Starting phenix.real_space_refine on Mon Apr 6 10:32:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8crs_26957/04_2026/8crs_26957.cif Found real_map, /net/cci-nas-00/data/ceres_data/8crs_26957/04_2026/8crs_26957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8crs_26957/04_2026/8crs_26957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8crs_26957/04_2026/8crs_26957.map" model { file = "/net/cci-nas-00/data/ceres_data/8crs_26957/04_2026/8crs_26957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8crs_26957/04_2026/8crs_26957.cif" } resolution = 2.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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 Mo 2 10.26 5 Fe 32 7.16 5 S 142 5.16 5 C 10296 2.51 5 N 2710 2.21 5 O 4706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17888 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {'1N7': 1, 'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {' FE': 1, '1N7': 2, 'CLF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' FE': 1, '1N7': 1, 'CLF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 343 Classifications: {'water': 343} Link IDs: {None: 342} Chain: "B" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 520 Classifications: {'water': 520} Link IDs: {None: 519} Chain: "C" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 315 Classifications: {'water': 315} Link IDs: {None: 314} Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 514 Classifications: {'water': 514} Link IDs: {None: 513} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 72.296 29.726 57.718 1.00 26.58 S ATOM 1170 SG CYS A 154 87.647 40.792 45.504 1.00 21.56 S ATOM 4549 SG CYS B 95 83.763 42.938 42.608 1.00 31.78 S ATOM 465 SG CYS A 62 81.899 39.378 47.987 1.00 19.53 S ATOM 652 SG CYS A 88 84.273 45.696 47.812 1.00 22.26 S ATOM 652 SG CYS A 88 84.273 45.696 47.812 1.00 22.26 S ATOM 5002 SG CYS B 153 88.254 45.480 44.148 1.00 33.02 S ATOM 4369 SG CYS B 70 82.615 49.630 42.687 1.00 28.57 S ATOM 4549 SG CYS B 95 83.763 42.938 42.608 1.00 31.78 S ATOM 10053 SG CYS C 275 38.130 98.999 57.789 1.00 26.52 S ATOM 9134 SG CYS C 154 22.859 87.896 45.508 1.00 21.04 S ATOM 12513 SG CYS D 95 26.734 85.706 42.618 1.00 30.17 S ATOM 8429 SG CYS C 62 28.601 89.326 47.993 1.00 19.48 S ATOM 8616 SG CYS C 88 26.245 83.072 47.781 1.00 22.88 S ATOM 8616 SG CYS C 88 26.245 83.072 47.781 1.00 22.88 S ATOM 12966 SG CYS D 153 22.230 83.223 44.155 1.00 26.81 S ATOM 12333 SG CYS D 70 27.931 79.052 42.817 1.00 24.97 S ATOM 12513 SG CYS D 95 26.734 85.706 42.618 1.00 30.17 S Time building chain proxies: 4.69, per 1000 atoms: 0.26 Number of scatterers: 17888 At special positions: 0 Unit cell: (111.15, 128.7, 96.2, 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) Mo 2 41.97 Fe 32 26.01 S 142 16.00 O 4706 8.00 N 2710 7.00 C 10296 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 653.6 milliseconds 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 12 sheets defined 58.8% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.975A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.591A pdb=" N GLY A 157 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.627A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.225A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 4.551A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.235A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 264 Processing helix chain 'A' and resid 265 through 268 Processing helix chain 'A' and resid 275 through 291 removed outlier: 5.780A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.147A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.562A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.588A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.511A pdb=" N TRP A 472 " --> pdb=" O ASN A 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 31 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 70 through 80 removed outlier: 4.014A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.974A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.857A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 320 through 337 removed outlier: 4.203A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.191A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.596A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 4.038A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 30 removed outlier: 3.963A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 4.294A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.630A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.218A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 4.539A pdb=" N ARG C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 245 removed outlier: 4.249A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 264 Processing helix chain 'C' and resid 265 through 268 Processing helix chain 'C' and resid 275 through 291 removed outlier: 5.758A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'C' and resid 317 through 347 Proline residue: C 333 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 