Starting phenix.real_space_refine on Mon Apr 6 09:43:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8enm_28273/04_2026/8enm_28273.cif Found real_map, /net/cci-nas-00/data/ceres_data/8enm_28273/04_2026/8enm_28273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8enm_28273/04_2026/8enm_28273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8enm_28273/04_2026/8enm_28273.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8enm_28273/04_2026/8enm_28273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8enm_28273/04_2026/8enm_28273.map" } resolution = 2.14 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= 0.029 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 138 5.16 5 C 10171 2.51 5 N 2703 2.21 5 O 4676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 17722 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3795 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 456} Chain breaks: 1 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: 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: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 349 Classifications: {'water': 349} Link IDs: {None: 348} Chain: "B" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 501 Classifications: {'water': 501} Link IDs: {None: 500} Chain: "C" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 352 Classifications: {'water': 352} Link IDs: {None: 351} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 491 Classifications: {'water': 491} Link IDs: {None: 490} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 101.479 35.100 60.219 1.00 58.39 S ATOM 1170 SG CYS A 154 102.167 54.066 48.155 1.00 48.05 S ATOM 4554 SG CYS B 95 97.965 52.385 45.312 1.00 42.86 S ATOM 465 SG CYS A 62 99.641 48.644 50.636 1.00 42.49 S ATOM 652 SG CYS A 88 96.265 54.353 50.367 1.00 52.20 S ATOM 652 SG CYS A 88 96.265 54.353 50.367 1.00 52.20 S ATOM 5007 SG CYS B 153 98.864 57.269 46.752 1.00 42.07 S ATOM 4374 SG CYS B 70 92.115 55.465 45.213 1.00 43.29 S ATOM 4554 SG CYS B 95 97.965 52.385 45.312 1.00 42.86 S ATOM 10058 SG CYS C 275 25.928 50.699 60.212 1.00 55.56 S ATOM 9139 SG CYS C 154 25.232 31.735 48.155 1.00 47.90 S ATOM 12518 SG CYS D 95 29.429 33.419 45.311 1.00 41.67 S ATOM 8434 SG CYS C 62 27.760 37.155 50.638 1.00 41.78 S ATOM 8621 SG CYS C 88 31.136 31.446 50.368 1.00 50.60 S ATOM 8621 SG CYS C 88 31.136 31.446 50.368 1.00 50.60 S ATOM 12971 SG CYS D 153 28.525 28.554 46.748 1.00 41.78 S ATOM 12338 SG CYS D 70 35.287 30.331 45.217 1.00 44.64 S ATOM 12518 SG CYS D 95 29.429 33.419 45.311 1.00 41.67 S Time building chain proxies: 4.30, per 1000 atoms: 0.24 Number of scatterers: 17722 At special positions: 0 Unit cell: (128.05, 86.45, 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 138 16.00 O 4676 8.00 N 2703 7.00 C 10171 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: 1.43 Conformation dependent library (CDL) restraints added in 668.5 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: 3666 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 12 sheets defined 59.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.047A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 4.172A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.619A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.144A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 4.519A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.723A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 5.777A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.963A 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 removed outlier: 3.595A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.395A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 4.043A 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: 4.586A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.360A 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: 3.546A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.519A pdb=" N GLU B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) 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: 3.965A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.110A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.865A pdb=" N PHE B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) 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: 3.748A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 284 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: 4.178A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.206A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.868A 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: 3.565A 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: 3.960A 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: 4.027A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 93 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: 4.177A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.605A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.149A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 4.512A pdb=" N ARG C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.716A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 291 removed outlier: 5.779A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.971A 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: 4.398A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 4.057A 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: 4.590A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.363A 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: 