Starting phenix.real_space_refine on Fri Jul 3 23:29:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctz_45923/07_2026/9ctz_45923.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctz_45923/07_2026/9ctz_45923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ctz_45923/07_2026/9ctz_45923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctz_45923/07_2026/9ctz_45923.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctz_45923/07_2026/9ctz_45923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctz_45923/07_2026/9ctz_45923.cif" } resolution = 2.67 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 32 7.16 5 S 139 5.16 5 C 10170 2.51 5 N 2702 2.21 5 O 3906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16951 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} bond proxies already assigned to first conformer: 3874 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3790 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3871 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "A" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 227 Classifications: {'water': 227} Link IDs: {None: 226} Chain: "B" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 237 Classifications: {'water': 237} Link IDs: {None: 236} Chain: "C" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 221 Classifications: {'water': 221} Link IDs: {None: 220} Chain: "D" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 239 Classifications: {'water': 239} Link IDs: {None: 238} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 31.097 44.142 58.378 1.00 74.35 S ATOM 4552 SG CYS B 95 40.714 29.137 43.156 1.00 52.29 S ATOM 1170 SG CYS A 154 37.260 25.809 46.230 1.00 46.60 S ATOM 465 SG CYS A 62 37.761 31.863 48.481 1.00 55.76 S ATOM 652 SG CYS A 88 43.366 27.528 48.403 1.00 53.29 S ATOM 652 SG CYS A 88 43.366 27.528 48.403 1.00 53.29 S ATOM 5005 SG CYS B 153 41.388 23.883 44.471 1.00 61.44 S ATOM 4372 SG CYS B 70 47.146 28.131 43.054 1.00 40.20 S ATOM 4552 SG CYS B 95 40.714 29.137 43.156 1.00 52.29 S ATOM 10056 SG CYS C 275 108.541 55.840 58.373 1.00 78.10 S ATOM 12516 SG CYS D 95 99.168 70.888 42.627 1.00 51.53 S ATOM 9134 SG CYS C 154 102.328 74.210 46.218 1.00 48.14 S ATOM 8429 SG CYS C 62 101.923 68.021 48.561 1.00 55.81 S ATOM 8616 SG CYS C 88 96.358 72.597 48.227 1.00 53.52 S ATOM 8616 SG CYS C 88 96.358 72.597 48.227 1.00 53.52 S ATOM 12969 SG CYS D 153 98.196 75.939 44.419 1.00 62.49 S ATOM 12336 SG CYS D 70 92.537 71.853 43.021 1.00 42.24 S ATOM 12516 SG CYS D 95 99.168 70.888 42.627 1.00 51.53 S Time building chain proxies: 5.64, per 1000 atoms: 0.33 Number of scatterers: 16951 At special positions: 0 Unit cell: (138.18, 100.695, 98.49, 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 3906 8.00 N 2702 7.00 C 10170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 921.3 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 12 sheets defined 58.2% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.191A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.809A pdb=" N LYS A 44 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.563A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 4.028A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.218A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 4.468A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.589A 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 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: 4.324A 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: 5.804A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.517A pdb=" N HIS A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 394 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.352A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.200A 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 removed outlier: 3.672A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.509A pdb=" N TRP A 472 " --> pdb=" O ASN A 469 " (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 57 Processing helix chain 'B' and resid 70 through 80 removed outlier: 4.024A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.253A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 173 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.804A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 320 through 337 removed outlier: 4.187A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 3.591A pdb=" N THR B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.704A 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: 3.730A 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: 4.438A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) 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: 4.208A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.513A