Starting phenix.real_space_refine on Mon Apr 6 08:11:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqx_45826/04_2026/9cqx_45826.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqx_45826/04_2026/9cqx_45826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cqx_45826/04_2026/9cqx_45826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqx_45826/04_2026/9cqx_45826.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cqx_45826/04_2026/9cqx_45826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqx_45826/04_2026/9cqx_45826.map" } resolution = 2.51 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= 0.010 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 4226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17271 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, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 255 Classifications: {'water': 255} Link IDs: {None: 254} Chain: "B" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Chain: "C" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 266 Classifications: {'water': 266} Link IDs: {None: 265} Chain: "D" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 352 Classifications: {'water': 352} Link IDs: {None: 351} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 26.516 37.482 35.803 1.00 39.70 S ATOM 4552 SG CYS B 95 31.305 54.422 51.245 1.00 32.41 S ATOM 1170 SG CYS A 154 27.406 56.770 48.066 1.00 39.79 S ATOM 465 SG CYS A 62 29.568 50.919 45.758 1.00 32.21 S ATOM 652 SG CYS A 88 33.734 56.590 45.776 1.00 46.41 S ATOM 652 SG CYS A 88 33.734 56.590 45.776 1.00 46.41 S ATOM 5005 SG CYS B 153 31.070 59.731 49.826 1.00 45.77 S ATOM 4372 SG CYS B 70 37.500 57.361 51.250 1.00 32.88 S ATOM 4552 SG CYS B 95 31.305 54.422 51.245 1.00 32.41 S ATOM 10056 SG CYS C 275 104.318 47.501 35.821 1.00 67.28 S ATOM 12516 SG CYS D 95 99.421 30.585 51.305 1.00 33.33 S ATOM 9134 SG CYS C 154 103.398 28.372 47.959 1.00 39.26 S ATOM 8429 SG CYS C 62 101.197 34.121 45.651 1.00 39.77 S ATOM 8616 SG CYS C 88 97.086 28.329 45.867 1.00 42.54 S ATOM 8616 SG CYS C 88 97.086 28.329 45.867 1.00 42.54 S ATOM 12969 SG CYS D 153 99.657 25.302 49.880 1.00 40.75 S ATOM 12336 SG CYS D 70 93.330 27.704 51.382 1.00 37.74 S ATOM 12516 SG CYS D 95 99.421 30.585 51.305 1.00 33.33 S Time building chain proxies: 5.26, per 1000 atoms: 0.30 Number of scatterers: 17271 At special positions: 0 Unit cell: (132.3, 87.465, 96.285, 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 4226 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: 1.33 Conformation dependent library (CDL) restraints added in 976.7 milliseconds 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: 103 helices and 12 sheets defined 58.5% alpha, 8.6% 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 29 Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.834A 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 93 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.644A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.857A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.227A 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: 4.469A 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: 3.563A pdb=" N MET A 279 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 removed outlier: 3.598A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.737A 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 434 removed outlier: 4.533A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.693A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.934A 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: 3.597A pdb=" N GLU B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.979A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.995A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.772A 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 removed outlier: 3.519A pdb=" N HIS B 297 " --> pdb=" O GLN B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 297' Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 321 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.113A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.694A 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: 3.799A 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: 4.398A 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 removed outlier: 3.541A pdb=" N ARG B 481 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 30 removed outlier: 4.086A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.578A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 160 " --> pdb=" O ILE C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.247A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.762A 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 290 removed outlier: 3.502A pdb=" N MET C 279 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 315 removed outlier: 4.295A pdb=" N LYS C 304 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 343 removed outlier: 3.525A pdb=" N GLN C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 358 through 369 removed outlier: 4.654A pdb=" N ILE C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY C 365 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA C 366 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.003A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 435 removed outlier: 4.408A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.233A 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: 3.595A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.525A pdb=" N TRP C 472 " --> pdb=" O ASN C 