3.598A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.520A pdb=" N GLU D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) 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: 3.967A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.115A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.870A pdb=" N PHE D 125 " --> pdb=" O ASP D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 159 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: 3.746A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 283 Processing helix chain 'D' and resid 284 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: 4.164A pdb=" N TRP D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.197A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.856A 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: 3.574A 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: 3.959A 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: 6.140A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.267A 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: 7.023A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.144A 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: 7.288A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 225 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP A 222 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU A 272 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA A 224 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN A 271 " --> pdb=" O MET A 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 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 250 through 253 removed outlier: 7.040A pdb=" N LYS B 223 " --> pdb=" O ASN B 289 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL B 291 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 6.368A 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: 8.346A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE B 367 " --> pdb=" O HIS B 392 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU B 394 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 369 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.235A pdb=" N VAL C 351 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY C 376 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.255A 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: 7.024A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.146A 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: 7.323A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP C 222 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU C 272 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA C 224 " --> pdb=" O LEU C 272 " (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 250 through 253 removed outlier: 7.032A pdb=" N LYS D 223 " --> pdb=" O ASN D 289 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N VAL D 291 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 6.365A 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: 8.341A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE D 367 " --> pdb=" O HIS D 392 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU D 394 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU D 369 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N MET D 442 " --> pdb=" O ILE D 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 776 hydrogen bonds defined for protein. 2214 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: 3.23 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 16168 1.57 - 1.91: 178 1.91 - 2.25: 34 2.25 - 2.60: 84 2.60 - 2.94: 18 Bond restraints: 16482 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 2.939 -0.739 2.00e-02 2.50e+03 1.37e+03 bond pdb="FE2 CLF B 600 " pdb="FE8 CLF B 600 " ideal model delta sigma weight residual 2.200 2.939 -0.739 2.00e-02 2.50e+03 1.36e+03 bond pdb="FE4 CLF B 600 " pdb="FE5 CLF B 600 " ideal model delta sigma weight residual 2.200 2.917 -0.717 2.00e-02 2.50e+03 1.29e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 2.917 -0.717 2.00e-02 2.50e+03 1.28e+03 bond pdb="FE6 CLF B 600 " pdb="FE7 CLF B 600 " ideal model delta sigma weight residual 2.200 2.852 -0.652 2.00e-02 2.50e+03 1.06e+03 ... (remaining 16477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.85: 22226 6.85 - 13.70: 4 13.70 - 20.55: 2 20.55 - 27.39: 0 27.39 - 34.24: 4 Bond angle restraints: 22236 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 55.76 34.24 3.00e+00 1.11e-01 1.30e+02 angle pdb=" S1 CLF B 600 " pdb="FE2 CLF B 600 " pdb="FE4 CLF B 600 " ideal model delta sigma weight residual 90.00 55.77 34.23 3.00e+00 1.11e-01 1.30e+02 angle pdb=" S1 CLF B 600 " pdb="FE2 CLF B 600 " pdb="FE1 CLF B 600 " ideal model delta sigma weight residual 90.00 57.04 32.96 3.00e+00 1.11e-01 1.21e+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 57.05 32.95 3.00e+00 1.11e-01 1.21e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE3 CLF D 602 " ideal model delta sigma weight residual 90.00 107.19 -17.19 3.00e+00 1.11e-01 3.28e+01 ... (remaining 22231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 8988 17.78 - 35.56: 821 35.56 - 53.34: 202 53.34 - 71.13: 64 71.13 - 88.91: 21 Dihedral angle restraints: 10096 sinusoidal: 4360 harmonic: 5736 Sorted by residual: 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 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+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 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA SER B 11 " pdb=" C SER B 11 " pdb=" N TYR B 12 " pdb=" CA TYR