Starting phenix.real_space_refine on Fri Jul 3 23:50:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mly_48381/07_2026/9mly_48381.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mly_48381/07_2026/9mly_48381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mly_48381/07_2026/9mly_48381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mly_48381/07_2026/9mly_48381.map" model { file = "/net/cci-nas-00/data/ceres_data/9mly_48381/07_2026/9mly_48381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mly_48381/07_2026/9mly_48381.cif" } resolution = 2.33 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= 0.011 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 4019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 17064 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: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 205 Classifications: {'water': 205} Link IDs: {None: 204} Chain: "B" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 324 Classifications: {'water': 324} Link IDs: {None: 323} Chain: "C" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Classifications: {'water': 197} Link IDs: {None: 196} Chain: "D" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 311 Classifications: {'water': 311} Link IDs: {None: 310} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 26.547 37.561 35.611 1.00 20.90 S ATOM 4552 SG CYS B 95 31.308 54.552 51.182 1.00 21.50 S ATOM 1170 SG CYS A 154 27.312 56.899 47.964 1.00 23.37 S ATOM 465 SG CYS A 62 29.496 51.084 45.607 1.00 14.67 S ATOM 652 SG CYS A 88 33.622 56.599 45.482 1.00 25.77 S ATOM 652 SG CYS A 88 33.622 56.599 45.482 1.00 25.77 S ATOM 5005 SG CYS B 153 30.873 60.108 49.650 1.00 24.80 S ATOM 4372 SG CYS B 70 37.355 57.592 51.124 1.00 24.06 S ATOM 4552 SG CYS B 95 31.308 54.552 51.182 1.00 21.50 S ATOM 10056 SG CYS C 275 104.257 47.606 35.523 1.00 20.86 S ATOM 12516 SG CYS D 95 99.467 30.710 51.153 1.00 24.65 S ATOM 9134 SG CYS C 154 103.523 28.450 47.834 1.00 24.93 S ATOM 8429 SG CYS C 62 101.372 34.215 45.501 1.00 15.75 S ATOM 8616 SG CYS C 88 97.266 28.457 45.621 1.00 27.26 S ATOM 8616 SG CYS C 88 97.266 28.457 45.621 1.00 27.26 S ATOM 12969 SG CYS D 153 99.913 25.206 49.582 1.00 32.88 S ATOM 12336 SG CYS D 70 93.407 27.726 51.082 1.00 18.77 S ATOM 12516 SG CYS D 95 99.467 30.710 51.153 1.00 24.65 S Time building chain proxies: 4.29, per 1000 atoms: 0.25 Number of scatterers: 17064 At special positions: 0 Unit cell: (132.3, 85.995, 95.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mo 2 41.97 Fe 32 26.01 S 139 16.00 O 4019 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: 1.18 Conformation dependent library (CDL) restraints added in 878.6 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 12 sheets defined 58.4% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.160A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.610A 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 removed outlier: 3.540A pdb=" N GLN A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.670A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.864A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 206 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: 4.096A 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: 3.606A pdb=" N MET A 279 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 317 through 343 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.562A 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 removed outlier: 4.008A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.033A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.240A 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: 3.686A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.574A pdb=" N LYS A 473 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 70 through 80 removed outlier: 4.057A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.004A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.907A 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 removed outlier: 3.502A pdb=" N HIS B 297 " --> pdb=" O GLN B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 297' Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 321 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.180A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.756A 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: 3.629A 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: 4.363A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 30 removed outlier: 4.039A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 92 removed outlier: 3.522A pdb=" N GLN C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.642A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.680A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.185A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) 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: 4.147A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 291 removed outlier: 3.570A pdb=" N MET C 279 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'C' and resid 317 through 347 Proline residue: C 333 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 370 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.429A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 434 removed outlier: 4.663A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.673A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.548A pdb=" N GLU D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 70 through 80 removed outlier: 