Starting phenix.real_space_refine on Sat Jul 4 00:56:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqy_45827/07_2026/9cqy_45827.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqy_45827/07_2026/9cqy_45827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cqy_45827/07_2026/9cqy_45827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqy_45827/07_2026/9cqy_45827.map" model { file = "/net/cci-nas-00/data/ceres_data/9cqy_45827/07_2026/9cqy_45827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqy_45827/07_2026/9cqy_45827.cif" } resolution = 2.39 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 4320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17365 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: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 231 Classifications: {'water': 231} Link IDs: {None: 230} Chain: "B" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 434 Classifications: {'water': 434} Link IDs: {None: 433} Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 245 Classifications: {'water': 245} Link IDs: {None: 244} Chain: "D" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 428 Classifications: {'water': 428} Link IDs: {None: 427} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 25.002 37.586 36.616 1.00 51.84 S ATOM 4552 SG CYS B 95 29.934 54.584 51.992 1.00 34.53 S ATOM 1170 SG CYS A 154 25.965 56.813 48.877 1.00 34.17 S ATOM 465 SG CYS A 62 28.059 51.066 46.547 1.00 31.59 S ATOM 652 SG CYS A 88 32.280 56.841 46.625 1.00 41.58 S ATOM 652 SG CYS A 88 32.280 56.841 46.625 1.00 41.58 S ATOM 5005 SG CYS B 153 29.731 60.053 50.559 1.00 36.33 S ATOM 4372 SG CYS B 70 36.069 57.573 51.994 1.00 29.20 S ATOM 4552 SG CYS B 95 29.934 54.584 51.992 1.00 34.53 S ATOM 10056 SG CYS C 275 102.882 47.631 36.607 1.00 52.20 S ATOM 12516 SG CYS D 95 97.913 30.637 52.029 1.00 32.62 S ATOM 9134 SG CYS C 154 101.906 28.398 48.831 1.00 34.18 S ATOM 8429 SG CYS C 62 99.857 34.177 46.525 1.00 32.40 S ATOM 8616 SG CYS C 88 95.583 28.420 46.612 1.00 42.50 S ATOM 8616 SG CYS C 88 95.583 28.420 46.612 1.00 42.50 S ATOM 12969 SG CYS D 153 98.153 25.166 50.570 1.00 35.17 S ATOM 12336 SG CYS D 70 91.826 27.690 52.000 1.00 29.92 S ATOM 12516 SG CYS D 95 97.913 30.637 52.029 1.00 32.62 S Time building chain proxies: 5.14, per 1000 atoms: 0.30 Number of scatterers: 17365 At special positions: 0 Unit cell: (130.83, 85.995, 96.285, 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 4320 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: 1.39 Conformation dependent library (CDL) restraints added in 759.6 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 58.6% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.791A 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: 3.500A 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: 3.795A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.743A 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: 4.264A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 5.838A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.725A pdb=" N LYS A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.504A pdb=" N HIS A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.838A 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: 4.733A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.457A 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: 3.608A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.562A pdb=" N GLU B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.988A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.995A 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: 3.874A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 320 through 337 removed outlier: 4.300A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.197A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.782A 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: 3.824A 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: 4.413A 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 29 Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.586A pdb=" N LYS C 44 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.741A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY C 160 " --> pdb=" O ILE C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.570A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 206 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 245 removed outlier: 4.390A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 291 removed outlier: 5.825A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.067A 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 369 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.207A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 4.037A 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: 4.711A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.621A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.885A 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: 