pdb=" N LYS C 44 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 119 through 125 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.501A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.645A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.226A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 4.415A pdb=" N ARG C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.606A 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 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: 4.366A 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 290 removed outlier: 5.784A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.672A 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 removed outlier: 3.516A pdb=" N GLN C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.046A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 434 removed outlier: 4.416A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.640A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.512A 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 32 removed outlier: 3.631A pdb=" N GLU D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 47 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 70 through 80 removed outlier: 4.005A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.059A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.849A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 3.575A pdb=" N THR D 345 " --> pdb=" O PRO D 341 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.694A 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: 3.823A 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: 4.407A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.571A pdb=" N ARG D 481 " --> pdb=" O HIS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.115A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.321A 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: 6.952A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 6.675A pdb=" N VAL A 223 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA A 251 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.385A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.543A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE B 367 " --> pdb=" O PRO B 390 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS B 392 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.583A pdb=" N VAL C 351 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N THR C 377 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU C 353 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR C 379 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.946A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.290A 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: 7.373A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 270 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.302A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.351A 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: 8.805A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE D 367 " --> pdb=" O PRO D 390 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS D 392 " --> pdb=" O PHE D 367 " (cutoff:3.500A) 784 hydrogen bonds defined for protein. 2274 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: 3.17 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.86: 16347 1.86 - 2.49: 105 2.49 - 3.13: 19 3.13 - 3.76: 8 3.76 - 4.40: 4 Bond restraints: 16483 Sorted by residual: bond pdb="FE2 CLF B 602 " pdb="FE8 CLF B 602 " ideal model delta sigma weight residual 2.200 4.397 -2.197 2.00e-02 2.50e+03 1.21e+04 bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 4.396 -2.196 2.00e-02 2.50e+03 1.21e+04 bond pdb="FE5 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.904 -1.704 2.00e-02 2.50e+03 7.26e+03 bond pdb="FE5 CLF B 602 " pdb="FE6 CLF B 602 " ideal model delta sigma weight residual 2.200 3.903 -1.703 2.00e-02 2.50e+03 7.25e+03 bond pdb="FE4 CLF B 602 " pdb="FE5 CLF B 602 " ideal model delta sigma weight residual 2.200 3.617 -1.417 2.00e-02 2.50e+03 5.02e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.79: 22236 6.79 - 13.57: 1 13.57 - 20.36: 2 20.36 - 27.14: 0 27.14 - 33.93: 4 Bond angle restraints: 22243 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 56.07 33.93 3.00e+00 1.11e-01 1.28e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 56.10 33.90 3.00e+00 1.11e-01 1.28e+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 60.62 29.38 3.00e+00 1.11e-01 9.59e+01 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE1 CLF B 602 " ideal model delta sigma weight residual 90.00 61.19 28.81 3.00e+00 1.11e-01 9.22e+01 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE3 CLF D 602 " ideal model delta sigma weight residual 