B 12 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 10093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1138 0.026 - 0.052: 702 0.052 - 0.079: 292 0.079 - 0.105: 130 0.105 - 0.131: 73 Chirality restraints: 2335 Sorted by residual: chirality pdb=" CA ILE A 81 " pdb=" N ILE A 81 " pdb=" C ILE A 81 " pdb=" CB ILE A 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE C 81 " pdb=" N ILE C 81 " pdb=" C ILE C 81 " pdb=" CB ILE C 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA PRO B 72 " pdb=" N PRO B 72 " pdb=" C PRO B 72 " pdb=" CB PRO B 72 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 2332 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 359 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO C 360 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 360 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 360 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 73 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO A 74 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 73 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 74 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.022 5.00e-02 4.00e+02 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 568 2.62 - 3.19: 16223 3.19 - 3.76: 34377 3.76 - 4.33: 50671 4.33 - 4.90: 74172 Nonbonded interactions: 176011 Sorted by model distance: nonbonded pdb="FE FE D 601 " pdb=" O HOH B 881 " model vdw 2.045 2.260 nonbonded pdb="FE FE B 601 " pdb=" O HOH D 883 " model vdw 2.046 2.260 nonbonded pdb="FE FE B 601 " pdb=" O HOH B 727 " model vdw 2.094 2.260 nonbonded pdb="FE FE D 601 " pdb=" O HOH D 725 " model vdw 2.094 2.260 nonbonded pdb=" OE1 GLU D 508 " pdb=" O HOH D 701 " model vdw 2.137 3.040 ... (remaining 176006 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 480 or resid 600 through 601)) selection = chain 'C' } ncs_group { reference = (chain 'B' and resid 2 through 523) selection = (chain 'D' and resid 2 through 523) } 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: 12.590 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 16.790 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 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 : 0.024 0.739 16498 Z= 1.177 Angle : 0.746 34.243 22236 Z= 0.348 Chirality : 0.044 0.131 2335 Planarity : 0.004 0.040 2856 Dihedral : 15.504 88.907 6430 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.75 % Allowed : 10.51 % Favored : 88.73 % 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: 0.86 (0.18), residues: 1990 helix: 1.52 (0.17), residues: 969 sheet: -0.52 (0.36), residues: 193 loop : -0.21 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 359 TYR 0.018 0.002 TYR C 446 PHE 0.015 0.002 PHE B 31 TRP 0.014 0.002 TRP B 296 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.02345 (16482) covalent geometry : angle 0.74613 (22236) hydrogen bonds : bond 0.12907 ( 776) hydrogen bonds : angle 6.55181 ( 2214) Misc. bond : bond 0.12075 ( 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 170 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.648 Fit side-chains REVERT: A 445 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8160 (m-30) outliers start: 13 outliers final: 8 residues processed: 169 average time/residue: 0.8154 time to fit residues: 150.7473 Evaluate side-chains 163 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 98 ASN B 518 ASN C 29 ASN C 98 ASN D 518 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.085405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.068014 restraints weight = 17463.809| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 1.23 r_work: 0.2594 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.223 16498 Z= 0.237 Angle : 0.748 29.105 22236 Z= 0.360 Chirality : 0.048 0.143 2335 Planarity : 0.005 0.070 2856 Dihedral : 5.601 58.260 2529 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.97 % Allowed : 9.35 % Favored : 88.68 % 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: 1.34 (0.16), residues: 994 sheet: -0.53 (0.37), residues: 189 loop : -0.13 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.021 0.002 TYR C 446 PHE 0.018 0.002 PHE D 31 TRP 0.014 0.002 TRP B 296 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00518 (16482) covalent geometry : angle 0.74822 (22236) hydrogen bonds : bond 0.05636 ( 776) hydrogen bonds : angle 5.72814 ( 2214) Misc. bond : bond 0.11140 ( 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 195 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.494 Fit side-chains REVERT: A 445 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: B 120 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8095 (mt-10) REVERT: C 25 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.8155 (ttp-110) outliers start: 34 outliers final: 15 residues processed: 182 average time/residue: 0.8022 time to fit residues: 159.7096 Evaluate side-chains 172 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 53 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 98 ASN C 29 ASN C 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.087027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.069448 restraints weight = 17560.367| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 1.24 r_work: 0.2620 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 16498 Z= 0.176 Angle : 0.707 29.233 22236 Z= 0.334 Chirality : 0.045 0.142 2335 Planarity : 0.004 0.057 2856 Dihedral : 5.408 58.577 2527 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.63 % Allowed : 9.99 % Favored : 88.39 % 