3.603A 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 58 Processing helix chain 'D' and resid 70 through 80 removed outlier: 3.988A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.981A 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 removed outlier: 3.531A pdb=" N ILE D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.889A 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: 5.198A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.783A 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: 3.993A 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: 4.415A 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: 10.016A pdb=" N LEU A 399 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 375 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N TYR A 401 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR A 377 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU A 353 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR A 377 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.313A 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: 6.931A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.169A 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: 7.170A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A 225 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN A 271 " --> pdb=" O MET A 295 " (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: 6.301A 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: 8.558A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE B 367 " --> pdb=" O PRO B 390 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS B 392 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 9.997A pdb=" N LEU C 399 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL C 375 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N TYR C 401 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR C 377 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU C 353 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR C 377 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.292A 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: 6.915A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.161A 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: 7.335A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN C 271 " --> pdb=" O MET C 295 " (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: 6.310A 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: 8.624A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N MET D 442 " --> pdb=" O ILE D 467 " (cutoff:3.500A) 777 hydrogen bonds defined for protein. 2229 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: 4.67 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.85: 16347 1.85 - 2.48: 102 2.48 - 3.11: 20 3.11 - 3.75: 6 3.75 - 4.38: 8 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 4.377 -2.177 2.00e-02 2.50e+03 1.18e+04 bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 4.375 -2.175 2.00e-02 2.50e+03 1.18e+04 bond pdb="FE5 CLF B 602 " pdb="FE6 CLF B 602 " ideal model delta sigma weight residual 2.200 3.927 -1.727 2.00e-02 2.50e+03 7.46e+03 bond pdb="FE5 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.926 -1.726 2.00e-02 2.50e+03 7.45e+03 bond pdb=" S1 CLF B 602 " pdb="FE5 CLF B 602 " ideal model delta sigma weight residual 2.200 3.779 -1.579 2.00e-02 2.50e+03 6.23e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.89: 22236 6.89 - 13.77: 1 13.77 - 20.66: 2 20.66 - 27.55: 0 27.55 - 34.43: 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 55.57 34.43 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 55.59 34.41 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 60.70 29.30 3.00e+00 1.11e-01 9.54e+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 60.75 29.25 3.00e+00 1.11e-01 9.50e+01 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE3 CLF B 602 " ideal model delta sigma weight residual 90.00 108.13 -18.13 3.00e+00 1.11e-01 3.65e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8846 17.97 - 35.93: 921 35.93 - 53.90: 251 53.90 - 71.86: 47 71.86 - 89.83: 36 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 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+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 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA SER D 11 " pdb=" C SER D 11 " pdb=" N TYR D 12 " pdb=" CA TYR D 12 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1369 0.035 - 0.070: 652 0.070 - 0.105: 228 0.105 - 0.141: 85 0.141 - 0.176: 2 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CB ILE A 355 " pdb=" CA ILE A 355 " pdb=" CG1 ILE A 355 " pdb=" CG2 ILE A 355 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA ILE A 355 " pdb=" N ILE A 355 " pdb=" C ILE A 355 " pdb=" CB ILE A 355 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA PRO B 373 " pdb=" N PRO B 373 " pdb=" C PRO B 373 " pdb=" CB PRO B 373 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 73 