Starting phenix.real_space_refine on Sat May 17 07:02:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cfx_45566/05_2025/9cfx_45566.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cfx_45566/05_2025/9cfx_45566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cfx_45566/05_2025/9cfx_45566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cfx_45566/05_2025/9cfx_45566.map" model { file = "/net/cci-nas-00/data/ceres_data/9cfx_45566/05_2025/9cfx_45566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cfx_45566/05_2025/9cfx_45566.cif" } resolution = 2.7 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 ------------------------------------------------------------------------------- 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= 0.031 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 3 5.21 5 S 93 5.16 5 C 9935 2.51 5 N 2696 2.21 5 O 3016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15749 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2826 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Chain: "C" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 19, 'TRANS': 352} Chain: "D" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2896 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "P" Number of atoms: 5874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5874 Classifications: {'peptide': 720} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 693} Chain: "R" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.93, per 1000 atoms: 0.57 Number of scatterers: 15749 At special positions: 0 Unit cell: (114.552, 195.804, 129.204, 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 93 16.00 P 6 15.00 Mg 3 11.99 O 3016 8.00 N 2696 7.00 C 9935 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: 3.48 Conformation dependent library (CDL) restraints added in 2.0 seconds 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3684 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 26 sheets defined 54.5% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.179A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.544A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.528A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.711A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.517A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.797A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Proline residue: B 258 - end of helix removed outlier: 4.552A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.690A pdb=" N ARG B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.501A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.185A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.558A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.632A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.565A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.508A pdb=" N SER C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.635A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.559A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.767A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.596A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.173A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.677A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.515A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.530A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.697A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.725A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.618A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 346 Processing helix chain 'D' and resid 347 through 348 No H-bonds generated for 'chain 'D' and resid 347 through 348' Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.521A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.193A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 8 removed outlier: 4.050A pdb=" N ALA P 4 " --> pdb=" O MET P 1 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR P 6 " --> pdb=" O SER P 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 19 Processing helix chain 'P' and resid 24 through 38 removed outlier: 3.505A pdb=" N GLU P 38 " --> pdb=" O ARG P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 61 removed outlier: 4.489A pdb=" N TYR P 61 " --> pdb=" O LEU P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 58 through 61' Processing helix chain 'P' and resid 62 through 67 Processing helix chain 'P' and resid 80 through 96 Processing helix chain 'P' and resid 110 through 125 removed outlier: 3.724A pdb=" N ALA P 123 " --> pdb=" O LEU P 119 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR P 125 " --> pdb=" O PHE P 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 142 removed outlier: 3.744A pdb=" N SER P 142 " --> pdb=" O ARG P 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 150 removed outlier: 3.615A pdb=" N PHE P 149 " --> pdb=" O VAL P 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 193 Processing helix chain 'P' and resid 203 through 211 Processing helix chain 'P' and resid 213 through 219 removed outlier: 3.947A pdb=" N ARG P 219 " --> pdb=" O GLU P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 228 Processing helix chain 'P' and resid 229 through 234 removed outlier: 3.614A pdb=" N VAL P 233 " --> pdb=" O TYR P 229 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS P 234 " --> pdb=" O LEU P 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 229 through 234' Processing helix chain 'P' and resid 244 through 259 removed outlier: 3.551A pdb=" N LYS P 254 " --> pdb=" O LYS P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 262 through 281 removed outlier: 3.543A pdb=" N GLY P 280 " --> pdb=" O VAL P 276 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN P 281 " --> pdb=" O LEU P 277 " (cutoff:3.500A) Processing helix chain 'P' and resid 296 through 307 removed outlier: 4.560A pdb=" N LEU P 300 " --> pdb=" O THR P 296 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR P 302 " --> pdb=" O ASN P 298 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG P 305 " --> pdb=" O LYS P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 318 Processing helix chain 'P' and resid 335 through 367 removed outlier: 3.534A pdb=" N SER P 365 " --> pdb=" O LYS P 361 " (cutoff:3.500A) Processing helix chain 'P' and resid 397 through 430 removed outlier: 3.739A pdb=" N GLU P 425 " --> pdb=" O SER P 421 " (cutoff:3.500A) Processing helix chain 'P' and resid 440 through 450 removed outlier: 4.432A pdb=" N ILE P 444 " --> pdb=" O ASN P 440 " (cutoff:3.500A) Processing helix chain 'P' and resid 454 through 463 Processing helix chain 'P' and resid 470 through 482 Processing helix chain 'P' and resid 497 through 501 removed outlier: 3.762A pdb=" N LYS P 500 " --> pdb=" O LYS P 497 " (cutoff:3.500A) Processing helix chain 'P' and resid 522 through 528 Processing helix chain 'P' and resid 532 through 540 Processing helix chain 'P' and resid 544 through 551 removed outlier: 3.528A pdb=" N GLN P 549 " --> pdb=" O PRO P 545 " (cutoff:3.500A) Processing helix chain 'P' and resid 552 through 558 Processing helix chain 'P' and resid 564 through 583 Processing helix chain 'P' and resid 603 through 614 removed outlier: 4.191A pdb=" N HIS P 609 " --> pdb=" O VAL P 605 " (cutoff:3.500A) Processing helix chain 'P' and resid 615 through 625 Processing helix chain 'P' and resid 633 through 641 Processing helix chain 'P' and resid 644 through 648 Processing helix chain 'P' and resid 654 through 666 removed outlier: 4.102A pdb=" N ARG P 664 " --> pdb=" O ALA P 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 684 through 719 removed outlier: 4.088A pdb=" N LEU P 688 " --> pdb=" O PHE P 684 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN P 700 " --> pdb=" O GLU P 696 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER P 701 " --> pdb=" O VAL P 697 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TRP P 715 " --> pdb=" O ARG P 711 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG P 716 " --> pdb=" O GLY P 712 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 22 removed outlier: 3.868A pdb=" N LEU R 19 " --> pdb=" O GLU R 15 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE R 20 " --> pdb=" O ALA R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 40 removed outlier: 4.102A pdb=" N THR R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 54 Processing helix chain 'R' and resid 55 through 60 removed outlier: 5.202A pdb=" N ALA R 58 " --> pdb=" O GLU R 55 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP R 59 " --> pdb=" O VAL R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 77 Processing helix chain 'R' and resid 82 through 94 removed outlier: 3.768A pdb=" N PHE R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 113 Processing helix chain 'R' and resid 118 through 130 removed outlier: 4.037A pdb=" N GLU R 128 " --> pdb=" O GLU R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 147 removed outlier: 3.669A pdb=" N GLN R 144 " --> pdb=" O GLU R 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.602A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.418A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.646A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.387A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'D' and resid 29 through 32 Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'D' and resid 169 through 170 removed outlier: 4.058A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'P' and resid 42 through 45 removed outlier: 6.584A pdb=" N LEU P 49 " --> pdb=" O ARG P 589 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE P 591 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER P 51 " --> pdb=" O ILE P 591 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA P 100 " --> pdb=" O ALA P 586 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE P 588 " --> pdb=" O ALA P 100 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N MET P 102 " --> pdb=" O ILE P 588 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N CYS P 590 " --> pdb=" O MET P 102 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER P 104 " --> pdb=" O CYS P 590 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS P 165 " --> pdb=" O ASP P 386 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY P 179 " --> pdb=" O GLN P 170 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASP P 172 " --> pdb=" O PRO P 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 151 through 152 Processing sheet with id=AC3, first strand: chain 'P' and resid 284 through 286 Processing sheet with id=AC4, first strand: chain 'P' and resid 320 through 325 Processing sheet with id=AC5, first strand: chain 'P' and resid 488 through 490 Processing sheet with id=AC6, first strand: chain 'P' and resid 629 through 632 Processing sheet with id=AC7, first strand: chain 'R' and resid 27 through 29 Processing sheet with id=AC8, first strand: chain 'R' and resid 100 through 102 787 hydrogen bonds defined for protein. 