Starting phenix.real_space_refine on Mon Apr 6 08:38:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqz_45828/04_2026/9cqz_45828.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqz_45828/04_2026/9cqz_45828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cqz_45828/04_2026/9cqz_45828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqz_45828/04_2026/9cqz_45828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cqz_45828/04_2026/9cqz_45828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqz_45828/04_2026/9cqz_45828.map" } resolution = 2.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 32 7.16 5 S 139 5.16 5 C 10170 2.51 5 N 2702 2.21 5 O 4417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17462 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} bond proxies already assigned to first conformer: 3874 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3790 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3871 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {' FE': 2, 'CLF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: "A" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 289 Classifications: {'water': 289} Link IDs: {None: 288} Chain: "B" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 412 Classifications: {'water': 412} Link IDs: {None: 411} Chain: "C" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 291 Classifications: {'water': 291} Link IDs: {None: 290} Chain: "D" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 443 Classifications: {'water': 443} Link IDs: {None: 442} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 26.532 37.622 35.721 1.00 21.85 S ATOM 4552 SG CYS B 95 31.284 54.548 51.248 1.00 15.89 S ATOM 1170 SG CYS A 154 27.329 56.794 47.891 1.00 25.02 S ATOM 465 SG CYS A 62 29.418 51.105 45.683 1.00 23.70 S ATOM 652 SG CYS A 88 33.711 57.040 45.729 1.00 30.06 S ATOM 652 SG CYS A 88 33.711 57.040 45.729 1.00 30.06 S ATOM 5005 SG CYS B 153 30.983 59.944 49.749 1.00 22.66 S ATOM 4372 SG CYS B 70 37.456 57.516 51.153 1.00 17.52 S ATOM 4552 SG CYS B 95 31.284 54.548 51.248 1.00 15.89 S ATOM 10056 SG CYS C 275 104.287 47.650 35.769 1.00 22.17 S ATOM 12516 SG CYS D 95 99.451 30.741 51.274 1.00 15.30 S ATOM 9134 SG CYS C 154 103.448 28.484 47.879 1.00 23.94 S ATOM 8429 SG CYS C 62 101.424 34.143 45.700 1.00 23.83 S ATOM 8616 SG CYS C 88 97.042 28.322 45.726 1.00 33.49 S ATOM 8616 SG CYS C 88 97.042 28.322 45.726 1.00 33.49 S ATOM 12969 SG CYS D 153 99.806 25.411 49.818 1.00 26.87 S ATOM 12336 SG CYS D 70 93.326 27.761 51.191 1.00 18.56 S ATOM 12516 SG CYS D 95 99.451 30.741 51.274 1.00 15.30 S Time building chain proxies: 5.47, per 1000 atoms: 0.31 Number of scatterers: 17462 At special positions: 0 Unit cell: (132.3, 85.995, 95.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mo 2 41.97 Fe 32 26.01 S 139 16.00 O 4417 8.00 N 2702 7.00 C 10170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 976.6 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 12 sheets defined 58.8% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 removed outlier: 3.636A pdb=" N VAL A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.032A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.533A pdb=" N LYS A 44 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.627A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.777A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.187A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.117A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 5.815A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.821A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.537A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.707A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.524A pdb=" N GLU B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 70 through 81 removed outlier: 4.024A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.077A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.880A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 320 through 337 removed outlier: 4.120A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.240A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.571A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 4.386A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 30 removed outlier: 4.109A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.554A 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 86 through 92 removed outlier: 3.509A pdb=" N GLN C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.612A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 160 " --> pdb=" O ILE