90.00 108.69 -18.69 3.00e+00 1.11e-01 3.88e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8715 17.89 - 35.78: 984 35.78 - 53.67: 303 53.67 - 71.56: 73 71.56 - 89.45: 26 Dihedral angle restraints: 10101 sinusoidal: 4359 harmonic: 5742 Sorted by residual: dihedral pdb=" CD ARG D 242 " pdb=" NE ARG D 242 " pdb=" CZ ARG D 242 " pdb=" NH1 ARG D 242 " ideal model delta sinusoidal sigma weight residual 0.00 89.05 -89.05 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CD ARG C 96 " pdb=" NE ARG C 96 " pdb=" CZ ARG C 96 " pdb=" NH1 ARG C 96 " ideal model delta sinusoidal sigma weight residual 0.00 -82.56 82.56 1 1.00e+01 1.00e-02 8.36e+01 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 180.00 158.09 21.91 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1716 0.046 - 0.092: 434 0.092 - 0.138: 166 0.138 - 0.184: 13 0.184 - 0.230: 7 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA PRO A 360 " pdb=" N PRO A 360 " pdb=" C PRO A 360 " pdb=" CB PRO A 360 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ILE D 175 " pdb=" N ILE D 175 " pdb=" C ILE D 175 " pdb=" CB ILE D 175 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL B 434 " pdb=" CA VAL B 434 " pdb=" CG1 VAL B 434 " pdb=" CG2 VAL B 434 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 242 " -1.115 9.50e-02 1.11e+02 5.00e-01 1.51e+02 pdb=" NE ARG D 242 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG D 242 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG D 242 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG D 242 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 96 " 1.096 9.50e-02 1.11e+02 4.91e-01 1.45e+02 pdb=" NE ARG C 96 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG C 96 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 96 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 96 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 96 " -0.543 9.50e-02 1.11e+02 2.43e-01 3.62e+01 pdb=" NE ARG A 96 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 96 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 96 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 96 " -0.018 2.00e-02 2.50e+03 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 431 2.64 - 3.20: 14897 3.20 - 3.77: 28633 3.77 - 4.33: 43290 4.33 - 4.90: 67873 Nonbonded interactions: 155124 Sorted by model distance: nonbonded pdb=" OD2 ASP D 353 " pdb="FE FE D 601 " model vdw 2.070 3.000 nonbonded pdb=" OD2 ASP B 353 " pdb="FE FE B 601 " model vdw 2.078 3.000 nonbonded pdb=" OG1 THR D 119 " pdb=" OD1 ASP D 121 " model vdw 2.139 3.040 nonbonded pdb=" OG1 THR B 119 " pdb=" OD1 ASP B 121 " model vdw 2.177 3.040 nonbonded pdb=" O LYS C 51 " pdb=" O HOH C 601 " model vdw 2.186 3.040 ... (remaining 155119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 248 or resid 250 through 502)) selection = (chain 'C' and (resid 4 through 248 or resid 250 through 502)) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 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: 6.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.090 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: 0.010 Load rotamer database and sin/cos tables:7.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 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 : 0.045 2.197 16499 Z= 2.296 Angle : 0.762 33.925 22243 Z= 0.406 Chirality : 0.047 0.230 2336 Planarity : 0.016 0.500 2858 Dihedral : 17.122 89.452 6433 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.16 % Allowed : 19.73 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 1992 helix: 1.28 (0.17), residues: 978 sheet: -0.43 (0.38), residues: 174 loop : -0.75 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 401 TYR 0.014 0.001 TYR D 142 PHE 0.014 0.001 PHE C 429 TRP 0.013 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.04476 / 2.24 (16483) covalent geometry : angle 0.76206 / 0.41 (22243) hydrogen bonds : bond 0.14493 / 9.79 ( 784) hydrogen bonds : angle 6.74707 / 4.86 ( 2274) Misc. bond : bond 0.16462 / 12.22 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 300 PHE cc_start: 0.6662 (m-80) cc_final: 0.6138 (t80) REVERT: A 332 LYS cc_start: 0.7632 (tttt) cc_final: 0.6723 (tttm) REVERT: B 93 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.6890 (tp40) REVERT: B 172 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: C 287 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7133 (tm-30) REVERT: C 300 PHE cc_start: 0.6860 (m-80) cc_final: 0.6216 (t80) REVERT: C 332 LYS cc_start: 0.7596 (tttt) cc_final: 0.6677 (tttm) REVERT: C 373 GLU cc_start: 0.7484 (mp0) cc_final: 0.6948 (pm20) REVERT: C 391 MET cc_start: 0.5949 (mtt) cc_final: 0.5710 (mtp) REVERT: D 172 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.6755 (mp0) outliers start: 20 