Starting phenix.real_space_refine on Sat Jul 4 03:57:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11ne_75858/07_2026/11ne_75858.cif Found real_map, /net/cci-nas-00/data/ceres_data/11ne_75858/07_2026/11ne_75858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11ne_75858/07_2026/11ne_75858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11ne_75858/07_2026/11ne_75858.map" model { file = "/net/cci-nas-00/data/ceres_data/11ne_75858/07_2026/11ne_75858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11ne_75858/07_2026/11ne_75858.cif" } resolution = 2.49 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= 0.009 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 139 5.16 5 C 10170 2.51 5 N 2702 2.21 5 O 4662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17707 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} bond proxies already assigned to first conformer: 3874 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: 2 Conformer: "A" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3871 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, 15 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 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, 15 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "A" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 341 Classifications: {'water': 341} Link IDs: {None: 340} Chain: "B" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 464 Classifications: {'water': 464} Link IDs: {None: 463} Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 381 Classifications: {'water': 381} Link IDs: {None: 380} Chain: "D" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 494 Classifications: {'water': 494} Link IDs: {None: 493} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 29.745 44.319 61.114 1.00 48.71 S ATOM 1170 SG CYS A 154 35.738 25.837 49.063 1.00 15.54 S ATOM 4552 SG CYS B 95 38.974 29.062 45.823 1.00 21.69 S ATOM 465 SG CYS A 62 36.289 31.947 51.449 1.00 10.15 S ATOM 652 SG CYS A 88 41.694 27.597 51.403 1.00 18.86 S ATOM 652 SG CYS A 88 41.694 27.597 51.403 1.00 18.86 S ATOM 5005 SG CYS B 153 40.156 23.675 47.402 1.00 23.16 S ATOM 4372 SG CYS B 70 45.761 28.097 45.780 1.00 16.87 S ATOM 4552 SG CYS B 95 38.974 29.062 45.823 1.00 21.69 S ATOM 10056 SG CYS C 275 106.832 55.753 61.037 1.00 26.69 S ATOM 12516 SG CYS D 95 97.564 70.850 45.794 1.00 18.81 S ATOM 9134 SG CYS C 154 100.883 74.115 49.103 1.00 17.56 S ATOM 8429 SG CYS C 62 100.407 67.983 51.450 1.00 13.99 S ATOM 8616 SG CYS C 88 94.931 72.147 51.451 1.00 17.76 S ATOM 8616 SG CYS C 88 94.931 72.147 51.451 1.00 17.76 S ATOM 12969 SG CYS D 153 96.482 76.198 47.391 1.00 20.35 S ATOM 12336 SG CYS D 70 90.805 71.782 45.790 1.00 15.68 S ATOM 12516 SG CYS D 95 97.564 70.850 45.794 1.00 18.81 S Time building chain proxies: 5.72, per 1000 atoms: 0.32 Number of scatterers: 17707 At special positions: 0 Unit cell: (136.71, 101.43, 100.695, 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 139 16.00 O 4662 8.00 N 2702 7.00 C 10170 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: 1.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 12 sheets defined 59.3% alpha, 8.7% 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: 3.999A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.812A pdb=" N LYS A 44 " --> pdb=" O GLN A 41 " (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 153 through 159 removed outlier: 3.735A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.766A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.282A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (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: 4.081A 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: 6.164A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.001A 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: 4.104A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 435 removed outlier: 4.097A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.643A 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: 3.722A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.841A 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: 3.533A 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 58 Processing helix chain 'B' and resid 70 through 81 removed outlier: 4.043A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.194A 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 158 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 216 removed outlier: 5.763A pdb=" N ASP B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP B 215 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.815A 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: 4.206A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.108A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.800A 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: 3.555A 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: 4.437A 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 29 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 removed outlier: 3.503A pdb=" N GLN C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) 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: 3.739A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.664A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.225A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 4.616A pdb=" N ARG C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 211' 