C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.668A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.226A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 4.539A pdb=" N ARG C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 211' Processing helix chain 'C' and resid 233 through 246 removed outlier: 3.754A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 291 removed outlier: 5.920A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'C' and resid 317 through 347 Proline residue: C 333 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 370 removed outlier: 3.631A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.320A 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 434 removed outlier: 4.721A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.707A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.594A pdb=" N GLU D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 70 through 80 removed outlier: 4.018A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.966A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.841A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.125A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.644A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.392A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.556A pdb=" N ARG D 481 " --> pdb=" O HIS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.618A pdb=" N VAL A 351 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N THR A 377 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 353 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR A 379 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.951A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 6.774A pdb=" N VAL A 223 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA A 251 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.335A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.355A 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: 8.774A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.062A pdb=" N VAL C 351 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY C 376 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 7.003A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 7.405A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.305A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.354A 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: 8.661A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) 777 hydrogen bonds defined for protein. 2238 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.86: 16347 1.86 - 2.49: 104 2.49 - 3.12: 18 3.12 - 3.75: 10 3.75 - 4.38: 4 Bond restraints: 16483 Sorted by residual: bond pdb="FE2 CLF D 601 " pdb="FE8 CLF D 601 " ideal model delta sigma weight residual 2.200 4.379 -2.179 2.00e-02 2.50e+03 1.19e+04 bond pdb="FE2 CLF B 602 " pdb="FE8 CLF B 602 " ideal model delta sigma weight residual 2.200 4.378 -2.178 2.00e-02 2.50e+03 1.19e+04 bond pdb="FE5 CLF D 601 " pdb="FE6 CLF D 601 " ideal model delta sigma weight residual 2.200 3.946 -1.746 2.00e-02 2.50e+03 7.62e+03 bond pdb="FE5 CLF B 602 " pdb="FE6 CLF B 602 " ideal model delta sigma weight residual 2.200 3.944 -1.744 2.00e-02 2.50e+03 7.60e+03 bond pdb=" S1 CLF D 601 " pdb="FE5 CLF D 601 " ideal model delta sigma weight residual 2.200 3.698 -1.498 2.00e-02 2.50e+03 5.61e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.89: 22237 6.89 - 13.78: 0 13.78 - 20.66: 2 20.66 - 27.55: 0 27.55 - 34.44: 4 Bond angle restraints: 22243 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 55.56 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 55.57 34.43 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE1 CLF B 602 " ideal model delta sigma weight residual 90.00 60.74 29.26 3.00e+00 1.11e-01 9.51e+01 angle pdb=" S1 CLF D 601 " pdb="FE2 CLF D 601 " pdb="FE1 CLF D 601 " ideal model delta sigma weight residual 90.00 60.75 29.25 3.00e+00 1.11e-01 9.51e+01 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE3 CLF B 602 " ideal model delta sigma weight residual 90.00 108.20 -18.20 3.00e+00 1.11e-01 3.68e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 8842 17.80 - 35.60: 891 35.60 - 53.40: 257 53.40 - 71.20: 70 71.20 - 89.00: 41 Dihedral angle restraints: 10101 sinusoidal: 4359 harmonic: 5742 Sorted by residual: dihedral pdb=" CA SER B 11 " pdb=" C SER B 11 " pdb=" N TYR B 12 " pdb=" CA TYR B 12 " ideal model delta harmonic sigma weight residual 180.00 161.99 18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ASP B 38 " pdb=" CB ASP B 38 " pdb=" CG ASP B 38 " pdb=" OD1 ASP B 38 " ideal model delta sinusoidal sigma weight residual -30.00 -89.38 59.38 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP B 215 " pdb=" CB ASP B 215 " pdb=" CG ASP