outliers final: 6 residues processed: 169 average time/residue: 0.7751 time to fit residues: 144.2195 Evaluate side-chains 162 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 172 GLU 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 D residue 172 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 ASN A 451 HIS B 4 GLN B 104 ASN B 185 HIS D 4 GLN D 104 ASN D 128 GLN D 185 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.105195 restraints weight = 18081.874| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.38 r_work: 0.3132 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.292 16499 Z= 0.233 Angle : 0.695 30.304 22243 Z= 0.321 Chirality : 0.044 0.133 2336 Planarity : 0.005 0.116 2858 Dihedral : 5.525 81.768 2538 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.55 % Allowed : 17.41 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.18), residues: 1992 helix: 1.29 (0.16), residues: 1016 sheet: -0.48 (0.38), residues: 176 loop : -0.62 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.013 0.001 TYR A 387 PHE 0.010 0.001 PHE D 44 TRP 0.015 0.001 TRP A 253 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.22 (16483) covalent geometry : angle 0.69522 / 0.32 (22243) hydrogen bonds : bond 0.04573 / 3.10 ( 784) hydrogen bonds : angle 5.48369 / 3.96 ( 2274) Misc. bond : bond 0.14051 / 8.64 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 332 LYS cc_start: 0.7720 (tttt) cc_final: 0.6891 (tttm) REVERT: B 172 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: B 268 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: C 129 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7616 (mttp) REVERT: C 300 PHE cc_start: 0.6596 (m-80) cc_final: 0.6174 (t80) REVERT: C 332 LYS cc_start: 0.7658 (tttt) cc_final: 0.6817 (tttm) REVERT: C 373 GLU cc_start: 0.7351 (mp0) cc_final: 0.7010 (pm20) REVERT: C 391 MET cc_start: 0.6212 (mtt) cc_final: 0.5941 (mtp) REVERT: D 172 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.6632 (mp0) outliers start: 44 outliers final: 13 residues processed: 190 average time/residue: 0.7380 time to fit residues: 154.4695 Evaluate side-chains 165 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 172 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 114 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 177 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 24 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 4 GLN D 4 GLN D 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.104037 restraints weight = 18135.604| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.38 r_work: 0.3117 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.274 16499 Z= 0.226 Angle : 0.684 30.694 22243 Z= 0.314 Chirality : 0.044 0.167 2336 Planarity : 0.004 0.060 2858 Dihedral : 5.121 63.518 2530 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.61 % Allowed : 17.12 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 1992 helix: 1.34 (0.16), residues: 1016 sheet: -0.53 (0.38), residues: 176 loop : -0.64 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 96 TYR 0.013 0.001 TYR D 142 PHE 0.012 0.001 PHE A 429 TRP 0.016 0.001 TRP A 253 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (16483) covalent geometry : angle 0.68377 / 0.31 (22243) hydrogen bonds : bond 0.04390 / 2.98 ( 784) hydrogen bonds : angle 5.29293 / 3.82 ( 2274) Misc. bond : bond 0.12686 / 7.84 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.708 Fit side-chains REVERT: A 119 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.6142 (mp10) REVERT: A 120 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: A 300 PHE cc_start: 0.6718 (m-80) cc_final: 0.6281 (t80) REVERT: A 332 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.6947 (tttm) REVERT: A 417 LYS cc_start: 0.7278 (mttp) cc_final: 0.6880 (mttp) REVERT: B 143 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8328 (mppt) REVERT: B 172 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: B 268 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.8003 (mt0) REVERT: C 10 GLU cc_start: 0.6669 (mm-30) cc_final: 0.6347 (tp30) REVERT: C 287 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: C 300 PHE cc_start: 0.6772 (m-80) cc_final: 0.6309 (t80) REVERT: C 332 LYS cc_start: 0.7758 (tttt) cc_final: 0.6953 (tttm) REVERT: C 373 GLU cc_start: 0.7328 (mp0) cc_final: 0.7050 (pm20) REVERT: C 391 MET cc_start: 0.6262 (mtt) cc_final: 0.6008 (mtp) REVERT: C 417 LYS cc_start: 0.7379 (mttp) cc_final: 0.6952 (mttp) REVERT: D 172 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.6705 (mp0) outliers start: 45 outliers final: 20 residues processed: 183 average time/residue: 0.7608 time to fit residues: 153.1668 Evaluate side-chains 176 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 