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8692 (mt-10) REVERT: C 225 ASP cc_start: 0.8704 (t0) cc_final: 0.8295 (t0) REVERT: D 130 GLN cc_start: 0.9020 (tp40) cc_final: 0.8687 (tp40) REVERT: D 207 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9294 (tm) REVERT: E 10 ASP cc_start: 0.8837 (t0) cc_final: 0.8337 (t0) REVERT: E 12 ASP cc_start: 0.9173 (p0) cc_final: 0.8956 (p0) REVERT: E 39 THR cc_start: 0.9443 (m) cc_final: 0.9101 (t) REVERT: E 150 ASP cc_start: 0.9107 (t0) cc_final: 0.8484 (t0) REVERT: E 153 ASN cc_start: 0.9406 (t0) cc_final: 0.9113 (t0) REVERT: G 51 MET cc_start: 0.8704 (mmm) cc_final: 0.8453 (mmt) REVERT: G 119 ASP cc_start: 0.8865 (p0) cc_final: 0.8542 (p0) REVERT: H 469 GLU cc_start: 0.8618 (pm20) cc_final: 0.8260 (pm20) REVERT: I 472 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8516 (tm-30) outliers start: 14 outliers final: 6 residues processed: 132 average time/residue: 0.7231 time to fit residues: 104.4523 Evaluate side-chains 126 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 266 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain G residue 120 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 47 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 365 GLN D 68 GLN E 124 GLN F 167 ASN G 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.057715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.040192 restraints weight = 46501.048| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 3.40 r_work: 0.2467 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1683 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= 0.169 Angle : 0.509 7.868 21478 Z= 0.272 Chirality : 0.043 0.154 2359 Planarity : 0.004 0.053 2755 Dihedral : 4.915 55.928 2165 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.41 % Favored : 96.49 % Rotamer: Outliers : 0.94 % Allowed : 8.82 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.20), residues: 1908 helix: 1.78 (0.21), residues: 702 sheet: 0.55 (0.27), residues: 391 loop : -0.85 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 143 TYR 0.016 0.001 TYR D 250 PHE 0.020 0.001 PHE F 90 TRP 0.021 0.001 TRP C 131 HIS 0.006 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00406 (15885) covalent geometry : angle 0.50895 (21478) hydrogen bonds : bond 0.04880 ( 669) hydrogen bonds : angle 3.74937 ( 1863) *********************** 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 141 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: C 9 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8669 (mt-10) REVERT: C 225 ASP cc_start: 0.8695 (t0) cc_final: 0.8275 (t0) REVERT: C 368 ARG cc_start: 0.8322 (mpp-170) cc_final: 0.8061 (mmp80) REVERT: D 130 GLN cc_start: 0.9013 (tp40) cc_final: 0.8778 (tp40) REVERT: D 207 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9306 (tm) REVERT: E 10 ASP cc_start: 0.8807 (t0) cc_final: 0.8321 (t0) REVERT: E 39 THR cc_start: 0.9443 (m) cc_final: 0.9106 (t) REVERT: E 150 ASP cc_start: 0.9082 (t0) cc_final: 0.8534 (t0) REVERT: E 153 ASN cc_start: 0.9449 (t0) cc_final: 0.9178 (t0) REVERT: G 51 MET cc_start: 0.8780 (mmm) cc_final: 0.8501 (mmt) REVERT: G 119 ASP cc_start: 0.8934 (p0) cc_final: 0.8569 (p0) REVERT: H 469 GLU cc_start: 0.8640 (pm20) cc_final: 0.8285 (pm20) REVERT: H 471 MET cc_start: 0.9039 (mmm) cc_final: 0.8107 (mmm) REVERT: I 472 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8637 (tm-30) outliers start: 16 outliers final: 7 residues processed: 133 average time/residue: 0.7394 time to fit residues: 107.7619 Evaluate side-chains 131 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 C residue 3 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain D residue 207 LEU 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 163 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 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 = 0.3155 r_free = 0.3155 target = 0.058621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.041135 restraints weight = 46220.068| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 3.39 r_work: 0.2508 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15885 Z= 0.112 Angle : 0.475 7.779 21478 Z= 0.254 Chirality : 0.042 0.169 2359 Planarity : 0.003 0.046 2755 Dihedral : 4.729 56.185 2165 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % Rotamer: Outliers : 0.94 % Allowed : 10.06 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.20), residues: 1908 helix: 1.91 (0.21), residues: 703 sheet: 0.65 (0.28), residues: 385 loop : -0.78 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 277 TYR 0.013 0.001 TYR D 250 PHE 0.016 0.001 PHE F 90 TRP 0.015 0.001 TRP C 131 HIS 0.003 0.000 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00259 (15885) covalent geometry : angle 