2088 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.47 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5017 1.34 - 1.47: 3391 1.47 - 1.60: 7503 1.60 - 1.73: 0 1.73 - 1.86: 161 Bond restraints: 16072 Sorted by residual: bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.346 0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" C5 ADP B 401 " pdb=" C6 ADP B 401 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C5 ADP C 401 " pdb=" C6 ADP C 401 " ideal model delta sigma weight residual 1.490 1.388 0.102 2.00e-02 2.50e+03 2.61e+01 ... (remaining 16067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 21229 4.37 - 8.75: 498 8.75 - 13.12: 13 13.12 - 17.50: 4 17.50 - 21.87: 2 Bond angle restraints: 21746 Sorted by residual: angle pdb=" CA ASP C 288 " pdb=" CB ASP C 288 " pdb=" CG ASP C 288 " ideal model delta sigma weight residual 112.60 120.78 -8.18 1.00e+00 1.00e+00 6.69e+01 angle pdb=" O2B ADP D 401 " pdb=" PB ADP D 401 " pdb=" O3B ADP D 401 " ideal model delta sigma weight residual 119.90 98.03 21.87 3.00e+00 1.11e-01 5.31e+01 angle pdb=" CA ASP C 25 " pdb=" CB ASP C 25 " pdb=" CG ASP C 25 " ideal model delta sigma weight residual 112.60 119.49 -6.89 1.00e+00 1.00e+00 4.74e+01 angle pdb=" O2B ADP B 401 " pdb=" PB ADP B 401 " pdb=" O3B ADP B 401 " ideal model delta sigma weight residual 119.90 100.12 19.78 3.00e+00 1.11e-01 4.35e+01 angle pdb=" C LEU P 19 " pdb=" CA LEU P 19 " pdb=" CB LEU P 19 " ideal model delta sigma weight residual 110.26 119.42 -9.16 1.50e+00 4.44e-01 3.73e+01 ... (remaining 21741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.17: 9256 25.17 - 50.35: 393 50.35 - 75.52: 60 75.52 - 100.69: 13 100.69 - 125.86: 4 Dihedral angle restraints: 9726 sinusoidal: 3997 harmonic: 5729 Sorted by residual: dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 65.87 -125.86 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.31 118.30 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 57.69 -117.69 1 2.00e+01 2.50e-03 3.52e+01 ... (remaining 9723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1754 0.103 - 0.207: 545 0.207 - 0.310: 81 0.310 - 0.414: 10 0.414 - 0.517: 4 Chirality restraints: 2394 Sorted by residual: chirality pdb=" CA SER B 14 " pdb=" N SER B 14 " pdb=" C SER B 14 " pdb=" CB SER B 14 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CA MET C 283 " pdb=" N MET C 283 " pdb=" C MET C 283 " pdb=" CB MET C 283 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.33e+00 chirality pdb=" CA LYS P 483 " pdb=" N LYS P 483 " pdb=" C LYS P 483 " pdb=" CB LYS P 483 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.79e+00 ... (remaining 2391 not shown) Planarity restraints: 2808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 340 " 0.224 2.00e-02 2.50e+03 1.12e-01 3.13e+02 pdb=" CG TRP D 340 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 340 " -0.079 2.00e-02 2.50e+03 pdb=" CD2 TRP D 340 " -0.082 2.00e-02 2.50e+03 pdb=" NE1 TRP D 340 " -0.060 2.00e-02 2.50e+03 pdb=" CE2 TRP D 340 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 340 " -0.137 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 340 " 0.137 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 340 " -0.075 2.00e-02 2.50e+03 pdb=" CH2 TRP D 340 " 0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 340 " 0.202 2.00e-02 2.50e+03 1.05e-01 2.77e+02 pdb=" CG TRP B 340 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 340 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 TRP B 340 " -0.087 2.00e-02 2.50e+03 pdb=" NE1 TRP B 340 " -0.072 2.00e-02 2.50e+03 pdb=" CE2 TRP B 340 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 340 " -0.139 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 340 " 0.134 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 340 " -0.055 2.00e-02 2.50e+03 pdb=" CH2 TRP B 340 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 337 " -0.203 2.00e-02 2.50e+03 1.08e-01 2.33e+02 pdb=" CG TYR C 337 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR C 337 " 0.109 2.00e-02 2.50e+03 pdb=" CD2 TYR C 337 " 0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR C 337 " 0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR C 337 " 0.062 2.00e-02 2.50e+03 pdb=" CZ TYR C 337 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR C 337 " -0.151 2.00e-02 2.50e+03 ... (remaining 2805 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 11 2.47 - 3.07: 9708 3.07 - 3.68: 23605 3.68 - 4.29: 36707 4.29 - 4.90: 61262 Nonbonded interactions: 131293 Sorted by model distance: nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 1.857 2.170 nonbonded pdb=" O3B ADP D 401 " pdb="MG MG D 402 " model vdw 1.868 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 1.875 2.170 nonbonded pdb=" O GLY D 13 " pdb="MG MG D 402 " model vdw 1.901 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 1.908 2.170 ... (remaining 131288 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 'B' selection = (chain 'C' and (resid 4 through 39 or resid 50 through 374 or resid 401 through \ 402)) selection = (chain 'D' and (resid 4 through 39 or resid 50 through 374 or resid 401 through \ 402)) } 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: 5.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.720 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 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:14.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 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 : 0.013 0.144 16072 Z= 0.767 Angle : 1.904 21.871 21746 Z= 1.258 Chirality : 0.098 0.517 2394 Planarity : 0.019 0.283 2808 Dihedral : 14.646 125.862 6042 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.44 % Favored : 95.26 % Rotamer: Outliers : 2.30 % Allowed : 4.19 % Favored : 93.51 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -2.20 (0.17), residues: 1960 helix: -2.35 (0.13), residues: 932 sheet: -0.77 (0.32), residues: 243 loop : -0.16 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.224 0.031 TRP D 340 HIS 0.013 0.004 HIS P 609 PHE 0.071 0.013 PHE D 21 TYR 0.203 0.025 TYR C 337 ARG 0.016 0.002 ARG C 116 Details of bonding type rmsd hydrogen bonds : bond 0.18375 ( 781) hydrogen bonds : angle 7.95682 ( 2088) covalent geometry : bond 0.01252 (16072) covalent geometry : angle 1.90376 (21746) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 373 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.6685 (m-30) cc_final: 0.5616 (p0) REVERT: B 59 GLN cc_start: 0.7340 (tt0) cc_final: 0.6497 (mm110) REVERT: B 91 TYR cc_start: 0.6527 (m-80) cc_final: 0.5997 (t80) REVERT: B 118 LYS cc_start: 0.7177 (tttt) cc_final: 0.6973 (mmmm) REVERT: B 119 MET cc_start: 0.7796 (mtt) cc_final: 0.7477 (mtp) REVERT: B 123 MET cc_start: 0.8362 (mmp) cc_final: 0.7987 (mpm) REVERT: B 128 ASN cc_start: 0.8119 (m-40) cc_final: 0.7556 (t0) REVERT: B 132 MET cc_start: 0.8299 (ppp) cc_final: 0.7710 (ppp) REVERT: B 137 GLN cc_start: 0.7724 (mt0) cc_final: 0.7291 (mt0) REVERT: B 208 ILE cc_start: 0.6217 (mt) cc_final: 0.5908 (mp) REVERT: B 221 LEU cc_start: 0.7994 (tp) cc_final: 0.7741 (mt) REVERT: B 227 MET cc_start: 0.7111 (mmm) cc_final: 0.6791 (mmt) REVERT: B 238 LYS cc_start: 0.6807 (mmtt) cc_final: 0.6044 (tttt) REVERT: B 246 GLN cc_start: 0.5744 (mt0) cc_final: 0.5533 (mt0) REVERT: B 250 ILE cc_start: 0.6619 (mt) cc_final: 0.6335 (mp) REVERT: B 291 LYS cc_start: 0.8703 (tttt) cc_final: 0.8394 (ttmm) REVERT: C 51 ASP cc_start: 0.7507 (p0) cc_final: 0.7269 (p0) REVERT: C 56 ASP cc_start: 0.7798 (m-30) cc_final: 0.7540 (m-30) REVERT: C 95 ARG cc_start: 0.7353 (mtp85) cc_final: 0.6795 (mmp-170) REVERT: C 210 ARG cc_start: 0.6720 (ttp-170) cc_final: 0.6337 (ttp-110) REVERT: C 214 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6641 (mt-10) REVERT: C 221 LEU cc_start: 0.8214 (tp) cc_final: 0.7825 (tm) REVERT: C 225 ASN cc_start: 0.6382 (t0) cc_final: 0.6003 (t0) REVERT: C 241 GLU cc_start: 0.7365 (tt0) cc_final: 0.6951 (tt0) REVERT: C 290 ARG cc_start: 0.4949 (OUTLIER) cc_final: 0.3383 (ttp-170) REVERT: C 292 ASP cc_start: 0.7471 (m-30) cc_final: 0.6987 (m-30) REVERT: C 316 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7022 (mm-30) REVERT: C 325 MET cc_start: 0.6926 (mmp) cc_final: 0.6714 (mmm) REVERT: C 328 LYS cc_start: 0.7311 (ttmt) cc_final: 0.7022 (ttpt) REVERT: C 363 ASP cc_start: 0.8572 (m-30) cc_final: 0.8321 (m-30) REVERT: D 25 ASP cc_start: 0.7378 (m-30) cc_final: 0.6356 (p0) REVERT: D 57 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6539 (mt-10) REVERT: D 75 ILE cc_start: 0.6943 (mt) cc_final: 0.6685 (mp) REVERT: D 80 ASP cc_start: 0.7297 (m-30) cc_final: 0.6441 (m-30) REVERT: D 81 ASP cc_start: 0.7907 (m-30) cc_final: 0.7465 (m-30) REVERT: D 107 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7896 (pt0) REVERT: D 119 MET cc_start: 0.7543 (mtm) cc_final: 0.7238 (mtm) REVERT: D 121 GLN cc_start: 0.7511 (tt0) cc_final: 0.7206 (tt0) REVERT: D 132 MET cc_start: 0.7880 (ppp) cc_final: 0.7472 (ppp) REVERT: D 176 MET cc_start: 0.6700 (mtt) cc_final: 0.6475 (mtp) REVERT: D 187 ASP cc_start: 0.7921 (m-30) cc_final: 0.7659 (m-30) REVERT: D 225 ASN cc_start: 0.7168 (t0) cc_final: 0.6878 (t0) REVERT: D 238 LYS cc_start: 0.7928 (mmtt) cc_final: 0.7252 (mtpt) REVERT: D 270 GLU cc_start: 0.6883 (tt0) cc_final: 0.6126 (mp0) REVERT: D 286 ASP cc_start: 0.6251 (OUTLIER) cc_final: 0.5530 (t0) REVERT: D 287 ILE cc_start: 0.6830 (tt) cc_final: 0.6515 (tp) REVERT: D 305 MET cc_start: 0.7987 (mmm) cc_final: 0.7287 (mmt) REVERT: D 326 LYS cc_start: 0.7499 (tppp) cc_final: 0.7070 (tptt) REVERT: D 328 LYS cc_start: 0.7412 (mttt) cc_final: 0.6773 (mtpp) REVERT: D 354 GLN cc_start: 0.7678 (pt0) cc_final: 0.6855 (pp30) REVERT: P 11 VAL cc_start: 0.7399 (OUTLIER) cc_final: 0.6801 (m) REVERT: P 19 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6357 (pt) REVERT: P 37 ARG cc_start: 0.7253 (ttm110) cc_final: 0.7015 (ttp80) REVERT: P 52 VAL cc_start: 0.8175 (p) cc_final: 0.7913 (t) REVERT: P 66 MET cc_start: 0.7897 (mtt) cc_final: 0.6889 (mtt) REVERT: P 97 ARG cc_start: 0.6434 (ttt180) cc_final: 0.6022 (ttt90) REVERT: P 116 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7464 (tptt) REVERT: P 156 ARG cc_start: 0.7793 (tpp80) cc_final: 0.6618 (tmt170) REVERT: P 183 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7713 (tt) REVERT: P 237 CYS cc_start: 0.6619 (t) cc_final: 0.6130 (t) REVERT: P 258 VAL cc_start: 0.7504 (t) cc_final: 0.7234 (m) REVERT: P 259 ILE cc_start: 0.7068 (mm) cc_final: 0.6730 (mm) REVERT: P 272 ILE cc_start: 0.7985 (mm) cc_final: 0.7784 (mm) REVERT: P 316 GLU cc_start: 0.7671 (tt0) cc_final: 0.7381 (tp30) REVERT: P 394 GLN cc_start: 0.8081 (mp10) cc_final: 0.7878 (mp10) REVERT: P 442 LYS cc_start: 0.8200 (tptp) cc_final: 0.7116 (ptpp) REVERT: P 446 ASP cc_start: 0.7509 (m-30) cc_final: 0.7170 (m-30) REVERT: P 460 ASP cc_start: 0.7042 (t70) cc_final: 0.6706 (t70) REVERT: P 525 ASP cc_start: 0.7746 (m-30) cc_final: 0.7399 (t70) REVERT: P 537 GLU cc_start: 0.7546 (tt0) cc_final: 0.7312 (pt0) REVERT: P 553 LYS cc_start: 0.7833 (mmtm) cc_final: 0.7060 (mppt) REVERT: P 563 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7181 (mt-10) REVERT: P 597 LYS cc_start: 0.7621 (mttt) cc_final: 0.7144 (tttp) REVERT: P 598 GLN cc_start: 0.7546 (tt0) cc_final: 0.7192 (tm-30) outliers start: 39 outliers final: 12 residues processed: 399 average time/residue: 1.3997 time to fit residues: 609.7229 Evaluate side-chains 263 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 245 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 323 ILE Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain R residue 45 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 153 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 114 optimal weight: 0.3980 chunk 177 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 314 GLN P 157 ASN P 227 GLN P 487 HIS P 511 HIS ** P 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 108 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.151747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.122873 restraints weight = 22716.378| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.08 r_work: 0.3560 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16072 Z= 0.185 Angle : 0.725 10.216 21746 Z= 0.375 Chirality : 0.047 0.240 2394 Planarity : 0.005 0.050 2808 Dihedral : 8.918 116.556 2230 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.30 % Rotamer: Outliers : 3.72 % Allowed : 11.69 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.59 (0.19), residues: 1960 helix: -0.69 (0.16), residues: 946 sheet: -0.38 (0.31), residues: 250 loop : 0.34 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 340 HIS 0.010 0.002 HIS P 487 PHE 0.037 0.002 PHE P 713 TYR 0.032 0.002 TYR P 629 ARG 0.006 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 781) hydrogen bonds : angle 5.32442 ( 2088) covalent geometry : bond 0.00428 (16072) covalent geometry : angle 0.72479 (21746) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 258 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.6787 (m-30) cc_final: 0.6485 (p0) REVERT: B 59 GLN cc_start: 0.8009 (tt0) cc_final: 0.7677 (mm110) REVERT: B 91 TYR cc_start: 0.7018 (m-80) cc_final: 0.6480 (t80) REVERT: B 95 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8098 (mtp85) REVERT: B 119 MET cc_start: 0.8337 (mtt) cc_final: 0.8085 (mtp) REVERT: B 137 GLN cc_start: 0.8029 (mt0) cc_final: 0.7710 (mt0) REVERT: B 190 MET cc_start: 0.8135 (mtm) cc_final: 0.7803 (mtp) REVERT: B 206 ARG cc_start: 0.7556 (ttp-110) cc_final: 0.7114 (mtm-85) REVERT: B 221 LEU cc_start: 0.8179 (tp) cc_final: 0.7950 (mt) REVERT: B 238 LYS cc_start: 0.7786 (mmtt) cc_final: 0.7428 (mttt) REVERT: B 323 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.8047 (t) REVERT: B 360 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7390 (pm20) REVERT: B 363 ASP cc_start: 0.7559 (m-30) cc_final: 0.7325 (m-30) REVERT: C 95 ARG cc_start: 0.7633 (mtp85) cc_final: 0.7023 (mmp-170) REVERT: C 122 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.6615 (mp) REVERT: C 132 MET cc_start: 0.7284 (ttp) cc_final: 0.6666 (ppp) REVERT: C 192 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7693 (mm) REVERT: C 206 ARG cc_start: 0.7745 (ttm110) cc_final: 0.7504 (mmm-85) REVERT: C 214 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7363 (mt-10) REVERT: C 241 GLU cc_start: 0.7637 (tt0) cc_final: 0.7216 (tt0) REVERT: C 290 ARG cc_start: 0.5346 (OUTLIER) cc_final: 0.4739 (mtt180) REVERT: C 292 ASP cc_start: 0.8132 (m-30) cc_final: 0.7804 (m-30) REVERT: C 328 LYS cc_start: 0.7571 (ttmt) cc_final: 0.7079 (pttp) REVERT: D 25 ASP cc_start: 0.7684 (m-30) cc_final: 0.6830 (p0) REVERT: D 28 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7790 (mtm-85) REVERT: D 57 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6887 (mt-10) REVERT: D 80 ASP cc_start: 0.7158 (m-30) cc_final: 0.6832 (m-30) REVERT: D 81 ASP cc_start: 0.8235 (m-30) cc_final: 0.7957 (m-30) REVERT: D 132 MET cc_start: 0.8048 (ppp) cc_final: 0.7704 (ppp) REVERT: D 225 ASN cc_start: 0.7461 (t0) cc_final: 0.6952 (t0) REVERT: D 238 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7471 (ttpt) REVERT: D 305 MET cc_start: 0.8506 (mmm) cc_final: 0.7964 (mmt) REVERT: D 326 LYS cc_start: 0.7853 (tppp) cc_final: 0.7562 (tptt) REVERT: D 328 LYS cc_start: 0.7952 (mttt) cc_final: 0.7564 (mtpp) REVERT: D 340 TRP cc_start: 0.7301 (t-100) cc_final: 0.6749 (t-100) REVERT: D 356 TRP cc_start: 0.8309 (OUTLIER) cc_final: 0.6649 (m-90) REVERT: D 372 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.7876 (mtp180) REVERT: P 37 ARG cc_start: 0.7447 (ttm110) cc_final: 0.7174 (ttp80) REVERT: P 64 GLN cc_start: 0.7265 (tp40) cc_final: 0.6880 (mp10) REVERT: P 66 MET cc_start: 0.7658 (mtt) cc_final: 0.7162 (mtt) REVERT: P 156 ARG cc_start: 0.7696 (tpp80) cc_final: 0.6445 (tmt170) REVERT: P 183 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7483 (tt) REVERT: P 210 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: P 233 VAL cc_start: 0.8105 (p) cc_final: 0.7761 (m) REVERT: P 316 GLU cc_start: 0.7779 (tt0) cc_final: 0.7475 (tp30) REVERT: P 442 LYS cc_start: 0.8156 (tptp) cc_final: 0.7024 (ptpp) REVERT: P 446 ASP cc_start: 0.7293 (m-30) cc_final: 0.6870 (m-30) REVERT: P 460 ASP cc_start: 0.6800 (t70) cc_final: 0.6533 (t70) REVERT: P 525 ASP cc_start: 0.7752 (m-30) cc_final: 0.7358 (t70) REVERT: P 553 LYS cc_start: 0.7453 (mmtm) cc_final: 0.6969 (mppt) REVERT: P 563 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6836 (mt-10) REVERT: P 597 LYS cc_start: 0.7790 (mttt) cc_final: 0.7317 (ttmp) REVERT: P 598 GLN cc_start: 0.7506 (tt0) cc_final: 0.7299 (tt0) REVERT: P 601 ARG cc_start: 0.7533 (ttp80) cc_final: 0.6633 (ttt90) REVERT: P 638 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7658 (tp40) REVERT: R 52 MET cc_start: 0.8856 (ttt) cc_final: 0.8289 (ttt) REVERT: R 145 MET cc_start: 0.8115 (tmt) cc_final: 0.7748 (tmt) outliers start: 63 outliers final: 26 residues processed: 294 average time/residue: 1.3578 time to fit residues: 437.7432 Evaluate side-chains 245 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 293 GLN Chi-restraints excluded: chain P residue 323 ILE Chi-restraints excluded: chain P residue 379 THR Chi-restraints excluded: chain P residue 473 THR Chi-restraints excluded: chain P residue 605 VAL Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain P residue 710 TRP Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 101 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 86 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 145 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 75 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN P 227 GLN P 395 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.151086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122137 restraints weight = 22598.393| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.05 r_work: 0.3516 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16072 Z= 0.167 Angle : 0.662 13.057 21746 Z= 0.335 Chirality : 0.044 0.197 2394 Planarity : 0.004 0.041 2808 Dihedral : 8.271 113.350 2220 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.91 % Favored : 96.99 % Rotamer: Outliers : 4.13 % Allowed : 13.64 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -0.15 (0.19), residues: 1960 helix: -0.24 (0.16), residues: 957 sheet: -0.43 (0.31), residues: 252 loop : 0.55 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 340 HIS 0.004 0.001 HIS P 320 PHE 0.037 0.002 