Starting phenix.real_space_refine on Mon Apr 6 04:08:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cjd_45628/04_2026/9cjd_45628.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cjd_45628/04_2026/9cjd_45628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cjd_45628/04_2026/9cjd_45628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cjd_45628/04_2026/9cjd_45628.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cjd_45628/04_2026/9cjd_45628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cjd_45628/04_2026/9cjd_45628.map" } resolution = 1.92 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= 0.080 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 134 5.16 5 C 9641 2.51 5 N 2560 2.21 5 O 3536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 15905 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" 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: "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: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2957 Classifications: {'peptide': 373} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 354} Chain breaks: 4 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'ICS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "B" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 269 Classifications: {'water': 269} Link IDs: {None: 268} Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "D" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 252 Classifications: {'water': 252} Link IDs: {None: 251} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 33.692 34.607 26.885 1.00 17.10 S ATOM 1170 SG CYS A 154 51.982 47.681 25.820 1.00 7.85 S ATOM 4549 SG CYS B 95 50.088 50.677 29.682 1.00 20.30 S ATOM 465 SG CYS A 62 46.784 45.009 28.375 1.00 10.93 S ATOM 652 SG CYS A 88 52.650 45.404 31.850 1.00 10.25 S ATOM 652 SG CYS A 88 52.650 45.404 31.850 1.00 10.25 S ATOM 5002 SG CYS B 153 55.250 49.250 28.991 1.00 15.55 S ATOM 4369 SG CYS B 70 53.461 50.887 35.750 1.00 14.58 S ATOM 4549 SG CYS B 95 50.088 50.677 29.682 1.00 20.30 S ATOM 9655 SG CYS C 275 50.574 37.295 101.786 1.00 44.63 S ATOM 8747 SG CYS C 154 31.304 48.353 103.084 1.00 13.35 S ATOM 11680 SG CYS D 95 32.890 51.311 98.997 1.00 17.89 S ATOM 8042 SG CYS C 62 36.737 46.010 100.461 1.00 14.67 S ATOM 8229 SG CYS C 88 30.902 45.715 97.024 1.00 10.21 S ATOM 8229 SG CYS C 88 30.902 45.715 97.024 1.00 10.21 S ATOM 12133 SG CYS D 153 27.924 49.440 99.833 1.00 18.75 S ATOM 11500 SG CYS D 70 29.494 50.952 92.951 1.00 13.16 S ATOM 11680 SG CYS D 95 32.890 51.311 98.997 1.00 17.89 S Time building chain proxies: 3.58, per 1000 atoms: 0.23 Number of scatterers: 15905 At special positions: 0 Unit cell: (84.5, 94.9, 125.45, 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 134 16.00 O 3536 8.00 N 2560 7.00 C 9641 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=15, symmetry=0 Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 655.7 milliseconds 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3474 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 12 sheets defined 59.5% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.023A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.576A pdb=" N GLY A 157 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.593A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.097A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.081A 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: 5.637A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 314 removed outlier: 4.332A pdb=" N LYS A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.304A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.515A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.335A 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 Processing helix chain 'B' and resid 4 through 8 removed outlier: 4.298A pdb=" N ILE B 8 " --> pdb=" O VAL B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 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: 3.969A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.071A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.766A 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 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.832A 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: 5.137A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 387 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.911A 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: 4.304A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 4.303A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.696A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 206 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 245 removed outlier: 4.047A 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: 5.749A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 315 removed outlier: 3.659A pdb=" N LYS C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) 