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: 0.86 (0.19), residues: 1990 helix: 1.41 (0.17), residues: 993 sheet: -0.58 (0.36), residues: 202 loop : -0.07 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.016 0.002 TYR C 446 PHE 0.013 0.002 PHE D 31 TRP 0.014 0.002 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00372 (16482) covalent geometry : angle 0.70654 (22236) hydrogen bonds : bond 0.04889 ( 776) hydrogen bonds : angle 5.54523 ( 2214) Misc. bond : bond 0.09296 ( 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 185 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.712 Fit side-chains REVERT: A 445 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8021 (m-30) REVERT: B 120 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8064 (mt-10) outliers start: 28 outliers final: 14 residues processed: 179 average time/residue: 0.7968 time to fit residues: 156.7177 Evaluate side-chains 171 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 145 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 158 optimal weight: 0.0970 chunk 177 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 98 ASN C 29 ASN C 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.085990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.068726 restraints weight = 17569.908| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 1.24 r_work: 0.2606 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.200 16498 Z= 0.197 Angle : 0.718 29.242 22236 Z= 0.341 Chirality : 0.046 0.143 2335 Planarity : 0.004 0.062 2856 Dihedral : 5.448 59.084 2527 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.68 % Allowed : 9.99 % Favored : 88.33 % 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: 0.85 (0.19), residues: 1990 helix: 1.41 (0.17), residues: 993 sheet: -0.54 (0.36), residues: 202 loop : -0.10 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.017 0.002 TYR C 446 PHE 0.015 0.002 PHE D 31 TRP 0.014 0.002 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00427 (16482) covalent geometry : angle 0.71840 (22236) hydrogen bonds : bond 0.05122 ( 776) hydrogen bonds : angle 5.52660 ( 2214) Misc. bond : bond 0.09634 ( 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 187 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.657 Fit side-chains REVERT: A 445 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: B 120 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: C 476 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7814 (tp-100) REVERT: D 26 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8289 (mtpm) outliers start: 29 outliers final: 15 residues processed: 179 average time/residue: 0.7854 time to fit residues: 154.0023 Evaluate side-chains 172 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 98 ASN C 29 ASN C 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.087308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.070174 restraints weight = 17326.992| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 1.22 r_work: 0.2633 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.178 16498 Z= 0.165 Angle : 0.696 29.180 22236 Z= 0.327 Chirality : 0.045 0.142 2335 Planarity : 0.004 0.054 2856 Dihedral : 5.362 59.205 2527 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.45 % Allowed : 10.28 % Favored : 88.27 % 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: 0.91 (0.19), residues: 1990 helix: 1.46 (0.17), residues: 995 sheet: -0.51 (0.36), residues: 202 loop : -0.07 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.015 0.002 TYR B 88 PHE 0.013 0.001 PHE A 429 TRP 0.014 0.002 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00350 (16482) covalent geometry : angle 0.69622 (22236) hydrogen bonds : bond 0.04651 ( 776) hydrogen bonds : angle 5.43437 ( 2214) Misc. bond : bond 0.08589 ( 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 183 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.633 Fit side-chains REVERT: A 445 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8039 (m-30) REVERT: B 120 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7997 (mt-10) REVERT: C 476 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7780 (tp-100) REVERT: D 26 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8281 (mtpm) outliers start: 25 outliers final: 14 residues processed: 174 average time/residue: 0.8034 time to fit residues: 153.0630 Evaluate side-chains 172 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 71 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 98 ASN C 29 ASN C 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.087275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.070149 restraints weight = 17377.662| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 1.22 r_work: 0.2633 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 16498 Z= 0.165 Angle : 0.697 29.191 22236 Z= 0.327 Chirality : 0.045 0.142 2335 Planarity : 0.004 0.054 2856 Dihedral : 5.344 59.420 2527 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.74 % Allowed : 10.05 % Favored : 88.21 % 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: 0.91 (0.19), residues: 1990 helix: 1.46 (0.17), residues: 997 sheet: -0.51 (0.36), residues: 202 loop : -0.09 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.016 0.002 TYR B 88 PHE 0.013 0.001 PHE A 429 TRP 0.014 0.002 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00350 (16482) covalent geometry : angle 0.69746 (22236) hydrogen bonds : bond 0.04657 ( 776) hydrogen bonds : angle 5.40564 ( 2214) Misc. bond : bond 0.08596 ( 