PHE R 69 TYR 0.026 0.002 TYR P 629 ARG 0.008 0.001 ARG P 97 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 781) hydrogen bonds : angle 4.99039 ( 2088) covalent geometry : bond 0.00391 (16072) covalent geometry : angle 0.66234 (21746) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 221 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.6860 (m-30) cc_final: 0.6417 (p0) REVERT: B 59 GLN cc_start: 0.7854 (tt0) cc_final: 0.7534 (mm110) REVERT: B 91 TYR cc_start: 0.6958 (m-80) cc_final: 0.6360 (t80) REVERT: B 95 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8005 (mtp85) REVERT: B 118 LYS cc_start: 0.8342 (mmmt) cc_final: 0.8127 (mmmt) REVERT: B 119 MET cc_start: 0.8295 (mtt) cc_final: 0.8007 (mtp) REVERT: B 128 ASN cc_start: 0.8082 (m-40) cc_final: 0.7535 (t0) REVERT: B 137 GLN cc_start: 0.7986 (mt0) cc_final: 0.7654 (mt0) REVERT: B 190 MET cc_start: 0.8074 (mtm) cc_final: 0.7804 (mtp) REVERT: B 221 LEU cc_start: 0.8113 (tp) cc_final: 0.7897 (mt) REVERT: B 237 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7376 (tt0) REVERT: B 238 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7302 (mttt) REVERT: B 323 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8011 (t) REVERT: B 360 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7848 (tm-30) REVERT: C 95 ARG cc_start: 0.7432 (mtp85) cc_final: 0.6903 (mmp-170) REVERT: C 99 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.5731 (tp30) REVERT: C 122 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6544 (mp) REVERT: C 132 MET cc_start: 0.7340 (ttp) cc_final: 0.6632 (ppp) REVERT: C 192 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7557 (mm) REVERT: C 214 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7327 (mt-10) REVERT: C 241 GLU cc_start: 0.7571 (tt0) cc_final: 0.7120 (tt0) REVERT: C 290 ARG cc_start: 0.5008 (OUTLIER) cc_final: 0.4627 (ttm170) REVERT: C 292 ASP cc_start: 0.8232 (m-30) cc_final: 0.8001 (m-30) REVERT: C 316 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6981 (mm-30) REVERT: C 328 LYS cc_start: 0.7641 (ttmt) cc_final: 0.7068 (pttp) REVERT: D 25 ASP cc_start: 0.7699 (m-30) cc_final: 0.6903 (p0) REVERT: D 57 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6789 (mt-10) REVERT: D 80 ASP cc_start: 0.7016 (m-30) cc_final: 0.6670 (m-30) REVERT: D 81 ASP cc_start: 0.8228 (m-30) cc_final: 0.7968 (m-30) REVERT: D 118 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6571 (mmpt) REVERT: D 125 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: D 132 MET cc_start: 0.7957 (ppp) cc_final: 0.7583 (ppp) REVERT: D 225 ASN cc_start: 0.7415 (t0) cc_final: 0.6945 (t0) REVERT: D 305 MET cc_start: 0.8317 (mmm) cc_final: 0.7779 (mmt) REVERT: D 326 LYS cc_start: 0.7796 (tppp) cc_final: 0.7526 (tptt) REVERT: D 328 LYS cc_start: 0.7959 (mttt) cc_final: 0.7539 (mtpp) REVERT: D 356 TRP cc_start: 0.8212 (OUTLIER) cc_final: 0.6537 (m-10) REVERT: D 372 ARG cc_start: 0.8340 (ttm-80) cc_final: 0.8111 (ttm170) REVERT: P 20 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: P 37 ARG cc_start: 0.7399 (ttm110) cc_final: 0.7160 (ttp80) REVERT: P 66 MET cc_start: 0.7670 (mtt) cc_final: 0.7088 (mtt) REVERT: P 156 ARG cc_start: 0.7808 (tpp80) cc_final: 0.6480 (tmt170) REVERT: P 157 ASN cc_start: 0.6769 (t0) cc_final: 0.6320 (t0) REVERT: P 183 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7501 (tt) REVERT: P 233 VAL cc_start: 0.7988 (p) cc_final: 0.7697 (t) REVERT: P 316 GLU cc_start: 0.7865 (tt0) cc_final: 0.7539 (tp30) REVERT: P 442 LYS cc_start: 0.8234 (tptp) cc_final: 0.7523 (ptpp) REVERT: P 460 ASP cc_start: 0.6669 (t70) cc_final: 0.6416 (t70) REVERT: P 492 LYS cc_start: 0.8413 (tttp) cc_final: 0.8099 (tttp) REVERT: P 525 ASP cc_start: 0.7788 (m-30) cc_final: 0.7354 (t70) REVERT: P 553 LYS cc_start: 0.7529 (mmtm) cc_final: 0.7135 (mppt) REVERT: P 563 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7044 (mt-10) REVERT: P 597 LYS cc_start: 0.7649 (mttt) cc_final: 0.7226 (ttmp) REVERT: P 598 GLN cc_start: 0.7558 (tt0) cc_final: 0.7331 (tm-30) REVERT: R 52 MET cc_start: 0.8899 (ttt) cc_final: 0.8587 (ttt) REVERT: R 83 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: R 125 MET cc_start: 0.5705 (pp-130) cc_final: 0.5143 (ttt) REVERT: R 145 MET cc_start: 0.8157 (tmt) cc_final: 0.7694 (tmt) outliers start: 70 outliers final: 30 residues processed: 269 average time/residue: 1.3940 time to fit residues: 411.6979 Evaluate side-chains 248 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 20 GLU Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 293 GLN Chi-restraints excluded: chain P residue 323 ILE Chi-restraints excluded: chain P residue 328 GLU Chi-restraints excluded: chain P residue 379 THR Chi-restraints excluded: chain P residue 444 ILE Chi-restraints excluded: chain P residue 473 THR Chi-restraints excluded: chain P residue 605 VAL Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain P residue 697 VAL Chi-restraints excluded: chain P residue 720 LEU Chi-restraints excluded: chain R residue 83 GLU Chi-restraints excluded: chain R residue 137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 HIS C 314 GLN D 41 GLN P 320 HIS P 395 HIS R 108 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.149850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.120524 restraints weight = 22620.552| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.06 r_work: 0.3528 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16072 Z= 0.222 Angle : 0.670 13.033 21746 Z= 0.338 Chirality : 0.046 0.192 2394 Planarity : 0.005 0.043 2808 Dihedral : 8.204 116.272 2219 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.21 % Favored : 96.68 % Rotamer: Outliers : 4.13 % Allowed : 15.23 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -0.16 (0.19), residues: 1960 helix: -0.17 (0.16), residues: 954 sheet: -0.48 (0.31), residues: 250 loop : 0.44 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 340 HIS 0.010 0.001 HIS R 108 PHE 0.030 0.002 PHE P 713 TYR 0.024 0.002 TYR P 629 ARG 0.008 0.001 ARG R 75 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 781) hydrogen bonds : angle 4.97346 ( 2088) covalent geometry : bond 0.00532 (16072) covalent geometry : angle 0.67023 (21746) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 219 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.6912 (m-30) cc_final: 0.6476 (p0) REVERT: B 59 GLN cc_start: 0.7921 (tt0) cc_final: 0.7620 (mm110) REVERT: B 91 TYR cc_start: 0.6956 (m-80) cc_final: 0.6477 (t80) REVERT: B 95 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8059 (mtp85) REVERT: B 119 MET cc_start: 0.8399 (mtt) cc_final: 0.8148 (mtp) REVERT: B 121 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: B 128 ASN cc_start: 0.8161 (m-40) cc_final: 0.7642 (t0) REVERT: B 132 MET cc_start: 0.8122 (ppp) cc_final: 0.7729 (ppp) REVERT: B 137 GLN cc_start: 0.8106 (mt0) cc_final: 0.7747 (mt0) REVERT: B 206 ARG cc_start: 0.7458 (ttp-110) cc_final: 0.6932 (ttt180) REVERT: B 237 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7568 (tt0) REVERT: B 238 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7561 (mttt) REVERT: B 323 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8109 (t) REVERT: B 360 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7931 (tm-30) REVERT: C 95 ARG cc_start: 0.7603 (mtp85) cc_final: 0.7076 (mmp-170) REVERT: C 122 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.6715 (mp) REVERT: C 132 MET cc_start: 0.7394 (ttp) cc_final: 0.6716 (ppp) REVERT: C 214 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7384 (mt-10) REVERT: C 241 GLU cc_start: 0.7611 (tt0) cc_final: 0.7224 (tt0) REVERT: C 290 ARG cc_start: 0.5471 (OUTLIER) cc_final: 0.4852 (ttm170) REVERT: C 292 ASP cc_start: 0.8302 (m-30) cc_final: 0.8050 (m-30) REVERT: C 316 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7333 (mm-30) REVERT: C 328 LYS cc_start: 0.7834 (ttmt) cc_final: 0.7263 (pttp) REVERT: D 25 ASP cc_start: 0.7702 (m-30) cc_final: 0.7012 (p0) REVERT: D 57 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6874 (mt-10) REVERT: D 80 ASP cc_start: 0.7179 (m-30) cc_final: 0.6804 (m-30) REVERT: D 118 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.6936 (mmpt) REVERT: D 132 MET cc_start: 0.8002 (ppp) cc_final: 0.7760 (ppp) REVERT: D 225 ASN cc_start: 0.7544 (t0) cc_final: 0.7077 (t0) REVERT: D 276 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7633 (tp30) REVERT: D 305 MET cc_start: 0.8412 (mmm) cc_final: 0.7950 (mmt) REVERT: D 328 LYS cc_start: 0.8044 (mttt) cc_final: 0.7667 (mtpp) REVERT: D 356 TRP cc_start: 0.8323 (OUTLIER) cc_final: 0.6680 (m-90) REVERT: P 20 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: P 37 ARG cc_start: 0.7443 (ttm110) cc_final: 0.7202 (ttp80) REVERT: P 66 MET cc_start: 0.7804 (mtt) cc_final: 0.7118 (mtt) REVERT: P 156 ARG cc_start: 0.7862 (tpp80) cc_final: 0.6590 (tmt170) REVERT: P 157 ASN cc_start: 0.6892 (t0) cc_final: 0.6509 (t0) REVERT: P 183 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7651 (tt) REVERT: P 316 GLU cc_start: 0.7992 (tt0) cc_final: 0.7151 (pp20) REVERT: P 391 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: P 433 TRP cc_start: 0.7836 (t-100) cc_final: 0.6214 (t-100) REVERT: P 442 LYS cc_start: 0.8325 (tptp) cc_final: 0.7630 (ptpp) REVERT: P 460 ASP cc_start: 0.6839 (t70) cc_final: 0.6553 (t70) REVERT: P 492 LYS cc_start: 0.8483 (tttp) cc_final: 0.8163 (tttp) REVERT: P 525 ASP cc_start: 0.7785 (m-30) cc_final: 0.7248 (OUTLIER) REVERT: P 537 GLU cc_start: 0.7435 (tt0) cc_final: 0.7059 (pt0) REVERT: P 553 LYS cc_start: 0.7515 (mmtm) cc_final: 0.7180 (mppt) REVERT: P 563 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7168 (mt-10) REVERT: P 571 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.5987 (mpm) REVERT: P 597 LYS cc_start: 0.7753 (mttt) cc_final: 0.7379 (ttmt) REVERT: R 37 MET cc_start: 0.7971 (pp-130) cc_final: 0.7766 (pp-130) REVERT: R 125 MET cc_start: 0.5839 (pp-130) cc_final: 0.5273 (ttt) REVERT: R 145 MET cc_start: 0.8174 (tmt) cc_final: 0.7697 (tmt) outliers start: 70 outliers final: 39 residues processed: 264 average time/residue: 1.3465 time to fit residues: 390.1650 Evaluate side-chains 262 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 213 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 20 GLU Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 102 MET Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 293 GLN Chi-restraints excluded: chain P residue 323 ILE Chi-restraints excluded: chain P residue 379 THR Chi-restraints excluded: chain P residue 391 GLU Chi-restraints excluded: chain P residue 444 ILE Chi-restraints excluded: chain P residue 473 THR Chi-restraints excluded: chain P residue 571 MET Chi-restraints excluded: chain P residue 578 GLU Chi-restraints excluded: chain P residue 605 VAL Chi-restraints excluded: chain P residue 666 LEU Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain P residue 697 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 137 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 60 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 170 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 173 optimal weight: 0.7980 chunk 141 optimal weight: 0.0670 chunk 46 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 HIS P 395 HIS ** P 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.150751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121882 restraints weight = 22784.260| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.04 r_work: 0.3516 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16072 Z= 0.143 Angle : 0.606 12.576 21746 Z= 0.303 Chirality : 0.043 0.170 2394 Planarity : 0.004 0.045 2808 Dihedral : 7.933 117.041 2219 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.76 % Favored : 97.14 % Rotamer: Outliers : 4.01 % Allowed : 16.29 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.12 (0.19), residues: 1960 helix: 0.14 (0.17), residues: 954 sheet: -0.39 (0.32), residues: 248 loop : 0.47 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.004 0.001 HIS C 161 PHE 0.027 0.001 PHE P 713 TYR 0.021 0.001 TYR P 629 ARG 0.010 0.001 ARG P 305 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 781) hydrogen bonds : angle 4.78606 ( 2088) covalent geometry : bond 0.00334 (16072) covalent geometry : angle 0.60597 (21746) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 228 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7658 (mtm-85) REVERT: B 51 ASP cc_start: 0.6890 (m-30) cc_final: 0.6437 (p0) REVERT: B 59 GLN cc_start: 0.7857 (tt0) cc_final: 0.7525 (mm110) REVERT: B 91 TYR cc_start: 0.6919 (m-80) cc_final: 0.6387 (t80) REVERT: B 95 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8019 (mtp85) REVERT: B 119 MET cc_start: 0.8188 (mtt) cc_final: 0.7980 (mtp) REVERT: B 121 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: B 132 MET cc_start: 0.7795 (ppp) cc_final: 0.7427 (ppp) REVERT: B 137 GLN cc_start: 0.8044 (mt0) cc_final: 0.7699 (mt0) REVERT: B 206 ARG cc_start: 0.7531 (ttp-110) cc_final: 0.6855 (mmm160) REVERT: B 237 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7593 (tt0) REVERT: B 238 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7432 (mttt) REVERT: B 323 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8083 (t) REVERT: B 354 GLN cc_start: 0.7998 (pt0) cc_final: 0.7486 (pm20) REVERT: B 360 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7913 (tm-30) REVERT: C 95 ARG cc_start: 0.7686 (mtp85) cc_final: 0.7077 (mmp-170) REVERT: C 122 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6603 (mp) REVERT: C 132 MET cc_start: 0.7357 (ttp) cc_final: 0.6731 (ppp) REVERT: C 241 GLU cc_start: 0.7531 (tt0) cc_final: 0.7143 (tt0) REVERT: C 290 ARG cc_start: 0.5354 (OUTLIER) cc_final: 0.4779 (ttm170) REVERT: C 292 ASP cc_start: 0.8303 (m-30) cc_final: 0.8016 (m-30) REVERT: C 316 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7228 (mm-30) REVERT: C 328 LYS cc_start: 0.7827 (ttmt) cc_final: 0.7213 (pttp) REVERT: D 25 ASP cc_start: 0.7676 (m-30) cc_final: 0.6979 (p0) REVERT: D 57 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6767 (mt-10) REVERT: D 80 ASP cc_start: 0.7241 (m-30) cc_final: 0.6888 (m-30) REVERT: D 118 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6768 (mmpt) REVERT: D 225 ASN cc_start: 0.7484 (t0) cc_final: 0.7049 (t0) REVERT: D 276 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: D 305 MET cc_start: 0.8338 (mmm) cc_final: 0.7797 (mmt) REVERT: D 328 LYS cc_start: 0.7960 (mttt) cc_final: 0.7472 (mtpp) REVERT: D 356 TRP cc_start: 0.8234 (OUTLIER) cc_final: 0.6494 (m-10) REVERT: P 20 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7539 (tp30) REVERT: P 37 ARG cc_start: 0.7418 (ttm110) cc_final: 0.7217 (ttp80) REVERT: P 66 MET cc_start: 0.7690 (mtt) cc_final: 0.7087 (mtt) REVERT: P 156 ARG cc_start: 0.7776 (tpp80) cc_final: 0.6447 (tmt170) REVERT: P 157 ASN cc_start: 0.6789 (t0) cc_final: 0.6423 (t0) REVERT: P 167 MET cc_start: 0.8253 (mtp) cc_final: 0.7956 (mtp) REVERT: P 183 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7669 (tt) REVERT: P 210 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: P 234 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7656 (mttm) REVERT: P 316 GLU cc_start: 0.7937 (tt0) cc_final: 0.7091 (pp20) REVERT: P 391 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: P 433 TRP cc_start: 0.7779 (t-100) cc_final: 0.6188 (t-100) REVERT: P 442 LYS cc_start: 0.8279 (tptp) cc_final: 0.7554 (ptpp) REVERT: P 460 ASP cc_start: 0.6743 (t70) cc_final: 0.6471 (t70) REVERT: P 492 LYS cc_start: 0.8455 (tttp) cc_final: 0.8220 (tttp) REVERT: P 510 LEU cc_start: 0.8782 (tm) cc_final: 0.8562 (tt) REVERT: P 525 ASP cc_start: 0.7772 (m-30) cc_final: 0.7182 (OUTLIER) REVERT: P 537 GLU cc_start: 0.7213 (tt0) cc_final: 0.6833 (pt0) REVERT: P 553 LYS cc_start: 0.7481 (mmtm) cc_final: 0.7131 (mppt) REVERT: P 571 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.5865 (mpm) REVERT: P 597 LYS cc_start: 0.7655 (mttt) cc_final: 0.7215 (tttp) REVERT: P 710 TRP cc_start: 0.7032 (OUTLIER) cc_final: 0.6765 (t-100) REVERT: R 145 MET cc_start: 0.8158 (tmt) cc_final: 0.7542 (tmt) REVERT: R 146 MET cc_start: 0.7620 (ttp) cc_final: 0.7256 (mtm) outliers start: 68 outliers final: 33 residues processed: 274 average time/residue: 1.4016 time to fit residues: 420.8918 Evaluate side-chains 255 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 20 GLU Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 102 MET Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 293 GLN Chi-restraints excluded: chain P residue 379 THR Chi-restraints excluded: chain P residue 391 GLU Chi-restraints excluded: chain P residue 444 ILE Chi-restraints excluded: chain P residue 571 MET Chi-restraints excluded: chain P residue 578 GLU Chi-restraints excluded: chain P residue 605 VAL Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain P residue 697 VAL Chi-restraints excluded: chain P residue 710 TRP Chi-restraints excluded: chain P residue 714 HIS Chi-restraints excluded: chain P residue 720 LEU Chi-restraints excluded: chain R residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 1 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 145 optimal weight: 0.4980 chunk 154 optimal weight: 0.8980 chunk 148 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN P 395 HIS R 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.150166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.120957 restraints weight = 22885.135| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.06 r_work: 0.3517 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16072 Z= 0.168 Angle : 0.627 13.320 21746 Z= 0.313 Chirality : 0.044 0.262 2394 Planarity : 0.004 0.044 2808 Dihedral : 7.814 116.791 2216 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.01 % Favored : 96.89 % Rotamer: Outliers : 4.19 % Allowed : 17.36 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.09 (0.19), residues: 1960 helix: 0.14 (0.17), residues: 956 sheet: -0.43 (0.32), residues: 248 loop : 0.44 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.010 0.001 HIS R 108 PHE 0.030 0.002 PHE P 713 TYR 0.021 0.002 TYR P 629 ARG 0.009 0.001 ARG P 305 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 781) hydrogen bonds : angle 4.79022 ( 2088) covalent geometry : bond 0.00397 (16072) covalent geometry : angle 0.62677 (21746) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 211 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.7926 (mtt-85) cc_final: 0.7625 (mtm-85) REVERT: B 51 ASP cc_start: 0.6981 (m-30) cc_final: 0.6511 (p0) REVERT: B 59 GLN cc_start: 0.7921 (tt0) cc_final: 0.7546 (mm110) REVERT: B 91 TYR cc_start: 0.6952 (m-80) cc_final: 0.6507 (t80) REVERT: B 95 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8034 (mtp85) REVERT: B 119 MET cc_start: 0.8241 (mtt) cc_final: 0.7955 (mtp) REVERT: B 121 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: B 132 MET cc_start: 0.7783 (ppp) cc_final: 0.7424 (ppp) REVERT: B 137 GLN cc_start: 0.7967 (mt0) cc_final: 0.7624 (mt0) REVERT: B 206 ARG cc_start: 0.7551 (ttp-110) cc_final: 0.6248 (tmm160) REVERT: B 238 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7525 (mttt) REVERT: B 323 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.8055 (t) REVERT: B 354 GLN cc_start: 0.8001 (pt0) cc_final: 0.7399 (pm20) REVERT: B 360 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7939 (mp10) REVERT: C 95 ARG cc_start: 0.7690 (mtp85) cc_final: 0.7104 (mmp-170) REVERT: C 100 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: C 122 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6518 (mp) REVERT: C 132 MET cc_start: 0.7381 (ttp) cc_final: 0.6741 (ppp) REVERT: C 241 GLU cc_start: 0.7574 (tt0) cc_final: 0.7179 (tt0) REVERT: C 290 ARG cc_start: 0.5356 (OUTLIER) cc_final: 0.4770 (ttm170) REVERT: C 292 ASP cc_start: 0.8316 (m-30) cc_final: 0.8016 (m-30) REVERT: C 316 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7325 (mm-30) REVERT: C 328 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7267 (pttp) REVERT: D 25 ASP cc_start: 0.7810 (m-30) cc_final: 0.7110 (p0) REVERT: D 57 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6809 (mt-10) REVERT: D 80 ASP cc_start: 0.7238 (m-30) cc_final: 0.6912 (m-30) REVERT: D 125 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: D 178 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.6976 (pp) REVERT: D 225 ASN cc_start: 0.7499 (t0) cc_final: 0.7054 (t0) REVERT: D 276 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: D 305 MET cc_start: 0.8344 (mmm) cc_final: 0.7810 (mmt) REVERT: D 356 TRP cc_start: 0.8276 (OUTLIER) cc_final: 0.6543 (m-10) REVERT: P 20 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: P 37 ARG cc_start: 0.7410 (ttm110) cc_final: 0.7200 (ttp80) REVERT: P 66 MET cc_start: 0.7746 (mtt) cc_final: 0.7063 (mtt) REVERT: P 156 ARG cc_start: 0.7752 (tpp80) cc_final: 0.6480 (tmt170) REVERT: P 157 ASN cc_start: 0.6655 (t0) cc_final: 0.6373 (t0) REVERT: P 167 MET cc_start: 0.8261 (mtp) cc_final: 0.7852 (mtp) REVERT: P 183 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7693 (tt) REVERT: P 210 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: P 316 GLU cc_start: 0.7977 (tt0) cc_final: 0.7127 (pp20) REVERT: P 391 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: P 433 TRP cc_start: 0.7620 (t-100) cc_final: 0.6052 (t-100) REVERT: P 442 LYS cc_start: 0.8267 (tptp) cc_final: 0.7562 (ptpp) REVERT: P 460 ASP cc_start: 0.6759 (t70) cc_final: 0.6494 (t70) REVERT: P 492 LYS cc_start: 0.8471 (tttp) cc_final: 0.8229 (tttp) REVERT: P 510 LEU cc_start: 0.8817 (tm) cc_final: 0.8601 (tt) REVERT: P 525 ASP cc_start: 0.7804 (m-30) cc_final: 0.7205 (t0) REVERT: P 537 GLU cc_start: 0.7138 (tt0) cc_final: 0.6803 (pt0) REVERT: P 553 LYS cc_start: 0.7658 (mmtm) cc_final: 0.7295 (mppt) REVERT: P 571 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.5870 (mpm) REVERT: P 597 LYS cc_start: 0.7566 (mttt) cc_final: 0.7092 (tttp) REVERT: R 52 MET cc_start: 0.9048 (ttt) cc_final: 0.8435 (ttt) REVERT: R 125 MET cc_start: 0.5791 (pp-130) cc_final: 0.5218 (ttt) REVERT: R 145 MET cc_start: 0.8158 (tmt) cc_final: 0.7956 (ppp) outliers start: 71 outliers final: 39 residues processed: 259 average time/residue: 1.3506 time to fit residues: 386.1576 Evaluate side-chains 260 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 206 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 20 GLU Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 102 MET Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 293 GLN Chi-restraints excluded: chain P residue 379 THR Chi-restraints excluded: chain P residue 391 GLU Chi-restraints excluded: chain P residue 444 ILE Chi-restraints excluded: chain P residue 453 LYS Chi-restraints excluded: chain P residue 524 LEU Chi-restraints excluded: chain P residue 571 MET Chi-restraints excluded: chain P residue 578 GLU Chi-restraints excluded: chain P residue 605 VAL Chi-restraints excluded: chain P residue 666 LEU Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain P residue 697 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 149 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 105 optimal weight: 0.0170 chunk 70 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.150607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.121470 restraints weight = 22823.611| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.07 r_work: 0.3507 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16072 Z= 0.156 Angle : 0.612 13.739 21746 Z= 0.305 Chirality : 0.043 0.230 2394 Planarity : 0.004 0.050 2808 Dihedral : 7.732 116.935 2216 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 4.43 % Allowed : 17.24 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.25 (0.19), residues: 1960 helix: 0.28 (0.17), residues: 950 sheet: -0.32 (0.32), residues: 254 loop : 0.49 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.005 0.001 HIS C 161 PHE 0.019 0.001 PHE R 69 TYR 0.020 0.001 TYR P 629 ARG 0.010 0.001 ARG P 305 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 781) hydrogen bonds : angle 4.71364 ( 2088) covalent geometry : bond 0.00369 (16072) covalent geometry : angle 0.61222 (21746) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 213 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.6858 (m-30) cc_final: 0.6380 (p0) REVERT: B 59 GLN cc_start: 0.7895 (tt0) cc_final: 0.7384 (mm-40) REVERT: B 91 TYR cc_start: 0.6898 (m-80) cc_final: 0.6329 (t80) REVERT: B 95 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7958 (mtp85) REVERT: B 119 MET cc_start: 0.8182 (mtt) cc_final: 0.7902 (mtp) REVERT: B 132 MET cc_start: 0.7764 (ppp) cc_final: 0.7432 (ppp) REVERT: B 137 GLN cc_start: 0.7924 (mt0) cc_final: 0.7597 (mt0) REVERT: B 206 ARG cc_start: 0.7631 (ttp-110) cc_final: 0.6298 (tmm160) REVERT: B 238 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7422 (mttt) REVERT: B 323 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.8030 (t) REVERT: B 354 GLN cc_start: 0.8023 (pt0) cc_final: 0.7400 (pm20) REVERT: B 360 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7669 (mp10) REVERT: C 95 ARG cc_start: 0.7643 (mtp85) cc_final: 0.7026 (mmp-170) REVERT: C 122 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6484 (mp) REVERT: C 132 MET cc_start: 0.7394 (ttp) cc_final: 0.6681 (ppp) REVERT: C 241 GLU cc_start: 0.7532 (tt0) cc_final: 0.7131 (tt0) REVERT: C 290 ARG cc_start: 0.5237 (OUTLIER) cc_final: 0.4674 (ttm170) REVERT: C 292 ASP cc_start: 0.8320 (m-30) cc_final: 0.8017 (m-30) REVERT: C 316 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7229 (mm-30) REVERT: C 328 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7163 (pttp) REVERT: D 25 ASP cc_start: 0.7798 (m-30) cc_final: 0.7233 (p0) REVERT: D 57 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6734 (mt-10) REVERT: D 80 ASP cc_start: 0.7141 (m-30) cc_final: 0.6832 (m-30) REVERT: D 118 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6845 (mmpt) REVERT: D 178 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.6931 (pp) REVERT: D 225 ASN cc_start: 0.7458 (t0) cc_final: 0.7028 (t0) REVERT: D 276 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: D 305 MET cc_start: 0.8309 (mmm) cc_final: 0.7752 (mmt) REVERT: D 329 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8213 (mp) REVERT: D 356 TRP cc_start: 0.8229 (OUTLIER) cc_final: 0.6471 (m-10) REVERT: P 20 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: P 37 ARG cc_start: 0.7404 (ttm110) cc_final: 0.7179 (ttp80) REVERT: P 64 GLN cc_start: 0.6713 (tp40) cc_final: 0.6223 (mp10) REVERT: P 66 MET cc_start: 0.7782 (mtt) cc_final: 0.7038 (mtt) REVERT: P 106 GLU cc_start: 0.6280 (mp0) cc_final: 0.5957 (mp0) REVERT: P 156 ARG cc_start: 0.7568 (tpp80) cc_final: 0.6196 (tmt170) REVERT: P 157 ASN cc_start: 0.6572 (t0) cc_final: 0.6298 (t0) REVERT: P 167 MET cc_start: 0.8249 (mtp) cc_final: 0.7840 (mtp) REVERT: P 183 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7689 (tt) REVERT: P 210 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: P 234 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7696 (mttm) REVERT: P 316 GLU cc_start: 0.7919 (tt0) cc_final: 0.7049 (pp20) REVERT: P 323 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7222 (pt) REVERT: P 391 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: P 442 LYS cc_start: 0.8253 (tptp) cc_final: 0.7515 (ptpp) REVERT: P 472 LEU cc_start: 0.7944 (mm) cc_final: 0.7660 (mt) REVERT: P 492 LYS cc_start: 0.8435 (tttp) cc_final: 0.8184 (tttp) REVERT: P 500 LYS cc_start: 0.7243 (mptp) cc_final: 0.6982 (mmtt) REVERT: P 525 ASP cc_start: 0.7767 (m-30) cc_final: 0.7154 (t0) REVERT: P 537 GLU cc_start: 0.7179 (tt0) cc_final: 0.6797 (pt0) REVERT: P 553 LYS cc_start: 0.7728 (mmtm) cc_final: 0.7352 (mppt) REVERT: P 571 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.5794 (mpm) REVERT: P 597 LYS cc_start: 0.7455 (mttt) cc_final: 0.6840 (mmmt) REVERT: P 598 GLN cc_start: 0.7426 (tm-30) cc_final: 0.7204 (tm-30) REVERT: P 674 LYS cc_start: 0.6531 (OUTLIER) cc_final: 0.6126 (mppt) REVERT: R 52 MET cc_start: 0.8982 (ttt) cc_final: 0.8369 (ttt) REVERT: R 75 ARG cc_start: 0.7380 (tpp-160) cc_final: 0.7063 (tpp-160) REVERT: R 125 MET cc_start: 0.6051 (pp-130) cc_final: 0.5480 (ttt) REVERT: R 142 PHE cc_start: 0.7743 (t80) cc_final: 0.7502 (t80) REVERT: R 146 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6909 (mtt) outliers start: 75 outliers final: 41 residues processed: 261 average time/residue: 1.3967 time to fit residues: 399.4648 Evaluate side-chains 265 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 20 GLU Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 102 MET Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 233 VAL Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 293 GLN Chi-restraints excluded: chain P residue 323 ILE Chi-restraints excluded: chain P residue 379 THR Chi-restraints excluded: chain P residue 381 VAL Chi-restraints excluded: chain P residue 391 GLU Chi-restraints excluded: chain P residue 444 ILE Chi-restraints excluded: chain P residue 453 LYS Chi-restraints excluded: chain P residue 482 VAL Chi-restraints excluded: chain P residue 571 MET Chi-restraints excluded: chain P residue 578 GLU Chi-restraints excluded: chain P residue 605 VAL Chi-restraints excluded: chain P residue 666 LEU Chi-restraints excluded: chain P residue 674 LYS Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain P residue 697 VAL Chi-restraints excluded: chain P residue 714 HIS Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 