Starting phenix.real_space_refine on Sat Jul 4 14:12:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cu0_45924/07_2026/9cu0_45924.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cu0_45924/07_2026/9cu0_45924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cu0_45924/07_2026/9cu0_45924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cu0_45924/07_2026/9cu0_45924.map" model { file = "/net/cci-nas-00/data/ceres_data/9cu0_45924/07_2026/9cu0_45924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cu0_45924/07_2026/9cu0_45924.cif" } resolution = 3.94 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 38 7.16 5 P 4 5.49 5 Mg 2 5.21 5 S 193 5.16 5 C 13402 2.51 5 N 3589 2.21 5 O 4141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21371 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" 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: "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: 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: "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: "E" Number of atoms: 2077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2077 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 8, 'TRANS': 265} Chain: "F" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2145 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "G" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'CLF': 1, 'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 2} Chain breaks: 2 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 56.167 65.641 82.521 1.00 96.56 S ATOM 4549 SG CYS B 95 39.327 48.870 85.179 1.00 86.05 S ATOM 1167 SG CYS A 154 37.457 52.502 80.916 1.00 87.82 S ATOM 462 SG CYS A 62 42.795 54.848 84.040 1.00 93.13 S ATOM 649 SG CYS A 88 36.256 54.415 86.974 1.00 84.72 S ATOM 649 SG CYS A 88 36.256 54.415 86.974 1.00 84.72 S ATOM 5002 SG CYS B 153 34.409 50.379 83.866 1.00 90.27 S ATOM 4369 SG CYS B 70 35.801 49.402 90.890 1.00 83.78 S ATOM 4549 SG CYS B 95 39.327 48.870 85.179 1.00 86.05 S ATOM 10056 SG CYS C 275 35.206 65.324 157.926 1.00126.38 S ATOM 12516 SG CYS D 95 53.459 50.987 155.989 1.00 91.09 S ATOM 9134 SG CYS C 154 55.400 54.712 159.632 1.00 94.00 S ATOM 8429 SG CYS C 62 50.133 56.089 157.194 1.00 93.45 S ATOM 12969 SG CYS D 153 59.125 52.721 156.673 1.00 94.64 S ATOM 12336 SG CYS D 70 57.455 51.753 149.878 1.00 94.08 S ATOM 18693 SG CYS F 98 38.091 48.013 41.531 1.00192.28 S ATOM 18964 SG CYS F 133 39.378 41.833 42.584 1.00189.75 S ATOM 16615 SG CYS E 98 43.006 45.298 45.502 1.00175.42 S ATOM 16886 SG CYS E 133 42.646 45.232 38.854 1.00202.72 S ATOM 20463 SG CYS G 42 37.083 43.661 57.638 1.00154.01 S ATOM 20498 SG CYS G 47 37.503 45.076 54.373 1.00159.61 S ATOM 20514 SG CYS G 50 37.103 50.187 56.718 1.00151.91 S ATOM 20925 SG CYS G 102 36.867 48.471 59.985 1.00147.31 S Time building chain proxies: 6.37, per 1000 atoms: 0.30 Number of scatterers: 21371 At special positions: 0 Unit cell: (88.935, 103.635, 183.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Mo 2 41.97 Fe 38 26.01 S 193 16.00 P 4 15.00 Mg 2 11.99 O 4141 8.00 N 3589 7.00 C 13402 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=17, symmetry=0 Number of additional bonds: simple=17, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES G 201 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 42 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 102 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 47 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 50 " pdb=" SF4 F 301 " pdb="FE2 SF4 F 301 " - pdb=" SG CYS F 133 " pdb="FE4 SF4 F 301 " - pdb=" SG CYS E 133 " pdb="FE1 SF4 F 301 " - pdb=" SG CYS F 98 " pdb="FE3 SF4 F 301 " - pdb=" SG CYS E 98 " Number of angles added : 18 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4894 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 15 sheets defined 54.4% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 removed outlier: 3.555A pdb=" N GLU A 18 " --> pdb=" O GLN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.690A pdb=" N LYS A 44 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.601A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 205 removed outlier: 4.078A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.996A pdb=" N ARG A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.530A pdb=" N MET A 245 " --> pdb=" O LEU A 241 " (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 290 removed outlier: 5.492A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 283 " --> pdb=" O MET A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'A' and resid 317 through 347 removed outlier: 3.550A pdb=" N GLN A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) 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: 3.552A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.489A 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 433 removed outlier: 4.233A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 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 31 Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 80 removed outlier: 4.071A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.984A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 127 through 143 removed outlier: 3.500A pdb=" N LYS B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'B' and resid 192 through 209 Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.626A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.531A pdb=" N MET B 281 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 294 through 297 removed outlier: 3.553A 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 322 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 3.531A pdb=" N THR B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.612A 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 426 through 437 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.674A pdb=" N ASN B 518 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 20 removed outlier: 3.573A pdb=" N VAL C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 30 removed outlier: 4.269A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.620A pdb=" N LYS C 44 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 85 through 92 removed outlier: 4.266A pdb=" N GLY C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER C 92 " --> pdb=" O CYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 163 through 175 Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.128A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.999A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 291 removed outlier: 3.514A pdb=" N MET C 279 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER C 283 " --> pdb=" O MET C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 315 removed outlier: 3.791A pdb=" N LYS C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 343 removed outlier: 3.718A 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 344 through 346 No H-bonds generated for 'chain 'C' and resid 344 through 346' Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 370 removed outlier: 3.697A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 394 removed outlier: 3.915A pdb=" N ARG C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) removed outlier: 3.780A 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 432 removed outlier: 4.580A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.507A 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: 3.736A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 removed outlier: 4.055A pdb=" N GLN C 476 " --> pdb=" O LYS C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 31 Processing helix chain 'D' and resid 36 through 47 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 71 through 80 removed outlier: 3.650A pdb=" N ALA D 75 " --> pdb=" O GLN D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.959A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.656A pdb=" N VAL D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 143 removed outlier: 3.525A pdb=" N LYS D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 209 Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.667A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 277 through 283 Processing helix chain 'D' and resid 284 through 287 Processing helix chain 'D' and resid 298 through 309 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 3.582A pdb=" N THR D 345 " --> pdb=" O PRO D 341 