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: 3.977A 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: 5.857A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 315 removed outlier: 3.646A pdb=" N LYS C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 343 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.399A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 4.037A 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: 4.593A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.401A 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: 3.654A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.831A 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 Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 70 through 80 removed outlier: 4.078A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.990A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 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 233 through 247 removed outlier: 3.779A 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 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.066A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 6.004A 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: 3.840A 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: 4.365A 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: 3.813A pdb=" N LEU A 399 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 401 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.348A 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: 6.891A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.130A 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: 7.008A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 225 " --> pdb=" O TRP A 253 " (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: 6.385A 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: 8.631A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.609A 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: 6.100A pdb=" N VAL C 351 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 376 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.339A 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: 6.974A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.155A 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: 7.139A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (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: 6.361A 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: 8.530A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2298 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: 3.50 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.84: 16347 1.84 - 2.48: 104 2.48 - 3.11: 25 3.11 - 3.75: 5 3.75 - 4.39: 2 Bond restraints: 16483 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 4.387 -2.187 2.00e-02 2.50e+03 1.20e+04 bond pdb="FE5 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.935 -1.735 2.00e-02 2.50e+03 7.53e+03 bond pdb=" S1 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 3.710 -1.510 2.00e-02 2.50e+03 5.70e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 3.707 -1.507 2.00e-02 2.50e+03 5.68e+03 bond pdb=" S1 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.663 -1.463 2.00e-02 2.50e+03 5.35e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.91: 22233 6.91 - 13.82: 4 13.82 - 20.74: 2 20.74 - 27.65: 0 27.65 - 34.56: 4 Bond angle restraints: 22243 Sorted by residual: angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 55.44 34.56 3.00e+00 1.11e-01 1.33e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.56 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE1 CLF B 602 " ideal model delta sigma weight residual 90.00 56.86 33.14 3.00e+00 1.11e-01 1.22e+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 60.80 29.20 3.00e+00 1.11e-01 9.47e+01 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE3 CLF D 602 " ideal model delta sigma weight residual 90.00 108.21 -18.21 3.00e+00 1.11e-01 3.69e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 9238 18.03 - 36.06: 689 36.06 - 54.09: 97 54.09 - 72.12: 49 72.12 - 90.15: 28 Dihedral angle restraints: 10101 sinusoidal: 4359 harmonic: 5742 Sorted by residual: dihedral pdb=" CA PHE D 367 " pdb=" C PHE D 367 " pdb=" N ALA D 368 " pdb=" CA ALA D 368 " ideal model delta harmonic sigma weight residual 180.00 157.05 22.95 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA SER D 11 " pdb=" C SER D 11 " pdb=" N TYR D 12 " pdb=" CA TYR D 12 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" C SER A 5 " pdb=" N SER A 5 " pdb=" CA SER A 5 " pdb=" CB SER A 5 " ideal model delta harmonic sigma weight residual -122.60 -131.31 8.71 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1710 0.054 - 0.109: 477 0.109 - 0.163: 115 0.163 - 0.218: 25 0.218 - 0.272: 9 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA SER A 423 " pdb=" N SER A 423 " pdb=" C SER A 423 " pdb=" CB SER A 423 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA SER A 5 " pdb=" N SER A 5 " pdb=" C SER A 5 " pdb=" CB SER A 5 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL A 351 " pdb=" CA VAL A 351 " pdb=" CG1 VAL A 351 " pdb=" CG2 VAL A 351 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 479 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C TRP C 479 " 0.050 2.00e-02 2.50e+03 pdb=" O TRP C 479 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU C 480 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 376 