146 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 125 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 129 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 395 HIS R 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.150915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121728 restraints weight = 22649.974| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.07 r_work: 0.3519 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16072 Z= 0.149 Angle : 0.611 13.749 21746 Z= 0.305 Chirality : 0.044 0.224 2394 Planarity : 0.004 0.049 2808 Dihedral : 7.611 116.102 2216 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % Rotamer: Outliers : 4.37 % Allowed : 17.89 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.33 (0.19), residues: 1960 helix: 0.36 (0.17), residues: 947 sheet: -0.31 (0.32), residues: 254 loop : 0.53 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP P 710 HIS 0.010 0.001 HIS R 108 PHE 0.036 0.001 PHE P 713 TYR 0.020 0.001 TYR P 629 ARG 0.011 0.001 ARG P 305 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 781) hydrogen bonds : angle 4.67362 ( 2088) covalent geometry : bond 0.00352 (16072) covalent geometry : angle 0.61080 (21746) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 215 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.6842 (m-30) cc_final: 0.6389 (p0) REVERT: B 59 GLN cc_start: 0.7926 (tt0) cc_final: 0.7426 (mm-40) REVERT: B 91 TYR cc_start: 0.6929 (m-80) cc_final: 0.6406 (t80) REVERT: B 95 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7998 (mtp85) REVERT: B 119 MET cc_start: 0.8205 (mtt) cc_final: 0.7843 (mtp) REVERT: B 123 MET cc_start: 0.8543 (mmp) cc_final: 0.7630 (mmm) REVERT: B 132 MET cc_start: 0.7782 (ppp) cc_final: 0.7470 (ppp) REVERT: B 137 GLN cc_start: 0.7960 (mt0) cc_final: 0.7640 (mt0) REVERT: B 206 ARG cc_start: 0.7662 (ttp-110) cc_final: 0.6350 (tmm160) REVERT: B 238 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7479 (mttt) REVERT: B 323 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.8058 (t) REVERT: B 354 GLN cc_start: 0.8103 (pt0) cc_final: 0.7497 (pm20) REVERT: B 360 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7540 (pm20) REVERT: C 95 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7124 (mmp-170) REVERT: C 100 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: C 122 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6506 (mp) REVERT: C 132 MET cc_start: 0.7426 (ttp) cc_final: 0.6730 (ppp) REVERT: C 241 GLU cc_start: 0.7604 (tt0) cc_final: 0.7204 (tt0) REVERT: C 292 ASP cc_start: 0.8342 (m-30) cc_final: 0.8058 (m-30) REVERT: C 316 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7304 (mm-30) REVERT: C 328 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7273 (pttp) REVERT: D 25 ASP cc_start: 0.7776 (m-30) cc_final: 0.7256 (p0) REVERT: D 57 GLU cc_start: 0.7511 (mm-30) cc_final: 0.6847 (mt-10) REVERT: D 78 ASN cc_start: 0.8224 (t0) cc_final: 0.7252 (t0) REVERT: D 80 ASP cc_start: 0.7155 (m-30) cc_final: 0.6846 (m-30) REVERT: D 118 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6921 (mmpt) REVERT: D 178 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.6949 (pp) REVERT: D 225 ASN cc_start: 0.7500 (t0) cc_final: 0.7070 (t0) REVERT: D 276 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: D 305 MET cc_start: 0.8368 (mmm) cc_final: 0.7796 (mmt) REVERT: D 329 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8237 (mp) REVERT: D 356 TRP cc_start: 0.8263 (OUTLIER) cc_final: 0.6491 (m-10) REVERT: P 11 VAL cc_start: 0.7168 (OUTLIER) cc_final: 0.6750 (m) REVERT: P 37 ARG cc_start: 0.7416 (ttm110) cc_final: 0.7192 (ttp80) REVERT: P 66 MET cc_start: 0.7834 (mtt) cc_final: 0.7109 (mtt) REVERT: P 106 GLU cc_start: 0.6303 (mp0) cc_final: 0.5966 (mp0) REVERT: P 156 ARG cc_start: 0.7564 (tpp80) cc_final: 0.6182 (tmt170) REVERT: P 157 ASN cc_start: 0.6571 (t0) cc_final: 0.6316 (t0) REVERT: P 167 MET cc_start: 0.8202 (mtp) cc_final: 0.7846 (mtp) REVERT: P 183 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7649 (tt) REVERT: P 234 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7770 (mttm) REVERT: P 316 GLU cc_start: 0.7974 (tt0) cc_final: 0.7120 (pp20) REVERT: P 391 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: P 442 LYS cc_start: 0.8300 (tptp) cc_final: 0.7561 (ptpp) REVERT: P 492 LYS cc_start: 0.8477 (tttp) cc_final: 0.8218 (tttp) REVERT: P 500 LYS cc_start: 0.7305 (mptp) cc_final: 0.7051 (mmtt) REVERT: P 525 ASP cc_start: 0.7779 (m-30) cc_final: 0.7193 (t0) REVERT: P 537 GLU cc_start: 0.7211 (tt0) cc_final: 0.6851 (pt0) REVERT: P 553 LYS cc_start: 0.7734 (mmtm) cc_final: 0.7350 (mppt) REVERT: P 571 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.5840 (mpm) REVERT: P 597 LYS cc_start: 0.7503 (mttt) cc_final: 0.6910 (mmmt) REVERT: P 674 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.6198 (mppt) REVERT: R 52 MET cc_start: 0.8994 (ttt) cc_final: 0.8411 (ttt) REVERT: R 75 ARG cc_start: 0.7306 (tpp-160) cc_final: 0.6973 (tpp-160) REVERT: R 125 MET cc_start: 0.5987 (pp-130) cc_final: 0.5390 (ttm) outliers start: 74 outliers final: 45 residues processed: 265 average time/residue: 1.3339 time to fit residues: 388.5673 Evaluate side-chains 264 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 204 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 102 MET Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 233 VAL Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 293 GLN Chi-restraints excluded: chain P residue 323 ILE Chi-restraints excluded: chain P residue 329 GLU Chi-restraints excluded: chain P residue 379 THR Chi-restraints excluded: chain P residue 381 VAL Chi-restraints excluded: chain P residue 391 GLU Chi-restraints excluded: chain P residue 444 ILE Chi-restraints excluded: chain P residue 453 LYS Chi-restraints excluded: chain P residue 482 VAL Chi-restraints excluded: chain P residue 571 MET Chi-restraints excluded: chain P residue 578 GLU Chi-restraints excluded: chain P residue 605 VAL Chi-restraints excluded: chain P residue 666 LEU Chi-restraints excluded: chain P residue 674 LYS Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain P residue 697 VAL Chi-restraints excluded: chain P residue 714 HIS Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 4 optimal weight: 0.0570 chunk 177 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 99 optimal weight: 0.3980 chunk 55 optimal weight: 0.0870 chunk 159 optimal weight: 0.0980 chunk 131 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 overall best weight: 0.1876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 395 HIS R 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.153884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.125487 restraints weight = 22594.075| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.01 r_work: 0.3555 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16072 Z= 0.107 Angle : 0.585 13.754 21746 Z= 0.292 Chirality : 0.042 0.252 2394 Planarity : 0.004 0.058 2808 Dihedral : 7.286 111.705 2212 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.19 % Rotamer: Outliers : 3.13 % Allowed : 19.24 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.69 (0.20), residues: 1960 helix: 0.63 (0.17), residues: 937 sheet: -0.21 (0.32), residues: 253 loop : 0.75 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 710 HIS 0.004 0.001 HIS C 161 PHE 0.018 0.001 PHE R 69 TYR 0.018 0.001 TYR P 629 ARG 0.009 0.000 ARG P 97 Details of bonding type rmsd hydrogen bonds : bond 0.03008 ( 781) hydrogen bonds : angle 4.53060 ( 2088) covalent geometry : bond 0.00242 (16072) covalent geometry : angle 0.58462 (21746) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.6728 (m-30) cc_final: 0.6318 (p0) REVERT: B 59 GLN cc_start: 0.7886 (tt0) cc_final: 0.7385 (mm-40) REVERT: B 91 TYR cc_start: 0.6896 (m-80) cc_final: 0.6336 (t80) REVERT: B 95 ARG cc_start: 0.8431 (ttp80) cc_final: 0.7964 (mtp85) REVERT: B 119 MET cc_start: 0.8084 (mtt) cc_final: 0.7811 (mtp) REVERT: B 123 MET cc_start: 0.8487 (mmp) cc_final: 0.7550 (mmm) REVERT: B 132 MET cc_start: 0.7750 (ppp) cc_final: 0.7452 (ppp) REVERT: B 137 GLN cc_start: 0.7921 (mt0) cc_final: 0.7625 (mt0) REVERT: B 206 ARG cc_start: 0.7560 (ttp-110) cc_final: 0.6231 (tmm160) REVERT: B 238 LYS cc_start: 0.7877 (mmtt) cc_final: 0.7445 (mttt) REVERT: B 354 GLN cc_start: 0.8085 (pt0) cc_final: 0.7469 (pm20) REVERT: B 360 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7499 (pm20) REVERT: C 95 ARG cc_start: 0.7662 (mtp85) cc_final: 0.7099 (mmp-170) REVERT: C 117 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6613 (mm-30) REVERT: C 132 MET cc_start: 0.7451 (ttp) cc_final: 0.6697 (ppp) REVERT: C 241 GLU cc_start: 0.7471 (tt0) cc_final: 0.7128 (tt0) REVERT: C 292 ASP cc_start: 0.8302 (m-30) cc_final: 0.8010 (m-30) REVERT: C 328 LYS cc_start: 0.7853 (ttmt) cc_final: 0.7264 (pttp) REVERT: D 25 ASP cc_start: 0.7553 (m-30) cc_final: 0.7116 (p0) REVERT: D 57 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6855 (mt-10) REVERT: D 78 ASN cc_start: 0.8262 (t0) cc_final: 0.7340 (t0) REVERT: D 80 ASP cc_start: 0.7067 (m-30) cc_final: 0.6748 (m-30) REVERT: D 118 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6651 (mmpt) REVERT: D 178 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6924 (pp) REVERT: D 225 ASN cc_start: 0.7442 (t0) cc_final: 0.7016 (t0) REVERT: D 305 MET cc_start: 0.8265 (mmm) cc_final: 0.7715 (mmt) REVERT: D 329 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8139 (mp) REVERT: D 356 TRP cc_start: 0.8216 (OUTLIER) cc_final: 0.6373 (m-10) REVERT: D 361 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7362 (mt-10) REVERT: P 11 VAL cc_start: 0.7056 (t) cc_final: 0.6692 (m) REVERT: P 37 ARG cc_start: 0.7345 (ttm110) cc_final: 0.7111 (ttp80) REVERT: P 64 GLN cc_start: 0.6707 (tp40) cc_final: 