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.527A 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 426 through 437 Processing helix chain 'D' and resid 445 through 447 No H-bonds generated for 'chain 'D' and resid 445 through 447' Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.511A 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 helix chain 'E' and resid 15 through 30 removed outlier: 3.811A pdb=" N GLU E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 51 Processing helix chain 'E' and resid 57 through 65 removed outlier: 3.614A pdb=" N MET E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 72 through 77 removed outlier: 3.787A pdb=" N VAL E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 114 removed outlier: 3.512A pdb=" N ILE E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 155 through 172 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 216 through 225 removed outlier: 3.692A pdb=" N ARG E 220 " --> pdb=" O ASN E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 235 through 250 Processing helix chain 'E' and resid 261 through 272 removed outlier: 3.579A pdb=" N LEU E 265 " --> pdb=" O THR E 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 31 Processing helix chain 'F' and resid 46 through 51 Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.517A pdb=" N MET F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 77 removed outlier: 3.880A pdb=" N VAL F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 114 removed outlier: 3.508A pdb=" N ILE F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 Processing helix chain 'F' and resid 155 through 172 Processing helix chain 'F' and resid 192 through 204 Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.618A pdb=" N ARG F 220 " --> pdb=" O ASN F 216 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG F 224 " --> pdb=" O ARG F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 235 through 250 Processing helix chain 'F' and resid 261 through 272 Processing helix chain 'F' and resid 279 through 283 removed outlier: 3.775A pdb=" N ILE F 282 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL F 283 " --> pdb=" O GLU F 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 279 through 283' Processing helix chain 'G' and resid 26 through 34 removed outlier: 3.576A pdb=" N ASN G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 Processing helix chain 'G' and resid 82 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 9.988A pdb=" N LEU A 399 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 375 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N TYR A 401 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR A 377 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 378 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.411A 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 182 removed outlier: 7.003A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 79 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLN A 151 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 81 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 7.001A pdb=" N ILE A 225 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN A 252 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY A 227 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N SER A 254 " --> pdb=" O GLY A 227 " (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: 6.563A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.586A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 4.498A pdb=" N LEU C 399 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C 351 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N GLY C 378 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 353 " --> pdb=" O GLY C 378 " (cutoff:3.500A) removed outlier: 6.583A 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: 6.519A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE C 79 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLN C 151 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE C 81 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 63 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 6.414A pdb=" N VAL C 223 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA C 251 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 250 through 253 removed outlier: 6.533A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N VAL D 291 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 6.315A 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: 8.741A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU D 369 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE D 393 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 85 through 88 removed outlier: 6.958A pdb=" N VAL E 34 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N VAL E 87 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE E 36 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET E 35 " --> pdb=" O PHE E 124 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASP E 126 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL E 37 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N LEU E 128 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY E 10 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN E 5 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N TYR E 149 " --> pdb=" O GLN E 5 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA E 7 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL E 151 " --> pdb=" O ALA E 7 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR E 9 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE E 148 " --> pdb=" O GLY E 181 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 183 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE E 150 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N CYS E 185 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS E 152 " --> pdb=" O CYS E 185 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE E 209 " --> pdb=" O GLY E 181 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU E 183 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE E 211 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS E 185 " --> pdb=" O PHE E 211 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 78 through 80 removed outlier: 6.519A pdb=" N VAL F 34 " --> pdb=" O LYS F 85 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL F 87 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE F 36 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N MET F 35 " --> pdb=" O PHE F 124 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASP F 126 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL F 37 " --> pdb=" O ASP F 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN F 5 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N TYR F 149 " --> pdb=" O GLN F 5 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA F 7 " --> pdb=" O TYR F 149 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL F 151 " --> pdb=" O ALA F 7 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR F 9 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE F 148 " --> pdb=" O GLY F 182 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILE F 184 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE F 150 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ASN F 186 " --> pdb=" O ILE F 150 " (cutoff:3.500A) removed outlier: 13.247A pdb=" N MET F 208 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N GLY F 181 " --> pdb=" O MET F 208 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N HIS F 210 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU F 183 " --> pdb=" O HIS F 210 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL F 212 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS F 185 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 15 through 18 956 hydrogen bonds defined for protein. 