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 363 through 370 removed outlier: 3.776A pdb=" N TYR C 367 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 434 Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 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 81 removed outlier: 4.016A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.014A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.654A pdb=" N VAL D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.813A 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 320 through 337 removed outlier: 4.091A pdb=" N TRP D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.351A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.626A 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: 4.045A 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: 7.347A pdb=" N LEU A 353 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR A 377 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.987A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.238A 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: 7.245A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE A 225 " --> pdb=" O TRP A 253 " (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 250 through 253 removed outlier: 7.062A pdb=" N LYS B 223 " --> pdb=" O ASN B 289 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL B 291 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 6.408A 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: 8.590A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 178 through 181 removed outlier: 4.235A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 248 through 254 removed outlier: 6.533A pdb=" N VAL C 223 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C 251 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP C 222 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU C 272 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA C 224 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 removed outlier: 6.548A pdb=" N MET D 86 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N SER D 150 " --> pdb=" O MET D 86 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR D 88 " --> pdb=" O SER D 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.399A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.544A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2172 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: 2.86 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.56: 15307 1.56 - 1.91: 171 1.91 - 2.25: 37 2.25 - 2.60: 81 2.60 - 2.95: 18 Bond restraints: 15614 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 2.947 -0.747 2.00e-02 2.50e+03 1.39e+03 bond pdb="FE2 CLF B 601 " pdb="FE8 CLF B 601 " ideal model delta sigma weight residual 2.200 2.913 -0.713 2.00e-02 2.50e+03 1.27e+03 bond pdb="FE4 CLF B 601 " pdb="FE5 CLF B 601 " ideal model delta sigma weight residual 2.200 2.893 -0.693 2.00e-02 2.50e+03 1.20e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 2.890 -0.690 2.00e-02 2.50e+03 1.19e+03 bond pdb="FE6 CLF D 602 " pdb="FE7 CLF D 602 " ideal model delta sigma weight residual 2.200 2.865 -0.665 2.00e-02 2.50e+03 1.11e+03 ... (remaining 15609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.86: 21056 6.86 - 13.72: 3 13.72 - 20.58: 2 20.58 - 27.43: 0 27.43 - 34.29: 4 Bond angle restraints: 21065 Sorted by residual: angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE4 CLF B 601 " ideal model delta sigma weight residual 90.00 55.71 34.29 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.74 34.26 3.00e+00 1.11e-01 1.30e+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 56.88 33.12 3.00e+00 1.11e-01 1.22e+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 57.03 32.97 3.00e+00 1.11e-01 1.21e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE3 CLF B 601 " ideal model delta sigma weight residual 90.00 106.92 -16.92 3.00e+00 1.11e-01 3.18e+01 ... (remaining 21060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8516 17.84 - 35.68: 750 35.68 - 53.52: 191 53.52 - 71.36: 68 71.36 - 89.20: 30 Dihedral angle restraints: 9555 sinusoidal: 4125 harmonic: 5430 Sorted by residual: dihedral pdb=" CA PHE B 367 " pdb=" C PHE B 367 " pdb=" N ALA B 368 " pdb=" CA ALA B 368 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 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 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ILE A 75 " pdb=" C ILE A 75 " pdb=" N LYS A 76 " pdb=" CA LYS A 76 " ideal model delta harmonic sigma weight residual -180.00 -158.36 -21.64 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 9552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1756 0.053 - 0.106: 385 0.106 - 0.159: 70 0.159 - 0.212: 1 0.212 - 0.265: 1 Chirality restraints: 2213 Sorted by residual: chirality pdb=" CA ARG C 277 " pdb=" N ARG C 277 " pdb=" C ARG C 277 " pdb=" CB ARG C 277 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE A 355 " pdb=" CA ILE A 355 " pdb=" CG1 ILE A 355 " pdb=" CG2 ILE A 355 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA ILE D 318 " pdb=" N ILE D 318 " pdb=" C ILE D 318 " pdb=" CB ILE D 318 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 2210 not shown) Planarity restraints: 2699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 453 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C ARG B 453 " -0.031 2.00e-02 2.50e+03 pdb=" O ARG B 453 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 454 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 277 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C ARG C 277 " 0.030 2.00e-02 2.50e+03 pdb=" O ARG C 277 " -0.011 2.00e-02 2.50e+03 pdb=" N SER C 278 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 453 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C ARG D 453 " 0.029 2.00e-02 2.50e+03 pdb=" O ARG D 453 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP D 454 " -0.010 2.00e-02 2.50e+03 ... (remaining 2696 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 166 2.50 - 3.10: 12448 3.10 - 3.70: 29456 3.70 - 4.30: 44512 4.30 - 4.90: 68869 Nonbonded interactions: 155451 Sorted by model distance: nonbonded pdb=" O VAL C 70 " pdb=" O HOH C 701 " model vdw 1.895 3.040 nonbonded pdb=" O ARG B 108 " pdb="FE FE D 601 " model vdw 2.078 2.260 nonbonded pdb=" OE2 GLU B 109 " pdb="FE FE D 601 " model vdw 2.110 2.260 nonbonded pdb=" OD2 ASP D 357 " pdb="FE FE D 601 " model vdw 2.125 2.260 nonbonded pdb=" O ARG D 108 " pdb="FE FE B 602 " model vdw 2.142 2.260 ... (remaining 155446 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 '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: 17.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 15.420 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 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 : 0.024 0.747 15629 Z= 1.198 Angle : 0.769 34.294 21065 Z= 0.361 Chirality : 0.044 0.265 2213 Planarity : 0.004 0.061 2699 Dihedral : 15.935 89.200 6081 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.80 % Allowed : 11.89 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % 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: 1878 helix: 1.45 (0.17), residues: 928 sheet: -1.07 (0.39), residues: 154 loop : -0.09 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 25 TYR 0.021 0.002 TYR A 446 PHE 0.020 0.002 PHE A 431 TRP 0.014 0.002 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.02391 (15614) covalent geometry : angle 0.76858 (21065) hydrogen bonds : bond 0.12976 ( 760) hydrogen bonds : angle 6.94026 ( 2172) Misc. bond : bond 0.03348 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.643 Fit side-chains REVERT: A 120 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7949 (pm20) REVERT: A 401 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8416 (p90) outliers start: 13 outliers final: 8 residues processed: 223 average time/residue: 0.8814 time to fit residues: 211.7912 Evaluate side-chains 219 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 210 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 384 ASN B 418 ASN C 98 ASN C 476 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125262 restraints weight = 7974.644| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 0.46 r_work: 0.3359 rms_B_bonded: 0.71 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work: 0.3108 rms_B_bonded: 3.43 restraints_weight: 0.1250 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.205 15629 Z= 0.162 Angle : 0.726 29.100 21065 Z= 0.345 Chirality : 0.044 0.145 2213 Planarity : 0.004 0.068 2699 Dihedral : 5.255 58.058 2388 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.41 % Allowed : 11.53 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % 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: 1878 helix: 1.46 (0.17), residues: 954 sheet: -0.96 (0.38), residues: 158 loop : -0.08 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.019 0.002 TYR A 446 PHE 0.018 0.002 PHE A 431 TRP 0.015 0.002 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00308 (15614) covalent geometry : angle 0.72609 (21065) hydrogen bonds : bond 0.05342 ( 760) hydrogen bonds : angle 5.97317 ( 2172) Misc. bond : bond 0.09606 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.590 Fit side-chains REVERT: A 51 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7484 (tptp) REVERT: A 120 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7855 (pm20) REVERT: A 218 SER cc_start: 0.8631 (p) cc_final: 0.8182 (t) REVERT: A 476 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: B 172 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: C 277 ARG cc_start: 0.5661 (ttm110) cc_final: 0.4942 (pmm-80) REVERT: D 121 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7509 (t0) outliers start: 23 outliers final: 3 residues processed: 228 average time/residue: 0.8867 time to fit residues: 217.3082 