0.6274 (mp10) REVERT: P 66 MET cc_start: 0.7820 (mtt) cc_final: 0.7112 (mtt) REVERT: P 106 GLU cc_start: 0.6356 (mp0) cc_final: 0.6031 (mp0) REVERT: P 156 ARG cc_start: 0.7567 (tpp80) cc_final: 0.6184 (tmt170) REVERT: P 157 ASN cc_start: 0.6685 (t0) cc_final: 0.6434 (t0) REVERT: P 167 MET cc_start: 0.8123 (mtp) cc_final: 0.7651 (mtp) REVERT: P 183 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7682 (tt) REVERT: P 234 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7799 (mttm) REVERT: P 316 GLU cc_start: 0.7954 (tt0) cc_final: 0.7071 (pp20) REVERT: P 391 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: P 442 LYS cc_start: 0.8290 (tptp) cc_final: 0.7495 (ptpp) REVERT: P 492 LYS cc_start: 0.8472 (tttp) cc_final: 0.8208 (tttp) REVERT: P 500 LYS cc_start: 0.7303 (mptp) cc_final: 0.7067 (mmtt) REVERT: P 510 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8621 (tm) REVERT: P 525 ASP cc_start: 0.7712 (m-30) cc_final: 0.7080 (t0) REVERT: P 537 GLU cc_start: 0.7153 (tt0) cc_final: 0.6833 (pt0) REVERT: P 553 LYS cc_start: 0.7724 (mmtm) cc_final: 0.7253 (mppt) REVERT: P 571 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.5658 (mpm) REVERT: P 597 LYS cc_start: 0.7425 (mttt) cc_final: 0.6869 (mmmt) REVERT: P 674 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.6175 (mppt) REVERT: R 52 MET cc_start: 0.8924 (ttt) cc_final: 0.8391 (ttt) REVERT: R 64 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8634 (mp) REVERT: R 125 MET cc_start: 0.5674 (pp-130) cc_final: 0.5095 (ttm) REVERT: R 145 MET cc_start: 0.8038 (ppp) cc_final: 0.7427 (ppp) REVERT: R 146 MET cc_start: 0.7191 (mtt) cc_final: 0.6987 (ttt) outliers start: 53 outliers final: 31 residues processed: 255 average time/residue: 1.3396 time to fit residues: 377.5287 Evaluate side-chains 245 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 203 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 102 MET Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 293 GLN Chi-restraints excluded: chain P residue 329 GLU Chi-restraints excluded: chain P residue 381 VAL Chi-restraints excluded: chain P residue 391 GLU Chi-restraints excluded: chain P residue 444 ILE Chi-restraints excluded: chain P residue 482 VAL Chi-restraints excluded: chain P residue 510 LEU Chi-restraints excluded: chain P residue 571 MET Chi-restraints excluded: chain P residue 578 GLU Chi-restraints excluded: chain P residue 605 VAL Chi-restraints excluded: chain P residue 674 LYS Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain P residue 697 VAL Chi-restraints excluded: chain P residue 714 HIS Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 26 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 0.0470 chunk 69 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 62 optimal weight: 0.0970 chunk 58 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN D 280 ASN P 395 HIS R 108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.153275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.124650 restraints weight = 22699.351| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.03 r_work: 0.3537 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16072 Z= 0.135 Angle : 0.605 13.757 21746 Z= 0.302 Chirality : 0.043 0.287 2394 Planarity : 0.004 0.057 2808 Dihedral : 7.494 109.430 2211 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 2.89 % Allowed : 19.89 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1960 helix: 0.55 (0.17), residues: 942 sheet: -0.15 (0.32), residues: 254 loop : 0.71 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 710 HIS 0.013 0.001 HIS R 108 PHE 0.037 0.001 PHE P 713 TYR 0.018 0.001 TYR P 629 ARG 0.014 0.001 ARG P 305 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 781) hydrogen bonds : angle 4.57981 ( 2088) covalent geometry : bond 0.00315 (16072) covalent geometry : angle 0.60535 (21746) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASP cc_start: 0.8141 (m-30) cc_final: 0.6772 (p0) REVERT: B 51 ASP cc_start: 0.6699 (m-30) cc_final: 0.6321 (p0) REVERT: B 59 GLN cc_start: 0.7876 (tt0) cc_final: 0.7387 (mm-40) REVERT: B 91 TYR cc_start: 0.6897 (m-80) cc_final: 0.6342 (t80) REVERT: B 95 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7974 (mtp85) REVERT: B 119 MET cc_start: 0.8251 (mtt) cc_final: 0.8009 (mtp) REVERT: B 123 MET cc_start: 0.8516 (mmp) cc_final: 0.7590 (mmm) REVERT: B 137 GLN cc_start: 0.7926 (mt0) cc_final: 0.7592 (mt0) REVERT: B 206 ARG cc_start: 0.7650 (ttp-110) cc_final: 0.6351 (tmm160) REVERT: B 238 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7451 (mttt) REVERT: B 354 GLN cc_start: 0.8107 (pt0) cc_final: 0.7477 (pm20) REVERT: B 360 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7500 (pm20) REVERT: C 95 ARG cc_start: 0.7653 (mtp85) cc_final: 0.7056 (mmp-170) REVERT: C 132 MET cc_start: 0.7429 (ttp) cc_final: 0.6778 (ppp) REVERT: C 241 GLU cc_start: 0.7493 (tt0) cc_final: 0.7149 (tt0) REVERT: C 292 ASP cc_start: 0.8304 (m-30) cc_final: 0.7971 (m-30) REVERT: C 328 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7257 (pttp) REVERT: D 25 ASP cc_start: 0.7334 (m-30) cc_final: 0.6930 (p0) REVERT: D 57 GLU cc_start: 0.7497 (mm-30) cc_final: 0.6850 (mt-10) REVERT: D 78 ASN cc_start: 0.8253 (t0) cc_final: 0.7352 (t0) REVERT: D 80 ASP cc_start: 0.7043 (m-30) cc_final: 0.6719 (m-30) REVERT: D 178 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6927 (pp) REVERT: D 225 ASN cc_start: 0.7435 (t0) cc_final: 0.7010 (t0) REVERT: D 305 MET cc_start: 0.8261 (mmm) cc_final: 0.7767 (mmt) REVERT: D 329 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8175 (mp) REVERT: D 356 TRP cc_start: 0.8253 (OUTLIER) cc_final: 0.6361 (m-10) REVERT: P 11 VAL cc_start: 0.7328 (t) cc_final: 0.7010 (m) REVERT: P 37 ARG cc_start: 0.7333 (ttm110) cc_final: 0.7092 (ttp80) REVERT: P 64 GLN cc_start: 0.6768 (tp40) cc_final: 0.6279 (mp10) REVERT: P 66 MET cc_start: 0.7869 (mtt) cc_final: 0.7119 (mtt) REVERT: P 106 GLU cc_start: 0.6372 (mp0) cc_final: 0.5863 (mp0) REVERT: P 156 ARG cc_start: 0.7574 (tpp80) cc_final: 0.6185 (tmt170) REVERT: P 157 ASN cc_start: 0.6698 (t0) cc_final: 0.6490 (t0) REVERT: P 167 MET cc_start: 0.8189 (mtp) cc_final: 0.7723 (mtp) REVERT: P 183 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7642 (tt) REVERT: P 234 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7764 (mttm) REVERT: P 305 ARG cc_start: 0.7514 (ttm110) cc_final: 0.7157 (ttm-80) REVERT: P 316 GLU cc_start: 0.7964 (tt0) cc_final: 0.7085 (pp20) REVERT: P 391 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: P 442 LYS cc_start: 0.8283 (tptp) cc_final: 0.7448 (ptpp) REVERT: P 492 LYS cc_start: 0.8446 (tttp) cc_final: 0.8175 (tttp) REVERT: P 500 LYS cc_start: 0.7606 (mptp) cc_final: 0.7353 (mmtt) REVERT: P 503 ASP cc_start: 0.8157 (m-30) cc_final: 0.7410 (t70) REVERT: P 525 ASP cc_start: 0.7764 (m-30) cc_final: 0.7178 (t0) REVERT: P 537 GLU cc_start: 0.7174 (tt0) cc_final: 0.6859 (pt0) REVERT: P 553 LYS cc_start: 0.7715 (mmtm) cc_final: 0.7340 (mppt) REVERT: P 571 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.5624 (mpm) REVERT: P 597 LYS cc_start: 0.7410 (mttt) cc_final: 0.6845 (mmmt) REVERT: P 674 LYS cc_start: 0.6597 (OUTLIER) cc_final: 0.6172 (mppt) REVERT: R 52 MET cc_start: 0.8974 (ttt) cc_final: 0.8373 (ttt) REVERT: R 75 ARG cc_start: 0.7495 (tpp-160) cc_final: 0.7236 (tpp-160) REVERT: R 125 MET cc_start: 0.5533 (pp-130) cc_final: 0.5178 (ppp) REVERT: R 145 MET cc_start: 0.8132 (ppp) cc_final: 0.7464 (ppp) REVERT: R 146 MET cc_start: 0.7206 (mtt) cc_final: 0.6777 (ttt) outliers start: 49 outliers final: 32 residues processed: 236 average time/residue: 1.3163 time to fit residues: 342.4819 Evaluate side-chains 243 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 102 MET Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 323 ILE Chi-restraints excluded: chain P residue 329 GLU Chi-restraints excluded: chain P residue 381 VAL Chi-restraints excluded: chain P residue 391 GLU Chi-restraints excluded: chain P residue 444 ILE Chi-restraints excluded: chain P residue 482 VAL Chi-restraints excluded: chain P residue 571 MET Chi-restraints excluded: chain P residue 578 GLU Chi-restraints excluded: chain P residue 605 VAL Chi-restraints excluded: chain P residue 674 LYS Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain P residue 697 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 152 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 30 optimal weight: 0.0470 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 103 optimal weight: 0.2980 chunk 183 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 395 HIS ** P 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.153933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.125352 restraints weight = 22573.152| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.02 r_work: 0.3548 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16072 Z= 0.127 Angle : 0.593 13.609 21746 Z= 0.296 Chirality : 0.042 0.193 2394 Planarity : 0.004 0.056 2808 Dihedral : 7.287 108.825 2211 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.19 % Rotamer: Outliers : 2.83 % Allowed : 20.07 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.67 (0.19), residues: 1960 helix: 0.59 (0.17), residues: 942 sheet: -0.09 (0.32), residues: 254 loop : 0.74 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 648 HIS 0.004 0.001 HIS C 275 PHE 0.017 0.001 PHE R 69 TYR 0.019 0.001 TYR P 629 ARG 0.012 0.000 ARG P 305 Details of bonding type rmsd hydrogen bonds : bond 0.03108 ( 781) hydrogen bonds : angle 4.54727 ( 2088) covalent geometry : bond 0.00295 (16072) covalent geometry : angle 0.59347 (21746) =============================================================================== Job complete usr+sys time: 13756.16 seconds wall clock time: 237 minutes 4.77 seconds (14224.77 seconds total)