2784 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: 4.18 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.84: 21606 1.84 - 2.48: 119 2.48 - 3.12: 22 3.12 - 3.76: 7 3.76 - 4.40: 4 Bond restraints: 21758 Sorted by residual: bond pdb="FE2 CLF A 503 " pdb="FE8 CLF A 503 " ideal model delta sigma weight residual 2.200 4.395 -2.195 2.00e-02 2.50e+03 1.20e+04 bond pdb="FE2 CLF D 601 " pdb="FE8 CLF D 601 " ideal model delta sigma weight residual 2.200 4.372 -2.172 2.00e-02 2.50e+03 1.18e+04 bond pdb="FE5 CLF D 601 " pdb="FE6 CLF D 601 " ideal model delta sigma weight residual 2.200 3.934 -1.734 2.00e-02 2.50e+03 7.52e+03 bond pdb="FE5 CLF A 503 " pdb="FE6 CLF A 503 " ideal model delta sigma weight residual 2.200 3.931 -1.731 2.00e-02 2.50e+03 7.49e+03 bond pdb="FE4 CLF A 503 " pdb="FE5 CLF A 503 " ideal model delta sigma weight residual 2.200 3.416 -1.216 2.00e-02 2.50e+03 3.69e+03 ... (remaining 21753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.85: 29345 6.85 - 13.70: 16 13.70 - 20.55: 2 20.55 - 27.40: 0 27.40 - 34.24: 4 Bond angle restraints: 29367 Sorted by residual: angle pdb=" S1 CLF D 601 " pdb="FE2 CLF D 601 " pdb="FE4 CLF D 601 " ideal model delta sigma weight residual 90.00 55.76 34.24 3.00e+00 1.11e-01 1.30e+02 angle pdb=" S1 CLF A 503 " pdb="FE2 CLF A 503 " pdb="FE4 CLF A 503 " ideal model delta sigma weight residual 90.00 55.89 34.11 3.00e+00 1.11e-01 1.29e+02 angle pdb=" S1 CLF D 601 " pdb="FE2 CLF D 601 " pdb="FE1 CLF D 601 " ideal model delta sigma weight residual 90.00 60.64 29.36 3.00e+00 1.11e-01 9.58e+01 angle pdb=" S1 CLF A 503 " pdb="FE2 CLF A 503 " pdb="FE1 CLF A 503 " ideal model delta sigma weight residual 90.00 61.06 28.94 3.00e+00 1.11e-01 9.30e+01 angle pdb=" S1 CLF A 503 " pdb="FE2 CLF A 503 " pdb="FE3 CLF A 503 " ideal model delta sigma weight residual 90.00 108.84 -18.84 3.00e+00 1.11e-01 3.95e+01 ... (remaining 29362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 11123 17.91 - 35.82: 1606 35.82 - 53.73: 454 53.73 - 71.64: 113 71.64 - 89.55: 40 Dihedral angle restraints: 13336 sinusoidal: 5673 harmonic: 7663 Sorted by residual: dihedral pdb=" CA GLU E 117 " pdb=" C GLU E 117 " pdb=" N ASP E 118 " pdb=" CA ASP E 118 " ideal model delta harmonic sigma weight residual 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" C5' ADP F 302 " pdb=" O5' ADP F 302 " pdb=" PA ADP F 302 " pdb=" O2A ADP F 302 " ideal model delta sinusoidal sigma weight residual -60.00 17.32 -77.32 1 2.00e+01 2.50e-03 1.87e+01 dihedral pdb=" C ILE F 14 " pdb=" N ILE F 14 " pdb=" CA ILE F 14 " pdb=" CB ILE F 14 " ideal model delta harmonic sigma weight residual -122.00 -131.45 9.45 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 13333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2679 0.068 - 0.137: 424 0.137 - 0.205: 39 0.205 - 0.273: 8 0.273 - 0.341: 2 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CA ILE G 38 " pdb=" N ILE G 38 " pdb=" C ILE G 38 " pdb=" CB ILE G 38 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB VAL D 260 " pdb=" CA VAL D 260 " pdb=" CG1 VAL D 260 " pdb=" CG2 VAL D 260 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB VAL B 464 " pdb=" CA VAL B 464 " pdb=" CG1 VAL B 464 " pdb=" CG2 VAL B 464 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3149 not shown) Planarity restraints: 3780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 131 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C VAL F 131 " 0.063 2.00e-02 2.50e+03 pdb=" O VAL F 131 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL F 132 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 231 " 0.027 2.00e-02 2.50e+03 2.39e-02 1.14e+01 pdb=" CG TYR E 231 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR E 231 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR E 231 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR E 231 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR E 231 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 231 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 231 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 145 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C ASN A 145 " -0.050 2.00e-02 2.50e+03 pdb=" O ASN A 145 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 146 " 0.017 2.00e-02 2.50e+03 ... (remaining 3777 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 275 2.58 - 3.16: 18041 3.16 - 3.74: 36183 3.74 - 4.32: 49102 4.32 - 4.90: 79810 Nonbonded interactions: 183411 Sorted by model distance: nonbonded pdb=" OE1 GLU E 147 " pdb=" O HOH E 401 " model vdw 2.005 3.040 nonbonded pdb=" OD2 ASP C 136 " pdb=" O HOH C 601 " model vdw 2.023 3.040 nonbonded pdb=" OE2 GLU C 22 " pdb=" O HOH C 602 " model vdw 2.026 3.040 nonbonded pdb=" OE1 GLN B 58 " pdb=" O HOH B 701 " model vdw 2.047 3.040 nonbonded pdb=" CA ALA E 235 " pdb=" O HOH E 409 " model vdw 2.054 3.470 ... (remaining 183406 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 248 or resid 250 through 502)) selection = (chain 'C' 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)) } ncs_group { reference = (chain 'B' and resid 2 through 523) selection = (chain 'D' and resid 2 through 523) } ncs_group { reference = (chain 'E' and (resid 3 through 82 or resid 84 through 302)) selection = (chain 'F' and (resid 3 through 276 or resid 302 through 303)) } 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=0.23 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.950 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 25.210 Find NCS groups from input model: 0.470 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: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.038 2.195 21783 Z= 1.932 Angle : 0.932 34.244 29385 Z= 0.513 Chirality : 0.051 0.341 3152 Planarity : 0.005 0.055 3780 Dihedral : 18.729 89.547 8442 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.35 % Allowed : 29.23 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: -0.01 (0.16), residues: 2664 helix: 0.92 (0.15), residues: 1237 sheet: -0.21 (0.29), residues: 297 loop : -0.95 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 28 TYR 0.056 0.002 TYR E 231 PHE 0.020 0.002 PHE F 272 TRP 0.017 0.002 TRP C 236 HIS 0.005 0.001 HIS D 429 Details of bonding type rmsd/Z covalent geometry : bond 0.03773 / 1.90 (21758) covalent geometry : angle 0.91150 / 0.51 (29367) hydrogen bonds : bond 0.15086 / 10.02 ( 956) hydrogen bonds : angle 6.61402 / 4.75 ( 2784) metal coordination : bond 0.07117 / 3.58 ( 8) metal coordination : angle 7.98909 / 4.77 ( 18) Misc. bond : bond 0.25911 / 20.46 ( 17) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 328 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.7766 (p0) REVERT: A 117 ASP cc_start: 0.8125 (t0) cc_final: 0.7901 (m-30) REVERT: A 427 GLU cc_start: 0.8713 (mp0) cc_final: 0.8513 (mp0) REVERT: A 441 MET cc_start: 0.8999 (mmm) cc_final: 0.8754 (mmm) REVERT: A 465 MET cc_start: 0.8939 (ttt) cc_final: 0.8250 (ttt) REVERT: B 131 MET cc_start: 0.8613 (tpp) cc_final: 0.8032 (tpp) REVERT: B 133 ASP cc_start: 0.7992 (m-30) cc_final: 0.7772 (m-30) REVERT: B 395 CYS cc_start: 0.8647 (t) cc_final: 0.8238 (t) REVERT: B 467 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8794 (pt) REVERT: C 4 MET cc_start: 0.5491 (pp-130) cc_final: 0.2520 (tpp) REVERT: C 57 MET cc_start: 0.9000 (ttt) cc_final: 0.8664 (tmm) REVERT: C 98 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.8731 (p0) REVERT: C 234 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7903 (t0) REVERT: C 256 ASP cc_start: 0.8440 (t0) cc_final: 0.7521 (t0) REVERT: C 277 ARG cc_start: 0.7989 (tpp-160) cc_final: 0.7356 (tpp-160) REVERT: C 362 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7742 (t70) REVERT: C 401 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6265 (p90) REVERT: D 95 CYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8534 (m) REVERT: D 131 MET cc_start: 0.9207 (tpp) cc_final: 0.8830 (tpp) REVERT: D 320 MET cc_start: 0.8354 (ttm) cc_final: 0.7758 (ttm) REVERT: D 453 ARG cc_start: 0.9151 (tmm-80) cc_final: 0.8912 (tmm-80) REVERT: E 60 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6490 (tt0) REVERT: E 237 GLN cc_start: 0.5493 (tp40) cc_final: 0.4949 (tp-100) REVERT: F 33 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.6492 (tttt) REVERT: F 45 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.7421 (p) REVERT: F 156 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.4841 (tpp) REVERT: G 65 MET cc_start: 0.8049 (ppp) cc_final: 0.7785 (pmm) outliers start: 98 outliers final: 34 residues processed: 389 average time/residue: 0.1449 time to fit residues: 89.9529 Evaluate side-chains 316 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 231 TYR Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 28 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN B 317 ASN ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.093327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072982 restraints weight = 103520.