B 215 " pdb=" OD1 ASP B 215 " ideal model delta sinusoidal sigma weight residual -30.00 -87.93 57.93 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1301 0.027 - 0.054: 607 0.054 - 0.082: 255 0.082 - 0.109: 117 0.109 - 0.136: 56 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA ILE C 81 " pdb=" N ILE C 81 " pdb=" C ILE C 81 " pdb=" CB ILE C 81 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE B 318 " pdb=" N ILE B 318 " pdb=" C ILE B 318 " pdb=" CB ILE B 318 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE A 81 " pdb=" N ILE A 81 " pdb=" C ILE A 81 " pdb=" CB ILE A 81 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 73 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO C 74 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 73 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 74 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 359 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 360 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " 0.023 5.00e-02 4.00e+02 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 537 2.57 - 3.15: 14460 3.15 - 3.73: 33077 3.73 - 4.32: 49239 4.32 - 4.90: 72279 Nonbonded interactions: 169592 Sorted by model distance: nonbonded pdb=" O HOH C 626 " pdb=" O HOH C 878 " model vdw 1.982 3.040 nonbonded pdb=" O HOH D1063 " pdb=" O HOH D1121 " model vdw 2.082 3.040 nonbonded pdb=" OE2 GLU D 109 " pdb="FE FE B 601 " model vdw 2.087 2.260 nonbonded pdb=" OD1 ASP C 136 " pdb=" O HOH C 601 " model vdw 2.093 3.040 nonbonded pdb=" OE2 GLU B 109 " pdb="FE FE B 603 " model vdw 2.095 2.260 ... (remaining 169587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 248 or resid 250 through 502)) selection = (chain 'C' and (resid 4 through 248 or resid 250 through 502)) } ncs_group { reference = (chain 'B' and resid 2 through 523) selection = (chain 'D' and resid 2 through 523) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.000 Find NCS groups from input model: 0.400 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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 : 0.048 2.179 16499 Z= 2.458 Angle : 0.690 34.440 22243 Z= 0.322 Chirality : 0.043 0.136 2336 Planarity : 0.004 0.042 2858 Dihedral : 16.821 89.001 6433 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.04 % Allowed : 15.38 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 1992 helix: 1.53 (0.17), residues: 974 sheet: -0.41 (0.37), residues: 174 loop : -0.56 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 415 TYR 0.016 0.001 TYR A 229 PHE 0.013 0.001 PHE C 429 TRP 0.014 0.001 TRP C 335 HIS 0.006 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.04817 (16483) covalent geometry : angle 0.69039 (22243) hydrogen bonds : bond 0.14040 ( 777) hydrogen bonds : angle 6.52095 ( 2238) Misc. bond : bond 0.16157 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7597 (tt0) cc_final: 0.7234 (mt-10) REVERT: A 209 LYS cc_start: 0.7743 (tttp) cc_final: 0.7093 (mmtt) REVERT: A 243 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: A 473 LYS cc_start: 0.8650 (mmtm) cc_final: 0.8003 (mppt) REVERT: B 54 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: B 404 LYS cc_start: 0.8841 (tttm) cc_final: 0.8501 (ttmp) REVERT: C 26 LYS cc_start: 0.8007 (ttpt) cc_final: 0.7487 (ttpp) REVERT: C 209 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7963 (mtpp) REVERT: C 243 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: C 393 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6803 (mm-30) REVERT: C 476 GLN cc_start: 0.7698 (tp40) cc_final: 0.7218 (tt0) REVERT: D 4 GLN cc_start: 0.7979 (mp10) cc_final: 0.7508 (mp10) REVERT: D 6 ASP cc_start: 0.7604 (m-30) cc_final: 0.6748 (p0) REVERT: D 7 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7522 (tppt) outliers start: 18 outliers final: 7 residues processed: 196 average time/residue: 0.9072 time to fit residues: 192.7044 Evaluate side-chains 189 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 7 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.0170 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 518 ASN C 98 ASN C 119 GLN D 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.103505 restraints weight = 15179.001| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.03 r_work: 0.3103 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.395 16499 Z= 0.268 Angle : 0.734 30.421 22243 Z= 0.349 Chirality : 0.045 0.145 2336 Planarity : 0.005 0.050 2858 Dihedral : 6.048 80.756 2543 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.21 % Allowed : 14.22 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.18), residues: 1992 helix: 1.51 (0.16), residues: 994 sheet: -0.38 (0.37), residues: 174 loop : -0.48 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 415 TYR 0.016 0.002 TYR A 229 PHE 0.013 0.001 PHE A 429 TRP 0.013 0.001 TRP C 335 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00513 (16483) covalent geometry : angle 0.73351 (22243) hydrogen bonds : bond 0.05515 ( 777) hydrogen bonds : angle 5.55011 ( 2238) Misc. bond : bond 0.17493 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.661 Fit side-chains REVERT: A 15 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6451 (tp30) REVERT: A 209 LYS cc_start: 0.7785 (tttp) cc_final: 0.7164 (mmtt) REVERT: A 373 GLU cc_start: 0.8351 (tt0) cc_final: 0.8122 (tt0) REVERT: A 473 LYS cc_start: 0.8497 (mmtm) cc_final: 0.7708 (mptt) REVERT: A 475 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8396 (mp) REVERT: B 299 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: B 404 LYS cc_start: 0.8794 (tttm) cc_final: 0.8459 (ttmp) REVERT: C 26 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7750 (tttm) REVERT: C 209 LYS cc_start: 0.8200 (ttmm) cc_final: 0.7944 (mtpp) REVERT: C 243 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: C 284 ARG cc_start: 0.8511 (mtm110) cc_final: 0.7666 (mtm-85) REVERT: C 393 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6858 (mm-30) REVERT: C 476 GLN cc_start: 0.7654 (tp40) cc_final: 0.7213 (tt0) REVERT: D 4 GLN cc_start: 0.8011 (mp10) cc_final: 0.7644 (mp10) REVERT: D 6 ASP cc_start: 0.7574 (m-30) cc_final: 0.6734 (p0) REVERT: D 7 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7518 (tppt) REVERT: D 175 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8219 (pt) REVERT: D 245 SER cc_start: 0.8628 (OUTLIER) cc_final: 0.8372 (m) outliers start: 38 outliers final: 14 residues processed: 209 average time/residue: 0.8646 time to fit residues: 196.6788 Evaluate side-chains 195 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 154 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 104 ASN C 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097541 restraints weight = 22977.468| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.30 r_work: 0.3011 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.417 16499 Z= 0.318 Angle : 0.784 30.638 22243 Z= 0.381 Chirality : 0.049 0.150 2336 Planarity : 0.005 0.065 2858 Dihedral : 5.979 83.346 2534 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.03 % Allowed : 13.99 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 1992 helix: 1.37 (0.16), residues: 1004 sheet: -0.34 (0.37), residues: 174 loop : -0.52 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 59 TYR 0.019 0.003 TYR D 142 PHE 0.017 0.002 PHE C 142 TRP 0.015 0.002 TRP C 335 HIS 0.008 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00632 (16483) covalent geometry : angle 0.78386 (22243) hydrogen bonds : bond 0.06703 ( 777) hydrogen bonds : angle 5.62318 ( 2238) Misc. bond : bond 0.19459 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 209 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7143 (mmtt) REVERT: A 473 LYS cc_start: 0.8623 (mmtm) cc_final: 0.7803 (mptt) REVERT: A 475 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8375 (mp) REVERT: B 54 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: B 299 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: B 404 LYS cc_start: 0.8859 (tttm) cc_final: 0.8491 (ttmp) REVERT: C 26 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7813 (tttm) REVERT: C 209 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7981 (mtpp) REVERT: C 243 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: C 284 ARG cc_start: 0.8552 (mtm110) cc_final: 0.7726 (mtt-85) REVERT: C 393 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7014 (mm-30) REVERT: C 476 GLN cc_start: 0.7765 (tp40) cc_final: 0.7247 (tt0) REVERT: D 4 GLN cc_start: 0.8065 (mp10) cc_final: 0.7613 (mp10) REVERT: D 6 ASP cc_start: 0.7583 (m-30) cc_final: 0.6651 (p0) REVERT: D 7 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7514 (tppt) REVERT: D 175 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8266 (pt) outliers start: 35 outliers final: 18 residues processed: 203 average time/residue: 0.8664 time to fit residues: 191.6261 Evaluate side-chains 196 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 127 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 142 optimal weight: 0.0980 chunk 138 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 98 ASN C 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102395 restraints weight = 24744.734| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.37 r_work: 0.3081 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.329 16499 Z= 0.236 Angle : 0.696 30.726 22243 Z= 0.328 Chirality : 0.044 