0.47500 (21478) hydrogen bonds : bond 0.04156 ( 669) hydrogen bonds : angle 3.59616 ( 1863) *********************** 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 141 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: C 9 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8637 (mt-10) REVERT: C 225 ASP cc_start: 0.8667 (t0) cc_final: 0.8083 (t0) REVERT: C 368 ARG cc_start: 0.8262 (mpp-170) cc_final: 0.7953 (mmp80) REVERT: D 130 GLN cc_start: 0.9005 (tp40) cc_final: 0.8555 (tp40) REVERT: D 207 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9333 (tm) REVERT: E 10 ASP cc_start: 0.8803 (t0) cc_final: 0.8260 (t0) REVERT: E 12 ASP cc_start: 0.9191 (p0) cc_final: 0.8963 (p0) REVERT: E 39 THR cc_start: 0.9441 (m) cc_final: 0.9129 (t) REVERT: E 150 ASP cc_start: 0.9091 (t0) cc_final: 0.8486 (t0) REVERT: E 153 ASN cc_start: 0.9498 (t0) cc_final: 0.9212 (t0) REVERT: G 51 MET cc_start: 0.8786 (mmm) cc_final: 0.8534 (mmt) REVERT: G 64 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8785 (mm) REVERT: G 119 ASP cc_start: 0.8904 (p0) cc_final: 0.8601 (p0) REVERT: H 469 GLU cc_start: 0.8606 (pm20) cc_final: 0.8246 (pm20) REVERT: H 471 MET cc_start: 0.9014 (mmm) cc_final: 0.8286 (mmm) REVERT: I 472 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8650 (tm-30) outliers start: 16 outliers final: 5 residues processed: 132 average time/residue: 0.7018 time to fit residues: 101.8802 Evaluate side-chains 128 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 C residue 3 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain G residue 64 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 177 optimal weight: 0.0370 overall best weight: 1.0862 ------------------------------------------------------------------------------- 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 = 0.3158 r_free = 0.3158 target = 0.058661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.040989 restraints weight = 45871.513| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 3.38 r_work: 0.2505 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1832 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= 0.123 Angle : 0.493 10.223 21478 Z= 0.261 Chirality : 0.042 0.170 2359 Planarity : 0.003 0.056 2755 Dihedral : 4.674 55.323 2165 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.99 % Favored : 96.91 % Rotamer: Outliers : 1.00 % Allowed : 10.47 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.20), residues: 1908 helix: 1.96 (0.21), residues: 704 sheet: 0.67 (0.28), residues: 385 loop : -0.71 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 277 TYR 0.014 0.001 TYR D 250 PHE 0.017 0.001 PHE F 90 TRP 0.014 0.001 TRP C 131 HIS 0.004 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00291 (15885) covalent geometry : angle 0.49291 (21478) hydrogen bonds : bond 0.04241 ( 669) hydrogen bonds : angle 3.59656 ( 1863) *********************** 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 138 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: C 9 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8684 (mt-10) REVERT: C 225 ASP cc_start: 0.8632 (t0) cc_final: 0.8043 (t0) REVERT: C 368 ARG cc_start: 0.8313 (mpp-170) cc_final: 0.8024 (mmp80) REVERT: D 130 GLN cc_start: 0.9046 (tp40) cc_final: 0.8591 (tp40) REVERT: D 207 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9338 (tm) REVERT: E 10 ASP cc_start: 0.8772 (t0) cc_final: 0.8203 (t0) REVERT: E 12 ASP cc_start: 0.9198 (p0) cc_final: 0.8975 (p0) REVERT: E 39 THR cc_start: 0.9455 (m) cc_final: 0.9162 (t) REVERT: E 150 ASP cc_start: 0.9112 (t0) cc_final: 0.8516 (t0) REVERT: E 153 ASN cc_start: 0.9523 (t0) cc_final: 0.9262 (t0) REVERT: G 51 MET cc_start: 0.8798 (mmm) cc_final: 0.8538 (mmt) REVERT: G 64 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8831 (mm) REVERT: G 119 ASP cc_start: 0.8897 (p0) cc_final: 0.8579 (p0) REVERT: H 469 GLU cc_start: 0.8618 (pm20) cc_final: 0.8250 (pm20) REVERT: H 471 MET cc_start: 0.9012 (mmm) cc_final: 0.8438 (mmm) REVERT: I 472 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8707 (tm-30) outliers start: 17 outliers final: 5 residues processed: 129 average time/residue: 0.6917 time to fit residues: 98.0101 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 : 0.781 ------------------------------------------------------------------------------- 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 C residue 3 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain G residue 64 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 132 optimal weight: 0.0770 chunk 157 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 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 = 0.3159 r_free = 0.3159 target = 0.058739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.041104 