Starting phenix.real_space_refine on Sat Jul 4 01:15:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqz_45828/07_2026/9cqz_45828.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqz_45828/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cqz_45828/07_2026/9cqz_45828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqz_45828/07_2026/9cqz_45828.map" model { file = "/net/cci-nas-00/data/ceres_data/9cqz_45828/07_2026/9cqz_45828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqz_45828/07_2026/9cqz_45828.cif" } 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-dev-6108/lib/python3.11/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, 15 Ad-hoc single atom residues: {' FE': 2} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain: "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: 4.32, per 1000 atoms: 0.25 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: 0.98 Conformation dependent library (CDL) restraints added in 649.0 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: 0.51 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: 3.10 Time building geometry restraints manager: 1.35 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 3.000 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 3.000 ... (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: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.240 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 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/Z covalent geometry : bond 0.04817 / 2.41 (16483) covalent geometry : angle 0.69039 / 0.32 (22243) hydrogen bonds : bond 0.14040 / 9.62 ( 777) hydrogen bonds : angle 6.52095 / 4.86 ( 2238) Misc. bond : bond 0.16157 / 12.28 ( 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 : 0.644 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: 0.7890 time to fit residues: 168.2425 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 : 0.592 ------------------------------------------------------------------------------- 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... 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 = 0.3412 r_free = 0.3412 target = 0.121953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103666 restraints weight = 14997.052| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.03 r_work: 0.3105 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 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 = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.393 16499 Z= 0.267 Angle : 0.735 30.667 22243 Z= 0.349 Chirality : 0.045 0.144 2336 Planarity : 0.005 0.050 2858 Dihedral : 6.050 80.765 2543 Min Nonbonded Distance : 1.914 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: 0.76 (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 0.014 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/Z covalent geometry : bond 0.00510 / 0.24 (16483) covalent geometry : angle 0.73518 / 0.35 (22243) hydrogen bonds : bond 0.05513 / 3.85 ( 777) hydrogen bonds : angle 5.56226 / 4.11 ( 2238) Misc. bond : bond 0.17524 / 11.22 ( 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 215 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.709 Fit side-chains REVERT: A 15 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6437 (tp30) REVERT: A 209 LYS cc_start: 0.7782 (tttp) cc_final: 0.7155 (mmtt) REVERT: A 373 GLU cc_start: 0.8346 (tt0) cc_final: 0.8117 (tt0) REVERT: A 473 LYS cc_start: 0.8498 (mmtm) cc_final: 0.7707 (mptt) REVERT: A 475 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8384 (mp) REVERT: B 299 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: B 404 LYS cc_start: 0.8782 (tttm) cc_final: 0.8441 (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: 0.7943 (mtpp) REVERT: C 243 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: C 284 ARG cc_start: 0.8517 (mtm110) cc_final: 0.7669 (mtm-85) REVERT: C 393 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6853 (mm-30) REVERT: C 476 GLN cc_start: 0.7655 (tp40) cc_final: 0.7211 (tt0) REVERT: D 4 GLN cc_start: 0.8012 (mp10) cc_final: 0.7646 (mp10) REVERT: D 6 ASP cc_start: 0.7577 (m-30) cc_final: 0.6737 (p0) REVERT: D 7 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7518 (tppt) REVERT: D 175 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8217 (pt) REVERT: D 245 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8364 (m) outliers start: 38 outliers final: 14 residues processed: 208 average time/residue: 0.7470 time to fit residues: 169.9183 Evaluate side-chains 194 