370 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.175A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 434 removed outlier: 4.533A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.629A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.558A pdb=" N TRP C 472 " --> pdb=" O ASN C 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 31 Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 70 through 80 removed outlier: 4.009A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.970A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.861A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 320 through 337 removed outlier: 4.174A pdb=" N TRP D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.194A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.584A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.026A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.149A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.966A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 7.315A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 225 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP A 222 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU A 272 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA A 224 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.379A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.623A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.152A pdb=" N VAL C 351 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 376 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.953A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 7.750A pdb=" N VAL C 223 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN C 252 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE C 225 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N SER C 254 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY C 227 " --> pdb=" O SER C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.354A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.514A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) 787 hydrogen bonds defined for protein. 2253 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: 3.76 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.54: 16210 1.54 - 1.90: 316 1.90 - 2.25: 32 2.25 - 2.60: 86 2.60 - 2.96: 18 Bond restraints: 16662 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 2.958 -0.758 2.00e-02 2.50e+03 1.44e+03 bond pdb="FE2 CLF B 601 " pdb="FE8 CLF B 601 " ideal model delta sigma weight residual 2.200 2.958 -0.758 2.00e-02 2.50e+03 1.43e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 2.893 -0.693 2.00e-02 2.50e+03 1.20e+03 bond pdb="FE4 CLF B 601 " pdb="FE5 CLF B 601 " ideal model delta sigma weight residual 2.200 2.891 -0.691 2.00e-02 2.50e+03 1.19e+03 bond pdb="FE6 CLF D 602 " pdb="FE7 CLF D 602 " ideal model delta sigma weight residual 2.200 2.861 -0.661 2.00e-02 2.50e+03 1.09e+03 ... (remaining 16657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.85: 22500 6.85 - 13.70: 11 13.70 - 20.56: 5 20.56 - 27.41: 0 27.41 - 34.26: 4 Bond angle restraints: 22520 Sorted by residual: angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.74 34.26 3.00e+00 1.11e-01 1.30e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE4 CLF B 601 " ideal model delta sigma weight residual 90.00 55.74 34.26 3.00e+00 1.11e-01 1.30e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 56.95 33.05 3.00e+00 1.11e-01 1.21e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE1 CLF B 601 " ideal model delta sigma weight residual 90.00 56.97 33.03 3.00e+00 1.11e-01 1.21e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE3 CLF B 601 " ideal model delta sigma weight residual 90.00 106.72 -16.72 3.00e+00 1.11e-01 3.11e+01 ... (remaining 22515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.25: 9337 20.25 - 40.51: 838 40.51 - 60.76: 199 60.76 - 81.02: 41 81.02 - 101.27: 11 Dihedral angle restraints: 10426 sinusoidal: 4692 harmonic: 5734 Sorted by residual: dihedral pdb=" CA PHE B 367 " pdb=" C PHE B 367 " pdb=" N ALA B 368 " pdb=" CA ALA B 368 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ILE C 75 " pdb=" C ILE C 75 " pdb=" N LYS C 76 " pdb=" CA LYS C 76 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ILE A 75 " pdb=" C ILE A 75 " pdb=" N LYS A 76 " pdb=" CA LYS A 76 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 10423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.457: 2378 0.457 - 0.914: 0 0.914 - 1.371: 0 1.371 - 1.828: 0 1.828 - 2.285: 4 Chirality restraints: 2382 Sorted by residual: chirality pdb=" C31 1N7 A 503 " pdb=" C28 1N7 A 503 " pdb=" C32 1N7 A 503 " pdb=" O5 1N7 A 503 " both_signs ideal model delta sigma weight residual False -2.34 -0.05 -2.29 2.00e-01 2.50e+01 1.31e+02 chirality pdb=" C31 1N7 D 603 " pdb=" C28 1N7 D 603 " pdb=" C32 1N7 D 603 " pdb=" O5 1N7 D 603 " both_signs ideal model delta sigma weight residual False -2.34 -0.07 -2.27 2.00e-01 2.50e+01 1.29e+02 chirality pdb=" C31 1N7 B 603 " pdb=" C28 1N7 B 603 " pdb=" C32 1N7 B 603 " pdb=" O5 1N7 B 603 " both_signs ideal model delta sigma weight residual False -2.34 -0.07 -2.27 2.00e-01 2.50e+01 1.29e+02 ... (remaining 2379 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 436 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO C 437 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 437 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 437 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 102 " -0.016 2.00e-02 2.50e+03 1.25e-02 3.14e+00 pdb=" CG TYR D 102 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR D 102 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR D 102 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 102 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 102 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 102 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 102 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 96 " -0.152 9.50e-02 1.11e+02 6.82e-02 2.93e+00 pdb=" NE ARG C 96 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG C 96 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 96 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C 96 " -0.007 2.00e-02 2.50e+03 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 249 2.45 - 3.06: 12913 3.06 - 3.67: 33207 3.67 - 4.29: 53563 4.29 - 4.90: 79498 Nonbonded interactions: 179430 Sorted by model distance: nonbonded pdb=" OE2 GLU D 109 " pdb=" O HOH D 701 " model vdw 1.832 3.040 nonbonded pdb=" OE2 GLU B 109 " pdb=" O HOH B 701 " model vdw 1.859 3.040 nonbonded pdb="FE FE B 604 " pdb=" O HOH B 704 " model vdw 2.035 2.260 nonbonded pdb="FE FE D 601 " pdb=" O HOH D 704 " model vdw 2.044 2.260 nonbonded pdb="FE FE B 604 " pdb=" O HOH D 701 " model vdw 2.054 2.260 ... (remaining 179425 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 'A' and resid 4 through 502) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 2 through 523 or resid 603)) selection = (chain 'D' and (resid 2 through 523 or resid 603)) } 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: 18.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.520 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 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 : 0.025 0.758 16678 Z= 1.226 Angle : 0.856 34.259 22520 Z= 0.380 Chirality : 0.105 2.285 2382 Planarity : 0.005 0.068 2860 Dihedral : 16.419 101.275 6762 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.99 % Allowed : 12.25 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 1990 helix: 1.26 (0.16), residues: 968 sheet: -0.56 (0.36), residues: 180 loop : -0.40 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 96 TYR 0.030 0.002 TYR D 102 PHE 0.018 0.002 PHE D 31 TRP 0.013 0.002 TRP C 253 HIS 0.008 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.02446 (16662) covalent geometry : angle 0.85606 (22520) hydrogen bonds : bond 0.12499 ( 787) hydrogen bonds : angle 6.75136 ( 2253) Misc. bond : bond 0.09548 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.772 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 201 average time/residue: 0.8475 time to fit residues: 185.8515 Evaluate side-chains 192 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 150 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 384 ASN B 268 GLN C 98 ASN D 268 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.094274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.078129 restraints weight = 17450.351| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.08 r_work: 0.2775 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 16678 Z= 0.177 Angle : 0.725 29.181 22520 Z= 0.345 Chirality : 0.045 0.141 2382 Planarity : 0.004 0.066 2860 Dihedral : 8.075 94.364 2867 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.39 % Allowed : 11.85 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.18), residues: 1990 helix: 1.30 (0.16), residues: 1002 sheet: -0.65 (0.36), residues: 184 loop : -0.28 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 96 TYR 0.020 0.002 TYR D 102 PHE 0.015 0.002 PHE D 31 TRP 0.013 0.002 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00370 (16662) covalent geometry : angle 0.72459 (22520) hydrogen bonds : bond 0.05217 ( 787) hydrogen bonds : angle 5.76787 ( 2253) Misc. bond : bond 0.08974 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.750 Fit side-chains REVERT: A 392 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8310 (pttt) REVERT: B 50 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8355 (tppt) REVERT: B 177 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8082 (t0) outliers start: 24 outliers final: 10 residues processed: 194 average time/residue: 0.8558 time to fit residues: 181.0159 Evaluate side-chains 191 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 417 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 78 optimal weight: 0.0970 chunk 85 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 384 ASN B 268 GLN C 98 ASN D 268 GLN D 317 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.093194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.076979 restraints