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 189 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.748 Fit side-chains REVERT: A 445 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8025 (m-30) REVERT: B 26 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8202 (mtpm) REVERT: B 120 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: C 445 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8237 (m-30) REVERT: C 476 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7775 (tp-100) REVERT: D 26 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8277 (mtpm) outliers start: 30 outliers final: 20 residues processed: 179 average time/residue: 0.7790 time to fit residues: 152.9033 Evaluate side-chains 181 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 47 ILE 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 445 ASP Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 165 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 445 ASP Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 503 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 5 optimal weight: 7.9990 chunk 151 optimal weight: 0.6980 chunk 171 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 48 optimal weight: 0.0870 chunk 163 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 183 optimal weight: 0.9980 chunk 53 optimal weight: 0.2980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 98 ASN C 29 ASN C 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.089308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.072323 restraints weight = 17417.628| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 1.23 r_work: 0.2673 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 16498 Z= 0.133 Angle : 0.674 29.120 22236 Z= 0.311 Chirality : 0.043 0.141 2335 Planarity : 0.004 0.045 2856 Dihedral : 5.215 59.105 2527 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.68 % Allowed : 10.28 % Favored : 88.04 % 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: 0.99 (0.19), residues: 1990 helix: 1.54 (0.17), residues: 997 sheet: -0.49 (0.36), residues: 202 loop : -0.06 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 25 TYR 0.014 0.001 TYR B 88 PHE 0.012 0.001 PHE A 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 0.00274 (16482) covalent geometry : angle 0.67357 (22236) hydrogen bonds : bond 0.04086 ( 776) hydrogen bonds : angle 5.29631 ( 2214) Misc. bond : bond 0.07214 ( 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 191 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.777 Fit side-chains REVERT: A 445 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: B 120 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: C 445 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8240 (m-30) REVERT: C 476 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7771 (tp-100) REVERT: D 26 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8284 (mtpm) outliers start: 29 outliers final: 15 residues processed: 183 average time/residue: 0.7854 time to fit residues: 157.4384 Evaluate side-chains 173 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 47 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 445 ASP Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 165 SER 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 445 ASP Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 26 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 18 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 61 optimal weight: 0.0670 chunk 39 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 98 ASN C 29 ASN C 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.087094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.069939 restraints weight = 17466.009| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 1.23 r_work: 0.2629 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 16498 Z= 0.177 Angle : 0.707 29.220 22236 Z= 0.331 Chirality : 0.045 0.143 2335 Planarity : 0.004 0.056 2856 Dihedral : 5.204 59.856 2522 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.80 % Allowed : 10.45 % Favored : 87.75 % 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: 0.94 (0.19), residues: 1990 helix: 1.49 (0.17), residues: 997 sheet: -0.47 (0.36), residues: 202 loop : -0.09 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.016 0.002 TYR B 88 PHE 0.013 0.002 PHE D 31 TRP 0.013 0.002 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00380 (16482) covalent geometry : angle 0.70710 (22236) hydrogen bonds : bond 0.04741 ( 776) hydrogen bonds : angle 5.37953 ( 2214) Misc. bond : bond 0.08842 ( 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 187 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.733 Fit side-chains REVERT: A 445 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: B 26 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8182 (mtpm) REVERT: B 120 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7982 (mt-10) REVERT: C 445 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8241 (m-30) REVERT: C 476 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7794 (tp-100) REVERT: D 26 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8285 (mtpm) outliers start: 31 outliers final: 15 residues processed: 177 average time/residue: 0.7631 time to fit residues: 148.1783 Evaluate side-chains 174 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 47 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 445 ASP Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 165 SER 