Starting phenix.real_space_refine on Mon Apr 6 07:29:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8enn_28274/04_2026/8enn_28274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8enn_28274/04_2026/8enn_28274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8enn_28274/04_2026/8enn_28274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8enn_28274/04_2026/8enn_28274.map" model { file = "/net/cci-nas-00/data/ceres_data/8enn_28274/04_2026/8enn_28274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8enn_28274/04_2026/8enn_28274.cif" } resolution = 2.58 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= 0.029 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 10093 2.51 5 N 2672 2.21 5 O 3811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16749 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3586 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 432} Chain breaks: 4 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: 1 Conformer: "" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} 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: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'ICS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' FE': 1, '1N7': 1, 'CLF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'CIT': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' FE': 1, '1N7': 1, 'CLF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 130 Classifications: {'water': 130} Link IDs: {None: 129} Chain: "B" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 273 Classifications: {'water': 273} Link IDs: {None: 272} Chain: "C" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 177 Classifications: {'water': 177} Link IDs: {None: 176} Chain: "D" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 278 Classifications: {'water': 278} Link IDs: {None: 277} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1978 SG CYS A 275 49.873 36.397 101.670 1.00 85.80 S ATOM 1059 SG CYS A 154 31.614 49.269 102.823 1.00 41.77 S ATOM 4345 SG CYS B 95 33.250 52.000 98.577 1.00 38.28 S ATOM 354 SG CYS A 62 36.804 46.716 100.018 1.00 33.83 S ATOM 541 SG CYS A 88 30.845 47.419 96.860 1.00 50.41 S ATOM 541 SG CYS A 88 30.845 47.419 96.860 1.00 50.41 S ATOM 4798 SG CYS B 153 28.473 50.872 99.635 1.00 48.92 S ATOM 4165 SG CYS B 70 30.115 52.565 92.825 1.00 55.47 S ATOM 4345 SG CYS B 95 33.250 52.000 98.577 1.00 38.28 S ATOM 9849 SG CYS C 275 32.957 37.671 26.402 1.00 41.73 S ATOM 8930 SG CYS C 154 52.364 48.841 25.418 1.00 34.19 S ATOM 12309 SG CYS D 95 50.919 51.714 29.671 1.00 48.70 S ATOM 8225 SG CYS C 62 46.929 46.663 28.126 1.00 25.03 S ATOM 8412 SG CYS C 88 52.777 46.760 31.392 1.00 42.60 S ATOM 8412 SG CYS C 88 52.777 46.760 31.392 1.00 42.60 S ATOM 12762 SG CYS D 153 55.582 50.106 28.613 1.00 60.25 S ATOM 12129 SG CYS D 70 53.989 51.737 35.515 1.00 54.91 S ATOM 12309 SG CYS D 95 50.919 51.714 29.671 1.00 48.70 S Time building chain proxies: 4.14, per 1000 atoms: 0.25 Number of scatterers: 16749 At special positions: 0 Unit cell: (85.15, 98.15, 128.7, 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 3811 8.00 N 2672 7.00 C 10093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 856.4 milliseconds 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3616 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 12 sheets defined 58.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 85 through 92 removed outlier: 4.601A pdb=" N GLY A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) 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: 4.067A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.735A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.158A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 4.549A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP A 211 " --> pdb=" O GLY A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 211' Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.702A 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: 5.865A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.033A 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 343 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 removed outlier: 3.644A pdb=" N TYR A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.277A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 434 removed outlier: 3.830A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.516A pdb=" N TRP A 472 " --> pdb=" O ASN A 469 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 474 " --> pdb=" O CYS A 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 31 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 80 removed outlier: 4.004A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.943A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.736A pdb=" N VAL B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) 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 233 through 247 removed outlier: 3.846A 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 321 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.135A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.772A 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: 3.981A 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: 4.046A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 removed outlier: 3.507A pdb=" N GLU B 463 " --> pdb=" O LYS B 460 " (cutoff:3.500A) No H-bonds generated for '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: 4.006A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.725A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.158A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 4.483A pdb=" N ARG C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.516A 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 245 removed outlier: 3.729A 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: 5.889A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.000A 