weight = 17784.318| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.10 r_work: 0.2777 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.219 16678 Z= 0.195 Angle : 0.727 29.264 22520 Z= 0.346 Chirality : 0.046 0.144 2382 Planarity : 0.004 0.074 2860 Dihedral : 7.809 89.918 2856 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.51 % Allowed : 12.49 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.18), residues: 1990 helix: 1.28 (0.16), residues: 1002 sheet: -0.61 (0.37), residues: 182 loop : -0.28 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 96 TYR 0.018 0.002 TYR D 102 PHE 0.016 0.002 PHE A 431 TRP 0.013 0.002 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00406 (16662) covalent geometry : angle 0.72743 (22520) hydrogen bonds : bond 0.05412 ( 787) hydrogen bonds : angle 5.70191 ( 2253) Misc. bond : bond 0.10334 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.733 Fit side-chains REVERT: A 318 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7143 (pp20) REVERT: B 50 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8362 (tppt) REVERT: C 318 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7156 (pp20) outliers start: 26 outliers final: 12 residues processed: 195 average time/residue: 0.8458 time to fit residues: 179.9621 Evaluate side-chains 194 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 417 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 122 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 167 optimal weight: 0.4980 chunk 181 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 268 GLN C 98 ASN D 268 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.092487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.076206 restraints weight = 17663.963| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.09 r_work: 0.2764 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.225 16678 Z= 0.215 Angle : 0.741 29.309 22520 Z= 0.354 Chirality : 0.047 0.145 2382 Planarity : 0.005 0.081 2860 Dihedral : 7.685 91.695 2856 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.28 % Allowed : 12.49 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 1990 helix: 1.25 (0.16), residues: 1002 sheet: -0.52 (0.37), residues: 180 loop : -0.33 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 96 TYR 0.019 0.002 TYR C 446 PHE 0.017 0.002 PHE A 431 TRP 0.014 0.002 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00458 (16662) covalent geometry : angle 0.74126 (22520) hydrogen bonds : bond 0.05645 ( 787) hydrogen bonds : angle 5.72221 ( 2253) Misc. bond : bond 0.10587 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.723 Fit side-chains REVERT: A 318 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7138 (pp20) REVERT: B 50 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8366 (tppt) REVERT: C 318 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7177 (pp20) outliers start: 22 outliers final: 12 residues processed: 193 average time/residue: 0.8349 time to fit residues: 175.8519 Evaluate side-chains 194 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 417 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 94 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 0.0770 chunk 187 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 268 GLN C 98 ASN D 268 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.094614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.078477 restraints weight = 17763.456| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.10 r_work: 0.2781 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 16678 Z= 0.157 Angle : 0.699 29.191 22520 Z= 0.328 Chirality : 0.044 0.142 2382 Planarity : 0.004 0.062 2860 Dihedral : 7.421 92.738 2856 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.45 % Allowed : 12.49 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 1990 helix: 1.36 (0.16), residues: 1002 sheet: -0.58 (0.37), residues: 182 loop : -0.27 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 25 TYR 0.016 0.002 TYR A 387 PHE 0.014 0.001 PHE C 429 TRP 0.014 0.002 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00322 (16662) covalent geometry : angle 0.69904 (22520) hydrogen bonds : bond 0.04792 ( 787) hydrogen bonds : angle 5.56789 ( 2253) Misc. bond : bond 0.08606 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.641 Fit side-chains REVERT: A 318 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7115 (pp20) REVERT: B 50 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8366 (tppt) REVERT: C 318 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7077 (pp20) outliers start: 25 outliers final: 13 residues processed: 195 average time/residue: 0.8350 time to fit residues: 178.0876 Evaluate side-chains 193 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 71 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 268 GLN C 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.092804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.076567 restraints weight = 17510.575| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.09 r_work: 0.2771 