Evaluate side-chains 221 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 214 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 121 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 418 ASN C 98 ASN C 191 GLN C 280 ASN C 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.139220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123640 restraints weight = 8040.955| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 0.46 r_work: 0.3334 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work: 0.3084 rms_B_bonded: 3.47 restraints_weight: 0.1250 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.0632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.252 15629 Z= 0.184 Angle : 0.739 29.311 21065 Z= 0.354 Chirality : 0.045 0.147 2213 Planarity : 0.004 0.078 2699 Dihedral : 5.154 59.357 2381 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.47 % Allowed : 11.34 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % 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: 1878 helix: 1.43 (0.17), residues: 953 sheet: -1.02 (0.38), residues: 158 loop : -0.13 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.022 0.002 TYR C 229 PHE 0.021 0.002 PHE A 431 TRP 0.015 0.002 TRP D 296 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00349 (15614) covalent geometry : angle 0.73921 (21065) hydrogen bonds : bond 0.05652 ( 760) hydrogen bonds : angle 5.95976 ( 2172) Misc. bond : bond 0.11561 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.656 Fit side-chains REVERT: A 51 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7589 (tptm) REVERT: A 120 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7823 (pm20) REVERT: A 218 SER cc_start: 0.8619 (p) cc_final: 0.8121 (t) REVERT: A 476 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: B 172 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: C 277 ARG cc_start: 0.5733 (ttm110) cc_final: 0.5053 (pmm-80) REVERT: D 417 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7650 (mmtm) outliers start: 24 outliers final: 5 residues processed: 222 average time/residue: 0.8760 time to fit residues: 209.1113 Evaluate side-chains 217 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 417 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 418 ASN C 98 ASN C 191 GLN C 476 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.124915 restraints weight = 8069.068| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 0.46 r_work: 0.3334 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.3090 rms_B_bonded: 3.39 restraints_weight: 0.1250 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.227 15629 Z= 0.166 Angle : 0.722 29.233 21065 Z= 0.343 Chirality : 0.044 0.146 2213 Planarity : 0.004 0.071 2699 Dihedral : 5.072 59.315 2381 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.41 % Allowed : 11.53 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % 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: 1878 helix: 1.49 (0.17), residues: 953 sheet: -0.99 (0.37), residues: 168 loop : -0.11 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.021 0.002 TYR C 229 PHE 0.018 0.002 PHE A 431 TRP 0.014 0.002 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00315 (15614) covalent geometry : angle 0.72164 (21065) hydrogen bonds : bond 0.05247 ( 760) hydrogen bonds : angle 5.86051 ( 2172) Misc. bond : bond 0.10401 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.629 Fit side-chains REVERT: A 51 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7592 (tptm) REVERT: A 120 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7832 (pm20) REVERT: A 476 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: B 51 GLU cc_start: 0.8573 (mp0) cc_final: 0.8314 (mp0) REVERT: B 172 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: B 222 LYS cc_start: 0.8440 (mmpt) cc_final: 0.8216 (mppt) REVERT: C 277 ARG cc_start: 0.5601 (ttm110) cc_final: 0.4849 (pmm-80) REVERT: C 467 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8719 (mt) REVERT: D 121 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7539 (t0) outliers start: 23 outliers final: 7 residues processed: 230 average time/residue: 0.8635 time to fit residues: 213.9672 Evaluate side-chains 226 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 121 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.1980 chunk 144 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 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 98 ASN B 418 ASN C 98 ASN C 191 GLN C 195 HIS C 199 ASN C 280 ASN C 476 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126512 restraints weight = 8218.027| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 0.47 r_work: 0.3355 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 1.24 restraints_weight: 0.2500 r_work: 0.3109 rms_B_bonded: 3.48 restraints_weight: 0.1250 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.205 15629 Z= 0.149 Angle : 0.703 29.152 21065 Z= 0.331 Chirality : 0.043 0.144 2213 Planarity : 0.004 0.063 2699 Dihedral : 4.954 59.093 2380 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.23 % Allowed : 11.71 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % 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: 0.95 (0.19), residues: 1878 helix: 1.56 (0.17), residues: 953 sheet: -0.96 (0.37), residues: 168 loop : -0.09 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.022 0.002 TYR C 276 PHE 0.017 0.001 PHE A 431 TRP 0.014 0.002 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00281 (15614) covalent geometry : angle 0.70349 (21065) hydrogen bonds : bond 0.04844 ( 760) hydrogen bonds : angle 5.75855 ( 2172) Misc. bond : bond 0.09374 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.676 Fit side-chains REVERT: A 51 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7550 (tptm) REVERT: A 120 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7803 (pm20) REVERT: A 218 SER cc_start: 0.8620 (p) cc_final: 0.8144 (t) REVERT: B 51 GLU cc_start: 0.8548 (mp0) cc_final: 0.8301 (mp0) REVERT: B 172 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: B 222 LYS cc_start: 0.8425 (mmpt) cc_final: 0.8220 (mppt) REVERT: C 277 ARG cc_start: 0.5403 (ttm110) cc_final: 0.4706 (pmm-80) REVERT: D 121 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7545 (t0) outliers start: 20 outliers final: 8 residues processed: 229 average time/residue: 0.8676 time to fit residues: 213.8111 Evaluate side-chains 222 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 121 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 126 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 418 ASN C 98 ASN C 191 GLN C 280 ASN C 476 GLN D 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124188 restraints weight = 8075.116| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 0.46 r_work: 0.3325 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work: 0.3077 rms_B_bonded: 3.44 restraints_weight: 0.1250 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 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 0.244 15629 Z= 0.178 Angle : 0.735 29.297 21065 Z= 0.351 Chirality : 0.045 0.148 2213 Planarity : 0.004 0.075 2699 Dihedral : 5.075 59.908 2380 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.35 % Allowed : 11.71 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % 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: 1878 helix: 1.48 (0.17), residues: 954 sheet: -0.99 (0.37), residues: 168 loop : -0.09 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 270 TYR 0.022 0.002 TYR C 229 PHE 0.021 0.002 PHE A 431 TRP 0.014 0.002 TRP D 296 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00339 (15614) covalent geometry : angle 0.73504 (21065) hydrogen bonds : bond 0.05481 ( 760) hydrogen bonds : angle 5.87894 ( 2172) Misc. bond : bond 0.11052 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.617 Fit side-chains REVERT: A 51 LYS cc_start: 0.8224 (ttmm) cc_final: 0.7632 (tptm) REVERT: A 120 GLU cc_start: 0.8466 (tm-30) cc_final: 0.7831 (pm20) REVERT: B 51 GLU cc_start: 0.8597 (mp0) cc_final: 0.8342 (mp0) REVERT: B 172 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: B 222 LYS cc_start: 0.8436 (mmpt) cc_final: 0.8224 (mppt) REVERT: C 277 ARG cc_start: 0.5522 (ttm110) cc_final: 0.4773 (pmm-80) outliers start: 22 outliers final: 10 residues processed: 228 average time/residue: 0.8737 time to fit residues: 214.3124 Evaluate side-chains 227 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 121 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 87 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 0.0030 chunk 170 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 156 optimal weight: 0.4980 chunk 177 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 418 ASN C 98 ASN C 191 GLN C 195 HIS C 280 ASN C 476 GLN D 4 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126818 restraints weight = 8181.618| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 0.47 r_work: 0.3377 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 1.25 restraints_weight: 0.2500 r_work: 0.3130 rms_B_bonded: 3.50 restraints_weight: 0.1250 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 15629 Z= 0.145 Angle : 0.703 29.107 21065 Z= 0.330 Chirality : 0.043 0.146 2213 Planarity : 0.004 0.061 2699 Dihedral : 4.936 58.833 2380 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.98 % Allowed : 12.20 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % 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: 0.96 (0.19), residues: 1878 helix: 1.56 (0.17), residues: 954 sheet: -0.96 (0.37), residues: 168 loop : -0.06 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 350 TYR 0.017 0.002 TYR A 446 PHE 0.015 0.001 PHE A 429 TRP 0.015 0.002 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00275 (15614) covalent geometry : angle 0.70338 (21065) hydrogen bonds : bond 0.04735 ( 760) hydrogen bonds : angle 5.73259 ( 2172) Misc. bond : bond 0.08995 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.622 Fit side-chains REVERT: A 51 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7553 (tptm) REVERT: A 120 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7795 (pm20) REVERT: A 218 SER cc_start: 0.8615 (p) cc_final: 0.8127 (t) REVERT: B 51 GLU cc_start: 0.8562 (mp0) cc_final: 0.8326 (mp0) REVERT: B 172 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: B 222 LYS cc_start: 0.8429 (mmpt) cc_final: 0.8217 (mppt) REVERT: C 277 ARG cc_start: 0.5337 (ttm110) cc_final: 0.4649 (pmm-80) REVERT: D 121 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7516 (t0) REVERT: D 178 GLU cc_start: 0.7720 (pm20) cc_final: 0.7387 (pm20) REVERT: D 303 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8684 (mtpm) outliers start: 16 outliers final: 10 residues processed: 226 average time/residue: 0.8613 time to fit residues: 209.8007 Evaluate side-chains 225 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 213 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 121 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 64 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 44 optimal weight: 0.0000 chunk 155 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 418 ASN C 98 ASN C 191 GLN C 195 HIS C 280 ASN C 476 GLN D 4 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.143633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128307 restraints weight = 8235.530| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 0.47 r_work: 0.3399 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 1.24 restraints_weight: 0.2500 r_work: 0.3153 rms_B_bonded: 3.53 restraints_weight: 0.1250 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 15629 Z= 0.137 Angle : 0.693 29.112 21065 Z= 0.323 Chirality : 0.043 0.144 2213 Planarity : 0.004 0.056 2699 Dihedral : 4.857 58.718 2380 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.98 % Allowed : 12.51 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % 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: 1.02 (0.19), residues: 1878 helix: 1.59 (0.17), residues: 955 sheet: -0.90 (0.38), residues: 168 loop : -0.03 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.016 0.001 TYR A 446 PHE 0.014 0.001 PHE A 429 TRP 0.015 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00261 (15614) covalent geometry : angle 0.69290 (21065) hydrogen bonds : bond 0.04468 ( 760) hydrogen bonds : angle 5.65252 ( 2172) Misc. bond : bond 0.08401 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.686 Fit side-chains REVERT: A 51 LYS cc_start: 0.8082 (ttmm) cc_final: 0.7544 (tptm) REVERT: A 120 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7775 (pm20) REVERT: A 218 SER cc_start: 0.8615 (p) cc_final: 0.8142 (t) REVERT: B 51 GLU cc_start: 0.8527 (mp0) cc_final: 0.8280 (mp0) REVERT: B 172 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: B 222 LYS cc_start: 0.8443 (mmpt) cc_final: 0.8217 (mppt) REVERT: C 277 ARG cc_start: 0.5198 (ttm110) cc_final: 0.4582 (pmm-80) REVERT: D 121 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7488 (t0) REVERT: D 178 GLU cc_start: 0.7750 (pm20) cc_final: 0.7411 (pm20) REVERT: D 303 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8708 (mtpm) outliers start: 16 outliers final: 7 residues processed: 229 average time/residue: 0.8698 time to fit residues: 214.6908 Evaluate side-chains 221 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 212 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 121 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 75 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 127 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 chunk 179 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 268 GLN B 418 ASN C 98 ASN C 191 GLN C 195 HIS C 280 ASN C 476 GLN D 4 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.127450 restraints weight = 8136.554| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 0.47 r_work: 0.3386 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work: 0.3138 rms_B_bonded: 3.54 restraints_weight: 0.1250 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 15629 Z= 0.145 Angle : 0.705 29.152 21065 Z= 0.331 Chirality : 0.043 0.188 2213 Planarity : 0.004 0.060 2699 Dihedral : 4.889 59.048 2380 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.86 % Allowed : 12.63 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % 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: 1.00 (0.19), residues: 1878 helix: 1.57 (0.17), residues: 955 sheet: -0.91 (0.38), residues: 168 loop : -0.02 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 25 TYR 0.017 0.002 TYR A 446 PHE 0.015 0.001 PHE A 429 TRP 0.014 0.002 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00277 (15614) covalent geometry : angle 0.70501 (21065) hydrogen bonds : bond 0.04666 ( 760) hydrogen bonds : angle 5.68578 ( 2172) Misc. bond : bond 0.09041 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 0.694 Fit side-chains REVERT: A 51 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7548 (tptm) REVERT: A 120 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7778 (pm20) REVERT: A 218 SER cc_start: 0.8621 (p) cc_final: 0.8131 (t) REVERT: A 288 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8017 (mt-10) REVERT: B 51 GLU cc_start: 0.8534 (mp0) cc_final: 0.8289 (mp0) REVERT: B 172 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: B 222 LYS cc_start: 0.8452 (mmpt) cc_final: 0.8218 (mppt) REVERT: C 277 ARG cc_start: 0.5167 (ttm110) cc_final: 0.4580 (pmm-80) REVERT: D 178 GLU cc_start: 0.7761 (pm20) cc_final: 0.7414 (pm20) REVERT: D 303 LYS cc_start: 0.8939 (mtpp) cc_final: 0.8722 (mtpm) outliers start: 14 outliers final: 10 residues processed: 223 average time/residue: 0.8753 time to fit residues: 209.8695 Evaluate side-chains 222 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 121 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 71 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 175 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 136 optimal weight: 0.2980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 268 GLN B 418 ASN C 98 ASN C 191 GLN C 195 HIS C 280 ASN C 476 GLN D 4 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.139806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124317 restraints weight = 8034.795| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 0.46 r_work: 0.3345 rms_B_bonded: 0.71 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work: 0.3094 rms_B_bonded: 3.44 restraints_weight: 0.1250 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.249 15629 Z= 0.186 Angle : 0.747 29.333 21065 Z= 0.358 Chirality : 0.045 0.189 2213 Planarity : 0.005 0.076 2699 Dihedral : 5.065 59.942 2380 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.86 % Allowed : 12.63 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % 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: 1878 helix: 1.47 (0.17), residues: 954 sheet: -0.94 (0.38), residues: 158 loop : -0.09 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 25 TYR 0.023 0.002 TYR C 229 PHE 0.022 0.002 PHE A 431 TRP 0.015 0.002 TRP A 205 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00357 (15614) covalent geometry : angle 0.74724 (21065) hydrogen bonds : bond 0.05547 ( 760) hydrogen bonds : angle 5.86191 ( 2172) Misc. bond : bond 0.11228 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.670 Fit side-chains REVERT: A 51 LYS cc_start: 0.8233 (ttmm) cc_final: 0.7639 (tptm) REVERT: A 120 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7817 (pm20) REVERT: A 288 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8039 (mt-10) REVERT: B 172 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: B 461 GLU cc_start: 0.8595 (pm20) cc_final: 0.8342 (pm20) REVERT: C 277 ARG cc_start: 0.5295 (ttm110) cc_final: 0.4674 (pmm-80) REVERT: D 178 GLU cc_start: 0.7789 (pm20) cc_final: 0.7368 (pm20) REVERT: D 303 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8730 (mtpm) outliers start: 14 outliers final: 11 residues processed: 226 average time/residue: 0.8863 time to fit residues: 215.5742 Evaluate side-chains 221 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 121 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 116 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 93 optimal weight: 0.0050 chunk 104 optimal weight: 0.0970 chunk 131 optimal weight: 6.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 268 GLN B 418 ASN C 98 ASN C 191 GLN C 195 HIS C 280 ASN C 476 GLN D 4 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125226 restraints weight = 8044.779| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 0.46 r_work: 0.3354 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 1.24 restraints_weight: 0.2500 r_work: 0.3106 rms_B_bonded: 3.46 restraints_weight: 0.1250 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.229 15629 Z= 0.169 Angle : 0.735 29.223 21065 Z= 0.350 Chirality : 0.044 0.169 2213 Planarity : 0.004 0.071 2699 Dihedral : 5.031 59.429 2380 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.92 % Allowed : 12.57 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % 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: 0.86 (0.19), residues: 1878 helix: 1.45 (0.17), residues: 954 sheet: -0.97 (0.37), residues: 168 loop : -0.08 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 25 TYR 0.021 0.002 TYR C 229 PHE 0.020 0.002 PHE A 431 TRP 0.015 0.002 TRP A 205 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00324 (15614) covalent geometry : angle 0.73478 (21065) hydrogen bonds : bond 0.05243 ( 760) hydrogen bonds : angle 5.82307 ( 2172) Misc. bond : bond 0.10373 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8005.24 seconds wall clock time: 137 minutes 3.09 seconds (8223.09 seconds total)