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.076304 restraints weight = 47211.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.078178 restraints weight = 25879.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.079091 restraints weight = 15600.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079857 restraints weight = 12560.821| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.644 21783 Z= 0.267 Angle : 0.819 29.840 29385 Z= 0.373 Chirality : 0.046 0.192 3152 Planarity : 0.005 0.043 3780 Dihedral : 7.106 76.941 3353 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.13 % Allowed : 27.38 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.06 (0.16), residues: 2664 helix: 1.11 (0.15), residues: 1245 sheet: -0.54 (0.29), residues: 305 loop : -0.97 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 224 TYR 0.019 0.002 TYR D 88 PHE 0.019 0.002 PHE B 382 TRP 0.023 0.002 TRP A 253 HIS 0.005 0.001 HIS D 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.25 (21758) covalent geometry : angle 0.78142 / 0.37 (29367) hydrogen bonds : bond 0.04635 / 3.08 ( 956) hydrogen bonds : angle 5.49397 / 3.93 ( 2784) metal coordination : bond 0.01787 / 1.13 ( 8) metal coordination : angle 9.92602 / 5.96 ( 18) Misc. bond : bond 0.21033 / 16.18 ( 17) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 289 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7865 (tp40) REVERT: A 98 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.7677 (p0) REVERT: A 151 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7331 (mt0) REVERT: A 465 MET cc_start: 0.8991 (ttt) cc_final: 0.8408 (ttt) REVERT: B 131 MET cc_start: 0.8543 (tpp) cc_final: 0.8056 (tpp) REVERT: B 395 CYS cc_start: 0.8437 (t) cc_final: 0.8086 (t) REVERT: B 467 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8844 (pt) REVERT: C 4 MET cc_start: 0.5592 (pp-130) cc_final: 0.2674 (tpp) REVERT: C 98 ASN cc_start: 0.9332 (OUTLIER) cc_final: 0.8811 (p0) REVERT: C 152 SER cc_start: 0.9503 (m) cc_final: 0.9230 (t) REVERT: C 256 ASP cc_start: 0.8522 (t0) cc_final: 0.7519 (t0) REVERT: C 277 ARG cc_start: 0.8011 (tpp-160) cc_final: 0.7655 (tpp-160) REVERT: C 394 MET cc_start: 0.5406 (tpp) cc_final: 0.5107 (tpp) REVERT: C 441 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7841 (mpp) REVERT: D 131 MET cc_start: 0.9202 (tpp) cc_final: 0.8978 (tpp) REVERT: D 200 MET cc_start: 0.8883 (tpt) cc_final: 0.8661 (tpt) REVERT: D 362 LEU cc_start: 0.9170 (mt) cc_final: 0.8901 (mt) REVERT: E 125 TYR cc_start: 0.8178 (m-80) cc_final: 0.7622 (m-80) REVERT: E 138 MET cc_start: 0.7966 (ttt) cc_final: 0.7689 (ttp) REVERT: E 237 GLN cc_start: 0.5392 (tp40) cc_final: 0.4942 (tp-100) REVERT: F 33 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.6365 (tttt) REVERT: F 125 TYR cc_start: 0.6706 (m-80) cc_final: 0.6417 (m-80) REVERT: F 138 MET cc_start: 0.8798 (tmm) cc_final: 0.8567 (tmm) REVERT: F 156 MET cc_start: 0.6041 (OUTLIER) cc_final: 0.5189 (tpp) REVERT: G 65 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7506 (ppp) outliers start: 93 outliers final: 54 residues processed: 352 average time/residue: 0.1424 time to fit residues: 81.0409 Evaluate side-chains 333 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 271 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 93 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 114 optimal weight: 7.9990 chunk 238 optimal weight: 8.9990 chunk 198 optimal weight: 8.9990 chunk 205 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 168 optimal weight: 0.3980 chunk 129 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 GLN D 199 ASN D 418 ASN ** D 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.093934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073535 restraints weight = 107811.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.076702 restraints weight = 50401.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.078570 restraints weight = 28920.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.079410 restraints weight = 16825.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.080548 restraints weight = 13715.503| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.588 21783 Z= 0.204 Angle : 0.782 30.705 29385 Z= 0.347 Chirality : 0.045 0.289 3152 Planarity : 0.004 0.044 3780 Dihedral : 6.243 72.027 3317 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.44 % Allowed : 26.64 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.11 (0.16), residues: 2664 helix: 1.19 (0.15), residues: 1240 sheet: -0.62 (0.29), residues: 305 loop : -0.95 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 97 TYR 0.017 0.001 TYR C 401 PHE 0.020 0.001 PHE E 124 TRP 0.020 0.001 TRP A 253 HIS 0.010 0.001 HIS D 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (21758) covalent geometry : angle 0.74380 / 0.35 (29367) hydrogen bonds : bond 0.03821 / 2.56 ( 956) hydrogen bonds : angle 5.25373 / 3.75 ( 2784) metal coordination : bond 0.01402 / 0.96 ( 8) metal coordination : angle 9.83519 / 5.87 ( 18) Misc. bond : bond 0.16925 / 13.41 ( 17) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 290 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.7667 (p0) REVERT: A 465 MET cc_start: 0.9013 (ttt) cc_final: 0.8741 (ttt) REVERT: B 131 MET cc_start: 0.8472 (tpp) cc_final: 0.8133 (tpp) REVERT: B 133 ASP cc_start: 0.7954 (m-30) cc_final: 0.7608 (m-30) REVERT: B 352 VAL cc_start: 0.9731 (t) cc_final: 0.9435 (p) REVERT: B 355 MET cc_start: 0.9239 (mtm) cc_final: 0.8963 (mtm) REVERT: B 395 CYS cc_start: 0.8420 (t) cc_final: 0.7974 (t) REVERT: B 467 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8815 (pt) REVERT: C 4 MET cc_start: 0.5489 (pp-130) cc_final: 0.2651 (tpp) REVERT: C 152 SER cc_start: 0.9510 (m) cc_final: 0.9203 (t) REVERT: C 256 ASP cc_start: 0.8412 (t0) cc_final: 0.7306 (t0) REVERT: C 394 MET cc_start: 0.5625 (tpp) cc_final: 0.5371 (tpp) REVERT: C 401 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.3926 (p90) REVERT: C 467 LEU cc_start: 0.9044 (tt) cc_final: 0.8570 (mm) REVERT: D 131 MET cc_start: 0.9247 (tpp) cc_final: 0.9028 (tpp) REVERT: D 504 ARG cc_start: 0.8976 (tpp80) cc_final: 0.8387 (tpt170) REVERT: E 9 TYR cc_start: 0.7093 (m-10) cc_final: 0.6638 (m-10) REVERT: E 60 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6674 (tt0) REVERT: E 138 MET cc_start: 0.8002 (ttt) cc_final: 0.7741 (ttp) REVERT: E 237 GLN cc_start: 0.5296 (tp40) cc_final: 0.4893 (tp-100) REVERT: E 269 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8008 (tp) REVERT: F 33 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.6279 (tttt) REVERT: F 125 TYR cc_start: 0.6565 (m-80) cc_final: 0.6245 (m-80) REVERT: F 138 MET cc_start: 0.8824 (tmm) cc_final: 0.8599 (tmm) REVERT: F 149 TYR cc_start: 0.8295 (m-80) cc_final: 0.7951 (m-80) REVERT: F 156 MET cc_start: 0.5971 (OUTLIER) cc_final: 0.5146 (tpp) REVERT: G 41 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: G 65 MET cc_start: 0.8124 (ppp) cc_final: 0.7538 (ppp) outliers start: 100 outliers final: 58 residues processed: 359 average time/residue: 0.1412 time to fit residues: 82.1739 Evaluate side-chains 333 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 268 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 41 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 63 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 243 optimal weight: 20.0000 chunk 224 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 69 optimal weight: 0.3980 chunk 184 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.095669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.075350 restraints weight = 97457.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078531 restraints weight = 47020.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.080314 restraints weight = 27091.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.081760 restraints weight = 16131.