3.986A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.970A 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 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.789A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.258A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.813A 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: 3.636A 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: 4.378A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 9.969A pdb=" N LEU A 399 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 375 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N TYR A 401 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR A 377 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.270A 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: 6.901A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 7.110A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE A 225 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.395A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.681A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.258A 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: 6.517A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.178A pdb=" N VAL C 351 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY C 376 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.977A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.222A 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: 7.392A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.424A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.830A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) 789 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: 2.53 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.84: 16347 1.84 - 2.47: 102 2.47 - 3.11: 20 3.11 - 3.75: 9 3.75 - 4.39: 5 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 4.388 -2.188 2.00e-02 2.50e+03 1.20e+04 bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 4.385 -2.185 2.00e-02 2.50e+03 1.19e+04 bond pdb="FE5 CLF B 602 " pdb="FE6 CLF B 602 " ideal model delta sigma weight residual 2.200 3.941 -1.741 2.00e-02 2.50e+03 7.58e+03 bond pdb="FE5 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.939 -1.739 2.00e-02 2.50e+03 7.56e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 3.778 -1.578 2.00e-02 2.50e+03 6.22e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.90: 22235 6.90 - 13.79: 2 13.79 - 20.69: 2 20.69 - 27.58: 0 27.58 - 34.48: 4 Bond angle restraints: 22243 Sorted by residual: angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 55.52 34.48 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.54 34.46 3.00e+00 1.11e-01 1.32e+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 60.78 29.22 3.00e+00 1.11e-01 9.49e+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 60.81 29.19 3.00e+00 1.11e-01 9.47e+01 angle pdb=" N GLY C 356 " pdb=" CA GLY C 356 " pdb=" C GLY C 356 " ideal model delta sigma weight residual 112.50 121.65 -9.15 1.16e+00 7.43e-01 6.22e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 9324 17.88 - 35.76: 616 35.76 - 53.64: 98 53.64 - 71.52: 35 71.52 - 89.40: 28 Dihedral angle restraints: 10101 sinusoidal: 4359 harmonic: 5742 Sorted by residual: dihedral pdb=" CA PHE B 367 " pdb=" C PHE B 367 " pdb=" N ALA B 368 " pdb=" CA ALA B 368 " ideal model delta harmonic sigma weight residual 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA PHE D 367 " pdb=" C PHE D 367 " pdb=" N ALA D 368 " pdb=" CA ALA D 368 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA SER B 11 " pdb=" C SER B 11 " pdb=" N TYR B 12 " pdb=" CA TYR B 12 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1791 0.053 - 0.106: 443 0.106 - 0.159: 93 0.159 - 0.211: 4 0.211 - 0.264: 5 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA ARG A 359 " pdb=" N ARG A 359 " pdb=" C ARG A 359 " pdb=" CB ARG A 359 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CG LEU B 369 " pdb=" CB LEU B 369 " pdb=" CD1 LEU B 369 " pdb=" CD2 LEU B 369 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA MET A 352 " pdb=" N MET A 352 " pdb=" C MET A 352 " pdb=" CB MET A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 444 " 0.017 2.00e-02 2.50e+03 2.41e-02 1.45e+01 pdb=" CG TRP A 444 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 444 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A 444 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 444 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 444 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 444 " 0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 444 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 444 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 444 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 446 " 0.027 2.00e-02 2.50e+03 1.97e-02 7.78e+00 pdb=" CG TYR C 446 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR C 446 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR C 446 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 446 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 446 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 446 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 446 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 357 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C GLY C 357 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY C 357 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU C 358 " -0.014 2.00e-02 2.50e+03 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1286 2.73 - 3.27: 18163 