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 74 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 73 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO C 74 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 453 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C ARG D 453 " 0.027 2.00e-02 2.50e+03 pdb=" O ARG D 453 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP D 454 " -0.009 2.00e-02 2.50e+03 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 6 2.04 - 2.75: 3163 2.75 - 3.47: 26417 3.47 - 4.18: 53475 4.18 - 4.90: 86846 Nonbonded interactions: 169907 Sorted by model distance: nonbonded pdb=" S5A ICS A 502 " pdb=" O HOH A 755 " model vdw 1.324 3.400 nonbonded pdb=" S5A ICS C 502 " pdb=" O HOH C 766 " model vdw 1.425 3.400 nonbonded pdb="FE7 ICS C 502 " pdb=" O HOH C 766 " model vdw 1.974 3.000 nonbonded pdb="FE7 ICS A 502 " pdb=" O HOH A 755 " model vdw 1.980 3.000 nonbonded pdb="FE FE B 601 " pdb=" O HOH D 801 " model vdw 2.010 3.000 ... (remaining 169902 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.730 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:8.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.050 2.177 16499 Z= 2.521 Angle : 0.760 34.434 22243 Z= 0.365 Chirality : 0.047 0.176 2336 Planarity : 0.005 0.047 2858 Dihedral : 16.661 89.831 6433 Min Nonbonded Distance : 1.324 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.04 % Allowed : 15.79 % Favored : 83.17 % 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: 0.46 (0.19), residues: 1992 helix: 1.20 (0.17), residues: 976 sheet: 0.08 (0.40), residues: 174 loop : -0.66 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 210 TYR 0.019 0.002 TYR D 88 PHE 0.015 0.002 PHE A 409 TRP 0.012 0.002 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.04949 / 2.47 (16483) covalent geometry : angle 0.76009 / 0.37 (22243) hydrogen bonds : bond 0.15055 / 10.25 ( 777) hydrogen bonds : angle 6.57523 / 4.80 ( 2229) Misc. bond : bond 0.16303 / 12.32 ( 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 193 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.689 Fit side-chains REVERT: A 15 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6520 (mt-10) REVERT: A 120 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: A 476 GLN cc_start: 0.7881 (tt0) cc_final: 0.7437 (tt0) REVERT: B 42 GLU cc_start: 0.8289 (tt0) cc_final: 0.7949 (tm-30) REVERT: B 259 GLU cc_start: 0.8522 (mm-30) cc_final: 0.6808 (mp0) REVERT: C 15 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6610 (mt-10) REVERT: D 42 GLU cc_start: 0.8299 (tt0) cc_final: 0.7850 (tm-30) REVERT: D 259 GLU cc_start: 0.8610 (mm-30) cc_final: 0.6838 (mp0) outliers start: 18 outliers final: 15 residues processed: 188 average time/residue: 0.7263 time to fit residues: 149.3992 Evaluate side-chains 189 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 274 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.099134 restraints weight = 15216.908| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.31 r_work: 0.2995 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.393 16499 Z= 0.286 Angle : 0.758 31.001 22243 Z= 0.361 Chirality : 0.046 0.147 2336 Planarity : 0.005 0.045 2858 Dihedral : 6.245 76.335 2553 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.80 % Allowed : 14.57 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 1992 helix: 1.20 (0.17), residues: 1006 sheet: -0.24 (0.38), residues: 190 loop : -0.65 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 210 TYR 0.017 0.002 TYR B 88 PHE 0.012 0.002 PHE C 409 TRP 0.012 0.002 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.26 (16483) covalent geometry : angle 0.75833 / 0.36 (22243) hydrogen bonds : bond 0.05745 / 3.90 ( 777) hydrogen bonds : angle 5.60865 / 4.10 ( 2229) Misc. bond : bond 0.17784 / 11.52 ( 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 210 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.574 Fit side-chains REVERT: A 15 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6523 (mt-10) REVERT: A 44 LYS cc_start: 0.5091 (OUTLIER) cc_final: 0.4730 (ptpt) REVERT: A 392 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6758 (pptt) REVERT: A 476 GLN cc_start: 0.7823 (tt0) cc_final: 0.7380 (tt0) REVERT: B 259 GLU cc_start: 0.8409 (mm-30) cc_final: 0.6639 (mp0) REVERT: C 15 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6596 (mt-10) REVERT: C 434 MET cc_start: 0.8302 (mtp) cc_final: 0.8091 (mtm) REVERT: C 480 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6431 (tp30) REVERT: D 259 GLU cc_start: 0.8477 (mm-30) cc_final: 0.6718 (mp0) outliers start: 31 outliers final: 16 residues processed: 205 average time/residue: 0.6940 time to fit residues: 156.2018 Evaluate side-chains 192 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 157 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 48 optimal weight: 0.0770 chunk 80 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 GLN C 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102924 