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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: 0.7980 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: 7.9990 chunk 35 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN B 104 ASN C 98 ASN C 119 GLN D 457 HIS D 518 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.095833 restraints weight = 22708.138| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.28 r_work: 0.2987 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.480 16499 Z= 0.369 Angle : 0.844 30.540 22243 Z= 0.417 Chirality : 0.053 0.179 2336 Planarity : 0.006 0.079 2858 Dihedral : 6.167 86.664 2534 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.21 % Allowed : 13.58 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 1992 helix: 1.30 (0.16), residues: 978 sheet: -0.34 (0.37), residues: 174 loop : -0.63 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 96 TYR 0.023 0.003 TYR D 142 PHE 0.020 0.003 PHE C 142 TRP 0.015 0.003 TRP C 335 HIS 0.009 0.002 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.34 (16483) covalent geometry : angle 0.84393 / 0.42 (22243) hydrogen bonds : bond 0.07706 / 5.35 ( 777) hydrogen bonds : angle 5.77860 / 4.29 ( 2238) Misc. bond : bond 0.21147 / 13.09 ( 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 216 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.594 Fit side-chains REVERT: A 209 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7119 (mmtt) REVERT: A 473 LYS cc_start: 0.8672 (mmtm) cc_final: 0.7858 (mptt) REVERT: A 475 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8401 (mp) REVERT: B 54 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: B 299 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: B 404 LYS cc_start: 0.8897 (tttm) cc_final: 0.8519 (ttmp) REVERT: C 26 LYS cc_start: 0.8116 (ttpt) cc_final: 0.7806 (tttm) REVERT: C 209 LYS cc_start: 0.8318 (ttmm) cc_final: 0.7988 (mtpp) REVERT: C 243 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: C 284 ARG cc_start: 0.8554 (mtm110) cc_final: 0.7666 (mtt-85) REVERT: C 393 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6972 (mm-30) REVERT: C 476 GLN cc_start: 0.7747 (tp40) cc_final: 0.7255 (tt0) REVERT: D 4 GLN cc_start: 0.8074 (mp10) cc_final: 0.7652 (mp10) REVERT: D 6 ASP cc_start: 0.7592 (m-30) cc_final: 0.6672 (p0) REVERT: D 7 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7516 (tppt) outliers start: 38 outliers final: 18 residues processed: 206 average time/residue: 0.7571 time to fit residues: 170.4154 Evaluate side-chains 195 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 465 MET 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 245 SER 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: 1.9990 chunk 11 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3393 r_free = 0.3393 target = 0.120509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.099646 restraints weight = 24331.198| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.35 r_work: 0.3041 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.363 16499 Z= 0.264 Angle : 0.734 30.729 22243 Z= 0.351 Chirality : 0.046 0.146 2336 Planarity : 0.004 0.051 2858 Dihedral : 5.946 81.028 2534 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.92 % Allowed : 13.99 % Favored : 84.10 % 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: 0.68 (0.18), residues: 1992 helix: 1.46 (0.16), residues: 992 sheet: -0.01 (0.36), residues: 194 loop : -0.66 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 25 TYR 0.017 0.002 TYR A 229 PHE 0.013 0.002 PHE C 142 TRP 0.014 0.001 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.24 (16483) covalent geometry : angle 0.73365 / 0.35 (22243) hydrogen bonds : bond 0.05547 / 3.87 ( 777) hydrogen bonds : angle 5.46597 / 4.02 ( 2238) Misc. bond : bond 0.16521 / 10.49 ( 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 206 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.457 Fit side-chains REVERT: A 15 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6554 (tp30) REVERT: A 209 LYS cc_start: 0.7808 (tttp) cc_final: 0.7145 (mmtt) REVERT: A 473 LYS cc_start: 0.8608 (mmtm) cc_final: 0.7792 (mptt) REVERT: A 475 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8377 (mp) REVERT: B 54 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6966 (tm-30) REVERT: B 299 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: B 404 LYS cc_start: 0.8842 (tttm) cc_final: 0.8473 (ttmp) REVERT: C 26 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7786 (tttm) REVERT: C 243 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: C 284 ARG cc_start: 0.8560 (mtm110) cc_final: 0.7730 (mtt-85) REVERT: C 393 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6998 (mm-30) REVERT: C 476 GLN cc_start: 0.7724 (tp40) cc_final: 0.7193 (tt0) REVERT: D 4 GLN cc_start: 0.8084 (mp10) cc_final: 0.7666 (mp10) REVERT: D 6 ASP cc_start: 0.7577 (m-30) cc_final: 0.6659 (p0) REVERT: D 7 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7505 (tppt) outliers start: 33 outliers final: 17 residues processed: 200 average time/residue: 0.7394 time to fit residues: 161.3576 Evaluate side-chains 191 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 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 401 TYR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 7 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 120 optimal weight: 0.4980 chunk 60 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3380 r_free = 0.3380 target = 0.119494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098865 restraints weight = 23206.548| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.31 r_work: 0.3031 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.366 16499 Z= 0.280 Angle : 0.750 30.773 22243 Z= 0.359 Chirality : 0.047 0.168 2336 Planarity : 0.005 0.057 2858 Dihedral : 5.957 82.088 2534 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.15 % Allowed : 13.76 % Favored : 84.10 % 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: 1.44 (0.16), residues: 1004 sheet: -0.00 (0.35), residues: 194 loop : -0.63 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.017 0.002 TYR B 88 PHE 0.014 0.002 PHE C 142 TRP 0.014 0.002 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.26 (16483) covalent geometry : angle 0.74950 / 0.36 (22243) hydrogen bonds : bond 0.05925 / 4.13 ( 777) hydrogen bonds : angle 5.47010 / 4.03 ( 2238) Misc. bond : bond 0.17096 / 10.69 ( 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 207 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 209 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7124 (mmtt) REVERT: A 391 MET cc_start: 0.8108 (mtt) cc_final: 0.7786 (mtp) REVERT: A 473 LYS cc_start: 0.8641 (mmtm) cc_final: 0.7843 (mptt) REVERT: A 475 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8354 (mp) REVERT: B 54 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: B 299 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: B 404 LYS cc_start: 0.8837 (tttm) cc_final: 0.8472 (ttmp) REVERT: C 26 LYS cc_start: 0.8065 (ttpt) cc_final: 0.7758 (tttm) REVERT: C 243 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: C 284 ARG cc_start: 0.8557 (mtm110) cc_final: 0.7707 (mtt-85) REVERT: C 393 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6980 (mm-30) REVERT: C 476 GLN cc_start: 0.7727 (tp40) cc_final: 0.7174 (tt0) REVERT: D 4 GLN cc_start: 0.8082 (mp10) cc_final: 0.7646 (mp10) REVERT: D 6 ASP cc_start: 0.7571 (m-30) cc_final: 0.6665 (p0) REVERT: D 7 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7507 (tppt) outliers start: 37 outliers final: 20 residues processed: 199 average time/residue: 0.6947 time to fit residues: 151.3411 Evaluate side-chains 193 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 475 LEU Chi-restraints excluded: chain D residue 7 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 43 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 119 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3423 r_free = 0.3423 target = 0.122787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101361 restraints weight = 27794.324| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.45 r_work: 0.3065 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.324 16499 Z= 0.237 Angle : 0.700 30.746 22243 Z= 0.330 Chirality : 0.045 0.147 2336 Planarity : 0.004 0.044 2858 Dihedral : 5.781 78.088 2534 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.97 % Allowed : 14.39 % Favored : 83.63 % 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: 0.83 (0.18), residues: 1992 helix: 1.57 (0.16), residues: 1006 sheet: -0.02 (0.35), residues: 194 loop : -0.58 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.015 0.002 TYR A 229 PHE 0.011 0.001 PHE C 429 TRP 0.013 0.001 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.22 (16483) covalent geometry : angle 0.69971 / 0.33 (22243) hydrogen bonds : bond 0.04840 / 3.39 ( 777) hydrogen bonds : angle 5.30167 / 3.89 ( 2238) Misc. bond : bond 0.14354 / 9.12 ( 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 204 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.708 Fit side-chains REVERT: A 4 MET cc_start: 0.5207 (pmm) cc_final: 0.4173 (pmm) REVERT: A 15 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6603 (tp30) REVERT: A 209 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7118 (mmtt) REVERT: A 334 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: A 401 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.7583 (p90) REVERT: A 473 LYS cc_start: 0.8584 (mmtm) cc_final: 0.7777 (mptt) REVERT: A 475 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8351 (mp) REVERT: B 54 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: B 299 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: C 26 LYS cc_start: 0.8059 (ttpt) cc_final: 0.7484 (ttpp) REVERT: C 209 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7910 (mtpp) REVERT: C 243 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: C 284 ARG cc_start: 0.8560 (mtm110) cc_final: 0.7637 (mtm-85) REVERT: C 393 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6996 (mm-30) REVERT: C 476 GLN cc_start: 0.7745 (tp40) cc_final: 0.7171 (tt0) REVERT: D 4 GLN cc_start: 0.8078 (mp10) cc_final: 0.7622 (mp10) REVERT: D 6 ASP cc_start: 0.7617 (m-30) cc_final: 0.6691 (p0) REVERT: D 7 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7492 (tppt) REVERT: D 258 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7993 (tm-30) outliers start: 34 outliers final: 18 residues processed: 197 average time/residue: 0.7580 time to fit residues: 163.3352 Evaluate side-chains 196 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 334 GLU 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 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 401 TYR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 36 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 113 optimal weight: 6.9990 chunk 163 optimal weight: 0.0060 chunk 1 optimal weight: 0.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100311 restraints weight = 23207.520| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.32 r_work: 0.3054 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.341 16499 Z= 0.262 Angle : 0.726 30.751 22243 Z= 0.345 Chirality : 0.046 0.148 2336 Planarity : 0.004 0.050 2858 Dihedral : 5.828 79.972 2534 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: 0.84 (0.18), residues: 1992 helix: 1.56 (0.16), residues: 1006 sheet: 0.01 (0.35), residues: 194 loop : -0.55 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.017 0.002 TYR B 88 PHE 0.013 0.002 PHE C 429 TRP 0.013 0.002 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.24 (16483) covalent geometry : angle 0.72648 / 0.35 (22243) hydrogen bonds : bond 0.05467 / 3.81 ( 777) hydrogen bonds : angle 5.35621 / 3.93 ( 2238) Misc. bond : bond 0.15767 / 9.91 ( 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 206 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.588 Fit side-chains REVERT: A 4 MET cc_start: 0.5053 (pmm) cc_final: 0.4142 (pmm) REVERT: A 15 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6562 (tp30) REVERT: A 209 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7145 (mmtt) REVERT: A 401 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.7597 (p90) REVERT: A 473 LYS cc_start: 0.8604 (mmtm) cc_final: 0.7808 (mptt) REVERT: A 475 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8350 (mp) REVERT: B 54 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: B 299 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: C 26 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7501 (ttpp) REVERT: C 243 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: C 284 ARG cc_start: 0.8546 (mtm110) cc_final: 0.7634 (mtm-85) REVERT: C 393 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6982 (mm-30) REVERT: C 476 GLN cc_start: 0.7740 (tp40) cc_final: 0.7176 (tt0) REVERT: D 4 GLN cc_start: 0.8067 (mp10) cc_final: 0.7613 (mp10) REVERT: D 6 ASP cc_start: 0.7601 (m-30) cc_final: 0.6690 (p0) REVERT: D 7 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7517 (tppt) outliers start: 34 outliers final: 18 residues processed: 199 average time/residue: 0.7432 time to fit residues: 161.5816 Evaluate side-chains 193 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 401 TYR 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 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: 0.9990 chunk 78 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3366 r_free = 0.3366 target = 0.118300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.097421 restraints weight = 25025.595| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.36 