377 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 183 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 104 optimal weight: 0.1980 chunk 60 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 4 GLN D 4 GLN D 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.102821 restraints weight = 24424.534| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.64 r_work: 0.3098 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.250 16499 Z= 0.218 Angle : 0.673 30.606 22243 Z= 0.308 Chirality : 0.044 0.154 2336 Planarity : 0.004 0.050 2858 Dihedral : 5.064 64.583 2530 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.38 % Allowed : 17.70 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 1992 helix: 1.41 (0.16), residues: 1018 sheet: -0.56 (0.38), residues: 176 loop : -0.62 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 96 TYR 0.012 0.001 TYR B 88 PHE 0.011 0.001 PHE A 429 TRP 0.015 0.001 TRP A 253 HIS 0.010 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (16483) covalent geometry : angle 0.67304 / 0.31 (22243) hydrogen bonds : bond 0.04170 / 2.84 ( 784) hydrogen bonds : angle 5.14991 / 3.72 ( 2274) Misc. bond : bond 0.11579 / 7.15 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 119 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.6184 (mp10) REVERT: A 120 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: A 300 PHE cc_start: 0.6849 (m-80) cc_final: 0.6518 (t80) REVERT: A 332 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7086 (tttm) REVERT: A 417 LYS cc_start: 0.7342 (mttp) cc_final: 0.6950 (mttp) REVERT: B 143 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8376 (mppt) REVERT: B 172 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6212 (mp0) REVERT: C 287 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: C 300 PHE cc_start: 0.6720 (m-80) cc_final: 0.6363 (t80) REVERT: C 332 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7020 (tttm) REVERT: C 373 GLU cc_start: 0.7350 (mp0) cc_final: 0.7011 (pm20) REVERT: C 391 MET cc_start: 0.6316 (mtt) cc_final: 0.6066 (mtp) REVERT: C 392 LYS cc_start: 0.6982 (ttpt) cc_final: 0.6715 (tttt) REVERT: C 417 LYS cc_start: 0.7412 (mttp) cc_final: 0.6925 (mttp) REVERT: D 172 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.6690 (mp0) outliers start: 41 outliers final: 18 residues processed: 182 average time/residue: 0.7643 time to fit residues: 153.1654 Evaluate side-chains 167 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 103 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 0.0010 chunk 101 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 80 optimal weight: 0.0270 overall best weight: 0.5848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 4 GLN D 4 GLN D 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.104928 restraints weight = 27997.645| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.80 r_work: 0.3122 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.221 16499 Z= 0.191 Angle : 0.646 30.614 22243 Z= 0.291 Chirality : 0.042 0.141 2336 Planarity : 0.004 0.044 2858 Dihedral : 4.851 65.531 2530 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.97 % Allowed : 18.86 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 1992 helix: 1.65 (0.17), residues: 1008 sheet: -0.56 (0.38), residues: 176 loop : -0.51 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 96 TYR 0.012 0.001 TYR A 387 PHE 0.011 0.001 PHE A 409 TRP 0.013 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (16483) covalent geometry : angle 0.64618 / 0.29 (22243) hydrogen bonds : bond 0.03516 / 2.38 ( 784) hydrogen bonds : angle 5.00820 / 3.62 ( 2274) Misc. bond : bond 0.10105 / 6.21 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.714 Fit side-chains REVERT: A 119 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.6191 (mp10) REVERT: A 120 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: A 300 PHE cc_start: 0.6839 (m-80) cc_final: 0.6429 (t80) REVERT: A 332 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7011 (tttm) REVERT: A 417 LYS cc_start: 0.7352 (mttp) cc_final: 0.6977 (mttp) REVERT: B 143 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8395 (mppt) REVERT: B 172 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.5918 (mp0) REVERT: C 129 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7586 (mttp) REVERT: C 300 PHE cc_start: 0.6694 (m-80) cc_final: 0.6270 (t80) REVERT: C 332 LYS cc_start: 0.7769 (tttt) cc_final: 0.6972 (tttm) REVERT: C 334 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: C 373 GLU cc_start: 0.7332 (mp0) cc_final: 0.7053 (pm20) REVERT: C 391 MET cc_start: 0.6275 (mtt) cc_final: 0.6021 (mtp) REVERT: C 392 LYS cc_start: 0.6981 (ttpt) cc_final: 0.6709 (tttt) REVERT: C 417 LYS cc_start: 0.7425 (mttp) cc_final: 