0.145 2336 Planarity : 0.004 0.043 2858 Dihedral : 5.739 77.787 2534 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.97 % Allowed : 14.34 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 1992 helix: 1.55 (0.16), residues: 996 sheet: -0.02 (0.36), residues: 194 loop : -0.58 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 25 TYR 0.015 0.001 TYR A 229 PHE 0.011 0.001 PHE C 429 TRP 0.014 0.001 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00448 (16483) covalent geometry : angle 0.69648 (22243) hydrogen bonds : bond 0.04782 ( 777) hydrogen bonds : angle 5.33369 ( 2238) Misc. bond : bond 0.14556 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.648 Fit side-chains REVERT: A 15 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6572 (tp30) REVERT: A 209 LYS cc_start: 0.7795 (tttp) cc_final: 0.7118 (mmtt) REVERT: A 401 TYR cc_start: 0.9144 (OUTLIER) cc_final: 0.7579 (p90) REVERT: A 473 LYS cc_start: 0.8565 (mmtm) cc_final: 0.7765 (mptt) REVERT: A 475 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8349 (mp) REVERT: B 54 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6959 (tm-30) REVERT: B 299 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: C 26 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7740 (tttm) REVERT: C 209 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7927 (mtpp) REVERT: C 243 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: C 284 ARG cc_start: 0.8544 (mtm110) cc_final: 0.7661 (mtm-85) REVERT: C 393 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6903 (mm-30) REVERT: C 476 GLN cc_start: 0.7760 (tp40) cc_final: 0.7242 (tt0) REVERT: D 4 GLN cc_start: 0.8043 (mp10) cc_final: 0.7597 (mp10) REVERT: D 6 ASP cc_start: 0.7588 (m-30) cc_final: 0.6676 (p0) REVERT: D 7 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7534 (tppt) REVERT: D 175 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8180 (pt) outliers start: 34 outliers final: 15 residues processed: 205 average time/residue: 0.8839 time to fit residues: 196.9727 Evaluate side-chains 198 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 53 optimal weight: 0.0870 chunk 195 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 193 optimal weight: 0.0170 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 98 ASN C 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103418 restraints weight = 23572.933| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.34 r_work: 0.3097 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.308 16499 Z= 0.230 Angle : 0.686 30.723 22243 Z= 0.321 Chirality : 0.044 0.147 2336 Planarity : 0.004 0.043 2858 Dihedral : 5.616 76.710 2534 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.09 % Allowed : 14.51 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.18), residues: 1992 helix: 1.63 (0.16), residues: 1008 sheet: 0.01 (0.36), residues: 194 loop : -0.51 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 25 TYR 0.014 0.001 TYR B 88 PHE 0.011 0.001 PHE A 429 TRP 0.013 0.001 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00439 (16483) covalent geometry : angle 0.68563 (22243) hydrogen bonds : bond 0.04624 ( 777) hydrogen bonds : angle 5.24376 ( 2238) Misc. bond : bond 0.13710 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.675 Fit side-chains REVERT: A 15 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6567 (tp30) REVERT: A 209 LYS cc_start: 0.7799 (tttp) cc_final: 0.7114 (mmtt) REVERT: A 373 GLU cc_start: 0.8394 (tt0) cc_final: 0.8171 (tt0) REVERT: A 384 ASN cc_start: 0.7803 (m110) cc_final: 0.7551 (m110) REVERT: A 391 MET cc_start: 0.8101 (mtt) cc_final: 0.7767 (mtp) REVERT: A 401 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.7569 (p90) REVERT: A 473 LYS cc_start: 0.8569 (mmtm) cc_final: 0.7775 (mptt) REVERT: A 475 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8322 (mp) REVERT: B 54 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: B 299 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: C 26 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7475 (ttpp) REVERT: C 243 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: C 284 ARG cc_start: 0.8544 (mtm110) cc_final: 0.7641 (mtm-85) REVERT: C 393 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6911 (mm-30) REVERT: C 476 GLN cc_start: 0.7751 (tp40) cc_final: 0.7228 (tt0) REVERT: D 4 GLN cc_start: 0.8036 (mp10) cc_final: 0.7578 (mp10) REVERT: D 6 ASP cc_start: 0.7552 (m-30) cc_final: 0.6655 (p0) REVERT: D 7 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7539 (tppt) REVERT: D 175 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8191 (pt) REVERT: D 245 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8370 (m) outliers