restraints weight = 46096.657| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 3.39 r_work: 0.2512 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15885 Z= 0.116 Angle : 0.500 11.367 21478 Z= 0.264 Chirality : 0.042 0.177 2359 Planarity : 0.003 0.045 2755 Dihedral : 4.635 55.521 2165 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.78 % Favored : 97.12 % Rotamer: Outliers : 0.71 % Allowed : 10.94 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.20), residues: 1908 helix: 1.99 (0.21), residues: 703 sheet: 0.69 (0.28), residues: 385 loop : -0.69 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 277 TYR 0.014 0.001 TYR D 250 PHE 0.015 0.001 PHE F 90 TRP 0.013 0.001 TRP C 131 HIS 0.003 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00272 (15885) covalent geometry : angle 0.49998 (21478) hydrogen bonds : bond 0.04100 ( 669) hydrogen bonds : angle 3.56189 ( 1863) *********************** 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 134 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 327 MET cc_start: 0.9200 (mmp) cc_final: 0.8981 (mmp) REVERT: C 1 MET cc_start: 0.8720 (mmm) cc_final: 0.8488 (mtt) REVERT: C 9 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8697 (mt-10) REVERT: C 225 ASP cc_start: 0.8617 (t0) cc_final: 0.8040 (t0) REVERT: C 368 ARG cc_start: 0.8319 (mpp-170) cc_final: 0.8015 (mmp80) REVERT: D 130 GLN cc_start: 0.9047 (tp40) cc_final: 0.8592 (tp40) REVERT: D 207 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9336 (tm) REVERT: E 10 ASP cc_start: 0.8793 (t0) cc_final: 0.8211 (t0) REVERT: E 12 ASP cc_start: 0.9189 (p0) cc_final: 0.8969 (p0) REVERT: E 39 THR cc_start: 0.9470 (m) cc_final: 0.9184 (t) REVERT: E 150 ASP cc_start: 0.9097 (t0) cc_final: 0.8507 (t0) REVERT: E 153 ASN cc_start: 0.9537 (t0) cc_final: 0.9283 (t0) REVERT: G 51 MET cc_start: 0.8736 (mmm) cc_final: 0.8471 (mmt) REVERT: G 64 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8820 (mm) REVERT: G 119 ASP cc_start: 0.8901 (p0) cc_final: 0.8589 (p0) REVERT: H 469 GLU cc_start: 0.8618 (pm20) cc_final: 0.8244 (pm20) outliers start: 12 outliers final: 6 residues processed: 130 average time/residue: 0.6863 time to fit residues: 98.3013 Evaluate side-chains 128 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 C residue 3 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain G residue 64 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 139 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 159 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 90 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 = 0.3160 r_free = 0.3160 target = 0.058842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.041095 restraints weight = 46232.294| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.40 r_work: 0.2508 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15885 Z= 0.121 Angle : 0.518 12.308 21478 Z= 0.271 Chirality : 0.042 0.177 2359 Planarity : 0.003 0.060 2755 Dihedral : 4.619 55.623 2165 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.09 % Favored : 96.80 % Rotamer: Outliers : 0.71 % Allowed : 11.24 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.20), residues: 1908 helix: 2.02 (0.21), residues: 704 sheet: 0.69 (0.28), residues: 385 loop : -0.65 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 474 TYR 0.014 0.001 TYR D 250 PHE 0.013 0.001 PHE F 90 TRP 0.013 0.001 TRP C 131 HIS 0.003 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00288 (15885) covalent geometry : angle 0.51751 (21478) hydrogen bonds : bond 0.04128 ( 669) hydrogen bonds : angle 3.56713 ( 1863) *********************** 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 130 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 327 MET cc_start: 0.9234 (mmp) cc_final: 0.8996 (mmp) REVERT: C 1 MET cc_start: 0.8686 (mmm) cc_final: 0.8403 (mtt) REVERT: C 9 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8702 (mt-10) REVERT: C 225 ASP cc_start: 0.8624 (t0) cc_final: 0.8043 (t0) REVERT: C 368 ARG cc_start: 0.8325 (mpp-170) cc_final: 0.8023 (mmp80) REVERT: D 130 GLN cc_start: 0.9046 (tp40) cc_final: 0.8677 (tp40) REVERT: D 207 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9337 (tm) REVERT: E 10 ASP cc_start: 0.8831 (t0) cc_final: 0.8262 (t0) REVERT: E 12 ASP cc_start: 0.9166 (p0) cc_final: 0.8940 (p0) REVERT: E 39 THR cc_start: 0.9470 (m) cc_final: 0.9192 (t) REVERT: E 90 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8391 (pt0) REVERT: E 150 ASP cc_start: 0.9098 (t0) cc_final: 0.8436 (t0) REVERT: E 153 ASN cc_start: 0.9556 (t0) cc_final: 0.9295 (t0) REVERT: G 51 MET cc_start: 0.8753 (mmm) cc_final: 0.8489 (mmt) REVERT: G 64 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.8842 (mm) REVERT: G 119 ASP cc_start: 0.8890 (p0) cc_final: 0.8577 (p0) REVERT: H 469 GLU cc_start: 0.8694 (pm20) cc_final: 0.8357 (pm20) REVERT: H 471 MET cc_start: 0.8985 (mmm) cc_final: 0.8205 (mmm) outliers start: 12 outliers final: 6 residues processed: 126 average time/residue: 0.6828 time to fit residues: 94.7791 Evaluate side-chains 127 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 C residue 3 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 90 GLN 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 3 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 66 optimal weight: 0.0060 chunk 183 optimal weight: 5.