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.666A pdb=" N GLU D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 70 through 80 removed outlier: 4.004A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.003A 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: 3.855A 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: 5.047A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.636A 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: 3.847A 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: 4.394A 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 removed outlier: 3.539A pdb=" N ARG D 481 " --> pdb=" O HIS D 478 " (cutoff:3.500A) 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: 7.594A pdb=" N LEU A 353 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR A 377 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.274A 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: 6.896A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.134A 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: 6.592A pdb=" N VAL A 223 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA A 251 " --> pdb=" O VAL A 223 " (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: 6.423A 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: 8.536A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.579A 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: 10.282A pdb=" N LEU C 399 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C 375 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N TYR C 401 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR C 377 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL C 351 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR C 377 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU C 353 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N TYR C 379 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.334A 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: 6.995A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.206A 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: 7.352A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN C 271 " --> pdb=" O MET C 295 " (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: 6.462A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.653A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE D 367 " --> pdb=" O HIS D 392 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU D 394 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU D 369 " --> pdb=" O LEU D 394 " (cutoff:3.500A) 781 hydrogen bonds defined for protein. 2247 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: 3.06 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.86: 16347 1.86 - 2.49: 103 2.49 - 3.12: 19 3.12 - 3.75: 6 3.75 - 4.38: 8 Bond restraints: 16483 Sorted by residual: bond pdb="FE2 CLF B 602 " pdb="FE8 CLF B 602 " ideal model delta sigma weight residual 2.200 4.382 -2.182 2.00e-02 2.50e+03 1.19e+04 bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 4.375 -2.175 2.00e-02 2.50e+03 1.18e+04 bond pdb="FE5 CLF B 602 " pdb="FE6 CLF B 602 " ideal model delta sigma weight residual 2.200 3.938 -1.738 2.00e-02 2.50e+03 7.56e+03 bond pdb="FE5 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.936 -1.736 2.00e-02 2.50e+03 7.53e+03 bond pdb="FE4 CLF B 602 " pdb="FE5 CLF B 602 " ideal model delta sigma weight residual 2.200 3.840 -1.640 2.00e-02 2.50e+03 6.72e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.89: 22236 6.89 - 13.78: 1 13.78 - 20.67: 2 20.67 - 27.56: 0 27.56 - 34.45: 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 55.55 34.45 3.00e+00 1.11e-01 1.32e+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 55.64 34.36 3.00e+00 1.11e-01 1.31e+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 60.76 29.24 3.00e+00 1.11e-01 9.50e+01 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE1 CLF B 602 " ideal model delta sigma weight residual 90.00 60.79 29.21 3.00e+00 1.11e-01 9.48e+01 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE3 CLF D 602 " ideal model delta sigma weight residual 90.00 108.26 -18.26 3.00e+00 1.11e-01 3.70e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8797 17.92 - 35.85: 926 35.85 - 53.77: 280 53.77 - 71.69: 69 71.69 - 89.61: 29 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 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE B 367 " pdb=" C PHE B 367 " pdb=" N ALA B 368 " pdb=" CA ALA B 368 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASP A 213 " pdb=" CB ASP A 213 " pdb=" CG ASP A 213 " pdb=" OD1 ASP A 213 " ideal model delta sinusoidal sigma weight residual -30.00 -89.44 59.44 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1778 0.048 - 0.096: 438 0.096 - 0.144: 119 0.144 - 0.192: 0 0.192 - 0.240: 1 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CB ILE C 355 " pdb=" CA ILE C 355 " pdb=" CG1 ILE C 355 " pdb=" CG2 ILE C 355 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE A 81 " pdb=" N ILE A 81 " pdb=" C ILE A 81 " pdb=" CB ILE A 81 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE C 81 " pdb=" N ILE C 81 " pdb=" C ILE C 81 " pdb=" CB ILE C 81 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 73 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 74 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 73 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO C 74 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 359 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 360 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " 0.022 5.00e-02 4.00e+02 