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.083042 restraints weight = 10410.293| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.627 21783 Z= 0.178 Angle : 0.759 30.686 29385 Z= 0.334 Chirality : 0.044 0.250 3152 Planarity : 0.004 0.043 3780 Dihedral : 5.990 67.160 3307 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.04 % Allowed : 26.99 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.21 (0.16), residues: 2664 helix: 1.31 (0.15), residues: 1234 sheet: -0.58 (0.29), residues: 315 loop : -0.93 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 210 TYR 0.036 0.001 TYR F 231 PHE 0.036 0.001 PHE A 412 TRP 0.013 0.001 TRP A 253 HIS 0.009 0.001 HIS D 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (21758) covalent geometry : angle 0.72777 / 0.33 (29367) hydrogen bonds : bond 0.03406 / 2.28 ( 956) hydrogen bonds : angle 5.09032 / 3.63 ( 2784) metal coordination : bond 0.00921 / 0.61 ( 8) metal coordination : angle 8.75859 / 5.17 ( 18) Misc. bond : bond 0.17070 / 13.70 ( 17) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 308 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.7672 (p0) REVERT: A 148 ILE cc_start: 0.9201 (mt) cc_final: 0.8990 (tp) REVERT: A 298 ASN cc_start: 0.7586 (t0) cc_final: 0.7343 (t0) REVERT: A 462 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: A 465 MET cc_start: 0.9003 (ttt) cc_final: 0.8471 (ttt) REVERT: B 131 MET cc_start: 0.8365 (tpp) cc_final: 0.8069 (tpp) REVERT: B 133 ASP cc_start: 0.7966 (m-30) cc_final: 0.7384 (m-30) REVERT: B 181 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8483 (m) REVERT: B 354 MET cc_start: 0.8580 (tpp) cc_final: 0.8061 (mmt) REVERT: B 395 CYS cc_start: 0.8300 (t) cc_final: 0.7778 (t) REVERT: B 409 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8867 (tp) REVERT: B 467 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8841 (pt) REVERT: B 479 LEU cc_start: 0.8774 (tp) cc_final: 0.8483 (tp) REVERT: C 4 MET cc_start: 0.5330 (pp-130) cc_final: 0.2575 (tpp) REVERT: C 152 SER cc_start: 0.9512 (m) cc_final: 0.9207 (t) REVERT: C 256 ASP cc_start: 0.8292 (t0) cc_final: 0.7159 (t0) REVERT: C 394 MET cc_start: 0.5659 (tpp) cc_final: 0.5402 (tpp) REVERT: C 401 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.3967 (p90) REVERT: C 441 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7544 (mtm) REVERT: C 467 LEU cc_start: 0.9063 (tt) cc_final: 0.8603 (mm) REVERT: D 117 SER cc_start: 0.8743 (m) cc_final: 0.8505 (p) REVERT: D 362 LEU cc_start: 0.9160 (mt) cc_final: 0.8816 (mt) REVERT: D 504 ARG cc_start: 0.8811 (tpp80) cc_final: 0.8225 (tpt170) REVERT: E 9 TYR cc_start: 0.7213 (m-10) cc_final: 0.6646 (m-10) REVERT: E 60 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6583 (tt0) REVERT: E 138 MET cc_start: 0.8041 (ttt) cc_final: 0.7786 (ttp) REVERT: E 269 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8042 (tp) REVERT: F 5 GLN cc_start: 0.3584 (OUTLIER) cc_final: 0.2822 (mt0) REVERT: F 33 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.6127 (ttmt) REVERT: F 125 TYR cc_start: 0.6462 (m-80) cc_final: 0.5983 (m-80) REVERT: F 138 MET cc_start: 0.8878 (tmm) cc_final: 0.8600 (tmm) REVERT: F 149 TYR cc_start: 0.8305 (m-80) cc_final: 0.7911 (m-80) REVERT: F 156 MET cc_start: 0.6035 (OUTLIER) cc_final: 0.5299 (tpp) REVERT: F 172 TYR cc_start: 0.8100 (m-80) cc_final: 0.6764 (m-80) REVERT: F 264 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7450 (tm-30) REVERT: F 270 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6498 (mmm) REVERT: G 65 MET cc_start: 0.8150 (ppp) cc_final: 0.7634 (ppp) outliers start: 91 outliers final: 51 residues processed: 369 average time/residue: 0.1381 time to fit residues: 83.5502 Evaluate side-chains 341 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 278 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 126 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 251 optimal weight: 8.9990 chunk 260 optimal weight: 8.9990 chunk 88 optimal weight: 0.0470 chunk 22 optimal weight: 0.9990 chunk 257 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 ASN ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN F 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.093373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.073137 restraints weight = 98698.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.076537 restraints weight = 47138.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.078263 restraints weight = 25992.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079671 restraints weight = 15347.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.080399 restraints weight = 9828.594| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.582 21783 Z= 0.201 Angle : 0.763 30.585 29385 Z= 0.338 Chirality : 0.044 0.146 3152 Planarity : 0.004 0.042 3780 Dihedral : 5.610 66.347 3298 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.53 % Allowed : 27.30 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.30 (0.17), residues: 2664 helix: 1.37 (0.15), residues: 1240 sheet: -0.43 (0.29), residues: 333 loop : -0.93 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 141 TYR 0.022 0.001 TYR F 231 PHE 0.021 0.001 PHE A 459 TRP 0.022 0.001 TRP A 253 HIS 0.010 0.001 HIS D 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (21758) covalent geometry : angle 0.73149 / 0.34 (29367) hydrogen bonds : bond 0.03492 / 2.36 ( 956) hydrogen bonds : angle 5.03883 / 3.60 ( 2784) metal coordination : bond 0.01493 / 1.01 ( 8) metal coordination : angle 8.86680 / 5.16 ( 18) Misc. bond : bond 0.15703 / 12.62 ( 17) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 278 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ILE cc_start: 0.9267 (mt) cc_final: 0.9038 (mm) REVERT: A 90 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7840 (tp40) REVERT: A 98 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.7646 (p0) REVERT: A 286 MET cc_start: 0.8791 (mtp) cc_final: 0.8569 (mtt) REVERT: A 462 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: A 465 MET cc_start: 0.9034 (ttt) cc_final: 0.8498 (ttt) REVERT: B 131 MET cc_start: 0.8411 (tpp) cc_final: 0.8162 (tpp) REVERT: B 133 ASP cc_start: 0.7987 (m-30) cc_final: 0.7682 (m-30) REVERT: B 181 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8599 (m) REVERT: B 271 MET cc_start: 0.8429 (ttm) cc_final: 0.7346 (tpp) REVERT: B 395 CYS cc_start: 0.8330 (t) cc_final: 0.7827 (t) REVERT: B 409 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8883 (tp) REVERT: B 467 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8821 (pt) REVERT: C 4 MET cc_start: 0.5466 (pp-130) cc_final: 0.2701 (tpp) REVERT: C 152 SER cc_start: 0.9547 (m) cc_final: 0.9325 (t) REVERT: C 256 ASP cc_start: 0.8299 (t0) cc_final: 0.7155 (t0) REVERT: C 394 MET cc_start: 0.5771 (tpp) cc_final: 0.5501 (tpp) REVERT: C 401 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.4213 (p90) REVERT: C 441 MET cc_start: 0.7953 (mpp) cc_final: 0.7625 (mtm) REVERT: C 467 LEU cc_start: 0.9075 (tt) cc_final: 0.8672 (mm) REVERT: D 186 THR cc_start: 0.9437 (OUTLIER) cc_final: 0.9147 (p) REVERT: D 200 MET cc_start: 0.8979 (tpt) cc_final: 0.8542 (tpt) REVERT: D 362 LEU cc_start: 0.9189 (mt) cc_final: 0.8817 (mt) REVERT: E 9 TYR cc_start: 0.7141 (m-10) cc_final: 0.6640 (m-10) REVERT: E 35 MET cc_start: 0.7849 (mmm) cc_final: 0.7605 (tpp) REVERT: E 60 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6749 (tt0) REVERT: E 138 MET cc_start: 0.8136 (ttt) cc_final: 0.7876 (ttp) REVERT: E 240 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6258 (tm-30) REVERT: E 269 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8116 (tp) REVERT: F 5 GLN cc_start: 0.3765 (OUTLIER) cc_final: 0.3097 (mt0) REVERT: F 30 MET cc_start: 0.7005 (mtm) cc_final: 0.6687 (ttt) REVERT: F 33 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.6169 (ttmt) REVERT: F 138 MET cc_start: 0.8861 (tmm) cc_final: 0.8580 (tmm) REVERT: F 149 TYR cc_start: 0.8333 (m-80) cc_final: 0.7932 (m-80) REVERT: F 156 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.5439 (tpp) REVERT: G 65 MET cc_start: 0.8207 (ppp) cc_final: 0.7994 (pmm) outliers start: 102 outliers final: 61 residues processed: 352 average time/residue: 0.1338 time to fit residues: 75.9990 Evaluate side-chains 341 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 267 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 202 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 174 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 244 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 ASN ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.093021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.073647 restraints weight = 80129.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076715 restraints weight = 40788.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.078211 restraints weight = 23901.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.079445 restraints weight = 14568.