restraints weight = 18098.898| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.41 r_work: 0.3046 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.303 16499 Z= 0.230 Angle : 0.692 30.721 22243 Z= 0.323 Chirality : 0.044 0.144 2336 Planarity : 0.004 0.043 2858 Dihedral : 5.600 63.545 2533 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.15 % Allowed : 14.34 % Favored : 83.52 % 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: 0.55 (0.19), residues: 1992 helix: 1.34 (0.17), residues: 1010 sheet: -0.36 (0.38), residues: 190 loop : -0.68 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 210 TYR 0.013 0.001 TYR D 88 PHE 0.012 0.001 PHE B 375 TRP 0.012 0.001 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (16483) covalent geometry : angle 0.69223 / 0.32 (22243) hydrogen bonds : bond 0.04485 / 3.03 ( 777) hydrogen bonds : angle 5.27558 / 3.85 ( 2229) Misc. bond : bond 0.13836 / 8.77 ( 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 238 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.758 Fit side-chains REVERT: A 15 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6604 (mt-10) REVERT: A 44 LYS cc_start: 0.5047 (OUTLIER) cc_final: 0.4697 (ptpt) REVERT: A 392 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6370 (pptt) REVERT: A 476 GLN cc_start: 0.7834 (tt0) cc_final: 0.7416 (tt0) REVERT: B 42 GLU cc_start: 0.8235 (tt0) cc_final: 0.7898 (tm-30) REVERT: B 259 GLU cc_start: 0.8425 (mm-30) cc_final: 0.6633 (mp0) REVERT: B 303 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7849 (ttpt) REVERT: C 15 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6613 (mt-10) REVERT: C 480 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6505 (tp30) REVERT: D 259 GLU cc_start: 0.8526 (mm-30) cc_final: 0.6795 (mp0) outliers start: 37 outliers final: 16 residues processed: 228 average time/residue: 0.6468 time to fit residues: 162.8828 Evaluate side-chains 202 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 132 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.125492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.099767 restraints weight = 21559.188| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.59 r_work: 0.2996 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- 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 = 0.42 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 = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.309 16499 Z= 0.244 Angle : 0.712 30.791 22243 Z= 0.332 Chirality : 0.045 0.146 2336 Planarity : 0.004 0.043 2858 Dihedral : 5.337 52.579 2528 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.26 % Allowed : 14.68 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 1992 helix: 1.37 (0.17), residues: 1010 sheet: -0.36 (0.38), residues: 190 loop : -0.68 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 210 TYR 0.016 0.001 TYR D 88 PHE 0.022 0.002 PHE B 375 TRP 0.012 0.001 TRP A 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 0.71164 / 0.33 (22243) hydrogen bonds : bond 0.04795 / 3.26 ( 777) hydrogen bonds : angle 5.23412 / 3.81 ( 2229) Misc. bond : bond 0.14477 / 9.13 ( 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 219 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.695 Fit side-chains REVERT: A 15 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6529 (mt-10) REVERT: A 44 LYS cc_start: 0.5014 (OUTLIER) cc_final: 0.4683 (ptpt) REVERT: A 120 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: A 392 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6351 (pptt) REVERT: A 476 GLN cc_start: 0.7822 (tt0) cc_final: 0.7399 (tt0) REVERT: B 42 GLU cc_start: 0.8219 (tt0) cc_final: 0.7883 (tm-30) REVERT: B 259 GLU cc_start: 0.8451 (mm-30) cc_final: 0.6608 (mp0) REVERT: C 15 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6618 (mt-10) REVERT: C 300 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7853 (t80) REVERT: C 480 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6522 (tp30) REVERT: D 259 GLU cc_start: 0.8498 (mm-30) cc_final: 0.6712 (mp0) outliers start: 39 outliers final: 20 residues processed: 209 average time/residue: 0.6834 time to fit residues: 157.1407 Evaluate side-chains 196 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 161 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 chunk 193 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100310 restraints weight = 21238.496| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.58 r_work: 0.3009 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.297 16499 Z= 0.238 Angle : 0.704 30.760 22243 Z= 0.327 Chirality : 0.045 0.148 2336 Planarity : 0.004 0.045 2858 Dihedral : 5.345 54.349 2528 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.32 % Allowed : 14.74 % Favored : 82.94 % 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: 0.60 (0.19), residues: 1992 helix: 1.37 (0.17), residues: 1022 sheet: -0.37 (0.38), residues: 190 loop : -0.65 