start: 36 outliers final: 16 residues processed: 210 average time/residue: 0.8634 time to fit residues: 197.3264 Evaluate side-chains 200 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 43 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 5 optimal weight: 0.0870 chunk 119 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 98 ASN C 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.098513 restraints weight = 28146.088| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.45 r_work: 0.3024 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.363 16499 Z= 0.278 Angle : 0.740 30.816 22243 Z= 0.354 Chirality : 0.047 0.180 2336 Planarity : 0.005 0.054 2858 Dihedral : 5.814 80.137 2534 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.92 % Allowed : 14.63 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 1992 helix: 1.55 (0.16), residues: 1006 sheet: -0.33 (0.36), residues: 174 loop : -0.50 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.018 0.002 TYR B 88 PHE 0.013 0.002 PHE C 142 TRP 0.013 0.002 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00544 (16483) covalent geometry : angle 0.74047 (22243) hydrogen bonds : bond 0.05792 ( 777) hydrogen bonds : angle 5.38601 ( 2238) Misc. bond : bond 0.16928 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.582 Fit side-chains REVERT: A 4 MET cc_start: 0.5169 (pmm) cc_final: 0.4099 (pmm) REVERT: A 15 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6582 (tp30) REVERT: A 209 LYS cc_start: 0.7805 (tttp) cc_final: 0.7117 (mmtt) REVERT: A 391 MET cc_start: 0.8136 (mtt) cc_final: 0.7840 (mtp) REVERT: A 473 LYS cc_start: 0.8610 (mmtm) cc_final: 0.7813 (mptt) REVERT: A 475 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8365 (mp) REVERT: B 54 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: B 299 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: C 26 LYS cc_start: 0.8082 (ttpt) cc_final: 0.7755 (tttm) REVERT: C 243 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: C 284 ARG cc_start: 0.8551 (mtm110) cc_final: 0.7630 (mtm-85) REVERT: C 393 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6924 (mm-30) REVERT: C 476 GLN cc_start: 0.7768 (tp40) cc_final: 0.7199 (tt0) REVERT: D 4 GLN cc_start: 0.8076 (mp10) cc_final: 0.7610 (mp10) REVERT: D 6 ASP cc_start: 0.7577 (m-30) cc_final: 0.6653 (p0) REVERT: D 7 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7510 (tppt) REVERT: D 175 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8216 (pt) REVERT: D 245 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8404 (m) outliers start: 33 outliers final: 17 residues processed: 200 average time/residue: 0.8446 time to fit residues: 184.1214 Evaluate side-chains 196 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 36 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 100 optimal weight: 0.0970 chunk 27 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 113 optimal weight: 10.0000 chunk 163 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 384 ASN C 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.125102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.104606 restraints weight = 23613.169| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.34 r_work: 0.3114 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.304 16499 Z= 0.219 Angle : 0.675 30.666 22243 Z= 0.314 Chirality : 0.043 0.147 2336 Planarity : 0.004 0.043 2858 Dihedral : 5.598 75.858 2534 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.97 % Allowed : 14.80 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 1992 helix: 1.68 (0.16), residues: 1008 sheet: -0.01 (0.35), residues: 194 loop : -0.50 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.013 0.001 TYR A 229 PHE 0.010 0.001 PHE A 429 TRP 0.014 0.001 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00413 (16483) covalent geometry : angle 0.67545 (22243) hydrogen bonds : bond 0.04270 ( 777) hydrogen bonds : angle 5.18929 ( 2238) Misc. bond : bond 0.13204 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.713 Fit side-chains REVERT: A 4 MET cc_start: 0.5060 (pmm) cc_final: 0.4132 (pmm) REVERT: A 209 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7150 (mmtt) REVERT: A 391 MET cc_start: 0.8051 (mtt) cc_final: 0.7793 (mtp) REVERT: A 401 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.7556 (p90) REVERT: A 473 LYS cc_start: 0.8536 (mmtm) cc_final: 0.7751 (mptt) REVERT: A 475 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8343 (mp) REVERT: B 54 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: B 299 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: C 26 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7470 (ttpp) REVERT: C 209 