3.27 - 3.81: 33706 3.81 - 4.36: 43095 4.36 - 4.90: 66040 Nonbonded interactions: 162290 Sorted by model distance: nonbonded pdb=" OD2 ASP D 353 " pdb="FE FE D 601 " model vdw 2.186 3.000 nonbonded pdb=" OD1 ASP B 326 " pdb=" OH TYR B 487 " model vdw 2.190 3.040 nonbonded pdb=" OH TYR A 450 " pdb=" OD2 ASP A 462 " model vdw 2.194 3.040 nonbonded pdb=" NZ LYS B 241 " pdb=" OD2 ASP B 256 " model vdw 2.200 3.120 nonbonded pdb=" OE2 GLU B 109 " pdb="FE FE D 601 " model vdw 2.204 3.000 ... (remaining 162285 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=0.36 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: 4.790 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.590 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.049 2.188 16499 Z= 2.483 Angle : 0.792 34.478 22243 Z= 0.420 Chirality : 0.048 0.264 2336 Planarity : 0.004 0.055 2858 Dihedral : 13.553 89.404 6433 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.58 % Allowed : 0.35 % Favored : 99.07 % 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: 0.36 (0.18), residues: 1992 helix: 1.19 (0.17), residues: 980 sheet: -0.41 (0.42), residues: 142 loop : -0.70 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 277 TYR 0.048 0.002 TYR C 446 PHE 0.026 0.002 PHE A 118 TRP 0.062 0.002 TRP A 444 HIS 0.009 0.001 HIS C 362 Details of bonding type rmsd/Z covalent geometry : bond 0.04908 / 2.46 (16483) covalent geometry : angle 0.79203 / 0.42 (22243) hydrogen bonds : bond 0.14244 / 9.38 ( 789) hydrogen bonds : angle 6.84881 / 4.87 ( 2274) Misc. bond : bond 0.12432 / 9.35 ( 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 356 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 346 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7385 (mt-10) REVERT: A 112 MET cc_start: 0.8977 (mtp) cc_final: 0.8729 (mtp) REVERT: A 120 GLU cc_start: 0.7891 (tp30) cc_final: 0.6657 (mp0) REVERT: A 122 ASP cc_start: 0.8108 (m-30) cc_final: 0.7881 (m-30) REVERT: A 209 LYS cc_start: 0.7706 (mmtt) cc_final: 0.7447 (mttt) REVERT: B 45 GLN cc_start: 0.7822 (tp40) cc_final: 0.7587 (mm110) REVERT: B 50 LYS cc_start: 0.8089 (tptp) cc_final: 0.7439 (mttp) REVERT: B 60 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8136 (mt-10) REVERT: B 211 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7950 (mttm) REVERT: B 315 LYS cc_start: 0.8212 (tptm) cc_final: 0.7531 (tptp) REVERT: B 503 GLU cc_start: 0.8231 (tt0) cc_final: 0.7725 (mt-10) REVERT: C 22 GLU cc_start: 0.7799 (tp30) cc_final: 0.6968 (pm20) REVERT: C 26 LYS cc_start: 0.7514 (tttt) cc_final: 0.7258 (mppt) REVERT: C 120 GLU cc_start: 0.8375 (tp30) cc_final: 0.8164 (tp30) REVERT: C 218 SER cc_start: 0.8301 (p) cc_final: 0.8095 (m) REVERT: C 318 GLU cc_start: 0.7338 (pt0) cc_final: 0.6610 (mm-30) REVERT: C 415 ARG cc_start: 0.7521 (tpp80) cc_final: 0.7291 (tpt-90) REVERT: C 473 LYS cc_start: 0.7964 (mmtm) cc_final: 0.7545 (mptt) REVERT: D 54 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7744 (mt-10) REVERT: D 163 ASN cc_start: 0.8364 (t0) cc_final: 0.8144 (t0) REVERT: D 214 ASP cc_start: 0.7616 (m-30) cc_final: 0.7330 (m-30) REVERT: D 259 GLU cc_start: 0.8228 (mm-30) cc_final: 0.8009 (tp30) REVERT: D 303 LYS cc_start: 0.8150 (mtmt) cc_final: 0.7859 (mttt) REVERT: D 404 LYS cc_start: 0.8189 (mttp) cc_final: 0.7663 (ttmt) REVERT: D 417 LYS cc_start: 0.7614 (pttm) cc_final: 0.7238 (mmpt) outliers start: 10 outliers final: 1 residues processed: 352 average time/residue: 0.7574 time to fit residues: 290.4757 Evaluate side-chains 222 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 355 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 145 ASN A 199 ASN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS A 469 ASN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN C 98 ASN C 199 ASN C 362 HIS D 106 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112096 restraints weight = 14609.605| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 0.88 r_work: 0.3229 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.417 16499 Z= 0.319 Angle : 0.797 31.255 22243 Z= 0.391 Chirality : 0.050 0.169 2336 Planarity : 0.005 0.065 2858 Dihedral : 5.121 47.805 2518 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.63 % Allowed : 6.79 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 1992 helix: 1.16 (0.16), residues: 996 sheet: -0.50 (0.36), residues: 188 loop : -0.57 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 277 TYR 0.024 0.003 TYR B 102 PHE 0.041 0.002 PHE A 118 TRP 0.051 0.002 TRP A 444 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.30 (16483) covalent geometry : angle 0.79746 / 0.39 (22243) hydrogen bonds : bond 0.06575 / 4.35 ( 789) hydrogen bonds : angle 5.78569 / 4.15 ( 2274) Misc. bond : bond 0.19281 / 11.72 ( 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 252 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7841 (tp30) cc_final: 0.7307 (mp0) REVERT: A 307 GLU cc_start: 0.8472 (tt0) cc_final: 0.8263 (tt0) REVERT: A 440 GLU cc_start: 0.7978 (tt0) cc_final: 0.7513 (tt0) REVERT: B 50 LYS cc_start: 0.8356 (tptp) cc_final: 0.7992 (mttp) REVERT: B 171 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7475 (pttt) REVERT: B 315 LYS cc_start: 0.8279 (tptm) cc_final: 0.7750 (tptp) REVERT: B 379 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8234 (tm) REVERT: B 417 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7631 (mmtp) REVERT: C 287 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.6796 (tm-30) REVERT: C 318 GLU cc_start: 0.7512 (pt0) cc_final: 0.6969 (mm-30) REVERT: C 322 LYS cc_start: 0.7566 (ttpp) cc_final: 0.7042 (tttt) REVERT: C 410 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: C 473 LYS cc_start: 0.8081 (mmtm) cc_final: 0.7800 (mppt) REVERT: C 476 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7754 (tp40) REVERT: D 177 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7200 (t70) REVERT: D 214 ASP cc_start: 0.7760 (m-30) cc_final: 0.7510 (m-30) REVERT: D 302 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8712 (tttt) REVERT: D 303 LYS cc_start: 0.8249 (mtmt) cc_final: 0.8019 (mttt) REVERT: D 430 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8693 (tm) outliers start: 28 outliers final: 7 residues processed: 243 average time/residue: 0.7514 time to fit residues: 198.4171 Evaluate side-chains 216 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 114 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 196 HIS A 252 GLN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS A 384 ASN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN C 98 ASN C 362 HIS C 384 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101019 restraints weight = 27756.926| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.52 r_work: 0.3031 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.336 16499 Z= 0.247 Angle : 0.710 30.716 22243 Z= 0.337 Chirality : 0.045 0.158 2336 Planarity : 0.004 0.044 2858 Dihedral : 4.868 47.172 2518 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.39 % Allowed : 8.94 % Favored : 89.67 % 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: 1.30 (0.17), residues: 1002 sheet: -0.47 (0.36), residues: 188 loop : -0.60 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 277 TYR 0.018 0.002 TYR B 102 PHE 0.026 0.002 PHE A 118 TRP 0.013 0.001 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.23 (16483) covalent geometry : angle 0.70974 / 0.34 (22243) hydrogen bonds : bond 0.05114 / 3.37 ( 789) hydrogen bonds : angle 5.54319 / 3.98 ( 2274) Misc. bond : bond 0.15394 / 9.66 ( 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 234 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.721 Fit side-chains REVERT: A 4 MET cc_start: 0.2199 (ppp) cc_final: 0.1558 (mtp) REVERT: A 120 GLU cc_start: 0.7957 (tp30) cc_final: 0.6890 (mp0) REVERT: A 287 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.6607 (tp30) REVERT: A 440 GLU cc_start: 0.8065 (tt0) cc_final: 0.7714 (tt0) REVERT: B 50 LYS cc_start: 0.8244 (tptp) cc_final: 0.7606 (mttp) REVERT: B 171 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7192 (pttt) REVERT: B 299 GLU cc_start: 0.7975 (mp0) cc_final: 0.7415 (mp0) REVERT: B 315 LYS cc_start: 0.8263 (tptm) cc_final: 0.7446 (tptp) REVERT: B 379 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8160 (tm) REVERT: B 417 LYS cc_start: 0.7834 (mmtm) cc_final: 0.7482 (mmtp) REVERT: B 503 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7804 (mt-10) REVERT: B 507 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: C 182 ARG cc_start: 0.8589 (mtt-85) cc_final: 0.8183 (mmt180) REVERT: C 318 GLU cc_start: 0.7430 (pt0) cc_final: 0.6539 (mm-30) REVERT: C 410 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: C 473 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7632 (mppt) REVERT: D 177 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7268 (t70) REVERT: D 214 ASP cc_start: 0.7703 (m-30) cc_final: 0.7395 (m-30) REVERT: D 303 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7785 (mttt) REVERT: D 346 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8434 (ttmm) REVERT: D 430 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8624 (tm) outliers start: 24 outliers final: 8 residues processed: 229 average time/residue: 0.7551 time to fit residues: 189.1731 Evaluate side-chains 213 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 161 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 274 HIS A 362 HIS A 383 HIS ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN D 268 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.101311 restraints weight = 22041.746| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.33 r_work: 0.3044 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 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 = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.320 16499 Z= 0.245 Angle : 0.710 30.782 22243 Z= 0.336 Chirality : 0.045 0.156 2336 Planarity : 0.004 0.048 2858 Dihedral : 4.810 47.804 2518 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.86 % Allowed : 9.52 % Favored : 88.62 % 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: 0.58 (0.18), residues: 1992 helix: 1.36 (0.17), residues: 1002 sheet: -0.36 (0.37), residues: 174 loop : -0.62 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 277 TYR 0.018 0.002 TYR B 102 PHE 0.023 0.002 PHE A 118 TRP 0.012 0.001 TRP C 479 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 (16483) covalent geometry : angle 0.71048 / 0.34 (22243) hydrogen bonds : bond 0.05151 / 3.40 ( 789) hydrogen bonds : angle 5.44937 / 3.91 ( 2274) Misc. bond : bond 0.14880 / 9.25 ( 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 239 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.686 Fit side-chains REVERT: A 4 MET cc_start: 0.2058 (ppp) cc_final: 0.1483 (mtp) REVERT: A 120 GLU cc_start: 0.7937 (tp30) cc_final: 0.6892 (mp0) REVERT: A 287 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.6564 (tp30) REVERT: A 321 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7630 (mt0) REVERT: B 50 LYS cc_start: 0.8239 (tptp) cc_final: 0.7615 (mttp) REVERT: B 171 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7174 (pttt) REVERT: B 315 LYS cc_start: 0.8236 (tptm) cc_final: 0.7438 (tptp) REVERT: B 379 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8141 (tm) REVERT: B 417 LYS cc_start: 0.7814 (mmtm) cc_final: 0.7414 (mmtp) REVERT: B 503 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7717 (mt-10) REVERT: B 507 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: C 182 ARG cc_start: 0.8581 (mtt-85) cc_final: 0.8188 (mmt180) REVERT: C 288 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7131 (mt-10) REVERT: C 305 THR cc_start: 0.8407 (t) cc_final: 0.8090 (m) REVERT: C 318 GLU cc_start: 0.7446 (pt0) cc_final: 0.6499 (mm-30) REVERT: C 322 LYS cc_start: 0.7270 (ttpp) cc_final: 0.6676 (tttt) REVERT: C 410 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: C 473 LYS cc_start: 0.8149 (mmtm) cc_final: 0.7652 (mppt) REVERT: D 177 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7178 (t70) REVERT: D 214 ASP cc_start: 0.7736 (m-30) cc_final: 0.7394 (m-30) REVERT: D 299 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: D 302 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8669 (tttt) REVERT: D 303 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7725 (mttt) REVERT: D 346 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8397 (ttmm) REVERT: D 430 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8584 (tm) outliers start: 32 outliers final: 10 residues processed: 229 average time/residue: 0.7788 time to fit residues: 194.8683 Evaluate side-chains 220 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 48 optimal weight: 0.3980 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 176 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 362 HIS A 383 HIS ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN D 268 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.099392 restraints weight = 16578.220| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.14 r_work: 0.3017 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.340 16499 Z= 0.273 Angle : 0.741 30.818 22243 Z= 0.356 Chirality : 0.047 0.161 2336 Planarity : 0.005 0.057 2858 Dihedral : 4.961 49.616 2518 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.03 % Allowed : 9.98 % Favored : 87.99 % 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: 1.30 (0.17), residues: 1002 sheet: -0.33 (0.37), residues: 174 loop : -0.65 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 277 TYR 0.018 0.002 TYR B 102 PHE 0.028 0.002 PHE A 118 TRP 0.010 0.002 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.25 (16483) covalent geometry : angle 0.74135 / 0.36 (22243) hydrogen bonds : bond 0.05812 / 3.84 ( 789) hydrogen bonds : angle 5.51222 / 3.96 ( 2274) Misc. bond : bond 0.16475 / 10.10 ( 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 239 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.648 Fit side-chains REVERT: A 4 MET cc_start: 0.2124 (ppp) cc_final: 0.1497 (mtp) REVERT: A 7 GLU cc_start: 0.6828 (mp0) cc_final: 0.6412 (mp0) REVERT: A 120 GLU cc_start: 0.7966 (tp30) cc_final: 0.6945 (mp0) REVERT: A 287 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.6558 (tp30) REVERT: A 321 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7632 (mt0) REVERT: A 345 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8120 (ptp-170) REVERT: B 50 LYS cc_start: 0.8221 (tptp) cc_final: 0.7581 (mttp) REVERT: B 171 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7154 (pttt) REVERT: B 315 LYS cc_start: 0.8248 (tptm) cc_final: 0.7396 (tptp) REVERT: B 379 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8110 (tm) REVERT: B 503 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7659 (mt-10) REVERT: B 507 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: C 8 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7411 (pt0) REVERT: C 182 ARG cc_start: 0.8565 (mtt-85) cc_final: 0.8175 (mmt180) REVERT: C 288 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7149 (mt-10) REVERT: C 305 THR cc_start: 0.8385 (t) cc_final: 0.8115 (m) REVERT: C 318 GLU cc_start: 0.7488 (pt0) cc_final: 0.6531 (mm-30) REVERT: C 410 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: C 473 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7618 (mppt) REVERT: D 214 ASP cc_start: 0.7771 (m-30) cc_final: 0.7399 (m-30) REVERT: D 299 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: D 302 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8660 (tttt) REVERT: D 303 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7762 (mttt) REVERT: D 346 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8427 (ttmm) REVERT: D 430 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8613 (tm) outliers start: 35 outliers final: 14 residues processed: 230 average time/residue: 0.7804 time to fit residues: 195.9855 Evaluate side-chains 224 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 13 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 119 optimal weight: 0.0670 chunk 147 optimal weight: 2.