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 210 TYR 0.016 0.001 TYR D 88 PHE 0.011 0.001 PHE A 409 TRP 0.012 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.22 (16483) covalent geometry : angle 0.70441 / 0.33 (22243) hydrogen bonds : bond 0.04656 / 3.16 ( 777) hydrogen bonds : angle 5.19076 / 3.77 ( 2229) Misc. bond : bond 0.13966 / 8.78 ( 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 222 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.542 Fit side-chains REVERT: A 15 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6535 (mt-10) REVERT: A 44 LYS cc_start: 0.5062 (OUTLIER) cc_final: 0.4736 (ptpt) REVERT: A 120 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: A 392 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6346 (pptt) REVERT: A 476 GLN cc_start: 0.7848 (tt0) cc_final: 0.7433 (tt0) REVERT: B 42 GLU cc_start: 0.8243 (tt0) cc_final: 0.7908 (tm-30) REVERT: B 54 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6778 (tm-30) REVERT: B 259 GLU cc_start: 0.8456 (mm-30) cc_final: 0.6616 (mp0) REVERT: C 15 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6614 (mt-10) REVERT: C 300 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7868 (t80) REVERT: C 391 MET cc_start: 0.6974 (mtm) cc_final: 0.6738 (mtm) REVERT: C 445 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.6747 (m-30) REVERT: C 480 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6528 (tp30) REVERT: D 259 GLU cc_start: 0.8501 (mm-30) cc_final: 0.6752 (mp0) outliers start: 40 outliers final: 20 residues processed: 213 average time/residue: 0.6946 time to fit residues: 163.1361 Evaluate side-chains 200 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 48 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.099520 restraints weight = 21161.275| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.58 r_work: 0.2989 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.302 16499 Z= 0.247 Angle : 0.713 30.793 22243 Z= 0.333 Chirality : 0.045 0.146 2336 Planarity : 0.004 0.044 2858 Dihedral : 5.383 54.888 2528 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.21 % Allowed : 15.09 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 1992 helix: 1.37 (0.17), residues: 1022 sheet: -0.36 (0.38), residues: 190 loop : -0.63 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 210 TYR 0.016 0.001 TYR B 88 PHE 0.022 0.002 PHE B 375 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 0.00486 / 0.23 (16483) covalent geometry : angle 0.71342 / 0.33 (22243) hydrogen bonds : bond 0.04846 / 3.30 ( 777) hydrogen bonds : angle 5.19633 / 3.77 ( 2229) Misc. bond : bond 0.14459 / 9.08 ( 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 217 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.980 Fit side-chains REVERT: A 15 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6513 (mt-10) REVERT: A 44 LYS cc_start: 0.5087 (OUTLIER) cc_final: 0.4742 (ptpt) REVERT: A 120 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: A 392 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6354 (pptt) REVERT: A 476 GLN cc_start: 0.7840 (tt0) cc_final: 0.7425 (tt0) REVERT: B 42 GLU cc_start: 0.8251 (tt0) cc_final: 0.7923 (tm-30) REVERT: B 54 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6799 (tm-30) REVERT: B 259 GLU cc_start: 0.8496 (mm-30) cc_final: 0.6726 (mp0) REVERT: C 15 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6639 (mt-10) REVERT: C 300 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7920 (t80) REVERT: C 480 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6539 (tp30) REVERT: D 259 GLU cc_start: 0.8524 (mm-30) cc_final: 0.6783 (mp0) outliers start: 38 outliers final: 22 residues processed: 207 average time/residue: 0.6758 time to fit residues: 154.1632 Evaluate side-chains 203 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 192 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 167 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 0.0040 chunk 113 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 518 ASN C 98 ASN D 518 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.104515 restraints weight = 17708.423| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.43 r_work: 0.3067 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.267 16499 Z= 0.213 Angle : 0.681 30.640 22243 Z= 0.313 Chirality : 0.044 0.154 2336 Planarity : 0.004 0.043 2858 Dihedral : 5.213 53.883 2528 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.26 % Allowed : 15.21 % Favored : 82.53 % 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: 0.67 (0.19), residues: 1992 helix: 1.45 (0.17), residues: 1022 sheet: -0.41 (0.37), residues: 190 loop : -0.63 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 187 TYR 0.012 0.001 TYR D 88 PHE 0.013 0.001 PHE B 375 TRP 0.013 0.001 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 (16483) covalent geometry : angle 0.68054 / 0.31 (22243) hydrogen bonds : bond 0.04065 / 2.75 ( 777) hydrogen bonds : angle 5.08457 / 3.69 ( 