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.59e+00 pdb=" C GLY C 376 " 0.048 2.00e-02 2.50e+03 pdb=" O GLY C 376 " -0.018 2.00e-02 2.50e+03 pdb=" N THR C 377 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 379 " 0.027 2.00e-02 2.50e+03 1.77e-02 6.28e+00 pdb=" CG TYR A 379 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 379 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 379 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 379 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 379 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 379 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 379 " 0.029 2.00e-02 2.50e+03 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 761 2.67 - 3.23: 17419 3.23 - 3.78: 32670 3.78 - 4.34: 47361 4.34 - 4.90: 70006 Nonbonded interactions: 168217 Sorted by model distance: nonbonded pdb=" O ASN C 98 " pdb=" OD1 ASN C 98 " model vdw 2.111 3.040 nonbonded pdb=" OD2 ASP D 357 " pdb="FE FE D 601 " model vdw 2.116 3.000 nonbonded pdb=" OE2 GLU D 109 " pdb="FE FE B 601 " model vdw 2.141 3.000 nonbonded pdb=" O ARG D 108 " pdb="FE FE B 601 " model vdw 2.272 3.000 nonbonded pdb=" OG1 THR A 177 " pdb=" NZ LYS A 209 " model vdw 2.299 3.120 ... (remaining 168212 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 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 248 or resid 250 through 502)) selection = (chain 'C' and (resid 4 through 248 or resid 250 through 502)) } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.270 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 20.220 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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 : 0.039 2.187 16499 Z= 1.977 Angle : 0.927 34.561 22243 Z= 0.555 Chirality : 0.056 0.272 2336 Planarity : 0.005 0.066 2858 Dihedral : 14.013 90.147 6433 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.21 % Favored : 97.74 % Rotamer: Outliers : 0.64 % Allowed : 1.45 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.36 (0.18), residues: 1992 helix: 1.14 (0.17), residues: 966 sheet: -0.34 (0.38), residues: 166 loop : -0.61 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 310 TYR 0.029 0.002 TYR A 379 PHE 0.025 0.002 PHE A 431 TRP 0.022 0.002 TRP C 444 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.03848 / 1.94 (16483) covalent geometry : angle 0.92712 / 0.56 (22243) hydrogen bonds : bond 0.15229 / 10.50 ( 805) hydrogen bonds : angle 6.78129 / 4.89 ( 2298) Misc. bond : bond 0.18446 / 13.00 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 337 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 35 ASN cc_start: 0.7991 (t0) cc_final: 0.7551 (t0) REVERT: A 288 GLU cc_start: 0.7868 (tt0) cc_final: 0.7229 (mp0) REVERT: A 364 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7250 (mm) REVERT: A 415 ARG cc_start: 0.7427 (tpp80) cc_final: 0.6129 (tmt170) REVERT: B 7 LYS cc_start: 0.7797 (tttt) cc_final: 0.7541 (mptt) REVERT: B 171 LYS cc_start: 0.7733 (tttt) cc_final: 0.7513 (mtpt) REVERT: C 26 LYS cc_start: 0.7360 (mmpt) cc_final: 0.6999 (mtmt) REVERT: C 168 LYS cc_start: 0.7841 (mtpt) cc_final: 0.7629 (mmpt) REVERT: C 284 ARG cc_start: 0.7843 (mtt-85) cc_final: 0.7408 (mtm110) REVERT: C 332 LYS cc_start: 0.8009 (tttt) cc_final: 0.7779 (tttm) REVERT: C 362 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.7524 (m90) REVERT: C 393 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7861 (mm-30) REVERT: D 303 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7580 (mttt) REVERT: D 400 LYS cc_start: 0.8381 (mttp) cc_final: 0.8007 (mmmt) outliers start: 11 outliers final: 3 residues processed: 348 average time/residue: 0.8715 time to fit residues: 330.6691 Evaluate side-chains 195 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 190 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 ASN A 145 ASN A 298 ASN ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN C 98 ASN C 362 HIS C 432 GLN C 469 ASN D 128 GLN D 168 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.108905 restraints weight = 18712.364| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.38 r_work: 0.3263 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.314 16499 Z= 0.205 Angle : 0.715 30.005 22243 Z= 0.340 Chirality : 0.045 0.143 2336 Planarity : 0.004 0.039 2858 Dihedral : 5.890 59.404 2525 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.32 % Allowed : 9.34 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.64 (0.19), residues: 1992 helix: 1.35 (0.17), residues: 988 sheet: -0.51 (0.37), residues: 178 loop : -0.42 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 277 TYR 0.017 0.002 TYR A 229 PHE 0.015 0.001 PHE A 118 TRP 0.017 0.001 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (16483) covalent geometry : angle 0.71525 / 0.34 (22243) hydrogen bonds : bond 0.04784 / 3.32 ( 805) hydrogen bonds : angle 5.54365 / 3.99 ( 2298) Misc. bond : bond 0.12596 / 8.21 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7038 (pt0) REVERT: A 284 ARG cc_start: 0.8444 (mtt90) cc_final: 0.7060 (mtm110) REVERT: A 288 GLU cc_start: 0.7698 (tt0) cc_final: 0.6988 (mp0) REVERT: A 415 ARG cc_start: 0.7946 (tpp80) cc_final: 0.6992 (tmt170) REVERT: B 7 LYS cc_start: 0.7856 (tttt) cc_final: 0.7387 (mptt) REVERT: B 171 LYS cc_start: 0.7568 (tttt) cc_final: 0.7078 (mtpt) REVERT: B 454 ASP cc_start: 0.8294 (m-30) cc_final: 0.8068 (m-30) REVERT: C 26 LYS cc_start: 0.7172 (mmpt) cc_final: 0.6862 (mtmt) REVERT: C 51 