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: 3.601A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 392 removed outlier: 3.529A pdb=" N TYR C 387 " --> pdb=" O HIS C 383 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 435 removed outlier: 4.425A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.601A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.504A pdb=" N TRP C 472 " --> pdb=" O ASN C 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 31 Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 70 through 80 removed outlier: 3.955A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.978A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.824A 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 321 through 337 Processing helix chain 'D' and resid 341 through 358 Processing helix chain 'D' and resid 358 through 363 Processing helix chain 'D' and resid 372 through 387 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.999A 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: 4.022A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 3.652A pdb=" N LEU A 399 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL A 351 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N THR A 377 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU A 353 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TYR A 379 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.300A 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: 7.028A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 7.222A pdb=" N ILE A 225 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN A 252 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLY A 227 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER A 254 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP A 222 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU A 272 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA A 224 " --> pdb=" O LEU A 272 " (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 ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.264A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE B 367 " --> pdb=" O HIS B 392 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU B 394 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU B 369 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.133A pdb=" N VAL C 351 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY C 376 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.299A 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: 4.241A 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: 7.893A pdb=" N VAL C 223 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN C 252 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 225 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N SER C 254 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N GLY C 227 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP C 222 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU C 272 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA C 224 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN C 271 " --> pdb=" O MET C 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 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: 6.447A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.297A 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: 8.427A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU D 369 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE D 393 " --> pdb=" O LEU D 369 " (cutoff:3.500A) 759 hydrogen bonds defined for protein. 2181 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: 3.33 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.54: 15922 1.54 - 1.89: 287 1.89 - 2.25: 32 2.25 - 2.60: 86 2.60 - 2.96: 18 Bond restraints: 16345 Sorted by residual: bond pdb="FE2 CLF B 601 " pdb="FE8 CLF B 601 " ideal model delta sigma weight residual 2.200 2.957 -0.757 2.00e-02 2.50e+03 1.43e+03 bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 2.949 -0.749 2.00e-02 2.50e+03 1.40e+03 bond pdb="FE4 CLF B 601 " pdb="FE5 CLF B 601 " ideal model delta sigma weight residual 2.200 2.930 -0.730 2.00e-02 2.50e+03 1.33e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 2.925 -0.725 2.00e-02 2.50e+03 1.31e+03 bond pdb="FE6 CLF D 602 " pdb="FE7 CLF D 602 " ideal model delta sigma weight residual 2.200 2.855 -0.655 2.00e-02 2.50e+03 1.07e+03 ... (remaining 16340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.84: 22052 6.84 - 13.69: 7 13.69 - 20.53: 4 20.53 - 27.38: 0 27.38 - 34.22: 4 Bond angle restraints: 22067 Sorted by residual: angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.78 34.22 3.00e+00 1.11e-01 1.30e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE4 CLF B 601 " ideal model delta sigma weight residual 90.00 55.83 34.17 3.00e+00 1.11e-01 1.30e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 57.07 32.93 3.00e+00 1.11e-01 1.20e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE1 CLF B 601 " ideal model delta sigma weight residual 90.00 57.08 32.92 3.00e+00 1.11e-01 1.20e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE3 CLF B 601 " ideal model delta sigma weight residual 90.00 107.34 -17.34 3.00e+00 1.11e-01 3.34e+01 ... (remaining 22062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.79: 9006 19.79 - 39.57: 834 39.57 - 59.36: 191 59.36 - 79.14: 53 79.14 - 98.93: 14 Dihedral angle restraints: 10098 sinusoidal: 4440 harmonic: 5658 Sorted by residual: dihedral pdb=" CA PHE D 367 " pdb=" C PHE D 367 " pdb=" N ALA D 368 " pdb=" CA ALA D 368 " ideal model delta harmonic sigma weight residual 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" C22 1N7 B 602 " pdb=" C23 1N7 B 602 " pdb=" C24 1N7 B 602 " pdb=" N1 1N7 B 602 " ideal model delta sinusoidal sigma weight residual 227.30 128.37 98.93 1 3.00e+01 1.11e-03 1.23e+01 dihedral