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 90 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 = 0.3145 r_free = 0.3145 target = 0.058180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.040540 restraints weight = 46094.365| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 3.38 r_work: 0.2491 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15885 Z= 0.154 Angle : 0.534 12.531 21478 Z= 0.280 Chirality : 0.043 0.176 2359 Planarity : 0.003 0.044 2755 Dihedral : 4.662 55.091 2165 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.88 % Favored : 97.01 % Rotamer: Outliers : 0.82 % Allowed : 11.29 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.20), residues: 1908 helix: 2.00 (0.21), residues: 703 sheet: 0.67 (0.27), residues: 385 loop : -0.66 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 277 TYR 0.016 0.001 TYR D 250 PHE 0.014 0.001 PHE F 90 TRP 0.014 0.001 TRP C 131 HIS 0.004 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00370 (15885) covalent geometry : angle 0.53405 (21478) hydrogen bonds : bond 0.04481 ( 669) hydrogen bonds : angle 3.63255 ( 1863) ********************** 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 132 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 327 MET cc_start: 0.9302 (mmp) cc_final: 0.8981 (mmp) REVERT: C 1 MET cc_start: 0.8663 (mmm) cc_final: 0.8380 (mtt) REVERT: C 9 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8687 (mt-10) REVERT: C 225 ASP cc_start: 0.8635 (t0) cc_final: 0.8040 (t0) REVERT: C 368 ARG cc_start: 0.8325 (mpp-170) cc_final: 0.7962 (mmp80) REVERT: D 130 GLN cc_start: 0.9043 (tp40) cc_final: 0.8672 (tp40) REVERT: D 207 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9340 (tm) REVERT: E 10 ASP cc_start: 0.8828 (t0) cc_final: 0.8248 (t0) REVERT: E 12 ASP cc_start: 0.9147 (p0) cc_final: 0.8908 (p0) REVERT: E 39 THR cc_start: 0.9478 (m) cc_final: 0.9209 (t) REVERT: E 90 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8581 (pt0) REVERT: E 150 ASP cc_start: 0.9083 (t0) cc_final: 0.8512 (t0) REVERT: E 153 ASN cc_start: 0.9573 (t0) cc_final: 0.9329 (t0) REVERT: G 51 MET cc_start: 0.8753 (mmm) cc_final: 0.8507 (mmt) REVERT: G 64 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8848 (mm) REVERT: G 119 ASP cc_start: 0.8890 (p0) cc_final: 0.8583 (p0) REVERT: H 469 GLU cc_start: 0.8702 (pm20) cc_final: 0.8344 (pm20) REVERT: H 471 MET cc_start: 0.9015 (mmm) cc_final: 0.8162 (mmm) outliers start: 14 outliers final: 7 residues processed: 125 average time/residue: 0.6568 time to fit residues: 90.4931 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 : 0.560 ------------------------------------------------------------------------------- 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 C residue 3 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 150 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 91 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 188 optimal weight: 30.0000 chunk 82 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3133 r_free = 0.3133 target = 0.057726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.040027 restraints weight = 46044.168| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 3.38 r_work: 0.2473 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15885 Z= 0.172 Angle : 0.549 12.571 21478 Z= 0.287 Chirality : 0.044 0.174 2359 Planarity : 0.003 0.044 2755 Dihedral : 4.733 54.819 2165 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.46 % Favored : 96.44 % Rotamer: Outliers : 0.82 % Allowed : 11.18 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.20), residues: 1908 helix: 1.96 (0.21), residues: 704 sheet: 0.57 (0.27), residues: 393 loop : -0.65 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 105 TYR 0.017 0.001 TYR D 250 PHE 0.014 0.001 PHE C 254 TRP 0.014 0.001 TRP C 131 HIS 0.005 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00416 (15885) covalent geometry : angle 0.54934 (21478) hydrogen bonds : bond 0.04775 ( 669) hydrogen bonds : angle 3.70772 ( 1863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4151.89 seconds wall clock time: 71 minutes 51.49 seconds (4311.49 seconds total)