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7887 (mtpp) REVERT: C 243 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: C 284 ARG cc_start: 0.8548 (mtm110) cc_final: 0.7680 (mtm-85) REVERT: C 393 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6983 (mm-30) REVERT: C 476 GLN cc_start: 0.7765 (tp40) cc_final: 0.7227 (tt0) REVERT: D 4 GLN cc_start: 0.8026 (mp10) cc_final: 0.7570 (mp10) REVERT: D 6 ASP cc_start: 0.7572 (m-30) cc_final: 0.6683 (p0) REVERT: D 7 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7553 (tppt) REVERT: D 175 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8193 (pt) REVERT: D 245 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8353 (m) outliers start: 34 outliers final: 17 residues processed: 208 average time/residue: 0.8488 time to fit residues: 192.1560 Evaluate side-chains 199 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 146 optimal weight: 0.0270 chunk 12 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 35 ASN C 98 ASN C 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.099667 restraints weight = 25447.177| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.39 r_work: 0.3042 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.345 16499 Z= 0.268 Angle : 0.730 30.761 22243 Z= 0.347 Chirality : 0.046 0.147 2336 Planarity : 0.004 0.051 2858 Dihedral : 5.468 58.897 2531 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.97 % Allowed : 14.57 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.18), residues: 1992 helix: 1.59 (0.16), residues: 1008 sheet: 0.03 (0.35), residues: 194 loop : -0.48 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.018 0.002 TYR B 88 PHE 0.013 0.002 PHE C 429 TRP 0.012 0.002 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00522 (16483) covalent geometry : angle 0.73034 (22243) hydrogen bonds : bond 0.05568 ( 777) hydrogen bonds : angle 5.33640 ( 2238) Misc. bond : bond 0.16138 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.4956 (pmm) cc_final: 0.4152 (pmm) REVERT: A 209 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7134 (mmtt) REVERT: A 391 MET cc_start: 0.8125 (mtt) cc_final: 0.7790 (mtp) REVERT: A 473 LYS cc_start: 0.8587 (mmtm) cc_final: 0.7805 (mptt) REVERT: A 475 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8356 (mp) REVERT: B 54 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: B 299 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: C 26 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7761 (tttm) REVERT: C 243 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: C 284 ARG cc_start: 0.8550 (mtm110) cc_final: 0.7646 (mtm-85) REVERT: C 393 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6928 (mm-30) REVERT: C 476 GLN cc_start: 0.7764 (tp40) cc_final: 0.7196 (tt0) REVERT: D 4 GLN cc_start: 0.8055 (mp10) cc_final: 0.7587 (mp10) REVERT: D 6 ASP cc_start: 0.7561 (m-30) cc_final: 0.6645 (p0) REVERT: D 7 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7513 (tppt) REVERT: D 175 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8226 (pt) outliers start: 34 outliers final: 19 residues processed: 202 average time/residue: 0.8577 time to fit residues: 188.6080 Evaluate side-chains 200 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 77 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 121 optimal weight: 0.0270 chunk 189 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 98 ASN C 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099571 restraints weight = 25721.281| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.39 r_work: 0.3042 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.348 16499 Z= 0.267 Angle : 0.732 30.775 22243 Z= 0.348 Chirality : 0.046 0.148 2336 Planarity : 0.005 0.052 2858 Dihedral : 5.529 58.961 2531 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.86 % Allowed : 14.86 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 1992 helix: 1.55 (0.16), residues: 1008 sheet: 0.02 (0.35), residues: 194 loop : -0.50 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.017 0.002 TYR D 88 PHE 0.013 0.002 PHE C 429 TRP 0.012 0.002 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00518 (16483) covalent geometry : angle 0.73175 (22243) hydrogen bonds : bond 0.05533 ( 777) hydrogen bonds : angle 5.35514 ( 2238) Misc. bond : bond 0.16196 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.4933 (pmm) cc_final: 0.4341 (pmm) REVERT: A 209 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7128 (mmtt) REVERT: A 391 MET cc_start: 0.8125 (mtt) cc_final: 0.7806 (mtp) REVERT: A 473 LYS cc_start: 0.8597 (mmtm) cc_final: 0.7812 (mptt) REVERT: A 475 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8356 (mp) REVERT: B 