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 445 ASP Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 7 optimal weight: 0.0870 chunk 83 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 125 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 98 ASN C 29 ASN C 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.088817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.071807 restraints weight = 17361.481| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 1.23 r_work: 0.2664 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 16498 Z= 0.140 Angle : 0.683 29.111 22236 Z= 0.316 Chirality : 0.044 0.142 2335 Planarity : 0.004 0.047 2856 Dihedral : 5.113 59.713 2522 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.45 % Allowed : 10.86 % Favored : 87.69 % 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: 0.99 (0.19), residues: 1990 helix: 1.55 (0.17), residues: 997 sheet: -0.46 (0.36), residues: 202 loop : -0.08 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.014 0.001 TYR B 88 PHE 0.012 0.001 PHE A 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 0.00291 (16482) covalent geometry : angle 0.68308 (22236) hydrogen bonds : bond 0.04212 ( 776) hydrogen bonds : angle 5.30402 ( 2214) Misc. bond : bond 0.07561 ( 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 182 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.783 Fit side-chains REVERT: A 445 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8009 (m-30) REVERT: B 120 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: C 445 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8213 (m-30) REVERT: C 476 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7787 (tp-100) REVERT: D 26 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8289 (mtpm) outliers start: 25 outliers final: 17 residues processed: 175 average time/residue: 0.7928 time to fit residues: 151.8999 Evaluate side-chains 174 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 47 ILE 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 445 ASP Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 165 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 445 ASP Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 91 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 0.0030 chunk 79 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 98 ASN C 29 ASN C 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.088233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.071188 restraints weight = 17353.601| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 1.23 r_work: 0.2652 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 16498 Z= 0.152 Angle : 0.693 29.173 22236 Z= 0.322 Chirality : 0.044 0.142 2335 Planarity : 0.004 0.050 2856 Dihedral : 5.135 59.999 2522 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.34 % Allowed : 10.98 % Favored : 87.69 % 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: 0.98 (0.19), residues: 1990 helix: 1.54 (0.17), residues: 997 sheet: -0.46 (0.35), residues: 202 loop : -0.09 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.015 0.002 TYR B 88 PHE 0.012 0.001 PHE A 429 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00319 (16482) covalent geometry : angle 0.69314 (22236) hydrogen bonds : bond 0.04397 ( 776) hydrogen bonds : angle 5.31822 ( 2214) Misc. bond : bond 0.08013 ( 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 182 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.727 Fit side-chains REVERT: A 445 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: B 120 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: C 445 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8228 (m-30) REVERT: C 476 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7795 (tp-100) outliers start: 23 outliers final: 17 residues processed: 176 average time/residue: 0.7921 time to fit residues: 152.7224 Evaluate side-chains 176 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 47 ILE 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 445 ASP Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 165 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 445 ASP Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 155 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 109 optimal weight: 0.0970 chunk 138 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 0.0370 chunk 9 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 29 ASN C 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.090334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.073388 restraints weight = 17520.595| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.23 r_work: 0.2693 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 16498 Z= 0.126 Angle : 0.673 29.084 22236 Z= 0.309 Chirality : 0.043 0.142 2335 Planarity : 0.004 0.041 2856 Dihedral : 5.028 59.810 2522 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.39 % Allowed : 10.86 % Favored : 87.75 % 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: 1.06 (0.19), residues: 1990 helix: 1.61 (0.17), residues: 997 sheet: -0.44 (0.36), residues: 196 loop : -0.05 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.013 0.001 TYR B 88 PHE 0.012 0.001 PHE A 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 0.00261 (16482) covalent geometry : angle 0.67293 (22236) hydrogen bonds : bond 0.03886 ( 776) hydrogen bonds : angle 5.23344 ( 2214) Misc. bond : bond 0.06777 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6264.04 seconds wall clock time: 107 minutes 40.82 seconds (6460.82 seconds total)