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8361 (ptpp) REVERT: C 168 LYS cc_start: 0.7699 (mtpt) cc_final: 0.7285 (mmpt) REVERT: C 284 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7042 (mtm110) REVERT: C 332 LYS cc_start: 0.7826 (tttt) cc_final: 0.7435 (tttm) REVERT: C 362 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7479 (m-70) REVERT: C 393 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7572 (mm-30) REVERT: D 50 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.8001 (ttpt) REVERT: D 172 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: D 177 ASP cc_start: 0.7554 (m-30) cc_final: 0.7345 (t70) REVERT: D 303 LYS cc_start: 0.7861 (mtpp) cc_final: 0.7237 (mttt) outliers start: 40 outliers final: 9 residues processed: 212 average time/residue: 0.8112 time to fit residues: 188.9604 Evaluate side-chains 179 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 172 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 191 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 35 ASN ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 ASN ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 ASN D 58 GLN D 518 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106576 restraints weight = 18676.967| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.36 r_work: 0.3216 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.287 16499 Z= 0.182 Angle : 0.680 30.556 22243 Z= 0.318 Chirality : 0.044 0.145 2336 Planarity : 0.004 0.043 2858 Dihedral : 5.555 57.660 2519 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.86 % Allowed : 11.14 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.73 (0.19), residues: 1992 helix: 1.44 (0.17), residues: 1010 sheet: -0.54 (0.37), residues: 178 loop : -0.43 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 277 TYR 0.014 0.001 TYR C 379 PHE 0.012 0.001 PHE C 429 TRP 0.014 0.001 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (16483) covalent geometry : angle 0.68003 / 0.32 (22243) hydrogen bonds : bond 0.04467 / 3.10 ( 805) hydrogen bonds : angle 5.28643 / 3.80 ( 2298) Misc. bond : bond 0.10928 / 7.26 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7055 (pt0) REVERT: A 284 ARG cc_start: 0.8417 (mtt90) cc_final: 0.7139 (mtm110) REVERT: A 288 GLU cc_start: 0.7755 (tt0) cc_final: 0.7180 (mp0) REVERT: A 415 ARG cc_start: 0.7963 (tpp80) cc_final: 0.6986 (tmt170) REVERT: A 473 LYS cc_start: 0.8192 (mttt) cc_final: 0.7927 (mttp) REVERT: B 6 ASP cc_start: 0.7510 (m-30) cc_final: 0.7066 (p0) REVERT: B 7 LYS cc_start: 0.7893 (tttt) cc_final: 0.7294 (mptt) REVERT: B 171 LYS cc_start: 0.7577 (tttt) cc_final: 0.7162 (mtpt) REVERT: B 202 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7478 (tm-30) REVERT: B 279 GLU cc_start: 0.7818 (mm-30) cc_final: 0.6961 (tp30) REVERT: B 454 ASP cc_start: 0.8304 (m-30) cc_final: 0.8028 (m-30) REVERT: C 26 LYS cc_start: 0.7304 (mmpt) cc_final: 0.6969 (mtmt) REVERT: C 168 LYS cc_start: 0.7796 (mtpt) cc_final: 0.7371 (mmpt) REVERT: C 214 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7740 (t) REVERT: C 284 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7138 (mtm110) REVERT: C 332 LYS cc_start: 0.7786 (tttt) cc_final: 0.7422 (tttm) REVERT: C 393 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7728 (mm-30) REVERT: D 50 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8064 (ttpt) REVERT: D 172 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: D 211 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8103 (mtpt) REVERT: D 212 SER cc_start: 0.9013 (m) cc_final: 0.8794 (m) REVERT: D 303 LYS cc_start: 0.8011 (mtpp) cc_final: 0.7337 (mttt) REVERT: D 354 MET cc_start: 0.8873 (mtp) cc_final: 0.8643 (mtp) outliers start: 32 outliers final: 7 residues processed: 195 average time/residue: 0.8251 time to fit residues: 176.5762 Evaluate side-chains 177 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 211 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 49 ASN A 53 GLN A 98 ASN A 383 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN C 98 ASN C 383 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.098147 restraints weight = 28197.716| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.71 r_work: 0.3083 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.331 16499 Z= 0.245 Angle : 0.749 30.793 22243 Z= 0.357 Chirality : 0.048 0.143 2336 Planarity : 0.005 0.045 2858 Dihedral : 5.763 59.840 2519 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.44 % Allowed : 11.20 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.50 (0.18), residues: 1992 helix: 1.24 (0.16), residues: 998 sheet: -0.32 (0.37), residues: 174 loop : -0.58 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 277 TYR 0.020 0.002 TYR B 142 PHE 0.015 0.002 PHE C 429 TRP 0.016 0.002 TRP A 472 HIS 0.014 0.002 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.23 (16483) covalent geometry : angle 0.74877 / 0.36 (22243) hydrogen bonds : bond 0.05791 / 3.98 ( 805) hydrogen bonds : angle 5.43780 / 3.91 ( 2298) Misc. bond : bond 0.13003 / 8.56 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 288 GLU cc_start: 0.7945 (tt0) cc_final: 0.7358 (mp0) REVERT: A 352 MET cc_start: 0.9245 (mtp) cc_final: 0.9017 (mtp) REVERT: A 393 GLU cc_start: 0.6503 (tp30) cc_final: 0.5866 (mp0) REVERT: A 415 ARG cc_start: 0.8057 (tpp80) cc_final: 0.6801 (tmt170) REVERT: A 473 LYS cc_start: 0.8260 (mttt) cc_final: 0.7653 (mptp) REVERT: A 476 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: B 6 ASP cc_start: 0.7692 (m-30) cc_final: 0.7187 (p0) REVERT: B 7 LYS cc_start: 0.8000 (tttt) cc_final: 0.7278 (mptt) REVERT: B 171 LYS cc_start: 0.7659 (tttt) cc_final: 0.7257 (mtpt) REVERT: B 202 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: B 279 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7163 (tp30) REVERT: B 312 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7494 (mm-30) REVERT: C 26 LYS cc_start: 0.7549 (mmpt) cc_final: 0.7207 (mtmt) REVERT: C 51 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8501 (ptpp) REVERT: C 120 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: C 168 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7491 (mmpt) REVERT: C 214 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7696 (t) REVERT: C 284 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7199 (mtm110) REVERT: C 332 LYS cc_start: 0.8003 (tttt) cc_final: 0.7627 (tttm) REVERT: C 345 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7634 (mtp180) REVERT: C 347 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7394 (tp30) REVERT: C 393 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7776 (mm-30) REVERT: D 60 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: D 120 GLU cc_start: 0.7747 (tt0) cc_final: 0.7505 (mp0) REVERT: D 211 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8099 (mtpt) REVERT: D 354 MET cc_start: 0.8877 (mtp) cc_final: 0.8619 (mtp) REVERT: D 400 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7889 (mmmt) outliers start: 42 outliers final: 11 residues processed: 205 average time/residue: 0.8332 time to fit residues: 187.5341 Evaluate side-chains 183 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 400 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 186 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 98 ASN C 98 ASN D 58 GLN D 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.100632 restraints weight = 22108.353| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.50 r_work: 0.3155 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.275 16499 Z= 0.180 Angle : 0.675 30.582 22243 Z= 0.314 Chirality : 0.044 0.146 2336 Planarity : 0.004 0.043 2858 Dihedral : 5.444 58.367 2519 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.74 % Allowed : 11.84 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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 (0.19), residues: 1992 helix: 1.37 (0.17), residues: 1010 sheet: -0.35 (0.37), residues: 174 loop : -0.53 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.016 0.001 TYR A 229 PHE 0.011 0.001 PHE C 429 TRP 0.014 0.001 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (16483) covalent geometry : angle 0.67498 / 0.31 (22243) hydrogen bonds : bond 0.04423 / 3.06 ( 805) hydrogen bonds : angle 5.23802 / 3.76 ( 2298) Misc. bond : bond 0.10549 / 6.95 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8405 (mtt90) cc_final: 0.7088 (mtm110) REVERT: A 288 GLU cc_start: 0.7874 (tt0) cc_final: 0.7354 (mp0) REVERT: A 391 MET cc_start: 0.8382 (mtt) cc_final: 0.8143 (mtp) REVERT: A 415 ARG cc_start: 0.8056 (tpp80) cc_final: 0.6770 (tmt170) REVERT: A 476 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: B 6 ASP cc_start: 0.7643 (m-30) cc_final: 0.7112 (p0) REVERT: B 7 LYS cc_start: 0.7980 (tttt) cc_final: 0.7235 (mptt) REVERT: B 171 LYS cc_start: 0.7573 (tttt) cc_final: 0.7198 (mtpt) REVERT: B 202 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: B 212 SER cc_start: 0.8197 (p) cc_final: 0.7702 (m) REVERT: B 223 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8633 (mtmt) REVERT: B 279 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7198 (tp30) REVERT: B 312 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7443 (mm-30) REVERT: C 15 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6291 (tt0) REVERT: C 25 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7401 (ttm170) REVERT: C 26 LYS cc_start: 0.7426 (mmpt) cc_final: 0.7108 (mtmt) REVERT: C 51 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8495 (ptpp) REVERT: C 168 LYS cc_start: 0.7919 (mtpt) cc_final: 0.7446 (mmpt) REVERT: C 214 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7726 (t) REVERT: C 284 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.7158 (mtm110) REVERT: C 332 LYS cc_start: 0.7849 (tttt) cc_final: 0.7485 (tttm) REVERT: C 347 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7291 (tp30) REVERT: D 120 GLU cc_start: 0.7769 (tt0) cc_final: 0.7522 (mp0) REVERT: D 172 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: D 354 MET cc_start: 0.8847 (mtp) cc_final: 0.8581 (mtp) outliers start: 30 outliers final: 9 residues processed: 189 average time/residue: 0.8405 time to fit residues: 174.1393 Evaluate side-chains 177 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 44 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 138 optimal weight: 10.0000 chunk 88 optimal weight: 0.0470 chunk 99 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 187 optimal weight: 0.0970 chunk 39 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 98 ASN B 518 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 = 0.3443 r_free = 0.3443 target = 0.122208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103229 restraints weight = 31122.057| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.85 r_work: 0.3185 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.222 16499 Z= 0.146 Angle : 0.642 30.136 22243 Z= 0.293 Chirality : 0.042 0.145 2336 Planarity : 0.004 0.041 2858 Dihedral : 5.112 58.923 2519 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.45 % Allowed : 12.65 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.87 (0.19), residues: 1992 helix: 1.58 (0.17), residues: 1004 sheet: -0.35 (0.38), residues: 174 loop : -0.42 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 343 TYR 0.012 0.001 TYR A 229 PHE 0.011 0.001 PHE D 375 TRP 0.013 0.001 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (16483) covalent geometry : angle 0.64173 / 0.29 (22243) hydrogen bonds : bond 0.03591 / 2.51 ( 805) hydrogen bonds : angle 5.06769 / 3.65 ( 2298) Misc. bond : bond 0.08144 / 5.47 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8425 (mtt90) cc_final: 0.7106 (mtm110) REVERT: A 288 GLU cc_start: 0.7906 (tt0) cc_final: 0.7340 (mp0) REVERT: A 391 MET cc_start: 0.8292 (mtt) cc_final: 0.8057 (mtp) REVERT: A 415 ARG cc_start: 0.8076 (tpp80) cc_final: 0.6742 (tmt170) REVERT: B 6 ASP cc_start: 0.7594 (m-30) cc_final: 0.7069 (p0) REVERT: B 7 LYS cc_start: 0.7991 (tttt) cc_final: 0.7249 (mptt) REVERT: B 171 LYS cc_start: 0.7572 (tttt) cc_final: 0.7235 (mtpt) REVERT: B 212 SER cc_start: 0.8205 (p) cc_final: 0.7727 (m) REVERT: B 279 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7243 (tp30) REVERT: B 312 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7443 (mm-30) REVERT: C 26 LYS cc_start: 0.7416 (mmpt) cc_final: 0.7079 (mtmt) REVERT: C 120 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: C 168 LYS cc_start: 0.7922 (mtpt) cc_final: 0.7667 (mtpp) REVERT: C 214 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7826 (t) REVERT: C 284 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7167 (mtm110) REVERT: C 332 LYS cc_start: 0.7782 (tttt) cc_final: 0.7367 (tttm) REVERT: C 347 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7252 (tp30) REVERT: C 393 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7515 (mm-30) REVERT: D 299 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7509 (mt-10) outliers start: 25 outliers final: 10 residues processed: 189 average time/residue: 0.8035 time to fit residues: 167.3640 Evaluate side-chains 172 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 299 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 149 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.0000 chunk 188 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 98 ASN C 98 ASN D 518 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.103139 restraints weight = 24992.743| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.59 r_work: 0.3171 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.239 16499 Z= 0.170 Angle : 0.665 30.401 22243 Z= 0.306 Chirality : 0.043 0.144 2336 Planarity : 0.004 0.043 2858 Dihedral : 5.058 59.024 2519 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.39 % Allowed : 13.29 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.89 (0.19), residues: 1992 helix: 1.56 (0.17), residues: 1012 sheet: -0.23 (0.38), residues: 172 loop : -0.40 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 206 TYR 0.013 0.001 TYR C 379 PHE 0.012 0.001 PHE C 429 TRP 0.012 0.001 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (16483) covalent geometry : angle 0.66462 / 0.31 (22243) hydrogen bonds : bond 0.04177 / 2.90 ( 805) hydrogen bonds : angle 5.10878 / 3.68 ( 2298) Misc. bond : bond 0.09357 / 6.16 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7137 (pt0) REVERT: A 173 GLU cc_start: 0.7941 (tt0) cc_final: 0.7716 (tt0) REVERT: A 284 ARG cc_start: 0.8404 (mtt90) cc_final: 0.7127 (mtm110) REVERT: A 288 GLU cc_start: 0.7870 (tt0) cc_final: 0.7380 (mp0) REVERT: A 391 MET cc_start: 0.8304 (mtt) cc_final: 0.8057 (mtp) REVERT: A 415 ARG cc_start: 0.8064 (tpp80) cc_final: 0.6948 (tmt170) REVERT: A 476 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7815 (mm-40) REVERT: B 6 ASP cc_start: 0.7651 (m-30) cc_final: 0.7143 (p0) REVERT: B 7 LYS cc_start: 0.7990 (tttt) cc_final: 0.7257 (mptt) REVERT: B 171 LYS cc_start: 0.7519 (tttt) cc_final: 0.7218 (mtpt) REVERT: B 212 SER cc_start: 0.8164 (p) cc_final: 0.7695 (m) REVERT: B 279 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7196 (tp30) REVERT: B 312 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7456 (mm-30) REVERT: C 26 LYS cc_start: 0.7452 (mmpt) cc_final: 0.7157 (mtmt) REVERT: C 120 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: C 168 LYS cc_start: 0.7934 (mtpt) cc_final: 0.7691 (mtpp) REVERT: C 214 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7872 (t) REVERT: C 284 ARG cc_start: 0.8084 (mtt-85) cc_final: 0.7173 (mtm110) REVERT: C 332 LYS cc_start: 0.7845 (tttt) cc_final: 0.7436 (tttm) REVERT: C 347 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7268 (tp30) REVERT: C 393 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7549 (mm-30) REVERT: D 120 GLU cc_start: 0.7722 (tt0) cc_final: 0.7459 (mp0) REVERT: D 211 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8136 (mtpt) REVERT: D 299 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: D 354 MET cc_start: 0.8783 (mtp) cc_final: 0.8494 (mtp) outliers start: 24 outliers final: 10 residues processed: 182 average time/residue: 0.8287 time to fit residues: 165.5347 Evaluate side-chains 176 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 299 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 73 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 41 GLN A 98 