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.219 16678 Z= 0.205 Angle : 0.734 29.315 22520 Z= 0.349 Chirality : 0.046 0.145 2382 Planarity : 0.004 0.077 2860 Dihedral : 7.403 91.517 2856 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.39 % Allowed : 12.54 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 1990 helix: 1.28 (0.16), residues: 1002 sheet: -0.60 (0.36), residues: 182 loop : -0.30 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 96 TYR 0.018 0.002 TYR C 446 PHE 0.017 0.002 PHE A 431 TRP 0.013 0.002 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00434 (16662) covalent geometry : angle 0.73362 (22520) hydrogen bonds : bond 0.05483 ( 787) hydrogen bonds : angle 5.66824 ( 2253) Misc. bond : bond 0.10224 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.662 Fit side-chains REVERT: A 318 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7133 (pp20) REVERT: A 475 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8673 (mp) REVERT: B 50 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8376 (tppt) REVERT: B 400 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8205 (mmtt) REVERT: C 318 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7162 (pp20) REVERT: C 475 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8642 (mp) REVERT: D 400 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8228 (mmtt) outliers start: 24 outliers final: 12 residues processed: 196 average time/residue: 0.8536 time to fit residues: 182.6786 Evaluate side-chains 197 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 400 LYS Chi-restraints excluded: chain D residue 417 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 189 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 157 optimal weight: 0.0770 chunk 165 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 268 GLN C 98 ASN D 268 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.095007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.078878 restraints weight = 17917.959| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.10 r_work: 0.2789 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 16678 Z= 0.151 Angle : 0.693 29.133 22520 Z= 0.324 Chirality : 0.044 0.143 2382 Planarity : 0.004 0.060 2860 Dihedral : 7.179 90.457 2856 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.51 % Allowed : 12.66 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.18), residues: 1990 helix: 1.38 (0.16), residues: 1002 sheet: -0.57 (0.37), residues: 182 loop : -0.26 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 25 TYR 0.017 0.002 TYR A 387 PHE 0.014 0.001 PHE C 429 TRP 0.014 0.002 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00306 (16662) covalent geometry : angle 0.69311 (22520) hydrogen bonds : bond 0.04665 ( 787) hydrogen bonds : angle 5.52375 ( 2253) Misc. bond : bond 0.08338 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.476 Fit side-chains REVERT: A 318 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7121 (pp20) REVERT: B 50 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8375 (tppt) REVERT: C 318 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7021 (pp20) outliers start: 26 outliers final: 13 residues processed: 200 average time/residue: 0.8114 time to fit residues: 177.2205 Evaluate side-chains 194 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 127 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 268 GLN C 98 ASN D 268 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.094922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.078803 restraints weight = 17814.623| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.10 r_work: 0.2788 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 16678 Z= 0.154 Angle : 0.697 29.189 22520 Z= 0.326 Chirality : 0.044 0.143 2382 Planarity : 0.004 0.060 2860 Dihedral : 7.069 88.548 2856 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.45 % Allowed : 12.72 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.18), residues: 1990 helix: 1.38 (0.16), residues: 1002 sheet: -0.49 (0.36), residues: 180 loop : -0.26 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 25 TYR 0.016 0.002 TYR A 387 PHE 0.014 0.001 PHE C 429 TRP 0.014 0.002 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00315 (16662) covalent geometry : angle 0.69703 (22520) hydrogen bonds : bond 0.04702 ( 787) hydrogen bonds : angle 5.51110 ( 2253) Misc. bond : bond 0.08535 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.706 Fit side-chains REVERT: A 318 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7099 (pp20) REVERT: A 475 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8670 (mp) REVERT: B 50 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8372 (tppt) REVERT: B 400 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8192 (mmtt) REVERT: C 318 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6994 (pp20) REVERT: D 400 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8216 (mmtt) outliers start: 25 outliers final: 16 residues processed: 198 average time/residue: 0.8236 time to fit residues: 177.9388 Evaluate