pdb=" CA ASP C 419 " pdb=" CB ASP C 419 " pdb=" CG ASP C 419 " pdb=" OD1 ASP C 419 " ideal model delta sinusoidal sigma weight residual -30.00 -89.61 59.61 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 10095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.478: 2323 0.478 - 0.957: 0 0.957 - 1.435: 0 1.435 - 1.913: 0 1.913 - 2.392: 2 Chirality restraints: 2325 Sorted by residual: chirality pdb=" C31 1N7 D 603 " pdb=" C28 1N7 D 603 " pdb=" C32 1N7 D 603 " pdb=" O5 1N7 D 603 " both_signs ideal model delta sigma weight residual False -2.34 0.05 -2.39 2.00e-01 2.50e+01 1.43e+02 chirality pdb=" C31 1N7 B 602 " pdb=" C28 1N7 B 602 " pdb=" C32 1N7 B 602 " pdb=" O5 1N7 B 602 " both_signs ideal model delta sigma weight residual False -2.34 -0.00 -2.34 2.00e-01 2.50e+01 1.36e+02 chirality pdb=" C2 1N7 B 602 " pdb=" C1 1N7 B 602 " pdb=" C15 1N7 B 602 " pdb=" C19 1N7 B 602 " both_signs ideal model delta sigma weight residual False -2.81 -2.54 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2322 not shown) Planarity restraints: 2814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 73 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO C 74 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 73 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO A 74 " 0.070 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 ILE A 436 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 437 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 437 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 437 " -0.022 5.00e-02 4.00e+02 ... (remaining 2811 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 285 2.53 - 3.13: 12777 3.13 - 3.72: 29835 3.72 - 4.31: 46953 4.31 - 4.90: 72105 Nonbonded interactions: 161955 Sorted by model distance: nonbonded pdb="FE FE D 601 " pdb=" O HOH B 758 " model vdw 1.943 2.260 nonbonded pdb="FE FE B 603 " pdb=" O HOH D 716 " model vdw 1.957 2.260 nonbonded pdb="FE FE D 601 " pdb=" O HOH B 812 " model vdw 2.024 2.260 nonbonded pdb=" OE2 GLU B 109 " pdb="FE FE D 601 " model vdw 2.074 2.260 nonbonded pdb=" OD2 ASP D 357 " pdb="FE FE D 601 " model vdw 2.084 2.260 ... (remaining 161950 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' selection = (chain 'C' and (resid 5 through 13 or resid 20 through 24 or resid 27 through 35 \ or resid 41 through 407 or resid 418 through 600)) } 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=1.00 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: 18.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.160 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 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 : 0.025 0.757 16361 Z= 1.211 Angle : 0.780 34.223 22067 Z= 0.348 Chirality : 0.084 2.392 2325 Planarity : 0.004 0.056 2814 Dihedral : 16.453 98.928 6482 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.88 % Allowed : 16.36 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.11 % 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: 0.41 (0.18), residues: 1958 helix: 1.05 (0.17), residues: 952 sheet: -0.41 (0.38), residues: 180 loop : -0.38 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.018 0.002 TYR A 229 PHE 0.020 0.002 PHE C 409 TRP 0.015 0.001 TRP C 335 HIS 0.010 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.02417 (16345) covalent geometry : angle 0.77973 (22067) hydrogen bonds : bond 0.13733 ( 759) hydrogen bonds : angle 6.84647 ( 2181) Misc. bond : bond 0.15804 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.505 Fit side-chains REVERT: A 51 LYS cc_start: 0.7935 (mtmm) cc_final: 0.7087 (mmmt) REVERT: B 39 LYS cc_start: 0.8188 (mmtp) cc_final: 0.7766 (mmtm) REVERT: B 315 LYS cc_start: 0.8464 (tppt) cc_final: 0.8220 (tmtm) REVERT: C 347 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7860 (tm-30) outliers start: 15 outliers final: 14 residues processed: 159 average time/residue: 0.8051 time to fit residues: 139.5324 Evaluate side-chains 156 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 465 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.104708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.082798 restraints weight = 17230.149| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.23 r_work: 0.2760 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.224 16361 Z= 0.178 Angle : 0.691 29.045 22067 Z= 0.322 Chirality : 0.044 0.158 2325 Planarity : 0.005 0.050 2814 Dihedral : 7.099 107.147 2651 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.06 % Allowed : 14.77 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 1958 helix: 1.16 (0.17), residues: 968 sheet: -0.56 (0.36), residues: 195 loop : -0.22 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.017 0.001 TYR A 229 PHE 0.016 0.001 PHE C 409 TRP 0.014 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00372 (16345) covalent geometry : angle 0.69077 (22067) hydrogen bonds : bond 0.04670 ( 759) hydrogen bonds : angle 5.85622 ( 2181) Misc. bond : bond 0.10956 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.454 Fit side-chains REVERT: A 51 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7271 (mmmt) REVERT: A 368 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: B 121 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: B 299 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7218 (mp0) outliers start: 35 outliers final: 13 residues processed: 168 average time/residue: 0.7913 time to fit residues: 144.9788 Evaluate side-chains 156 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain D residue 303 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN D 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.104145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.082214 restraints weight = 17449.303| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.23 r_work: 0.2750 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.173 16361 Z= 0.185 Angle : 0.689 29.127 22067 Z= 0.319 Chirality : 0.045 0.158 2325 Planarity : 0.004 0.049 2814 Dihedral : 6.710 113.512 2633 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.12 % Allowed : 14.83 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.11 % 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: 0.59 (0.19), residues: 1958 helix: 1.19 (0.17), residues: 970 sheet: -0.65 (0.35), residues: 205 loop : -0.21 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.017 0.002 TYR A 229 PHE 0.016 0.002 PHE C 409 TRP 0.014 0.001 TRP C 335 HIS 0.010 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00412 (16345) covalent geometry : angle 0.68852 (22067) hydrogen bonds : bond 0.04597 ( 759) hydrogen bonds : angle 5.67716 ( 2181) Misc. bond : bond 0.08633 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.427 Fit side-chains REVERT: A 368 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: A 401 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6947 (p90) REVERT: B 299 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: B 400 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8395 (mmmt) REVERT: C 287 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.6927 (tp30) REVERT: D 389 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8264 (mt-10) REVERT: D 461 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8197 (pt0) outliers start: 36 outliers final: 12 residues processed: 170 average time/residue: 0.7492 time to fit residues: 139.5476 Evaluate side-chains 156 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.104418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.082527 restraints weight = 17153.153| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.22 r_work: 0.2758 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 16361 Z= 0.177 Angle : 0.681 29.115 22067 Z= 0.314 Chirality : 0.045 0.170 2325 Planarity : 0.004 0.048 2814 Dihedral : 6.574 118.679 2631 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.06 % Allowed : 15.07 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.11 % 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: 0.60 (0.19), residues: 1958 helix: 1.21 (0.17), residues: 973 sheet: -0.65 (0.35), residues: 205 loop : -0.22 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 345 TYR 0.017 0.001 TYR A 229 PHE 0.014 0.001 PHE C 409 TRP 0.014 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00397 (16345) covalent geometry : angle 0.68143 (22067) hydrogen bonds : bond 0.04440 ( 759) hydrogen bonds : angle 5.59216 ( 2181) Misc. bond : bond 0.07832 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.607 Fit side-chains REVERT: A 51 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7434 (mmmt) REVERT: A 368 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: A 401 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.7021 (p90) REVERT: B 299 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: B 400 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8382 (mmmt) REVERT: C 47 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8153 (mp) REVERT: C 287 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.6992 (tp30) REVERT: D 171 LYS cc_start: 0.8381 (ttmm) cc_final: 0.8153 (mtmm) REVERT: D 389 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8271 (mt-10) REVERT: D 461 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8187 (pt0) outliers start: 35 outliers final: 14 residues processed: 173 average time/residue: 0.7224 time to fit residues: 137.3777 Evaluate side-chains 163 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 461 GLU Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 8 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.084254 restraints weight = 17130.574| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.22 r_work: 0.2789 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 16361 Z= 0.137 Angle : 0.654 29.076 22067 Z= 0.298 Chirality : 0.043 0.149 2325 Planarity : 0.004 0.046 2814 Dihedral : 6.419 120.375 2631 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.71 % Allowed : 15.42 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1958 helix: 1.35 (0.17), residues: 974 sheet: -0.63 (0.35), residues: 205 loop : -0.19 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 345 TYR 0.015 0.001 TYR A 229 PHE 0.014 0.001 PHE C 409 TRP 0.014 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00294 (16345) covalent geometry : angle 0.65387 (22067) hydrogen bonds : bond 0.03946 ( 759) hydrogen bonds : angle 5.46252 ( 2181) Misc. bond : bond 0.06679 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.738 Fit side-chains REVERT: A 368 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: B 299 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: C 15 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7680 (mt-10) REVERT: C 47 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8138 (mp) REVERT: C 287 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.6915 (tp30) REVERT: C 355 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7906 (mt) REVERT: D 38 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8002 (p0) REVERT: D 171 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8113 (mtmm) REVERT: D 389 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8276 (mt-10) outliers start: 29 outliers final: 11 residues processed: 168 average time/residue: 0.7699 time to fit residues: 141.6088 Evaluate side-chains 159 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 163 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.083107 restraints weight = 17173.100| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.22 r_work: 0.2769 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 16361 Z= 0.166 Angle : 0.672 29.133 22067 Z= 0.309 Chirality : 0.044 0.188 2325 Planarity : 0.004 0.047 2814 Dihedral : 6.365 119.598 2629 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.88 % Allowed : 15.13 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1958 helix: 1.34 (0.17), residues: 974 sheet: -0.62 (0.35), residues: 205 loop : -0.18 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.015 0.001 TYR A 229 PHE 0.015 0.001 PHE C 409 TRP 0.013 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00371 (16345) covalent geometry : angle 0.67246 (22067) hydrogen bonds : bond 0.04223 ( 759) hydrogen bonds : angle 5.48332 ( 2181) Misc. bond : bond 0.07253 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.649 Fit side-chains REVERT: A 334 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: A 368 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: B 299 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: C 15 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7638 (mt-10) REVERT: C 47 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8170 (mp) REVERT: C 287 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.6946 (tp30) REVERT: C 355 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7976 (mt) REVERT: D 38 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8003 (p0) REVERT: D 171 LYS cc_start: 0.8335 (ttmm) cc_final: 0.8115 (mtmm) REVERT: D 389 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8283 (mt-10) REVERT: D 461 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8164 (pt0) outliers start: 32 outliers final: 15 residues processed: 169 average time/residue: 0.7877 time to fit residues: 145.2632 Evaluate side-chains 169 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 461 GLU Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 110 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 139 optimal weight: 0.0000 chunk 166 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN C 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.083977 restraints weight = 17073.967| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.22 r_work: 0.2770 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 16361 Z= 0.143 Angle : 0.661 29.102 22067 Z= 0.302 Chirality : 0.043 0.166 2325 Planarity : 0.004 0.048 2814 Dihedral : 6.311 119.728 2629 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.82 % Allowed : 15.30 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1958 helix: 1.38 (0.17), residues: 974 sheet: -0.61 (0.35), residues: 205 loop : -0.16 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 345 TYR 0.015 0.001 TYR A 229 PHE 0.018 0.001 PHE C 409 TRP 0.014 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00313 (16345) covalent geometry : angle 0.66143 (22067) hydrogen bonds : bond 0.04011 ( 759) hydrogen bonds : angle 5.44410 ( 2181) Misc. bond : bond 0.06693 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.653 Fit side-chains REVERT: A 334 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: A 368 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: B 299 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: C 15 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7650 (mt-10) REVERT: C 47 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8154 (mp) REVERT: C 287 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.6975 (tp30) REVERT: C 355 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7936 (mt) REVERT: D 38 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7997 (p0) REVERT: D 171 LYS cc_start: 0.8330 (ttmm) cc_final: 0.8113 (mtmm) REVERT: D 389 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8289 (mt-10) REVERT: D 461 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8140 (pt0) outliers start: 31 outliers final: 14 residues processed: 171 average time/residue: 0.7646 time to fit residues: 143.0190 Evaluate side-chains 166 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 351 VAL 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 C residue 465 MET Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 461 GLU Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 30 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 39 optimal weight: 0.0060 chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.105206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.083370 restraints weight = 17120.490| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 1.22 r_work: 0.2773 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 16361 Z= 0.160 Angle : 0.670 29.119 22067 Z= 0.307 Chirality : 0.044 0.157 2325 Planarity : 0.004 0.047 2814 Dihedral : 6.303 118.761 2629 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.94 % Allowed : 15.13 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.11 % 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 (0.19), residues: 1958 helix: 1.36 (0.17), residues: 974 sheet: -0.59 (0.35), residues: 205 loop : -0.16 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.015 0.001 TYR A 229 PHE 0.018 0.001 PHE C 409 TRP 0.013 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00356 (16345) covalent geometry : angle 0.66982 (22067) hydrogen bonds : bond 0.04166 ( 759) hydrogen bonds : angle 5.46398 ( 2181) Misc. bond : bond 0.07045 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.561 Fit side-chains REVERT: A 334 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: A 368 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: B 299 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: C 15 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7655 (mt-10) REVERT: C 47 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8159 (mp) REVERT: C 287 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.6989 (tp30) REVERT: C 355 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7985 (mt) REVERT: D 38 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7978 (p0) REVERT: D 171 LYS cc_start: 0.8350 (ttmm) cc_final: 0.8134 (mtmm) REVERT: D 389 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8295 (mt-10) outliers start: 33 outliers