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.102668 restraints weight = 27263.542| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.71 r_work: 0.3165 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.234 16499 Z= 0.165 Angle : 0.661 30.380 22243 Z= 0.304 Chirality : 0.043 0.144 2336 Planarity : 0.004 0.042 2858 Dihedral : 4.995 59.996 2519 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.51 % Allowed : 13.41 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.92 (0.19), residues: 1992 helix: 1.57 (0.17), residues: 1012 sheet: -0.21 (0.38), residues: 172 loop : -0.36 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 343 TYR 0.013 0.001 TYR C 379 PHE 0.011 0.001 PHE C 429 TRP 0.013 0.001 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (16483) covalent geometry : angle 0.66100 / 0.30 (22243) hydrogen bonds : bond 0.04041 / 2.81 ( 805) hydrogen bonds : angle 5.08253 / 3.66 ( 2298) Misc. bond : bond 0.09112 / 5.99 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7151 (pt0) REVERT: A 173 GLU cc_start: 0.7946 (tt0) cc_final: 0.7709 (tt0) REVERT: A 284 ARG cc_start: 0.8395 (mtt90) cc_final: 0.7095 (mtm110) REVERT: A 288 GLU cc_start: 0.7900 (tt0) cc_final: 0.7352 (mp0) REVERT: A 391 MET cc_start: 0.8349 (mtt) cc_final: 0.8110 (mtp) REVERT: A 393 GLU cc_start: 0.6269 (tp30) cc_final: 0.5845 (mp0) REVERT: A 415 ARG cc_start: 0.8084 (tpp80) cc_final: 0.6939 (tmt170) REVERT: A 476 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7811 (mm-40) REVERT: B 6 ASP cc_start: 0.7634 (m-30) cc_final: 0.7082 (p0) REVERT: B 7 LYS cc_start: 0.7977 (tttt) cc_final: 0.7160 (mptt) REVERT: B 171 LYS cc_start: 0.7539 (tttt) cc_final: 0.7227 (mtpt) REVERT: B 212 SER cc_start: 0.8194 (p) cc_final: 0.7721 (m) REVERT: B 279 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7198 (tp30) REVERT: B 312 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7438 (mm-30) REVERT: C 25 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7369 (ttm170) REVERT: C 26 LYS cc_start: 0.7468 (mmpt) cc_final: 0.7163 (mtmt) REVERT: C 120 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: C 168 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7647 (mtpp) REVERT: C 214 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7866 (t) REVERT: C 284 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7175 (mtm110) REVERT: C 332 LYS cc_start: 0.7808 (tttt) cc_final: 0.7401 (tttm) REVERT: D 120 GLU cc_start: 0.7743 (tt0) cc_final: 0.7474 (mp0) REVERT: D 211 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8133 (mtpt) REVERT: D 299 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: D 354 MET cc_start: 0.8779 (mtp) cc_final: 0.8487 (mtp) REVERT: D 379 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8250 (tt) REVERT: D 400 LYS cc_start: 0.8489 (mmtt) cc_final: 0.7885 (mmmt) outliers start: 26 outliers final: 12 residues processed: 186 average time/residue: 0.8256 time to fit residues: 168.5910 Evaluate side-chains 179 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 379 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 31 HIS A 41 GLN A 98 ASN B 518 ASN C 98 ASN D 518 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.098376 restraints weight = 31372.134| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.78 r_work: 0.3083 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.291 16499 Z= 0.226 Angle : 0.724 30.752 22243 Z= 0.342 Chirality : 0.046 0.142 2336 Planarity : 0.005 0.045 2858 Dihedral : 5.272 58.731 2519 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.68 % Allowed : 13.52 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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 (0.19), residues: 1992 helix: 1.35 (0.16), residues: 1014 sheet: -0.20 (0.38), residues: 172 loop : -0.52 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 277 TYR 0.018 0.002 TYR C 379 PHE 0.015 0.002 PHE C 429 TRP 0.015 0.002 TRP A 472 HIS 0.010 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (16483) covalent geometry : angle 0.72396 / 0.34 (22243) hydrogen bonds : bond 0.05283 / 3.64 ( 805) hydrogen bonds : angle 5.27710 / 3.80 ( 2298) Misc. bond : bond 0.11738 / 7.69 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7067 (pt0) REVERT: A 284 ARG cc_start: 0.8430 (mtt90) cc_final: 0.7341 (mtm110) REVERT: A 288 GLU cc_start: 0.7966 (tt0) cc_final: 0.7651 (mt-10) REVERT: A 391 MET cc_start: 0.8385 (mtt) cc_final: 0.8138 (mtp) REVERT: A 393 GLU cc_start: 0.6354 (tp30) cc_final: 0.5767 (mp0) REVERT: A 415 ARG cc_start: 0.8088 (tpp80) cc_final: 0.6848 (tmt170) REVERT: A 476 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7834 (mm-40) REVERT: B 6 ASP cc_start: 0.7687 (m-30) cc_final: 0.7197 (p0) REVERT: B 7 LYS cc_start: 0.8019 (tttt) cc_final: 0.7180 (mptt) REVERT: B 171 LYS cc_start: 0.7580 (tttt) cc_final: 0.7248 (mtpt) REVERT: B 212 SER cc_start: 0.8245 (p) cc_final: 0.7777 (m) REVERT: B 279 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7245 (tp30) REVERT: B 312 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7458 (mm-30) REVERT: C 25 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7397 (ttm170) REVERT: C 26 LYS cc_start: 0.7455 (mmpt) cc_final: 0.7150 (mtmt) REVERT: C 120 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: C 168 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7518 (mmpt) REVERT: C 214 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7811 (t) REVERT: C 284 ARG cc_start: 0.8124 (mtt-85) cc_final: 0.7207 (mtm110) REVERT: C 332 LYS cc_start: 0.7965 (tttt) cc_final: 0.7607 (tttm) REVERT: C 345 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7566 (mtp180) REVERT: C 393 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7649 (mm-30) REVERT: D 120 GLU cc_start: 0.7862 (tt0) cc_final: 0.7531 (mp0) REVERT: D 172 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: D 211 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8119 (mtpt) REVERT: D 299 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: D 354 MET cc_start: 0.8830 (mtp) cc_final: 0.8531 (mtp) REVERT: D 379 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8253 (tt) REVERT: D 400 LYS cc_start: 0.8561 (mmtt) cc_final: 0.7989 (mmmt) outliers start: 29 outliers final: 13 residues processed: 184 average time/residue: 0.8261 time to fit residues: 166.8060 Evaluate side-chains 185 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 379 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 100 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 41 GLN A 98 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.101765 restraints weight = 22269.247| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.51 r_work: 0.3146 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.260 16499 Z= 0.179 Angle : 0.676 30.529 22243 Z= 0.314 Chirality : 0.044 0.142 2336 Planarity : 0.004 0.044 2858 Dihedral : 5.054 55.848 2519 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.45 % Allowed : 13.87 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.78 (0.19), residues: 1992 helix: 1.48 (0.17), residues: 1010 sheet: -0.22 (0.38), residues: 172 loop : -0.48 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 206 TYR 0.015 0.001 TYR A 229 PHE 0.011 0.001 PHE C 429 TRP 0.013 0.001 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (16483) covalent geometry : angle 0.67629 / 0.31 (22243) hydrogen bonds : bond 0.04365 / 3.03 ( 805) hydrogen bonds : angle 5.16505 / 3.72 ( 2298) Misc. bond : bond 0.10134 / 6.66 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7077 (pt0) REVERT: A 284 ARG cc_start: 0.8385 (mtt90) cc_final: 0.7306 (mtm110) REVERT: A 288 GLU cc_start: 0.7833 (tt0) cc_final: 0.7528 (mt-10) REVERT: A 391 MET cc_start: 0.8336 (mtt) cc_final: 0.8073 (mtp) REVERT: A 393 GLU cc_start: 0.6274 (tp30) cc_final: 0.5883 (mp0) REVERT: A 415 ARG cc_start: 0.8049 (tpp80) cc_final: 0.6839 (tmt170) REVERT: A 476 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7834 (mm-40) REVERT: B 6 ASP cc_start: 0.7645 (m-30) cc_final: 0.7164 (p0) REVERT: B 7 LYS cc_start: 0.7960 (tttt) cc_final: 0.7138 (mptt) REVERT: B 171 LYS cc_start: 0.7556 (tttt) cc_final: 0.7245 (mtpt) REVERT: B 212 SER cc_start: 0.8234 (p) cc_final: 0.7788 (m) REVERT: B 279 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7132 (tp30) REVERT: B 312 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7450 (mm-30) REVERT: C 25 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7347 (ttm170) REVERT: C 26 LYS cc_start: 0.7445 (mmpt) cc_final: 0.7146 (mtmt) REVERT: C 120 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: C 168 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7699 (mtpp) REVERT: C 214 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7870 (t) REVERT: C 284 ARG cc_start: 0.8056 (mtt-85) cc_final: 0.7155 (mtm110) REVERT: C 332 LYS cc_start: 0.7845 (tttt) cc_final: 0.7417 (tttm) REVERT: C 345 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7379 (mtp180) REVERT: D 120 GLU cc_start: 0.7810 (tt0) cc_final: 0.7525 (mp0) REVERT: D 171 LYS cc_start: 0.7230 (mppt) cc_final: 0.7009 (tttm) REVERT: D 172 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: D 299 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: D 354 MET cc_start: 0.8776 (mtp) cc_final: 0.8483 (mtp) REVERT: D 400 LYS cc_start: 0.8494 (mmtt) cc_final: 0.7876 (mmmt) outliers start: 25 outliers final: 13 residues processed: 178 average time/residue: 0.8262 time to fit residues: 161.7646 Evaluate side-chains 179 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 299 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 125 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 98 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 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 = 0.3416 r_free = 0.3416 target = 0.119652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.101834 restraints weight = 27821.908| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.68 r_work: 0.3140 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.243 16499 Z= 0.172 Angle : 0.668 30.442 22243 Z= 0.309 Chirality : 0.044 0.145 2336 Planarity : 0.004 0.044 2858 Dihedral : 4.929 55.811 2519 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.51 % Allowed : 13.76 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % 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: 0.84 (0.19), residues: 1992 helix: 1.52 (0.17), residues: 1012 sheet: -0.21 (0.38), residues: 172 loop : -0.44 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 277 TYR 0.013 0.001 TYR A 229 PHE 0.012 0.001 PHE C 429 TRP 0.013 0.001 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (16483) covalent geometry : angle 0.66823 / 0.31 (22243) hydrogen bonds : bond 0.04219 / 2.93 ( 805) hydrogen bonds : angle 5.12412 / 3.69 ( 2298) Misc. bond : bond 0.09510 / 6.24 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6931.34 seconds wall clock time: 119 minutes 23.25 seconds (7163.25 seconds total)