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 362 HIS A 383 HIS B 168 ASN C 98 ASN D 268 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.114591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.097047 restraints weight = 16222.865| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.19 r_work: 0.2979 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.364 16499 Z= 0.290 Angle : 0.764 30.763 22243 Z= 0.370 Chirality : 0.048 0.162 2336 Planarity : 0.005 0.062 2858 Dihedral : 5.087 51.339 2518 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.92 % Allowed : 10.10 % Favored : 87.99 % 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: 0.41 (0.18), residues: 1992 helix: 1.22 (0.16), residues: 998 sheet: -0.36 (0.37), residues: 174 loop : -0.71 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 277 TYR 0.017 0.002 TYR D 88 PHE 0.029 0.002 PHE A 118 TRP 0.012 0.002 TRP A 444 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.27 (16483) covalent geometry : angle 0.76434 / 0.37 (22243) hydrogen bonds : bond 0.06212 / 4.11 ( 789) hydrogen bonds : angle 5.56651 / 4.00 ( 2274) Misc. bond : bond 0.17259 / 10.47 ( 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 235 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.668 Fit side-chains REVERT: A 7 GLU cc_start: 0.6768 (mp0) cc_final: 0.6437 (mp0) REVERT: A 120 GLU cc_start: 0.7992 (tp30) cc_final: 0.6770 (mp0) REVERT: A 168 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7208 (mmmm) REVERT: A 287 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.6514 (tp30) REVERT: A 321 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: A 345 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8227 (ptp-170) REVERT: B 50 LYS cc_start: 0.8137 (tptp) cc_final: 0.7416 (mttp) REVERT: B 171 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7055 (pttt) REVERT: B 315 LYS cc_start: 0.8227 (tptm) cc_final: 0.7327 (tptp) REVERT: B 379 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8028 (tm) REVERT: B 503 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7613 (mt-10) REVERT: B 507 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: C 8 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7345 (pt0) REVERT: C 288 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7121 (mt-10) REVERT: C 305 THR cc_start: 0.8333 (t) cc_final: 0.8093 (m) REVERT: C 318 GLU cc_start: 0.7513 (pt0) cc_final: 0.6532 (mm-30) REVERT: C 322 LYS cc_start: 0.7202 (ttpp) cc_final: 0.6565 (tttt) REVERT: C 410 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: C 473 LYS cc_start: 0.8098 (mmtm) cc_final: 0.7520 (mppt) REVERT: D 4 GLN cc_start: 0.7591 (mp10) cc_final: 0.7244 (mt0) REVERT: D 214 ASP cc_start: 0.7790 (m-30) cc_final: 0.7388 (m-30) REVERT: D 299 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: D 302 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8557 (tttt) REVERT: D 303 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7658 (mttt) REVERT: D 346 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8348 (ttmm) REVERT: D 430 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8569 (tm) outliers start: 33 outliers final: 15 residues processed: 224 average time/residue: 0.7621 time to fit residues: 186.0775 Evaluate side-chains 229 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 152 optimal weight: 0.0040 chunk 169 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 362 HIS A 383 HIS C 98 ASN D 268 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.097982 restraints weight = 26192.074| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.55 r_work: 0.2978 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 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 = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.311 16499 Z= 0.246 Angle : 0.711 30.764 22243 Z= 0.339 Chirality : 0.045 0.154 2336 Planarity : 0.004 0.050 2858 Dihedral : 4.903 48.625 2518 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.92 % Allowed : 10.62 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 1992 helix: 1.34 (0.17), residues: 1002 sheet: -0.35 (0.37), residues: 174 loop : -0.64 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 277 TYR 0.015 0.002 TYR C 229 PHE 0.022 0.002 PHE A 118 TRP 0.012 0.001 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.23 (16483) covalent geometry : angle 0.71148 / 0.34 (22243) hydrogen bonds : bond 0.05163 / 3.40 ( 789) hydrogen bonds : angle 5.43552 / 3.91 ( 2274) Misc. bond : bond 0.14787 / 9.11 ( 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 235 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.566 Fit side-chains REVERT: A 4 MET cc_start: 0.2385 (pmm) cc_final: 0.1724 (mtp) REVERT: A 120 GLU cc_start: 0.8052 (tp30) cc_final: 0.6765 (mp0) REVERT: A 287 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.6482 (tp30) REVERT: A 321 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7497 (mt0) REVERT: B 50 LYS cc_start: 0.8140 (tptp) cc_final: 0.7377 (mttp) REVERT: B 171 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6973 (pttt) REVERT: B 315 LYS cc_start: 0.8246 (tptm) cc_final: 0.7293 (tptp) REVERT: B 379 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8024 (tm) REVERT: B 507 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: C 8 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7200 (pt0) REVERT: C 288 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7107 (mt-10) REVERT: C 305 THR cc_start: 0.8309 (t) cc_final: 0.8071 (m) REVERT: C 318 GLU cc_start: 0.7465 (pt0) cc_final: 0.6313 (mm-30) REVERT: C 322 LYS cc_start: 0.7153 (ttpp) cc_final: 0.6500 (tttt) REVERT: C 410 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: C 473 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7493 (mppt) REVERT: D 4 GLN cc_start: 0.7561 (mp10) cc_final: 0.7213 (mt0) REVERT: D 177 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7082 (t70) REVERT: D 214 ASP cc_start: 0.7856 (m-30) cc_final: 0.7404 (m-30) REVERT: D 299 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: D 302 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8526 (tttt) REVERT: D 303 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7565 (mttt) REVERT: D 346 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8324 (ttmm) REVERT: D 430 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8552 (tm) outliers start: 33 outliers final: 14 residues processed: 226 average time/residue: 0.7173 time to fit residues: 177.5474 Evaluate side-chains 224 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 21 optimal weight: 0.4980 chunk 140 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 145 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 362 HIS A 383 HIS C 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.101432 restraints weight = 22278.034| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.43 r_work: 0.3027 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 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 = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.293 16499 Z= 0.224 Angle : 0.686 30.655 22243 Z= 0.322 Chirality : 0.044 0.148 2336 Planarity : 0.004 0.043 2858 Dihedral : 4.698 46.085 2518 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.68 % Allowed : 11.14 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.18), residues: 1992 helix: 1.46 (0.17), residues: 1002 sheet: -0.34 (0.37), residues: 174 loop : -0.59 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.014 0.001 TYR B 88 PHE 0.018 0.001 PHE A 118 TRP 0.013 0.001 TRP C 479 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (16483) covalent geometry : angle 0.68559 / 0.32 (22243) hydrogen bonds : bond 0.04581 / 3.02 ( 789) hydrogen bonds : angle 5.32807 / 3.83 ( 2274) Misc. bond : bond 0.13090 / 8.14 ( 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 236 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.706 Fit side-chains REVERT: A 4 MET cc_start: 0.2102 (pmm) cc_final: 0.1666 (mtp) REVERT: A 120 GLU cc_start: 0.8007 (tp30) cc_final: 0.6756 (mp0) REVERT: A 287 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.6444 (tp30) REVERT: A 321 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7507 (mt0) REVERT: A 388 ASP cc_start: 0.7966 (m-30) cc_final: 0.7761 (m-30) REVERT: B 50 LYS cc_start: 0.8131 (tptp) cc_final: 0.7389 (mttp) REVERT: B 171 LYS cc_start: 0.7613 (ptmt) cc_final: 0.6995 (pttt) REVERT: B 246 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7918 (mt-10) REVERT: B 315 LYS cc_start: 0.8219 (tptm) cc_final: 0.7262 (tptp) REVERT: B 323 ASP cc_start: 0.8542 (m-30) cc_final: 0.8315 (m-30) REVERT: B 379 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8024 (tm) REVERT: B 507 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: C 8 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: C 288 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7061 (mt-10) REVERT: C 305 THR cc_start: 0.8314 (t) cc_final: 0.8074 (m) REVERT: C 318 GLU cc_start: 0.7377 (pt0) cc_final: 0.6296 (mm-30) REVERT: C 322 LYS cc_start: 0.7122 (ttpp) cc_final: 0.6581 (ttpp) REVERT: C 410 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: C 473 LYS cc_start: 0.8057 (mmtm) cc_final: 0.7496 (mppt) REVERT: D 214 ASP cc_start: 0.7870 (m-30) cc_final: 0.7427 (m-30) REVERT: D 299 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: D 303 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7529 (mttt) REVERT: D 346 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8302 (ttmm) REVERT: D 430 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8516 (tm) outliers start: 29 outliers final: 11 residues processed: 227 average time/residue: 0.7125 time to fit residues: 176.8819 Evaluate side-chains 221 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 45 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 192 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 362 HIS A 383 HIS C 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.101584 restraints weight = 23266.895| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.38 r_work: 0.3044 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 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 = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.291 16499 Z= 0.230 Angle : 0.694 30.660 22243 Z= 0.326 Chirality : 0.045 0.150 2336 Planarity : 0.004 0.043 2858 Dihedral : 4.632 46.498 2516 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.51 % Allowed : 11.67 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 1992 helix: 1.46 (0.17), residues: 1004 sheet: -0.32 (0.37), residues: 174 loop : -0.56 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 25 TYR 0.015 0.001 TYR B 88 PHE 0.018 0.001 PHE A 118 TRP 0.013 0.001 TRP C 479 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (16483) covalent geometry : angle 0.69369 / 0.33 (22243) hydrogen bonds : bond 0.04719 / 3.11 ( 789) hydrogen bonds : angle 5.33211 / 3.84 ( 2274) Misc. bond : bond 0.13604 / 8.39 ( 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 232 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.679 Fit side-chains REVERT: A 120 GLU cc_start: 0.7982 (tp30) cc_final: 0.6818 (mp0) REVERT: A 287 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.6514 (tp30) REVERT: A 321 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: A 388 ASP cc_start: 0.8063 (m-30) cc_final: 0.7859 (m-30) REVERT: B 50 LYS cc_start: 0.8232 (tptp) cc_final: 0.7566 (mttp) REVERT: B 171 LYS cc_start: 0.7710 (ptmt) cc_final: 0.7088 (pttt) REVERT: B 246 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7959 (mt-10) REVERT: B 315 LYS cc_start: 0.8276 (tptm) cc_final: 0.7354 (tptp) REVERT: B 323 ASP cc_start: 0.8572 (m-30) cc_final: 0.8350 (m-30) REVERT: B 379 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8112 (tm) REVERT: B 507 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: C 8 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7267 (pt0) REVERT: C 288 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7125 (mt-10) REVERT: C 305 THR cc_start: 0.8391 (t) cc_final: 0.8171 (m) REVERT: C 318 GLU cc_start: 0.7429 (pt0) cc_final: 0.6395 (mm-30) REVERT: C 410 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: C 473 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7641 (mppt) REVERT: D 214 ASP cc_start: 0.7911 (m-30) cc_final: 0.7476 (m-30) REVERT: D 299 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: D 303 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7697 (mttt) REVERT: D 346 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8388 (ttmm) REVERT: D 430 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8571 (tm) outliers start: 26 outliers final: 11 residues processed: 223 average time/residue: 0.7406 time to fit residues: 180.8553 Evaluate side-chains 223 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 50 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 362 HIS A 383 HIS C 98 ASN D 268 GLN D 363 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.098440 restraints weight = 22400.740| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.35 r_work: 0.2997 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.323 16499 Z= 0.266 Angle : 0.737 30.749 22243 Z= 0.353 Chirality : 0.046 0.156 2336 Planarity : 0.005 0.054 2858 Dihedral : 4.854 49.754 2516 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.45 % Allowed : 11.78 % Favored : 86.77 % 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: 0.59 (0.18), residues: 1992 helix: 1.35 (0.17), residues: 1004 sheet: -0.33 (0.36), residues: 174 loop : -0.60 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 277 TYR 0.017 0.002 TYR B 88 PHE 0.023 0.002 PHE A 118 TRP 0.011 0.002 TRP A 444 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.25 (16483) covalent geometry : angle 0.73685 / 0.35 (22243) hydrogen bonds : bond 0.05594 / 3.70 ( 789) hydrogen bonds : angle 5.44039 / 3.91 ( 2274) Misc. bond : bond 0.15861 / 9.66 ( 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 225 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.661 Fit side-chains REVERT: A 7 GLU cc_start: 0.6843 (mp0) cc_final: 0.6406 (mp0) REVERT: A 120 GLU cc_start: 0.8001 (tp30) cc_final: 0.6906 (mp0) REVERT: A 287 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.6575 (tp30) REVERT: A 321 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: B 50 LYS cc_start: 0.8244 (tptp) cc_final: 0.7576 (mttp) REVERT: B 171 LYS cc_start: 0.7725 (ptmt) cc_final: 0.7098 (pttt) REVERT: B 315 LYS cc_start: 0.8308 (tptm) cc_final: 0.7403 (tptp) REVERT: B 379 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8129 (tm) REVERT: C 8 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7330 (pt0) REVERT: C 288 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7196 (mt-10) REVERT: C 318 GLU cc_start: 0.7524 (pt0) cc_final: 0.6472 (mm-30) REVERT: C 322 LYS cc_start: 0.7293 (ttpp) cc_final: 0.6723 (ttpp) REVERT: C 410 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: C 473 LYS cc_start: 0.8175 (mmtm) cc_final: 0.7647 (mppt) REVERT: D 4 GLN cc_start: 0.7612 (mp10) cc_final: 0.7270 (mt0) REVERT: D 177 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7072 (t70) REVERT: D 214 ASP cc_start: 0.7930 (m-30) cc_final: 0.7488 (m-30) REVERT: D 299 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: D 303 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7777 (mttt) REVERT: D 346 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8440 (ttmm) REVERT: D 430 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8628 (tm) outliers start: 25 outliers final: 11 residues processed: 216 average time/residue: 0.7113 time to fit residues: 167.9267 Evaluate side-chains 217 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 192 optimal weight: 0.9980 chunk 53 optimal weight: 0.0370 chunk 120 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 33 optimal weight: 0.0170 chunk 146 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 362 HIS A 383 HIS C 98 ASN D 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.103625 restraints weight = 23622.922| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.40 r_work: 0.3073 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.271 16499 Z= 0.214 Angle : 0.677 30.615 22243 Z= 0.316 Chirality : 0.044 0.146 2336 Planarity : 0.004 0.041 2858 Dihedral : 4.566 44.728 2516 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.45 % Allowed : 11.84 % Favored : 86.71 % 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: 0.78 (0.19), residues: 1992 helix: 1.49 (0.17), residues: 1016 sheet: -0.32 (0.36), residues: 174 loop : -0.50 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.012 0.001 TYR B 88 PHE 0.016 0.001 PHE A 118 TRP 0.014 0.001 TRP C 479 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 (16483) covalent geometry : angle 0.67723 / 0.32 (22243) hydrogen bonds : bond 0.04232 / 2.78 ( 789) hydrogen bonds : angle 5.27411 / 3.79 ( 2274) Misc. bond : bond 0.12383 / 7.67 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6262.72 seconds wall clock time: 107 minutes 34.19 seconds (6454.19 seconds total)