2229) Misc. bond : bond 0.12119 / 7.61 ( 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 236 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.505 Fit side-chains REVERT: A 44 LYS cc_start: 0.4978 (OUTLIER) cc_final: 0.4679 (ptpt) REVERT: A 362 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7018 (m90) REVERT: A 392 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6259 (pptt) REVERT: A 476 GLN cc_start: 0.7746 (tt0) cc_final: 0.7379 (tt0) REVERT: B 42 GLU cc_start: 0.8183 (tt0) cc_final: 0.7836 (tm-30) REVERT: B 54 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: B 259 GLU cc_start: 0.8389 (mm-30) cc_final: 0.6534 (mp0) REVERT: B 303 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7817 (ttpt) REVERT: C 15 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6506 (mt-10) REVERT: C 300 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7805 (t80) REVERT: C 391 MET cc_start: 0.7127 (mtm) cc_final: 0.6896 (mtm) REVERT: C 445 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.6704 (m-30) REVERT: D 259 GLU cc_start: 0.8477 (mm-30) cc_final: 0.6711 (mp0) outliers start: 39 outliers final: 19 residues processed: 226 average time/residue: 0.6382 time to fit residues: 159.1908 Evaluate side-chains 200 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.099689 restraints weight = 23531.602| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.67 r_work: 0.2990 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.290 16499 Z= 0.240 Angle : 0.708 30.729 22243 Z= 0.330 Chirality : 0.045 0.167 2336 Planarity : 0.004 0.045 2858 Dihedral : 5.322 55.867 2528 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.97 % Allowed : 15.90 % Favored : 82.12 % 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: 0.65 (0.19), residues: 1992 helix: 1.40 (0.17), residues: 1022 sheet: -0.36 (0.37), residues: 190 loop : -0.61 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 187 TYR 0.017 0.001 TYR D 88 PHE 0.023 0.002 PHE B 375 TRP 0.014 0.001 TRP A 253 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (16483) covalent geometry : angle 0.70840 / 0.33 (22243) hydrogen bonds : bond 0.04695 / 3.19 ( 777) hydrogen bonds : angle 5.13702 / 3.73 ( 2229) Misc. bond : bond 0.13786 / 8.63 ( 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 212 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.702 Fit side-chains REVERT: A 15 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6383 (mt-10) REVERT: A 44 LYS cc_start: 0.5024 (OUTLIER) cc_final: 0.4695 (ptpt) REVERT: A 120 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: A 362 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7116 (m90) REVERT: A 392 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6335 (pptt) REVERT: A 476 GLN cc_start: 0.7812 (tt0) cc_final: 0.7452 (tt0) REVERT: B 42 GLU cc_start: 0.8264 (tt0) cc_final: 0.7936 (tm-30) REVERT: B 54 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: B 259 GLU cc_start: 0.8505 (mm-30) cc_final: 0.6666 (mp0) REVERT: C 15 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6558 (mt-10) REVERT: C 300 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7895 (t80) REVERT: C 391 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6894 (mtm) REVERT: C 445 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.6781 (m-30) REVERT: C 475 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8158 (mp) REVERT: C 480 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6550 (tp30) REVERT: D 259 GLU cc_start: 0.8536 (mm-30) cc_final: 0.6787 (mp0) REVERT: D 303 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7899 (ttpt) outliers start: 34 outliers final: 20 residues processed: 204 average time/residue: 0.6877 time to fit residues: 154.4405 Evaluate side-chains 204 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 47 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.097763 restraints weight = 26410.598| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.77 r_work: 0.2960 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.306 16499 Z= 0.255 Angle : 0.725 30.800 22243 Z= 0.339 Chirality : 0.046 0.163 2336 Planarity : 0.004 0.045 2858 Dihedral : 5.412 55.766 2528 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.15 % Allowed : 15.90 % Favored : 81.95 % 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: 0.63 (0.19), residues: 1992 helix: 1.37 (0.17), residues: 1020 sheet: -0.34 (0.37), residues: 190 loop : -0.59 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 187 TYR 0.018 0.002 TYR D 88 PHE 0.015 0.002 PHE A 409 TRP 0.018 0.002 TRP A 253 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.24 (16483) covalent geometry : angle 0.72533 / 0.34 (22243) hydrogen bonds : bond 0.04996 / 3.40 ( 777) hydrogen bonds : angle 5.18888 / 3.76 ( 2229) Misc. bond : bond 0.14735 / 9.22 ( 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 209 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.560 Fit side-chains REVERT: A 44 LYS cc_start: 0.5010 (OUTLIER) cc_final: 0.4673 (ptpt) REVERT: A 120 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: A 362 HIS cc_start: 0.8044 (OUTLIER) cc_final: 0.7125 (m90) REVERT: A 392 LYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6339 (pptt) REVERT: A 476 GLN cc_start: 0.7835 (tt0) cc_final: 0.7471 (tt0) REVERT: B 42 GLU cc_start: 0.8288 (tt0) cc_final: 0.7967 (tm-30) REVERT: B 54 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: B 259 GLU cc_start: 0.8508 (mm-30) cc_final: 0.6654 (mp0) REVERT: C 15 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6559 (mt-10) REVERT: C 300 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7950 (t80) REVERT: C 391 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6921 (mtm) REVERT: C 445 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.6795 (m-30) REVERT: C 475 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8138 (mp) REVERT: C 480 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6544 (tp30) REVERT: D 259 GLU cc_start: 0.8543 (mm-30) cc_final: 0.6805 (mp0) REVERT: D 303 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7911 (ttpt) outliers start: 37 outliers final: 23 residues processed: 198 average time/residue: 0.6616 time to fit residues: 144.5532 Evaluate side-chains 203 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 94 optimal weight: 0.0060 chunk 163 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.101824 restraints weight = 22326.670| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.62 r_work: 0.3023 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 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: 0.8424 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.277 16499 Z= 0.223 Angle : 0.696 30.662 22243 Z= 0.322 Chirality : 0.044 0.157 2336 Planarity : 0.004 0.044 2858 Dihedral : 5.293 55.710 2528 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.15 % Allowed : 15.96 % Favored : 81.89 % 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: 0.65 (0.19), residues: 1992 helix: 1.41 (0.17), residues: 1022 sheet: -0.39 (0.37), residues: 190 loop : -0.61 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 187 TYR 0.014 0.001 TYR D 88 PHE 0.020 0.001 PHE B 375 TRP 0.015 0.001 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (16483) covalent geometry : angle 0.69598 / 0.32 (22243) hydrogen bonds : bond 0.04304 / 2.92 ( 777) hydrogen bonds : angle 5.09852 / 3.70 ( 2229) Misc. bond : bond 0.12821 / 8.02 ( 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 213 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.634 Fit side-chains REVERT: A 44 LYS cc_start: 0.4959 (OUTLIER) cc_final: 0.4647 (ptpt) REVERT: A 120 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: A 362 HIS cc_start: 0.8001 (OUTLIER) cc_final: 0.7185 (m90) REVERT: A 384 ASN cc_start: 0.6787 (m110) cc_final: 0.6517 (m-40) REVERT: A 392 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6351 (pptt) REVERT: A 476 GLN cc_start: 0.7821 (tt0) cc_final: 0.7465 (tt0) REVERT: B 42 GLU cc_start: 0.8251 (tt0) cc_final: 0.7917 (tm-30) REVERT: B 54 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6800 (tm-30) REVERT: B 259 GLU cc_start: 0.8472 (mm-30) cc_final: 0.6621 (mp0) REVERT: C 15 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6611 (mt-10) REVERT: C 391 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.7005 (mtm) REVERT: C 475 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8123 (mp) REVERT: C 480 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6557 (tp30) REVERT: D 259 GLU cc_start: 0.8526 (mm-30) cc_final: 0.6807 (mp0) REVERT: D 303 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7914 (ttpt) outliers start: 37 outliers final: 18 residues processed: 204 average time/residue: 0.6495 time to fit residues: 145.7774 Evaluate side-chains 196 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 194 optimal weight: 8.9990 chunk 176 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.099595 restraints weight = 23556.509| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.67 r_work: 0.2989 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.294 16499 Z= 0.240 Angle : 0.714 30.734 22243 Z= 0.332 Chirality : 0.045 0.178 2336 Planarity : 0.004 0.045 2858 Dihedral : 5.364 56.635 2528 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.74 % Allowed : 16.48 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 1992 helix: 1.40 (0.17), residues: 1022 sheet: -0.36 (0.37), residues: 190 loop : -0.61 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 187 TYR 0.016 0.001 TYR D 88 PHE 0.016 0.002 PHE A 409 TRP 0.017 0.001 TRP A 253 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (16483) covalent geometry : angle 0.71370 / 0.33 (22243) hydrogen bonds : bond 0.04704 / 3.20 ( 777) hydrogen bonds : angle 5.14001 / 3.73 ( 2229) Misc. bond : bond 0.13876 / 8.67 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6156.38 seconds wall clock time: 105 minutes 40.12 seconds (6340.12 seconds total)