0.6984 (mttp) REVERT: D 172 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6596 (mp0) REVERT: D 258 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7674 (pt0) outliers start: 34 outliers final: 16 residues processed: 180 average time/residue: 0.7560 time to fit residues: 149.8839 Evaluate side-chains 167 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 258 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 15 optimal weight: 0.0030 chunk 176 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 145 optimal weight: 0.3980 chunk 167 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN B 4 GLN D 4 GLN D 168 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.105247 restraints weight = 17661.066| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.36 r_work: 0.3137 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 16499 Z= 0.207 Angle : 0.661 30.609 22243 Z= 0.300 Chirality : 0.043 0.133 2336 Planarity : 0.004 0.045 2858 Dihedral : 4.944 66.068 2530 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.09 % Allowed : 18.69 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 1992 helix: 1.63 (0.17), residues: 1010 sheet: -0.57 (0.38), residues: 176 loop : -0.49 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 96 TYR 0.012 0.001 TYR B 88 PHE 0.011 0.001 PHE A 429 TRP 0.013 0.001 TRP A 253 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (16483) covalent geometry : angle 0.66089 / 0.30 (22243) hydrogen bonds : bond 0.03896 / 2.65 ( 784) hydrogen bonds : angle 5.01153 / 3.63 ( 2274) Misc. bond : bond 0.10597 / 6.50 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.704 Fit side-chains REVERT: A 119 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.6190 (mp10) REVERT: A 120 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: A 300 PHE cc_start: 0.6933 (m-80) cc_final: 0.6556 (t80) REVERT: A 332 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7087 (tttm) REVERT: A 417 LYS cc_start: 0.7382 (mttp) cc_final: 0.7029 (mttp) REVERT: B 143 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8402 (mppt) REVERT: B 172 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.5862 (mp0) REVERT: B 268 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7904 (mt0) REVERT: C 287 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: C 300 PHE cc_start: 0.6777 (m-80) cc_final: 0.6412 (t80) REVERT: C 332 LYS cc_start: 0.7848 (tttt) cc_final: 0.7049 (tttm) REVERT: C 334 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: C 373 GLU cc_start: 0.7290 (mp0) cc_final: 0.7027 (pm20) REVERT: C 391 MET cc_start: 0.6397 (mtt) cc_final: 0.6135 (mtp) REVERT: C 392 LYS cc_start: 0.7016 (ttpt) cc_final: 0.6765 (tttt) REVERT: C 417 LYS cc_start: 0.7437 (mttp) cc_final: 0.7009 (mttp) REVERT: D 172 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: D 258 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7752 (pt0) outliers start: 36 outliers final: 17 residues processed: 169 average time/residue: 0.7534 time to fit residues: 140.2218 Evaluate side-chains 167 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 258 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 4 GLN D 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.104151 restraints weight = 23195.903| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.60 r_work: 0.3114 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.225 16499 Z= 0.204 Angle : 0.660 30.603 22243 Z= 0.299 Chirality : 0.043 0.184 2336 Planarity : 0.004 0.045 2858 Dihedral : 4.879 66.315 2530 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.44 % Allowed : 18.51 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1992 helix: 1.66 (0.17), residues: 1008 sheet: -0.56 (0.38), residues: 176 loop : -0.52 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 359 TYR 0.012 0.001 TYR D 88 PHE 0.010 0.001 PHE C 431 TRP 0.013 0.001 TRP A 253 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (16483) covalent geometry : angle 0.65987 / 0.30 (22243) hydrogen bonds : bond 0.03843 / 2.61 ( 784) hydrogen bonds : angle 4.99302 / 3.62 ( 2274) Misc. bond : bond 0.10506 / 6.44 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.719 Fit side-chains REVERT: A 119 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.6197 (mp10) REVERT: A 120 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: A 300 PHE cc_start: 0.6860 (m-80) cc_final: 0.6562 (t80) REVERT: A 332 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7082 (tttm) REVERT: A 417 LYS cc_start: 0.7390 (mttp) cc_final: 0.7049 (mttp) REVERT: B 143 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8424 (mppt) REVERT: B 172 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.5820 (mp0) REVERT: B 268 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7925 (mt0) REVERT: C 287 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: C 300 PHE cc_start: 0.6837 (m-80) cc_final: 0.6442 (t80) REVERT: C 332 LYS cc_start: 0.7840 (tttt) cc_final: 0.7036 (tttm) REVERT: C 334 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: C 373 GLU cc_start: 0.7297 (mp0) cc_final: 0.7028 (pm20) REVERT: C 391 MET cc_start: 0.6375 (mtt) cc_final: 0.6114 (mtp) REVERT: C 392 LYS cc_start: 0.6963 (ttpt) cc_final: 0.6732 (tttt) REVERT: C 417 LYS cc_start: 0.7489 (mttp) cc_final: 0.7064 (mttp) REVERT: D 172 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.6602 (mp0) REVERT: D 258 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7726 (pt0) outliers start: 42 outliers final: 23 residues processed: 176 average time/residue: 0.7297 time to fit residues: 141.9840 Evaluate side-chains 174 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 377 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 170 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 4 GLN D 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.100653 restraints weight = 34856.587| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.95 r_work: 0.3045 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.246 16499 Z= 0.237 Angle : 0.691 30.626 22243 Z= 0.317 Chirality : 0.045 0.186 2336 Planarity : 0.004 0.046 2858 Dihedral : 5.043 66.212 2530 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.26 % Allowed : 18.86 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.18), residues: 1992 helix: 1.54 (0.16), residues: 1008 sheet: -0.57 (0.37), residues: 176 loop : -0.59 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.015 0.001 TYR D 88 PHE 0.013 0.001 PHE A 429 TRP 0.016 0.001 TRP A 253 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (16483) covalent geometry : angle 0.69095 / 0.32 (22243) hydrogen bonds : bond 0.04455 / 3.03 ( 784) hydrogen bonds : angle 5.08633 / 3.68 ( 2274) Misc. bond : bond 0.11635 / 7.16 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 59 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.7988 (mm) REVERT: A 119 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.6223 (mp10) REVERT: A 120 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: A 300 PHE cc_start: 0.6966 (m-80) cc_final: 0.6658 (t80) REVERT: A 332 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7073 (tttm) REVERT: A 417 LYS cc_start: 0.7358 (mttp) cc_final: 0.7010 (mttp) REVERT: B 143 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8414 (mppt) REVERT: C 59 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8085 (mm) REVERT: C 287 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: C 300 PHE cc_start: 0.6942 (m-80) cc_final: 0.6563 (t80) REVERT: C 332 LYS cc_start: 0.7855 (tttt) cc_final: 0.7030 (tttm) REVERT: C 334 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: C 373 GLU cc_start: 0.7328 (mp0) cc_final: 0.7076 (pm20) REVERT: C 391 MET cc_start: 0.6342 (mtt) cc_final: 0.6089 (mtp) REVERT: C 392 LYS cc_start: 0.6953 (ttpt) cc_final: 0.6730 (tttt) REVERT: C 417 LYS cc_start: 0.7459 (mttp) cc_final: 0.7029 (mttp) REVERT: D 172 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.6600 (mp0) outliers start: 39 outliers final: 23 residues processed: 171 average time/residue: 0.7395 time to fit residues: 139.6209 Evaluate side-chains 173 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 376 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 59 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 chunk 187 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 4 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.100626 restraints weight = 24132.702| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.43 r_work: 0.3073 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.221 16499 Z= 0.194 Angle : 0.652 30.597 22243 Z= 0.295 Chirality : 0.043 0.183 2336 Planarity : 0.004 0.044 2858 Dihedral : 4.816 66.693 2530 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.86 % Allowed : 19.38 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.19), residues: 1992 helix: 1.69 (0.17), residues: 1010 sheet: -0.61 (0.37), residues: 176 loop : -0.51 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 359 TYR 0.012 0.001 TYR A 387 PHE 0.010 0.001 PHE C 431 TRP 0.013 0.001 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (16483) covalent geometry : angle 0.65246 / 0.29 (22243) hydrogen bonds : bond 0.03562 / 2.42 ( 784) hydrogen bonds : angle 4.95681 / 3.59 ( 2274) Misc. bond : bond 0.10169 / 6.24 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.704 Fit side-chains REVERT: A 119 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.6405 (mp10) REVERT: A 120 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: A 300 PHE cc_start: 0.6993 (m-80) cc_final: 