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.080222 restraints weight = 9803.015| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.576 21783 Z= 0.198 Angle : 0.767 30.577 29385 Z= 0.339 Chirality : 0.044 0.148 3152 Planarity : 0.004 0.045 3780 Dihedral : 5.634 65.099 3298 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.53 % Allowed : 27.52 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.29 (0.17), residues: 2664 helix: 1.36 (0.15), residues: 1243 sheet: -0.43 (0.29), residues: 323 loop : -0.95 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 179 TYR 0.015 0.001 TYR D 88 PHE 0.018 0.001 PHE A 459 TRP 0.021 0.001 TRP A 253 HIS 0.007 0.001 HIS D 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (21758) covalent geometry : angle 0.73496 / 0.34 (29367) hydrogen bonds : bond 0.03462 / 2.35 ( 956) hydrogen bonds : angle 4.99509 / 3.57 ( 2784) metal coordination : bond 0.01244 / 0.83 ( 8) metal coordination : angle 8.87150 / 5.11 ( 18) Misc. bond : bond 0.15485 / 12.45 ( 17) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 276 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ILE cc_start: 0.9256 (mt) cc_final: 0.9019 (mm) REVERT: A 98 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.7625 (p0) REVERT: A 465 MET cc_start: 0.9025 (ttt) cc_final: 0.8459 (ttt) REVERT: B 116 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8269 (p0) REVERT: B 131 MET cc_start: 0.8395 (tpp) cc_final: 0.8114 (tpp) REVERT: B 133 ASP cc_start: 0.7984 (m-30) cc_final: 0.7676 (m-30) REVERT: B 258 GLU cc_start: 0.8504 (pm20) cc_final: 0.7961 (pp20) REVERT: B 271 MET cc_start: 0.8460 (ttm) cc_final: 0.7422 (tpp) REVERT: B 395 CYS cc_start: 0.8300 (t) cc_final: 0.7755 (t) REVERT: B 409 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8889 (tp) REVERT: B 467 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8833 (pt) REVERT: B 517 TYR cc_start: 0.8438 (p90) cc_final: 0.8132 (p90) REVERT: C 4 MET cc_start: 0.5408 (pp-130) cc_final: 0.2781 (tpp) REVERT: C 20 TYR cc_start: 0.7955 (m-80) cc_final: 0.7726 (m-80) REVERT: C 161 ASP cc_start: 0.4660 (OUTLIER) cc_final: 0.4333 (m-30) REVERT: C 256 ASP cc_start: 0.8244 (t0) cc_final: 0.7085 (t0) REVERT: C 380 GLU cc_start: 0.7914 (tt0) cc_final: 0.7605 (tm-30) REVERT: C 394 MET cc_start: 0.6023 (tpp) cc_final: 0.5794 (tpp) REVERT: C 401 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.4238 (p90) REVERT: C 441 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7644 (mtm) REVERT: C 467 LEU cc_start: 0.9081 (tt) cc_final: 0.8681 (mm) REVERT: D 186 THR cc_start: 0.9441 (OUTLIER) cc_final: 0.9159 (p) REVERT: D 200 MET cc_start: 0.8973 (tpt) cc_final: 0.8557 (tpt) REVERT: E 9 TYR cc_start: 0.7212 (m-10) cc_final: 0.6984 (m-10) REVERT: E 35 MET cc_start: 0.7893 (mmm) cc_final: 0.7660 (tpp) REVERT: E 78 LYS cc_start: 0.6798 (mttp) cc_final: 0.6400 (ptpt) REVERT: E 117 GLU cc_start: 0.5744 (pm20) cc_final: 0.4352 (mt-10) REVERT: E 138 MET cc_start: 0.8090 (ttt) cc_final: 0.7819 (ttp) REVERT: E 269 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8097 (tp) REVERT: F 5 GLN cc_start: 0.3813 (OUTLIER) cc_final: 0.3117 (mt0) REVERT: F 30 MET cc_start: 0.7116 (mtm) cc_final: 0.6816 (ttt) REVERT: F 33 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.6168 (ttmt) REVERT: F 138 MET cc_start: 0.8866 (tmm) cc_final: 0.8601 (tmm) REVERT: F 149 TYR cc_start: 0.8246 (m-80) cc_final: 0.7966 (m-80) REVERT: F 156 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.5542 (tpp) REVERT: F 231 TYR cc_start: 0.6357 (OUTLIER) cc_final: 0.6105 (m-80) REVERT: F 264 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7516 (tm-30) outliers start: 102 outliers final: 67 residues processed: 349 average time/residue: 0.1418 time to fit residues: 80.2049 Evaluate side-chains 346 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 266 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 231 TYR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 66 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 235 optimal weight: 10.0000 chunk 144 optimal weight: 0.7980 chunk 202 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 256 optimal weight: 0.5980 chunk 239 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.092973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.073877 restraints weight = 74108.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.076831 restraints weight = 38436.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.078281 restraints weight = 22612.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.079195 restraints weight = 14282.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.080332 restraints weight = 10146.485| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.565 21783 Z= 0.197 Angle : 0.776 30.562 29385 Z= 0.345 Chirality : 0.045 0.184 3152 Planarity : 0.004 0.042 3780 Dihedral : 5.672 63.571 3298 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.00 % Allowed : 28.00 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.31 (0.17), residues: 2664 helix: 1.37 (0.15), residues: 1239 sheet: -0.42 (0.29), residues: 322 loop : -0.92 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 468 TYR 0.022 0.001 TYR F 241 PHE 0.037 0.001 PHE A 412 TRP 0.021 0.001 TRP A 253 HIS 0.007 0.001 HIS D 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (21758) covalent geometry : angle 0.74441 / 0.34 (29367) hydrogen bonds : bond 0.03510 / 2.37 ( 956) hydrogen bonds : angle 4.98987 / 3.57 ( 2784) metal coordination : bond 0.01194 / 0.79 ( 8) metal coordination : angle 8.93458 / 5.11 ( 18) Misc. bond : bond 0.15202 / 12.22 ( 17) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 271 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.7737 (p0) REVERT: A 465 MET cc_start: 0.9016 (ttt) cc_final: 0.8496 (ttt) REVERT: B 98 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.8582 (m-10) REVERT: B 116 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8285 (p0) REVERT: B 133 ASP cc_start: 0.7981 (m-30) cc_final: 0.7654 (m-30) REVERT: B 258 GLU cc_start: 0.8573 (pm20) cc_final: 0.8156 (pp20) REVERT: B 271 MET cc_start: 0.8486 (ttm) cc_final: 0.7514 (tpp) REVERT: B 395 CYS cc_start: 0.8285 (t) cc_final: 0.7716 (t) REVERT: B 409 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8890 (tp) REVERT: B 467 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8788 (pt) REVERT: B 517 TYR cc_start: 0.8449 (p90) cc_final: 0.8158 (p90) REVERT: C 4 MET cc_start: 0.5417 (pp-130) cc_final: 0.2858 (tpp) REVERT: C 161 ASP cc_start: 0.4815 (OUTLIER) cc_final: 0.4354 (m-30) REVERT: C 256 ASP cc_start: 0.8200 (t0) cc_final: 0.7036 (t0) REVERT: C 380 GLU cc_start: 0.7911 (tt0) cc_final: 0.7634 (tm-30) REVERT: C 394 MET cc_start: 0.6408 (tpp) cc_final: 0.6200 (tpp) REVERT: C 401 TYR cc_start: 0.7630 (OUTLIER) cc_final: 0.4444 (p90) REVERT: C 441 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7551 (mtm) REVERT: C 467 LEU cc_start: 0.9082 (tt) cc_final: 0.8703 (mm) REVERT: D 200 MET cc_start: 0.8981 (tpt) cc_final: 0.8651 (tpt) REVERT: D 247 MET cc_start: 0.7244 (tpp) cc_final: 0.6746 (mtt) REVERT: E 9 TYR cc_start: 0.7146 (m-10) cc_final: 0.6669 (m-10) REVERT: E 35 MET cc_start: 0.7951 (mmm) cc_final: 0.7702 (tpp) REVERT: E 78 LYS cc_start: 0.6852 (mttp) cc_final: 0.6468 (ptpt) REVERT: E 117 GLU cc_start: 0.5810 (pm20) cc_final: 0.4723 (pt0) REVERT: E 138 MET cc_start: 0.8106 (ttt) cc_final: 0.7846 (ttp) REVERT: E 155 GLU cc_start: 0.7441 (tt0) cc_final: 0.7097 (tt0) REVERT: E 159 MET cc_start: 0.8861 (mmt) cc_final: 0.8496 (mtm) REVERT: F 5 GLN cc_start: 0.3826 (OUTLIER) cc_final: 0.3128 (mt0) REVERT: F 30 MET cc_start: 0.7025 (mtm) cc_final: 0.6713 (ttt) REVERT: F 33 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.6195 (ttmt) REVERT: F 138 MET cc_start: 0.8893 (tmm) cc_final: 0.8600 (tmm) REVERT: F 149 TYR cc_start: 0.8248 (m-80) cc_final: 0.8023 (m-80) REVERT: F 156 MET cc_start: 0.5981 (OUTLIER) cc_final: 0.5695 (tpp) REVERT: F 157 MET cc_start: 0.6678 (ttp) cc_final: 0.6342 (ttm) REVERT: F 226 MET cc_start: 0.6296 (tpt) cc_final: 0.5982 (tpt) REVERT: F 231 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.6274 (m-80) REVERT: F 264 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7506 (tm-30) REVERT: G 72 ARG cc_start: 0.7611 (ttm170) cc_final: 0.7353 (ttm-80) outliers start: 90 outliers final: 69 residues processed: 332 average time/residue: 0.1362 time to fit residues: 72.4755 Evaluate side-chains 339 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 258 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 231 TYR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 66 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 118 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 228 optimal weight: 20.0000 chunk 198 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.093785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074589 restraints weight = 78124.