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 734 2.63 - 3.20: 15501 3.20 - 3.76: 31673 3.76 - 4.33: 47172 4.33 - 4.90: 71174 Nonbonded interactions: 166254 Sorted by model distance: nonbonded pdb=" O ILE C 430 " pdb=" O HOH C 601 " model vdw 2.062 3.040 nonbonded pdb=" OE2 GLU D 109 " pdb="FE FE B 601 " model vdw 2.096 2.260 nonbonded pdb=" O LEU D 494 " pdb=" O HOH D 701 " model vdw 2.100 3.040 nonbonded pdb=" O HOH D 701 " pdb=" O HOH D 953 " model vdw 2.115 3.040 nonbonded pdb=" OD2 ASP D 353 " pdb="FE FE D 601 " model vdw 2.119 2.260 ... (remaining 166249 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=0.37 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: 3.480 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.950 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 : 0.050 2.182 16499 Z= 2.534 Angle : 0.701 34.450 22243 Z= 0.327 Chirality : 0.044 0.240 2336 Planarity : 0.004 0.045 2858 Dihedral : 16.963 89.615 6433 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.57 % Allowed : 19.33 % Favored : 79.11 % 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: 0.69 (0.19), residues: 1992 helix: 1.45 (0.17), residues: 974 sheet: -0.39 (0.42), residues: 142 loop : -0.49 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 270 TYR 0.014 0.001 TYR D 88 PHE 0.012 0.001 PHE A 429 TRP 0.015 0.001 TRP A 335 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.04974 (16483) covalent geometry : angle 0.70071 (22243) hydrogen bonds : bond 0.13620 ( 781) hydrogen bonds : angle 6.42108 ( 2247) Misc. bond : bond 0.16116 ( 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 215 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.489 Fit side-chains REVERT: A 4 MET cc_start: 0.4504 (tmm) cc_final: 0.2685 (ttt) REVERT: A 22 GLU cc_start: 0.7323 (tp30) cc_final: 0.6840 (mm-30) REVERT: A 214 THR cc_start: 0.8025 (p) cc_final: 0.7713 (t) REVERT: A 391 MET cc_start: 0.7945 (mtm) cc_final: 0.7570 (mtt) REVERT: A 475 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8466 (mp) REVERT: B 60 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7311 (pt0) REVERT: B 171 LYS cc_start: 0.7439 (ttpp) cc_final: 0.6520 (mtmt) REVERT: B 259 GLU cc_start: 0.8464 (mm-30) cc_final: 0.6905 (mp0) REVERT: B 400 LYS cc_start: 0.8473 (mttt) cc_final: 0.7623 (mmtt) REVERT: B 503 GLU cc_start: 0.8389 (tt0) cc_final: 0.7934 (pt0) REVERT: C 22 GLU cc_start: 0.5669 (tp30) cc_final: 0.5181 (tm-30) REVERT: C 23 LYS cc_start: 0.5149 (ttmm) cc_final: 0.4454 (ttpm) REVERT: C 243 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: C 392 LYS cc_start: 0.6613 (pttt) cc_final: 0.6121 (pttp) REVERT: C 394 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.5946 (mmm) REVERT: C 400 LEU cc_start: 0.6829 (mt) cc_final: 0.6508 (mt) REVERT: C 473 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7585 (mptt) REVERT: D 2 SER cc_start: 0.7705 (m) cc_final: 0.7199 (p) REVERT: D 7 LYS cc_start: 0.7351 (tttp) cc_final: 0.6636 (ptpt) REVERT: D 38 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7577 (p0) REVERT: D 268 GLN cc_start: 0.8067 (pt0) cc_final: 0.7435 (pt0) REVERT: D 315 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8152 (mmtp) outliers start: 27 outliers final: 15 residues processed: 207 average time/residue: 0.7131 time to fit residues: 162.4999 Evaluate side-chains 200 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 369 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS B 518 ASN C 29 ASN C 98 ASN C 432 GLN ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.095154 restraints weight = 16337.109| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.21 r_work: 0.2933 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.422 16499 Z= 0.369 Angle : 0.814 30.380 22243 Z= 0.395 Chirality : 0.052 0.226 2336 Planarity : 0.005 0.055 2858 Dihedral : 6.583 65.769 2567 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.90 % Allowed : 17.18 % Favored : 79.92 % 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: 0.38 (0.18), residues: 1992 helix: 1.09 (0.16), residues: 986 sheet: -0.33 (0.38), residues: 164 loop : -0.56 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 97 TYR 0.021 0.003 TYR D 88 PHE 0.017 0.002 PHE D 82 TRP 0.017 0.002 TRP C 253 HIS 0.011 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00796 (16483) covalent geometry : angle 0.81409 (22243) hydrogen bonds : bond 0.06821 ( 781) hydrogen bonds : angle 5.62268 ( 2247) Misc. bond : bond 0.19118 ( 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 233 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 0.591 Fit side-chains REVERT: A 4 MET cc_start: 0.4859 (tmm) cc_final: 0.2967 (ttt) REVERT: A 23 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7041 (ttmt) REVERT: A 214 THR cc_start: 0.8000 (p) cc_final: 0.7620 (t) REVERT: A 287 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6551 (tp30) REVERT: A 391 MET cc_start: 0.7773 (mtm) cc_final: 0.7425 (mtt) REVERT: B 60 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6974 (pt0) REVERT: B 171 LYS cc_start: 0.7364 (ttpp) cc_final: 0.6310 (mttt) REVERT: B 259 GLU cc_start: 0.8339 (mm-30) cc_final: 0.6735 (mp0) REVERT: B 279 GLU cc_start: 0.7371 (mp0) cc_final: 0.6752 (mm-30) REVERT: B 400 LYS cc_start: 0.8439 (mttt) cc_final: 0.7474 (mmtt) REVERT: B 488 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: B 503 GLU cc_start: 0.8203 (tt0) cc_final: 0.7836 (pt0) REVERT: B 516 ASP cc_start: 0.8279 (p0) cc_final: 0.8026 (p0) REVERT: C 22 GLU cc_start: 0.5761 (tp30) cc_final: 0.5237 (tm-30) REVERT: C 23 LYS cc_start: 0.5343 (ttmm) cc_final: 0.4567 (ttpm) REVERT: C 59 ILE cc_start: 0.7731 (mt) cc_final: 0.7379 (mm) REVERT: C 213 ASP cc_start: 0.6174 (t0) cc_final: 0.5455 (m-30) REVERT: C 243 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: C 392 LYS cc_start: 0.6495 (pttt) cc_final: 0.5975 (ptmt) REVERT: C 394 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.5915 (mmm) REVERT: C 410 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5663 (mt-10) REVERT: C 473 LYS cc_start: 0.8377 (mmpt) cc_final: 0.7543 (mptt) REVERT: D 2 SER cc_start: 0.7689 (m) cc_final: 0.7148 (p) REVERT: D 6 ASP cc_start: 0.7062 (m-30) cc_final: 0.6051 (p0) REVERT: D 7 LYS cc_start: 0.7301 (tttp) cc_final: 0.6415 (tptp) REVERT: D 50 LYS cc_start: 0.7810 (tptp) cc_final: 0.7498 (mmmt) REVERT: D 54 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: D 202 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: D 268 GLN cc_start: 0.8017 (pt0) cc_final: 0.7095 (pt0) outliers start: 50 outliers final: 19 residues processed: 221 average time/residue: 0.7580 time to fit residues: 183.6655 Evaluate side-chains 205 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 63 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 168 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 GLN C 29 ASN C 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.104696 restraints weight = 18969.936| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.18 r_work: 0.3054 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.322 16499 Z= 0.254 Angle : 0.709 30.699 22243 Z= 0.334 Chirality : 0.045 0.154 2336 Planarity : 0.004 0.046 2858 Dihedral : 5.806 59.939 2544 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.67 % Allowed : 17.59 % Favored : 79.74 % 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: 0.49 (0.18), residues: 1992 helix: 1.24 (0.17), residues: 994 sheet: -0.53 (0.40), residues: 154 loop : -0.54 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 187 TYR 0.015 0.002 TYR D 88 PHE 0.012 0.001 PHE D 31 TRP 0.015 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00504 (16483) covalent geometry : angle 0.70918 (22243) hydrogen bonds : bond 0.05086 ( 781) hydrogen bonds : angle 5.37890 ( 2247) Misc. bond : bond 0.15172 ( 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 237 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 0.560 Fit side-chains REVERT: A 4 MET cc_start: 0.4732 (tmm) cc_final: 0.2854 (ttt) REVERT: A 214 THR cc_start: 0.8162 (p) cc_final: 0.7771 (t) REVERT: A 284 ARG cc_start: 0.8249 (mtm110) cc_final: 0.8039 (mtm110) REVERT: A 391 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7518 (mtt) REVERT: B 171 LYS cc_start: 0.7745 (ttpp) cc_final: 0.6769 (mtmt) REVERT: B 259 GLU cc_start: 0.8567 (mm-30) cc_final: 0.7324 (mp0) REVERT: B 279 GLU cc_start: 0.7697 (mp0) cc_final: 0.7351 (mm-30) REVERT: B 400 LYS cc_start: 0.8668 (mttt) cc_final: 0.7933 (mmtt) REVERT: C 22 GLU cc_start: 0.5957 (tp30) cc_final: 0.5499 (tm-30) REVERT: C 23 LYS cc_start: 0.5728 (ttmm) cc_final: 0.5039 (ttpm) REVERT: C 59 ILE cc_start: 0.7831 (mt) cc_final: 0.7544 (mm) REVERT: C 213 ASP cc_start: 0.6349 (t0) cc_final: 0.5676 (m-30) REVERT: C 243 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: C 300 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7838 (t80) REVERT: C 392 LYS cc_start: 0.6921 (pttt) cc_final: 0.6399 (pttp) REVERT: C 394 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6545 (mmm) REVERT: C 410 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.6075 (mt-10) REVERT: C 473 LYS cc_start: 0.8584 (mmpt) cc_final: 0.7991 (mptt) REVERT: D 2 SER cc_start: 0.7850 (m) cc_final: 0.7394 (p) REVERT: D 6 ASP cc_start: 0.7226 (m-30) cc_final: 0.6326 (p0) REVERT: D 7 LYS cc_start: 0.7468 (tttp) cc_final: 0.6813 (tptp) REVERT: D 268 GLN cc_start: 0.8240 (pt0) cc_final: 0.7487 (pt0) REVERT: D 315 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8328 (mmtp) outliers start: 46 outliers final: 20 residues processed: 224 average time/residue: 0.7433 time to fit residues: 182.8184 Evaluate side-chains 206 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 135 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 128 GLN C 29 ASN C 98 ASN D 53 GLN D 477 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.102305 restraints weight = 27535.128| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.46 r_work: 0.3014 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.308 16499 Z= 0.255 Angle : 0.710 30.776 22243 Z= 0.334 Chirality : 0.046 0.194 2336 Planarity : 0.004 0.047 2858 Dihedral : 5.500 59.673 2537 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.84 % Allowed : 17.41 % Favored : 79.74 % 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: 0.49 (0.18), residues: 1992 helix: 1.26 (0.17), residues: 994 sheet: -0.50 (0.40), residues: 154 loop : -0.58 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 187 TYR 0.016 0.002 TYR D 88 PHE 0.012 0.001 PHE D 31 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00513 (16483) covalent geometry : angle 0.71014 (22243) hydrogen bonds : bond 0.05111 ( 781) hydrogen bonds : angle 5.31835 ( 2247) Misc. bond : bond 0.14745 ( 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 240 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.561 Fit side-chains REVERT: A 4 MET cc_start: 0.4670 (tmm) cc_final: 0.2843 (ttt) REVERT: A 214 THR cc_start: 0.8163 (p) cc_final: 0.7758 (t) REVERT: A 391 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7560 (mtt) REVERT: A 475 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8587 (mt) REVERT: B 171 LYS cc_start: 0.7782 (ttpp) cc_final: 0.6755 (mttt) REVERT: B 259 GLU cc_start: 0.8654 (mm-30) cc_final: 0.7338 (mp0) REVERT: B 279 GLU cc_start: 0.7734 (mp0) cc_final: 0.7359 (mm-30) REVERT: B 400 LYS cc_start: 0.8713 (mttt) cc_final: 0.7963 (mmtt) REVERT: B 453 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8197 (ttp-170) REVERT: C 22 GLU cc_start: 0.6014 (tp30) cc_final: 0.5553 (tm-30) REVERT: C 23 LYS cc_start: 0.5734 (ttmm) cc_final: 0.5016 (ttpm) REVERT: C 59 ILE cc_start: 0.7854 (mt) cc_final: 0.7569 (mm) REVERT: C 213 ASP cc_start: 0.6410 (t0) cc_final: 0.5714 (m-30) REVERT: C 243 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: C 300 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7939 (t80) REVERT: C 392 LYS cc_start: 0.6952 (pttt) cc_final: 0.6407 (pttp) REVERT: C 394 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6510 (mmm) REVERT: C 410 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.6079 (mt-10) REVERT: C 473 LYS cc_start: 0.8612 (mmpt) cc_final: 0.8003 (mptt) REVERT: D 2 SER cc_start: 0.7871 (m) cc_final: 0.7405 (p) REVERT: D 6 ASP cc_start: 0.7297 (m-30) cc_final: 0.6353 (p0) REVERT: D 7 LYS cc_start: 0.7465 (tttp) cc_final: 0.6789 (tptp) REVERT: D 54 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: D 223 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8527 (mttt) REVERT: D 268 GLN cc_start: 0.8264 (pt0) cc_final: 0.7468 (pt0) outliers start: 49 outliers final: 22 residues processed: 228 average time/residue: 0.7454 time to fit residues: 186.2275 Evaluate side-chains 215 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 117 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 29 ASN C 98 ASN D 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101597 restraints weight = 24696.176| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.47 r_work: 0.3029 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.287 16499 Z= 0.236 Angle : 0.692 30.722 22243 Z= 0.323 Chirality : 0.045 0.168 2336 Planarity : 0.004 0.046 2858 Dihedral : 5.354 59.825 2535 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.38 % Allowed : 17.88 % Favored : 79.74 % 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: 0.57 (0.18), residues: 1992 helix: 1.29 (0.17), residues: 1010 sheet: -0.54 (0.40), residues: 154 loop : -0.52 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.015 0.001 TYR D 88 PHE 0.011 0.001 PHE B 375 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00466 (16483) covalent geometry : angle 0.69249 (22243) hydrogen bonds : bond 0.04716 ( 781) hydrogen bonds : angle 5.23902 ( 2247) Misc. bond : bond 0.13592 ( 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 230 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.671 Fit side-chains REVERT: A 214 THR cc_start: 0.8126 (p) cc_final: 0.7709 (t) REVERT: A 391 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7511 (mtt) REVERT: A 475 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8544 (mp) REVERT: B 60 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7323 (pt0) REVERT: B 171 LYS cc_start: 0.7689 (ttpp) cc_final: 0.6643 (mttt) REVERT: B 259 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7212 (mp0) REVERT: B 279 GLU cc_start: 0.7661 (mp0) cc_final: 0.7224 (mm-30) REVERT: B 400 LYS cc_start: 0.8652 (mttt) cc_final: 0.7859 (mmtt) REVERT: B 453 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8118 (ttp-170) REVERT: B 488 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: C 22 GLU cc_start: 0.5842 (tp30) cc_final: 0.5373 (tm-30) REVERT: C 23 LYS cc_start: 0.5582 (ttmm) cc_final: 0.4823 (ttpm) REVERT: C 59 ILE cc_start: 0.7764 (mt) cc_final: 0.7443 (mm) REVERT: C 213 ASP cc_start: 0.6347 (t0) cc_final: 0.5745 (m-30) REVERT: C 243 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: C 300 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7891 (t80) REVERT: C 392 LYS cc_start: 0.6850 (pttt) cc_final: 0.6309 (pttp) REVERT: C 394 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6427 (mmm) REVERT: C 410 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5932 (mt-10) REVERT: C 473 LYS cc_start: 0.8557 (mmpt) cc_final: 0.7833 (mptt) REVERT: D 2 SER cc_start: 0.7838 (m) cc_final: 0.7363 (p) REVERT: D 6 ASP cc_start: 0.7227 (m-30) cc_final: 0.6262 (p0) REVERT: D 7 LYS cc_start: 0.7428 (tttp) cc_final: 0.6681 (tptp) REVERT: D 54 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: D 223 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8439 (mttt) REVERT: D 268 GLN cc_start: 0.8163 (pt0) cc_final: 0.7341 (pt0) outliers start: 41 outliers final: 22 residues processed: 219 average time/residue: 0.7261 time to fit residues: 174.7835 Evaluate side-chains 216 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 154 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 119 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN C 98 ASN D 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.102589 restraints weight = 23908.598| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.45 r_work: 0.3043 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.273 16499 Z= 0.227 Angle : 0.686 30.699 22243 Z= 0.318 Chirality : 0.044 0.152 2336 Planarity : 0.004 0.046 2858 Dihedral : 5.165 59.788 2531 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.55 % Allowed : 17.99 % Favored : 79.45 % 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: 0.62 (0.18), residues: 1992 helix: 1.35 (0.17), residues: 1010 sheet: -0.53 (0.40), residues: 154 loop : -0.52 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.015 0.001 TYR D 88 PHE 0.013 0.001 PHE B 375 TRP 0.014 0.001 