final: 15 residues processed: 169 average time/residue: 0.7526 time to fit residues: 139.2077 Evaluate side-chains 167 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 351 VAL 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 C residue 465 MET Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 132 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 7 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 190 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.083980 restraints weight = 17083.969| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.22 r_work: 0.2782 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 16361 Z= 0.143 Angle : 0.662 29.102 22067 Z= 0.302 Chirality : 0.043 0.220 2325 Planarity : 0.004 0.047 2814 Dihedral : 6.269 118.608 2629 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.65 % Allowed : 15.30 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.11 % 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: 0.79 (0.19), residues: 1958 helix: 1.39 (0.17), residues: 974 sheet: -0.60 (0.35), residues: 205 loop : -0.15 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.015 0.001 TYR A 229 PHE 0.021 0.001 PHE C 409 TRP 0.014 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00312 (16345) covalent geometry : angle 0.66171 (22067) hydrogen bonds : bond 0.04016 ( 759) hydrogen bonds : angle 5.43877 ( 2181) Misc. bond : bond 0.06701 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.550 Fit side-chains REVERT: A 334 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: A 368 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: B 299 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: C 15 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7720 (mt-10) REVERT: C 47 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8155 (mp) REVERT: C 287 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.6976 (tp30) REVERT: C 355 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7955 (mt) REVERT: D 38 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7980 (p0) REVERT: D 171 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8124 (mtmm) REVERT: D 389 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8297 (mt-10) outliers start: 28 outliers final: 17 residues processed: 163 average time/residue: 0.7737 time to fit residues: 138.0383 Evaluate side-chains 169 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 351 VAL 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 C residue 463 MET Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 0.0170 chunk 119 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.084266 restraints weight = 17015.281| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.22 r_work: 0.2787 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 16361 Z= 0.141 Angle : 0.660 29.103 22067 Z= 0.301 Chirality : 0.043 0.210 2325 Planarity : 0.004 0.047 2814 Dihedral : 6.234 118.089 2629 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.53 % Allowed : 15.48 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.11 % 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: 0.82 (0.19), residues: 1958 helix: 1.41 (0.17), residues: 974 sheet: -0.59 (0.35), residues: 205 loop : -0.13 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 96 TYR 0.015 0.001 TYR A 229 PHE 0.022 0.001 PHE C 409 TRP 0.014 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00307 (16345) covalent geometry : angle 0.65967 (22067) hydrogen bonds : bond 0.03955 ( 759) hydrogen bonds : angle 5.41764 ( 2181) Misc. bond : bond 0.06548 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.569 Fit side-chains REVERT: A 334 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: A 368 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: B 299 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: C 15 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7624 (mt-10) REVERT: C 47 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8160 (mp) REVERT: C 287 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.6963 (tp30) REVERT: C 355 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7955 (mt) REVERT: D 38 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7974 (p0) REVERT: D 171 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8127 (mtmm) REVERT: D 389 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8299 (mt-10) outliers start: 26 outliers final: 16 residues processed: 165 average time/residue: 0.7862 time to fit residues: 141.7323 Evaluate side-chains 167 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 351 VAL 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 C residue 463 MET Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 155 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.0980 chunk 100 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.085439 restraints weight = 17038.403| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.22 r_work: 0.2808 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 16361 Z= 0.123 Angle : 0.647 29.095 22067 Z= 0.293 Chirality : 0.042 0.205 2325 Planarity : 0.004 0.046 2814 Dihedral : 6.167 117.785 2629 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.59 % Allowed : 15.30 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.11 % 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: 0.88 (0.19), residues: 1958 helix: 1.47 (0.17), residues: 974 sheet: -0.58 (0.35), residues: 205 loop : -0.11 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 96 TYR 0.014 0.001 TYR A 229 PHE 0.022 0.001 PHE C 409 TRP 0.015 0.001 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00261 (16345) covalent geometry : angle 0.64666 (22067) hydrogen bonds : bond 0.03722 ( 759) hydrogen bonds : angle 5.36637 ( 2181) Misc. bond : bond 0.05912 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5500.33 seconds wall clock time: 94 minutes 50.23 seconds (5690.23 seconds total)