54 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: B 299 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: C 26 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7777 (tttm) REVERT: C 209 LYS cc_start: 0.8271 (ttmm) cc_final: 0.7973 (mtpp) REVERT: C 243 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: C 284 ARG cc_start: 0.8550 (mtm110) cc_final: 0.7704 (mtt-85) REVERT: C 393 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6931 (mm-30) REVERT: C 476 GLN cc_start: 0.7755 (tp40) cc_final: 0.7187 (tt0) REVERT: D 4 GLN cc_start: 0.8066 (mp10) cc_final: 0.7596 (mp10) REVERT: D 6 ASP cc_start: 0.7567 (m-30) cc_final: 0.6652 (p0) REVERT: D 7 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7530 (tppt) REVERT: D 175 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8215 (pt) outliers start: 32 outliers final: 20 residues processed: 201 average time/residue: 0.8881 time to fit residues: 193.9945 Evaluate side-chains 199 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 129 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 180 optimal weight: 0.4980 chunk 176 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 14 GLN C 98 ASN C 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101303 restraints weight = 25506.524| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.39 r_work: 0.3068 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.323 16499 Z= 0.243 Angle : 0.706 30.744 22243 Z= 0.332 Chirality : 0.045 0.147 2336 Planarity : 0.004 0.044 2858 Dihedral : 5.439 59.110 2531 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.51 % Allowed : 15.15 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.18), residues: 1992 helix: 1.62 (0.16), residues: 1008 sheet: -0.35 (0.36), residues: 174 loop : -0.45 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 25 TYR 0.015 0.002 TYR B 88 PHE 0.012 0.001 PHE A 429 TRP 0.013 0.001 TRP C 335 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00467 (16483) covalent geometry : angle 0.70563 (22243) hydrogen bonds : bond 0.04969 ( 777) hydrogen bonds : angle 5.26847 ( 2238) Misc. bond : bond 0.14670 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.4798 (pmm) cc_final: 0.4333 (pmm) REVERT: A 209 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7130 (mmtt) REVERT: A 391 MET cc_start: 0.8076 (mtt) cc_final: 0.7820 (mtp) REVERT: A 473 LYS cc_start: 0.8569 (mmtm) cc_final: 0.7783 (mptt) REVERT: A 475 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8334 (mp) REVERT: B 54 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: B 299 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: C 26 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7478 (ttpp) REVERT: C 209 LYS cc_start: 0.8245 (ttmm) cc_final: 0.7944 (mtpp) REVERT: C 243 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: C 284 ARG cc_start: 0.8546 (mtm110) cc_final: 0.7637 (mtm-85) REVERT: C 393 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6954 (mm-30) REVERT: C 476 GLN cc_start: 0.7745 (tp40) cc_final: 0.7177 (tt0) REVERT: D 4 GLN cc_start: 0.8067 (mp10) cc_final: 0.7596 (mp10) REVERT: D 6 ASP cc_start: 0.7584 (m-30) cc_final: 0.6675 (p0) REVERT: D 7 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7541 (tppt) REVERT: D 175 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8211 (pt) REVERT: D 245 SER cc_start: 0.8586 (m) cc_final: 0.8367 (m) outliers start: 26 outliers final: 17 residues processed: 195 average time/residue: 0.8761 time to fit residues: 185.2853 Evaluate side-chains 198 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 106 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 98 ASN C 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103102 restraints weight = 22762.202| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.31 r_work: 0.3095 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.307 16499 Z= 0.233 Angle : 0.694 30.675 22243 Z= 0.325 Chirality : 0.044 0.146 2336 Planarity : 0.004 0.044 2858 Dihedral : 5.364 59.028 2531 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.68 % Allowed : 15.15 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.18), residues: 1992 helix: 1.67 (0.16), residues: 1008 sheet: 0.01 (0.35), residues: 194 loop : -0.46 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.014 0.002 TYR B 88 PHE 0.011 0.001 PHE A 429 TRP 0.014 0.001 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00446 (16483) covalent geometry : angle 0.69430 (22243) hydrogen bonds : bond 0.04699 ( 777) hydrogen bonds : angle 5.21720 ( 2238) Misc. bond : bond 0.13829 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7825.39 seconds wall clock time: 133 minutes 56.57 seconds (8036.57 seconds total)