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00447 (16483) covalent geometry : angle 0.68574 (22243) hydrogen bonds : bond 0.04519 ( 781) hydrogen bonds : angle 5.19505 ( 2247) Misc. bond : bond 0.12902 ( 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 228 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.670 Fit side-chains REVERT: A 22 GLU cc_start: 0.7460 (tp30) cc_final: 0.7214 (mm-30) REVERT: A 119 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7056 (mp-120) REVERT: A 214 THR cc_start: 0.8133 (p) cc_final: 0.7714 (t) REVERT: A 391 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7496 (mtt) REVERT: A 475 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8529 (mp) REVERT: B 60 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: B 171 LYS cc_start: 0.7686 (ttpp) cc_final: 0.6642 (mttt) REVERT: B 259 GLU cc_start: 0.8616 (mm-30) cc_final: 0.7230 (mp0) REVERT: B 279 GLU cc_start: 0.7676 (mp0) cc_final: 0.7237 (mm-30) REVERT: B 400 LYS cc_start: 0.8666 (mttt) cc_final: 0.7898 (mmtt) REVERT: B 453 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8108 (ttp-170) REVERT: C 22 GLU cc_start: 0.5876 (tp30) cc_final: 0.5419 (tm-30) REVERT: C 23 LYS cc_start: 0.5535 (ttmm) cc_final: 0.4772 (ttpm) REVERT: C 59 ILE cc_start: 0.7730 (mt) cc_final: 0.7427 (mm) REVERT: C 213 ASP cc_start: 0.6345 (t0) cc_final: 0.6118 (t0) REVERT: C 243 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: C 300 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7950 (t80) REVERT: C 392 LYS cc_start: 0.6924 (pttt) cc_final: 0.6379 (pttp) REVERT: C 394 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6529 (mmm) REVERT: C 410 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5912 (mt-10) REVERT: C 473 LYS cc_start: 0.8559 (mmpt) cc_final: 0.7831 (mptt) REVERT: D 2 SER cc_start: 0.7804 (m) cc_final: 0.7333 (p) REVERT: D 6 ASP cc_start: 0.7215 (m-30) cc_final: 0.6254 (p0) REVERT: D 7 LYS cc_start: 0.7426 (tttp) cc_final: 0.6665 (tptp) REVERT: D 223 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8446 (mttt) REVERT: D 268 GLN cc_start: 0.8130 (pt0) cc_final: 0.7302 (pt0) outliers start: 44 outliers final: 21 residues processed: 216 average time/residue: 0.7518 time to fit residues: 178.1202 Evaluate side-chains 212 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 3 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 119 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN C 98 ASN D 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.104506 restraints weight = 18735.678| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.25 r_work: 0.3076 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.266 16499 Z= 0.222 Angle : 0.688 30.686 22243 Z= 0.317 Chirality : 0.044 0.230 2336 Planarity : 0.004 0.046 2858 Dihedral : 5.122 59.893 2531 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.55 % Allowed : 18.34 % Favored : 79.11 % 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: 0.66 (0.18), residues: 1992 helix: 1.41 (0.17), residues: 1008 sheet: -0.53 (0.40), residues: 154 loop : -0.53 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.015 0.001 TYR D 88 PHE 0.013 0.001 PHE B 375 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00436 (16483) covalent geometry : angle 0.68767 (22243) hydrogen bonds : bond 0.04405 ( 781) hydrogen bonds : angle 5.16728 ( 2247) Misc. bond : bond 0.12513 ( 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 236 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.483 Fit side-chains REVERT: A 4 MET cc_start: 0.4847 (ppp) cc_final: 0.2300 (ttt) REVERT: A 22 GLU cc_start: 0.7447 (tp30) cc_final: 0.7189 (mm-30) REVERT: A 119 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8405 (tp40) REVERT: A 214 THR cc_start: 0.8137 (p) cc_final: 0.7717 (t) REVERT: A 391 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7492 (mtt) REVERT: A 475 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8513 (mp) REVERT: B 60 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7254 (pt0) REVERT: B 171 LYS cc_start: 0.7696 (ttpp) cc_final: 0.6698 (mtmt) REVERT: B 259 GLU cc_start: 0.8563 (mm-30) cc_final: 0.7234 (mp0) REVERT: B 279 GLU cc_start: 0.7633 (mp0) cc_final: 0.7238 (mm-30) REVERT: B 400 LYS cc_start: 0.8612 (mttt) cc_final: 0.7843 (mmtt) REVERT: B 453 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8110 (ttp-170) REVERT: B 507 GLU cc_start: 0.8571 (tt0) cc_final: 0.8287 (tt0) REVERT: C 22 GLU cc_start: 0.5867 (tp30) cc_final: 0.5418 (tm-30) REVERT: C 23 LYS cc_start: 0.5568 (ttmm) cc_final: 0.4807 (ttpm) REVERT: C 59 ILE cc_start: 0.7750 (mt) cc_final: 0.7451 (mm) REVERT: C 213 ASP cc_start: 0.6341 (t0) cc_final: 0.6095 (t0) REVERT: C 243 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: C 300 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7929 (t80) REVERT: C 392 LYS cc_start: 0.6970 (pttt) cc_final: 0.6419 (pttp) REVERT: C 394 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6719 (mmm) REVERT: C 410 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5931 (mt-10) REVERT: C 441 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6989 (mmm) REVERT: C 473 LYS cc_start: 0.8550 (mmpt) cc_final: 0.7831 (mptt) REVERT: D 2 SER cc_start: 0.7795 (m) cc_final: 0.7331 (p) REVERT: D 6 ASP cc_start: 0.7196 (m-30) cc_final: 0.6264 (p0) REVERT: D 7 LYS cc_start: 0.7438 (tttp) cc_final: 0.6692 (tptp) REVERT: D 223 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8457 (mttt) REVERT: D 268 GLN cc_start: 0.8120 (pt0) cc_final: 0.7297 (pt0) outliers start: 44 outliers final: 22 residues processed: 224 