r_work: 0.3009 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.391 16499 Z= 0.306 Angle : 0.778 30.755 22243 Z= 0.376 Chirality : 0.048 0.150 2336 Planarity : 0.005 0.063 2858 Dihedral : 6.009 83.020 2534 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.92 % Allowed : 14.34 % Favored : 83.75 % 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: 0.71 (0.18), residues: 1992 helix: 1.42 (0.16), residues: 1006 sheet: 0.02 (0.35), residues: 194 loop : -0.59 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.020 0.002 TYR B 88 PHE 0.016 0.002 PHE C 142 TRP 0.013 0.002 TRP C 335 HIS 0.008 0.002 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.28 (16483) covalent geometry : angle 0.77776 / 0.38 (22243) hydrogen bonds : bond 0.06484 / 4.51 ( 777) hydrogen bonds : angle 5.52747 / 4.07 ( 2238) Misc. bond : bond 0.18052 / 11.23 ( 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 200 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.4991 (pmm) cc_final: 0.4263 (pmm) REVERT: A 209 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7138 (mmtt) REVERT: A 473 LYS cc_start: 0.8667 (mmtm) cc_final: 0.7872 (mptt) REVERT: A 475 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8390 (mp) REVERT: B 54 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: B 299 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: B 404 LYS cc_start: 0.8860 (tttm) cc_final: 0.8513 (ttmp) REVERT: C 26 LYS cc_start: 0.8082 (ttpt) cc_final: 0.7531 (ttpp) REVERT: C 209 LYS cc_start: 0.8309 (ttmm) cc_final: 0.8022 (mtpp) REVERT: C 243 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: C 284 ARG cc_start: 0.8581 (mtm110) cc_final: 0.7718 (mtt-85) REVERT: C 393 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6997 (mm-30) REVERT: C 476 GLN cc_start: 0.7791 (tp40) cc_final: 0.7208 (tt0) REVERT: D 4 GLN cc_start: 0.8099 (mp10) cc_final: 0.7650 (mp10) REVERT: D 6 ASP cc_start: 0.7622 (m-30) cc_final: 0.6688 (p0) REVERT: D 7 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7552 (tppt) outliers start: 33 outliers final: 16 residues processed: 192 average time/residue: 0.7218 time to fit residues: 151.6299 Evaluate side-chains 187 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 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 C residue 467 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 245 SER 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: 0.9980 chunk 125 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3361 r_free = 0.3361 target = 0.117952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.096981 restraints weight = 25298.487| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.37 r_work: 0.3003 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.397 16499 Z= 0.311 Angle : 0.787 30.717 22243 Z= 0.382 Chirality : 0.049 0.149 2336 Planarity : 0.005 0.067 2858 Dihedral : 6.086 84.089 2534 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.57 % Allowed : 14.74 % 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: 0.64 (0.18), residues: 1992 helix: 1.34 (0.16), residues: 1006 sheet: 0.04 (0.35), residues: 194 loop : -0.62 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 25 TYR 0.019 0.002 TYR B 88 PHE 0.016 0.002 PHE C 142 TRP 0.013 0.002 TRP C 335 HIS 0.008 0.002 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.29 (16483) covalent geometry : angle 0.78682 / 0.38 (22243) hydrogen bonds : bond 0.06567 / 4.56 ( 777) hydrogen bonds : angle 5.57399 / 4.11 ( 2238) Misc. bond : bond 0.18112 / 11.27 ( 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 197 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.5009 (pmm) cc_final: 0.4353 (pmm) REVERT: A 209 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7146 (mmtt) REVERT: A 334 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: A 473 LYS cc_start: 0.8672 (mmtm) cc_final: 0.7872 (mptt) REVERT: A 475 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8397 (mp) REVERT: B 54 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: B 299 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: B 404 LYS cc_start: 0.8852 (tttm) cc_final: 0.8489 (ttmp) REVERT: C 26 LYS cc_start: 0.8083 (ttpt) cc_final: 0.7537 (ttpp) REVERT: C 243 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: C 284 ARG cc_start: 0.8581 (mtm110) cc_final: 0.7717 (mtt-85) REVERT: C 393 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6985 (mm-30) REVERT: C 476 GLN cc_start: 0.7816 (tp40) cc_final: 0.7248 (tt0) REVERT: D 4 GLN cc_start: 0.8079 (mp10) cc_final: 0.7646 (mp10) REVERT: D 6 ASP cc_start: 0.7609 (m-30) cc_final: 0.6683 (p0) REVERT: D 7 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7554 (tppt) outliers start: 27 outliers final: 16 residues processed: 190 average time/residue: 0.7284 time to fit residues: 150.7724 Evaluate side-chains 188 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 334 GLU 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 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 245 SER 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: 1.9990 chunk 43 optimal weight: 0.0870 chunk 95 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 chunk 196 optimal weight: 0.