0.6791 (t80) REVERT: A 332 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7349 (tttm) REVERT: A 417 LYS cc_start: 0.7433 (mttp) cc_final: 0.7142 (mttp) REVERT: B 143 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8458 (mppt) REVERT: B 172 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.5814 (mp0) REVERT: C 300 PHE cc_start: 0.6909 (m-80) cc_final: 0.6618 (t80) REVERT: C 332 LYS cc_start: 0.8128 (tttt) cc_final: 0.7353 (tttm) REVERT: C 334 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: C 373 GLU cc_start: 0.7277 (mp0) cc_final: 0.7050 (pm20) REVERT: C 391 MET cc_start: 0.6538 (mtt) cc_final: 0.6254 (mtp) REVERT: C 392 LYS cc_start: 0.6993 (ttpt) cc_final: 0.6777 (tttt) REVERT: C 417 LYS cc_start: 0.7561 (mttp) cc_final: 0.7164 (mttp) REVERT: D 172 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: D 258 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: D 312 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7832 (mt-10) outliers start: 32 outliers final: 18 residues processed: 167 average time/residue: 0.7596 time to fit residues: 140.1723 Evaluate side-chains 167 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 376 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 138 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 179 optimal weight: 0.1980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 432 GLN B 4 GLN D 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.098423 restraints weight = 26561.037| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.51 r_work: 0.3039 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.228 16499 Z= 0.215 Angle : 0.673 30.603 22243 Z= 0.306 Chirality : 0.044 0.176 2336 Planarity : 0.004 0.045 2858 Dihedral : 4.942 66.721 2530 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.63 % Allowed : 19.67 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1992 helix: 1.64 (0.17), residues: 1008 sheet: -0.56 (0.37), residues: 176 loop : -0.54 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 359 TYR 0.014 0.001 TYR D 88 PHE 0.011 0.001 PHE C 431 TRP 0.014 0.001 TRP A 253 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (16483) covalent geometry : angle 0.67284 / 0.31 (22243) hydrogen bonds : bond 0.04041 / 2.75 ( 784) hydrogen bonds : angle 5.00110 / 3.62 ( 2274) Misc. bond : bond 0.10696 / 6.57 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.821 Fit side-chains REVERT: A 119 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.6475 (mp10) REVERT: A 332 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7481 (tttm) REVERT: A 417 LYS cc_start: 0.7509 (mttp) cc_final: 0.7212 (mttp) REVERT: B 143 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8499 (mppt) REVERT: B 172 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.5858 (mp0) REVERT: C 59 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8220 (mm) REVERT: C 300 PHE cc_start: 0.7076 (m-80) cc_final: 0.6792 (t80) REVERT: C 332 LYS cc_start: 0.8243 (tttt) cc_final: 0.7492 (tttm) REVERT: C 334 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: C 391 MET cc_start: 0.6575 (mtt) cc_final: 0.6295 (mtp) REVERT: C 392 LYS cc_start: 0.7020 (ttpt) cc_final: 0.6808 (tttt) REVERT: C 417 LYS cc_start: 0.7624 (mttp) cc_final: 0.7232 (mttp) REVERT: D 172 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: D 258 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7878 (pt0) outliers start: 28 outliers final: 17 residues processed: 164 average time/residue: 0.7555 time to fit residues: 136.5893 Evaluate side-chains 165 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 376 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 HIS B 4 GLN D 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.098402 restraints weight = 25378.559| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.47 r_work: 0.3035 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.235 16499 Z= 0.216 Angle : 0.674 30.608 22243 Z= 0.307 Chirality : 0.044 0.181 2336 Planarity : 0.004 0.045 2858 Dihedral : 4.829 66.757 2528 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.57 % Allowed : 20.02 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.19), residues: 1992 helix: 1.63 (0.17), residues: 1006 sheet: -0.55 (0.37), residues: 176 loop : -0.56 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 359 TYR 0.015 0.001 TYR D 88 PHE 0.011 0.001 PHE A 431 TRP 0.015 0.001 TRP A 253 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (16483) covalent geometry : angle 0.67410 / 0.31 (22243) hydrogen bonds : bond 0.04077 / 2.77 ( 784) hydrogen bonds : angle 5.01389 / 3.63 ( 2274) Misc. bond : bond 0.10932 / 6.72 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6453.53 seconds wall clock time: 111 minutes 9.24 seconds (6669.24 seconds total)