side-chains 200 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 400 LYS Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 130 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 268 GLN C 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.092781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.076603 restraints weight = 17689.864| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.09 r_work: 0.2769 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.219 16678 Z= 0.204 Angle : 0.735 29.306 22520 Z= 0.349 Chirality : 0.046 0.146 2382 Planarity : 0.004 0.074 2860 Dihedral : 7.151 87.343 2856 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.57 % Allowed : 12.72 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.18), residues: 1990 helix: 1.29 (0.16), residues: 1002 sheet: -0.57 (0.36), residues: 182 loop : -0.28 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 25 TYR 0.018 0.002 TYR C 446 PHE 0.016 0.002 PHE A 431 TRP 0.013 0.002 TRP B 296 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00433 (16662) covalent geometry : angle 0.73487 (22520) hydrogen bonds : bond 0.05447 ( 787) hydrogen bonds : angle 5.65010 ( 2253) Misc. bond : bond 0.10169 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.781 Fit side-chains REVERT: A 318 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7187 (pp20) REVERT: A 475 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8663 (mp) REVERT: B 50 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8382 (tppt) REVERT: B 400 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8190 (mmtt) REVERT: C 318 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7166 (pp20) REVERT: D 400 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8201 (mmtt) outliers start: 27 outliers final: 14 residues processed: 196 average time/residue: 0.8757 time to fit residues: 187.1472 Evaluate side-chains 199 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 400 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 143 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 268 GLN C 98 ASN D 268 GLN D 418 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.094557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.078506 restraints weight = 17728.535| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.09 r_work: 0.2784 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 16678 Z= 0.158 Angle : 0.703 29.169 22520 Z= 0.330 Chirality : 0.044 0.143 2382 Planarity : 0.004 0.062 2860 Dihedral : 6.972 86.420 2854 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.34 % Allowed : 12.83 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.18), residues: 1990 helix: 1.37 (0.16), residues: 1002 sheet: -0.50 (0.36), residues: 180 loop : -0.29 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 25 TYR 0.017 0.002 TYR A 387 PHE 0.014 0.001 PHE C 429 TRP 0.014 0.002 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00323 (16662) covalent geometry : angle 0.70300 (22520) hydrogen bonds : bond 0.04788 ( 787) hydrogen bonds : angle 5.54123 ( 2253) Misc. bond : bond 0.08656 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.664 Fit side-chains REVERT: A 318 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7112 (pp20) REVERT: B 50 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8399 (tppt) REVERT: B 400 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8197 (mmtt) REVERT: C 318 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7106 (pp20) REVERT: D 400 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8199 (mmtt) outliers start: 23 outliers final: 14 residues processed: 193 average time/residue: 0.8503 time to fit residues: 179.1647 Evaluate side-chains 196 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 400 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 36 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 106 optimal weight: 0.0370 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 268 GLN C 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.095288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.079204 restraints weight = 17889.583| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.10 r_work: 0.2796 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 16678 Z= 0.149 Angle : 0.697 29.168 22520 Z= 0.325 Chirality : 0.044 0.143 2382 Planarity : 0.004 0.059 2860 Dihedral : 6.839 84.641 2854 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.28 % Allowed : 12.83 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.18), residues: 1990 helix: 1.40 (0.16), residues: 1002 sheet: -0.49 (0.36), residues: 180 loop : -0.25 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 25 TYR 0.016 0.002 TYR A 387 PHE 0.014 0.001 PHE C 429 TRP 0.014 0.001 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00304 (16662) covalent geometry : angle 0.69703 (22520) hydrogen bonds : bond 0.04579 ( 787) hydrogen bonds : angle 5.48939 ( 2253) Misc. bond : bond 0.08227 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7679.11 seconds wall clock time: 131 minutes 41.52 seconds (7901.52 seconds total)