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077583 restraints weight = 39977.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.078954 restraints weight = 22459.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.080209 restraints weight = 14824.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081763 restraints weight = 9778.398| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.569 21783 Z= 0.177 Angle : 0.769 30.598 29385 Z= 0.338 Chirality : 0.044 0.193 3152 Planarity : 0.004 0.042 3780 Dihedral : 5.599 60.801 3298 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.00 % Allowed : 27.96 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.30 (0.17), residues: 2664 helix: 1.37 (0.15), residues: 1240 sheet: -0.43 (0.29), residues: 322 loop : -0.93 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 468 TYR 0.017 0.001 TYR F 241 PHE 0.020 0.001 PHE A 459 TRP 0.017 0.001 TRP A 253 HIS 0.006 0.001 HIS D 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (21758) covalent geometry : angle 0.73908 / 0.34 (29367) hydrogen bonds : bond 0.03352 / 2.26 ( 956) hydrogen bonds : angle 4.93978 / 3.53 ( 2784) metal coordination : bond 0.00868 / 0.56 ( 8) metal coordination : angle 8.60914 / 4.92 ( 18) Misc. bond : bond 0.15190 / 12.23 ( 17) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 274 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.7700 (p0) REVERT: A 462 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: A 465 MET cc_start: 0.8999 (ttt) cc_final: 0.8490 (ttt) REVERT: B 62 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8200 (tp) REVERT: B 98 TYR cc_start: 0.9140 (OUTLIER) cc_final: 0.8601 (m-10) REVERT: B 107 PHE cc_start: 0.9420 (m-80) cc_final: 0.9010 (m-10) REVERT: B 116 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8322 (p0) REVERT: B 131 MET cc_start: 0.8358 (tpp) cc_final: 0.8096 (tpp) REVERT: B 133 ASP cc_start: 0.7968 (m-30) cc_final: 0.7439 (m-30) REVERT: B 258 GLU cc_start: 0.8499 (pm20) cc_final: 0.7896 (pp20) REVERT: B 271 MET cc_start: 0.8476 (ttm) cc_final: 0.7555 (tpp) REVERT: B 354 MET cc_start: 0.8563 (tpp) cc_final: 0.8159 (mmm) REVERT: B 395 CYS cc_start: 0.8258 (t) cc_final: 0.7667 (t) REVERT: B 409 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8907 (tp) REVERT: B 467 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8798 (pt) REVERT: B 517 TYR cc_start: 0.8421 (p90) cc_final: 0.8178 (p90) REVERT: C 4 MET cc_start: 0.5253 (pp-130) cc_final: 0.2784 (tpp) REVERT: C 161 ASP cc_start: 0.4853 (OUTLIER) cc_final: 0.4357 (m-30) REVERT: C 256 ASP cc_start: 0.8111 (t0) cc_final: 0.6984 (t0) REVERT: C 380 GLU cc_start: 0.7771 (tt0) cc_final: 0.7531 (tm-30) REVERT: C 401 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.4531 (p90) REVERT: C 441 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7414 (mtm) REVERT: C 463 MET cc_start: 0.9079 (mmp) cc_final: 0.8848 (mmm) REVERT: C 467 LEU cc_start: 0.9090 (tt) cc_final: 0.8722 (mm) REVERT: D 247 MET cc_start: 0.7181 (tpp) cc_final: 0.6619 (mtt) REVERT: E 9 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6781 (m-10) REVERT: E 35 MET cc_start: 0.8041 (mmm) cc_final: 0.7796 (tpp) REVERT: E 78 LYS cc_start: 0.6874 (mttp) cc_final: 0.6471 (ptpt) REVERT: E 117 GLU cc_start: 0.5842 (pm20) cc_final: 0.4728 (pt0) REVERT: E 138 MET cc_start: 0.8080 (ttt) cc_final: 0.7823 (ttp) REVERT: E 155 GLU cc_start: 0.7487 (tt0) cc_final: 0.7152 (tt0) REVERT: E 156 MET cc_start: 0.7894 (ppp) cc_final: 0.7634 (ppp) REVERT: E 159 MET cc_start: 0.8824 (mmt) cc_final: 0.8533 (mtm) REVERT: E 275 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.4894 (ttm) REVERT: F 5 GLN cc_start: 0.3780 (OUTLIER) cc_final: 0.3080 (mt0) REVERT: F 30 MET cc_start: 0.7015 (mtm) cc_final: 0.6686 (ttt) REVERT: F 33 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6131 (ttmt) REVERT: F 138 MET cc_start: 0.8882 (tmm) cc_final: 0.8582 (tmm) REVERT: F 149 TYR cc_start: 0.8269 (m-80) cc_final: 0.8044 (m-80) REVERT: F 157 MET cc_start: 0.6717 (ttp) cc_final: 0.6384 (ttm) REVERT: F 226 MET cc_start: 0.6277 (tpt) cc_final: 0.5915 (tpt) REVERT: F 231 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.6307 (m-80) REVERT: G 53 LYS cc_start: 0.8315 (tppt) cc_final: 0.7599 (mmmt) REVERT: G 72 ARG cc_start: 0.7623 (ttm170) cc_final: 0.7342 (ttm-80) outliers start: 90 outliers final: 64 residues processed: 337 average time/residue: 0.1386 time to fit residues: 76.3101 Evaluate side-chains 339 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 260 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 231 TYR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 66 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 39 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 134 optimal weight: 40.0000 chunk 148 optimal weight: 6.9990 chunk 62 optimal weight: 30.0000 chunk 190 optimal weight: 9.9990 chunk 184 optimal weight: 0.0980 chunk 5 optimal weight: 20.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 HIS ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.093093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.073636 restraints weight = 80240.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076664 restraints weight = 41623.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.078038 restraints weight = 23613.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.079148 restraints weight = 15415.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079559 restraints weight = 10601.411| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.551 21783 Z= 0.192 Angle : 0.781 30.549 29385 Z= 0.346 Chirality : 0.045 0.226 3152 Planarity : 0.004 0.043 3780 Dihedral : 5.479 58.769 3294 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.60 % Allowed : 28.35 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.27 (0.16), residues: 2664 helix: 1.35 (0.15), residues: 1237 sheet: -0.44 (0.29), residues: 322 loop : -0.95 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 187 TYR 0.016 0.001 TYR E 125 PHE 0.052 0.001 PHE A 412 TRP 0.021 0.001 TRP A 253 HIS 0.007 0.001 HIS D 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (21758) covalent geometry : angle 0.75066 / 0.35 (29367) hydrogen bonds : bond 0.03460 / 2.34 ( 956) hydrogen bonds : angle 4.97505 / 3.56 ( 2784) metal coordination : bond 0.01097 / 0.72 ( 8) metal coordination : angle 8.77984 / 4.98 ( 18) Misc. bond : bond 0.14736 / 11.86 ( 17) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 263 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.7653 (p0) REVERT: A 462 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7907 (m-30) REVERT: A 465 MET cc_start: 0.9000 (ttt) cc_final: 0.8477 (ttt) REVERT: B 98 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.8615 (m-10) REVERT: B 116 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8383 (p0) REVERT: B 120 GLU cc_start: 0.8657 (mp0) cc_final: 0.8266 (mp0) REVERT: B 131 MET cc_start: 0.8379 (tpp) cc_final: 0.8084 (tpp) REVERT: B 133 ASP cc_start: 0.8054 (m-30) cc_final: 0.7783 (m-30) REVERT: B 213 MET cc_start: 0.7531 (tpp) cc_final: 0.7312 (tpp) REVERT: B 258 GLU cc_start: 0.8503 (pm20) cc_final: 0.7969 (pp20) REVERT: B 271 MET cc_start: 0.8504 (ttm) cc_final: 0.7574 (tpp) REVERT: B 395 CYS cc_start: 0.8315 (t) cc_final: 0.7730 (t) REVERT: B 409 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8894 (tp) REVERT: B 467 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8794 (pt) REVERT: C 4 MET cc_start: 0.5311 (pp-130) cc_final: 0.2828 (tpp) REVERT: C 161 ASP cc_start: 0.4895 (OUTLIER) cc_final: 0.4434 (m-30) REVERT: C 256 ASP cc_start: 0.8099 (t0) cc_final: 0.6960 (t0) REVERT: C 380 GLU cc_start: 0.7972 (tt0) cc_final: 0.7657 (tm-30) REVERT: C 401 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.4625 (p90) REVERT: C 441 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7437 (mtm) REVERT: C 463 MET cc_start: 0.9146 (mmp) cc_final: 0.8934 (mmm) REVERT: C 467 LEU cc_start: 0.9075 (tt) cc_final: 0.8718 (mm) REVERT: D 247 MET cc_start: 0.7060 (tpp) cc_final: 0.6695 (mtt) REVERT: E 9 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.6871 (m-10) REVERT: E 35 MET cc_start: 0.8093 (mmm) cc_final: 0.7800 (tpp) REVERT: E 78 LYS cc_start: 0.6862 (mttp) cc_final: 0.6482 (ptpt) REVERT: E 117 GLU cc_start: 0.5746 (pm20) cc_final: 0.4519 (pt0) REVERT: E 126 ASP cc_start: 0.6311 (t0) cc_final: 0.5752 (p0) REVERT: E 155 GLU cc_start: 0.7501 (tt0) cc_final: 0.7201 (tt0) REVERT: E 156 MET cc_start: 0.7968 (ppp) cc_final: 0.7729 (ppp) REVERT: E 159 MET cc_start: 0.8836 (mmt) cc_final: 0.8537 (mtm) REVERT: E 275 MET cc_start: 0.6573 (ppp) cc_final: 0.5481 (ttm) REVERT: F 5 GLN cc_start: 0.3825 (OUTLIER) cc_final: 0.3111 (mt0) REVERT: F 30 MET cc_start: 0.6997 (mtm) cc_final: 0.6710 (ttt) REVERT: F 33 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.6262 (ttmt) REVERT: F 138 MET cc_start: 0.8903 (tmm) cc_final: 0.8574 (tmm) REVERT: F 156 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.5947 (tmm) REVERT: F 160 TYR cc_start: 0.7827 (t80) cc_final: 0.7525 (t80) REVERT: F 208 MET cc_start: 0.3575 (mtt) cc_final: 0.3225 (mmm) REVERT: F 226 MET cc_start: 0.6397 (tpt) cc_final: 0.6012 (tpt) REVERT: F 231 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: G 53 LYS cc_start: 0.8356 (tppt) cc_final: 0.7614 (mmmt) REVERT: G 72 ARG cc_start: 0.7623 (ttm170) cc_final: 0.7066 (ttm170) outliers start: 81 outliers final: 60 residues processed: 319 average time/residue: 0.1314 time to fit residues: 68.7852 Evaluate side-chains 329 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 255 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 231 TYR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 41 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 262 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 171 optimal weight: 0.5980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS ** D 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.092520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072716 restraints weight = 91030.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.075710 restraints weight = 44789.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077372 restraints weight = 25944.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.078464 restraints weight = 15911.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.079709 restraints weight = 10925.780| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.545 21783 Z= 0.200 Angle : 0.811 35.052 29385 Z= 0.352 Chirality : 0.045 0.215 3152 Planarity : 0.004 0.045 3780 Dihedral : 5.510 58.768 3293 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.30 % Allowed : 28.57 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.20 (0.17), residues: 2664 helix: 1.26 (0.15), residues: 1248 sheet: -0.41 (0.30), residues: 315 loop : -0.99 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 468 TYR 0.021 0.001 TYR F 9 PHE 0.020 0.001 PHE A 459 TRP 0.023 0.001 TRP A 253 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (21758) covalent geometry : angle 0.75984 / 0.35 (29367) hydrogen bonds : bond 0.03524 / 2.39 ( 956) hydrogen bonds : angle 5.00942 / 3.59 ( 2784) metal coordination : bond 0.01269 / 0.81 ( 8) metal coordination : angle 11.49259 / 6.22 ( 18) Misc. bond : bond 0.14609 / 11.75 ( 17) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 262 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.7654 (p0) REVERT: A 462 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7940 (m-30) REVERT: A 465 MET cc_start: 0.9005 (ttt) cc_final: 0.8501 (ttt) REVERT: B 98 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8660 (m-10) REVERT: B 116 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8368 (p0) REVERT: B 120 GLU cc_start: 0.8650 (mp0) cc_final: 0.8253 (mp0) REVERT: B 133 ASP cc_start: 0.8029 (m-30) cc_final: 0.7728 (m-30) REVERT: B 258 GLU cc_start: 0.8562 (pm20) cc_final: 0.8008 (pp20) REVERT: B 271 MET cc_start: 0.8510 (ttm) cc_final: 0.7575 (tpp) REVERT: B 354 MET cc_start: 0.8517 (tpp) cc_final: 0.7980 (mmt) REVERT: B 395 CYS cc_start: 0.8271 (t) cc_final: 0.7707 (t) REVERT: B 409 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8893 (tp) REVERT: B 467 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8790 (pt) REVERT: B 468 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.7772 (mtt90) REVERT: C 4 MET cc_start: 0.5296 (pp-130) cc_final: 0.2873 (tpp) REVERT: C 113 ASN cc_start: 0.9014 (t0) cc_final: 0.8660 (t0) REVERT: C 161 ASP cc_start: 0.4906 (OUTLIER) cc_final: 0.4458 (m-30) REVERT: C 256 ASP cc_start: 0.8099 (t0) cc_final: 0.6948 (t0) REVERT: C 380 GLU cc_start: 0.7938 (tt0) cc_final: 0.7675 (tm-30) REVERT: C 401 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.4717 (p90) REVERT: C 441 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7398 (mtm) REVERT: C 463 MET cc_start: 0.9187 (mmp) cc_final: 0.8967 (mmm) REVERT: D 247 MET cc_start: 0.7069 (tpp) cc_final: 0.6717 (mtt) REVERT: E 35 MET cc_start: 0.8238 (mmm) cc_final: 0.7965 (tpp) REVERT: E 78 LYS cc_start: 0.6885 (mttp) cc_final: 0.6463 (ptpp) REVERT: E 117 GLU cc_start: 0.5722 (pm20) cc_final: 0.4293 (mt-10) REVERT: E 126 ASP cc_start: 0.6240 (t0) cc_final: 0.5714 (p0) REVERT: E 155 GLU cc_start: 0.7523 (tt0) cc_final: 0.7249 (tt0) REVERT: E 156 MET cc_start: 0.8007 (ppp) cc_final: 0.7778 (ppp) REVERT: E 159 MET cc_start: 0.8826 (mmt) cc_final: 0.8564 (mtm) REVERT: E 275 MET cc_start: 0.6459 (ppp) cc_final: 0.5628 (ttm) REVERT: F 5 GLN cc_start: 0.3908 (OUTLIER) cc_final: 0.3167 (mt0) REVERT: F 30 MET cc_start: 0.7040 (mtm) cc_final: 0.6771 (ttt) REVERT: F 33 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.6267 (ttmt) REVERT: F 138 MET cc_start: 0.8902 (tmm) cc_final: 0.8559 (tmm) REVERT: F 160 TYR cc_start: 0.7842 (t80) cc_final: 0.7641 (t80) REVERT: F 226 MET cc_start: 0.6568 (tpt) cc_final: 0.6150 (tpt) REVERT: F 231 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.6374 (m-80) REVERT: F 264 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7701 (tm-30) REVERT: G 53 LYS cc_start: 0.8406 (tppt) cc_final: 0.7664 (mmmt) REVERT: G 72 ARG cc_start: 0.7601 (ttm170) cc_final: 0.7036 (ttm170) outliers start: 74 outliers final: 58 residues processed: 315 average time/residue: 0.1361 time to fit residues: 69.8567 Evaluate side-chains 327 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 257 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 396 HIS Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 231 TYR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 105 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 210 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 253 optimal weight: 30.0000 chunk 80 optimal weight: 0.0370 chunk 70 optimal weight: 7.9990 chunk 142 optimal weight: 0.0070 overall best weight: 2.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS F 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.092996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.074274 restraints weight = 68096.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.076570 restraints weight = 34768.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.078082 restraints weight = 21021.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.079043 restraints weight = 14314.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.079819 restraints weight = 10875.952| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.544 21783 Z= 0.190 Angle : 0.816 34.162 29385 Z= 0.353 Chirality : 0.045 0.254 3152 Planarity : 0.004 0.044 3780 Dihedral : 5.475 58.408 3291 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.38 % Allowed : 28.62 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.20 (0.17), residues: 2664 helix: 1.25 (0.15), residues: 1247 sheet: -0.42 (0.29), residues: 322 loop : -0.98 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 468 TYR 0.023 0.001 TYR C 20 PHE 0.019 0.001 PHE A 459 TRP 0.021 0.001 TRP A 253 HIS 0.017 0.001 HIS D 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (21758) covalent geometry : angle 0.76981 / 0.35 (29367) hydrogen bonds : bond 0.03467 / 2.35 ( 956) hydrogen bonds : angle 5.00305 / 3.58 ( 2784) metal coordination : bond 0.01234 / 0.74 ( 8) metal coordination : angle 10.99489 / 5.92 ( 18) Misc. bond : bond 0.14563 / 11.71 ( 17) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3779.40 seconds wall clock time: 66 minutes 30.15 seconds (3990.15 seconds total)