average time/residue: 0.7308 time to fit residues: 179.7903 Evaluate side-chains 215 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 139 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN C 53 GLN C 98 ASN D 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.102843 restraints weight = 23533.475| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.43 r_work: 0.3047 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.265 16499 Z= 0.227 Angle : 0.692 30.686 22243 Z= 0.320 Chirality : 0.045 0.206 2336 Planarity : 0.004 0.046 2858 Dihedral : 5.096 59.826 2531 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.21 % Allowed : 18.98 % Favored : 78.82 % 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: 0.66 (0.18), residues: 1992 helix: 1.41 (0.17), residues: 1008 sheet: -0.50 (0.40), residues: 154 loop : -0.54 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 97 TYR 0.015 0.001 TYR D 88 PHE 0.013 0.001 PHE B 375 TRP 0.014 0.001 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00451 (16483) covalent geometry : angle 0.69180 (22243) hydrogen bonds : bond 0.04506 ( 781) hydrogen bonds : angle 5.16936 ( 2247) Misc. bond : bond 0.12664 ( 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 222 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.572 Fit side-chains REVERT: A 4 MET cc_start: 0.4831 (ppp) cc_final: 0.2320 (ttt) REVERT: A 22 GLU cc_start: 0.7485 (tp30) cc_final: 0.7232 (mm-30) REVERT: A 214 THR cc_start: 0.8144 (p) cc_final: 0.7724 (t) REVERT: A 391 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7496 (mtt) REVERT: A 475 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8512 (mp) REVERT: B 60 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7291 (pt0) REVERT: B 171 LYS cc_start: 0.7682 (ttpp) cc_final: 0.6670 (mtmt) REVERT: B 259 GLU cc_start: 0.8645 (mm-30) cc_final: 0.7255 (mp0) REVERT: B 279 GLU cc_start: 0.7697 (mp0) cc_final: 0.7263 (mm-30) REVERT: B 400 LYS cc_start: 0.8633 (mttt) cc_final: 0.7864 (mmtt) REVERT: B 453 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8109 (ttp-170) REVERT: B 507 GLU cc_start: 0.8609 (tt0) cc_final: 0.8325 (tt0) REVERT: C 22 GLU cc_start: 0.5865 (tp30) cc_final: 0.5414 (tm-30) REVERT: C 23 LYS cc_start: 0.5562 (ttmm) cc_final: 0.4799 (ttpm) REVERT: C 59 ILE cc_start: 0.7774 (mt) cc_final: 0.7480 (mm) REVERT: C 213 ASP cc_start: 0.6376 (t0) cc_final: 0.6094 (t0) REVERT: C 243 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: C 300 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7965 (t80) REVERT: C 392 LYS cc_start: 0.7021 (pttt) cc_final: 0.6465 (pttp) REVERT: C 410 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5937 (mt-10) REVERT: C 441 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6995 (mmm) REVERT: C 473 LYS cc_start: 0.8565 (mmpt) cc_final: 0.7838 (mptt) REVERT: D 2 SER cc_start: 0.7809 (m) cc_final: 0.7345 (p) REVERT: D 6 ASP cc_start: 0.7239 (m-30) cc_final: 0.6278 (p0) REVERT: D 7 LYS cc_start: 0.7437 (tttp) cc_final: 0.6679 (tptp) REVERT: D 223 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8478 (mttt) REVERT: D 268 GLN cc_start: 0.8132 (pt0) cc_final: 0.7302 (pt0) outliers start: 38 outliers final: 22 residues processed: 211 average time/residue: 0.7404 time to fit residues: 171.3766 Evaluate side-chains 212 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 169 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 119 GLN C 29 ASN C 98 ASN D 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102808 restraints weight = 24768.940| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.37 r_work: 0.3023 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.300 16499 Z= 0.256 Angle : 0.719 30.730 22243 Z= 0.337 Chirality : 0.046 0.209 2336 Planarity : 0.004 0.048 2858 Dihedral : 5.132 59.623 2528 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.50 % Allowed : 18.86 % Favored : 78.64 % 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: 0.57 (0.18), residues: 1992 helix: 1.31 (0.17), residues: 1008 sheet: -0.48 (0.40), residues: 154 loop : -0.56 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 210 TYR 0.018 0.002 TYR D 88 PHE 0.014 0.002 PHE B 375 TRP 0.014 0.001 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00519 (16483) covalent geometry : angle 0.71917 (22243) hydrogen bonds : bond 0.05106 ( 781) hydrogen bonds : angle 5.26232 ( 2247) Misc. bond : bond 0.14243 ( 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 228 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.709 Fit side-chains REVERT: A 4 MET cc_start: 0.5080 (ppp) cc_final: 0.2494 (ttt) REVERT: A 22 GLU cc_start: 0.7511 (tp30) cc_final: 0.7256 (mm-30) REVERT: A 119 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.6950 (mp-120) REVERT: A 214 THR cc_start: 0.8160 (p) cc_final: 0.7724 (t) REVERT: A 391 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7542 (mtt) REVERT: A 475 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8543 (mp) REVERT: B 60 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7324 (pt0) REVERT: B 171 LYS cc_start: 0.7731 (ttpp) cc_final: 0.6681 (mttt) REVERT: B 259 GLU cc_start: 0.8657 (mm-30) cc_final: 0.7330 (mp0) REVERT: B 279 GLU cc_start: 0.7715 (mp0) cc_final: 0.7323 (mm-30) REVERT: B 400 LYS cc_start: 0.8670 (mttt) cc_final: 0.7923 (mmtt) REVERT: B 453 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8217 (ttp-170) REVERT: C 22 GLU cc_start: 0.5902 (tp30) cc_final: 0.5452 (tm-30) REVERT: C 23 LYS cc_start: 0.5651 (ttmm) cc_final: 0.4887 (ttpm) REVERT: C 59 ILE cc_start: 0.7814 (mt) cc_final: 0.7517 (mm) REVERT: C 213 ASP cc_start: 0.6463 (t0) cc_final: 0.6047 (t0) REVERT: C 243 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: C 300 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.8103 (t80) REVERT: C 392 LYS cc_start: 0.7010 (pttt) cc_final: 0.6444 (pttp) REVERT: C 410 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.6019 (mt-10) REVERT: C 473 LYS cc_start: 0.8557 (mmpt) cc_final: 0.7932 (mptt) REVERT: D 2 SER cc_start: 0.7849 (m) cc_final: 0.7395 (p) REVERT: D 6 ASP cc_start: 0.7247 (m-30) cc_final: 0.6289 (p0) REVERT: D 7 LYS cc_start: 0.7467 (tttp) cc_final: 0.6722 (tptp) REVERT: D 223 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8524 (mttt) REVERT: D 268 GLN cc_start: 0.8189 (pt0) cc_final: 0.7336 (pt0) outliers start: 43 outliers final: 20 residues processed: 213 average time/residue: 0.7326 time to fit residues: 171.1666 Evaluate side-chains 210 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 69 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 197 optimal weight: 0.9990 chunk 163 optimal weight: 0.0050 chunk 156 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 119 GLN A 274 HIS C 29 ASN C 98 ASN D 53 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.104131 restraints weight = 20090.846| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.22 r_work: 0.3046 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.297 16499 Z= 0.257 Angle : 0.890 59.199 22243 Z= 0.464 Chirality : 0.045 0.201 2336 Planarity : 0.004 0.048 2858 Dihedral : 5.126 59.661 2528 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.03 % Allowed : 19.21 % Favored : 78.76 % Cbeta Deviations : 0.05 % 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: 0.57 (0.18), residues: 1992 helix: 1.31 (0.17), residues: 1008 sheet: -0.48 (0.40), residues: 154 loop : -0.56 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG C 210 TYR 0.018 0.002 TYR D 88 PHE 0.013 0.001 PHE B 375 TRP 0.014 0.001 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00501 (16483) covalent geometry : angle 0.88966 (22243) hydrogen bonds : bond 0.04994 ( 781) hydrogen bonds : angle 5.26231 ( 2247) Misc. bond : bond 0.14171 ( 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 215 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.654 Fit side-chains REVERT: A 4 MET cc_start: 0.5080 (ppp) cc_final: 0.2490 (ttt) REVERT: A 22 GLU cc_start: 0.7486 (tp30) cc_final: 0.7237 (mm-30) REVERT: A 214 THR cc_start: 0.8167 (p) cc_final: 0.7731 (t) REVERT: A 391 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7532 (mtt) REVERT: A 475 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8539 (mp) REVERT: B 60 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7290 (pt0) REVERT: B 171 LYS cc_start: 0.7738 (ttpp) cc_final: 0.6693 (mttt) REVERT: B 259 GLU cc_start: 0.8612 (mm-30) cc_final: 0.7313 (mp0) REVERT: B 279 GLU cc_start: 0.7671 (mp0) cc_final: 0.7309 (mm-30) REVERT: B 400 LYS cc_start: 0.8647 (mttt) cc_final: 0.7907 (mmtt) REVERT: B 453 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8163 (ttp-170) REVERT: C 22 GLU cc_start: 0.5900 (tp30) cc_final: 0.5464 (tm-30) REVERT: C 23 LYS cc_start: 0.5684 (ttmm) cc_final: 0.4930 (ttpm) REVERT: C 59 ILE cc_start: 0.7811 (mt) cc_final: 0.7514 (mm) REVERT: C 213 ASP cc_start: 0.6425 (t0) cc_final: 0.6084 (t0) REVERT: C 243 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: C 300 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.8080 (t80) REVERT: C 392 LYS cc_start: 0.7039 (pttt) cc_final: 0.6471 (pttp) REVERT: C 410 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.6045 (mt-10) REVERT: C 473 LYS cc_start: 0.8544 (mmpt) cc_final: 0.7928 (mptt) REVERT: D 2 SER cc_start: 0.7848 (m) cc_final: 0.7401 (p) REVERT: D 6 ASP cc_start: 0.7230 (m-30) cc_final: 0.6294 (p0) REVERT: D 7 LYS cc_start: 0.7458 (tttp) cc_final: 0.6732 (tptp) REVERT: D 38 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7787 (p0) REVERT: D 223 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8466 (mttt) REVERT: D 268 GLN cc_start: 0.8183 (pt0) cc_final: 0.7337 (pt0) outliers start: 35 outliers final: 20 residues processed: 205 average time/residue: 0.7569 time to fit residues: 170.2209 Evaluate side-chains 208 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 189 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 chunk 116 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN C 98 ASN D 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.126958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.103518 restraints weight = 22322.485| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.30 r_work: 0.3028 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.297 16499 Z= 0.257 Angle : 0.890 59.199 22243 Z= 0.464 Chirality : 0.045 0.201 2336 Planarity : 0.004 0.048 2858 Dihedral : 5.126 59.661 2528 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.86 % Allowed : 19.38 % Favored : 78.76 % Cbeta Deviations : 0.05 % 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: 0.57 (0.18), residues: 1992 helix: 1.31 (0.17), residues: 1008 sheet: -0.48 (0.40), residues: 154 loop : -0.56 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG C 210 TYR 0.018 0.002 TYR D 88 PHE 0.013 0.001 PHE B 375 TRP 0.014 0.001 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00501 (16483) covalent geometry : angle 0.88966 (22243) hydrogen bonds : bond 0.04994 ( 781) hydrogen bonds : angle 5.26231 ( 2247) Misc. bond : bond 0.14171 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6610.25 seconds wall clock time: 113 minutes 11.62 seconds (6791.62 seconds total)