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3434 r_free = 0.3434 target = 0.123620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.102829 restraints weight = 25131.200| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.37 r_work: 0.3088 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.317 16499 Z= 0.229 Angle : 0.695 30.689 22243 Z= 0.327 Chirality : 0.044 0.144 2336 Planarity : 0.004 0.043 2858 Dihedral : 5.789 77.428 2534 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.39 % Allowed : 15.03 % 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: 0.86 (0.18), residues: 1992 helix: 1.57 (0.16), residues: 1008 sheet: -0.01 (0.35), residues: 194 loop : -0.54 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.015 0.001 TYR A 229 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/Z covalent geometry : bond 0.00435 / 0.21 (16483) covalent geometry : angle 0.69545 / 0.33 (22243) hydrogen bonds : bond 0.04595 / 3.22 ( 777) hydrogen bonds : angle 5.28528 / 3.86 ( 2238) Misc. bond : bond 0.13740 / 8.79 ( 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 193 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.685 Fit side-chains REVERT: A 4 MET cc_start: 0.4789 (pmm) cc_final: 0.4236 (pmm) REVERT: A 15 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6541 (tp30) REVERT: A 209 LYS cc_start: 0.7775 (tttp) cc_final: 0.7112 (mmtt) REVERT: A 473 LYS cc_start: 0.8562 (mmtm) cc_final: 0.7766 (mptt) REVERT: A 475 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8335 (mp) REVERT: B 54 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6975 (tm-30) REVERT: B 299 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: C 26 LYS cc_start: 0.8067 (ttpt) cc_final: 0.7504 (ttpp) REVERT: C 209 LYS cc_start: 0.8246 (ttmm) cc_final: 0.7959 (mtpp) REVERT: C 243 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: C 284 ARG cc_start: 0.8562 (mtm110) cc_final: 0.7713 (mtt-85) REVERT: C 393 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6978 (mm-30) REVERT: C 476 GLN cc_start: 0.7761 (tp40) cc_final: 0.7189 (tt0) REVERT: D 4 GLN cc_start: 0.8049 (mp10) cc_final: 0.7596 (mp10) REVERT: D 6 ASP cc_start: 0.7539 (m-30) cc_final: 0.6648 (p0) REVERT: D 7 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7522 (tppt) outliers start: 24 outliers final: 12 residues processed: 187 average time/residue: 0.7167 time to fit residues: 146.3785 Evaluate side-chains 184 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 258 GLU Chi-restraints excluded: chain B residue 299 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 D residue 7 LYS Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 369 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 106 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102697 restraints weight = 22457.645| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.29 r_work: 0.3089 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 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 = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.315 16499 Z= 0.236 Angle : 0.701 30.727 22243 Z= 0.329 Chirality : 0.044 0.146 2336 Planarity : 0.004 0.044 2858 Dihedral : 5.711 77.790 2534 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.22 % Allowed : 15.38 % 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: 0.93 (0.18), residues: 1992 helix: 1.62 (0.16), residues: 1006 sheet: 0.02 (0.35), residues: 194 loop : -0.48 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.015 0.002 TYR A 229 PHE 0.012 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/Z covalent geometry : bond 0.00452 / 0.22 (16483) covalent geometry : angle 0.70070 / 0.33 (22243) hydrogen bonds : bond 0.04813 / 3.36 ( 777) hydrogen bonds : angle 5.26210 / 3.85 ( 2238) Misc. bond : bond 0.14157 / 8.89 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6382.41 seconds wall clock time: 109 minutes 38.84 seconds (6578.84 seconds total)