Starting phenix.real_space_refine on Mon Apr 6 08:21:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqy_45827/04_2026/9cqy_45827.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqy_45827/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cqy_45827/04_2026/9cqy_45827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqy_45827/04_2026/9cqy_45827.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cqy_45827/04_2026/9cqy_45827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqy_45827/04_2026/9cqy_45827.map" } 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-2.1rc1-6017/lib/python3.9/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, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 5.73, per 1000 atoms: 0.33 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: 1.31 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.75 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: 3.50 Time building geometry restraints manager: 1.78 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 2.260 ... (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: 4.980 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.210 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:9.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 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 covalent geometry : bond 0.04949 (16483) covalent geometry : angle 0.76009 (22243) hydrogen bonds : bond 0.15055 ( 777) hydrogen bonds : angle 6.57523 ( 2229) Misc. bond : bond 0.16303 ( 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 : 0.692 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: 0.8441 time to fit residues: 172.6118 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 : 0.646 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.122934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.099195 restraints weight = 15278.057| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.31 r_work: 0.2997 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.20 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.392 16499 Z= 0.284 Angle : 0.756 31.051 22243 Z= 0.359 Chirality : 0.046 0.145 2336 Planarity : 0.005 0.043 2858 Dihedral : 6.236 75.810 2553 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -0.23 (0.38), residues: 190 loop : -0.64 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 210 TYR 0.017 0.002 TYR B 88 PHE 0.012 0.002 PHE C 409 TRP 0.012 0.001 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00557 (16483) covalent geometry : angle 0.75557 (22243) hydrogen bonds : bond 0.05768 ( 777) hydrogen bonds : angle 5.57323 ( 2229) Misc. bond : bond 0.18307 ( 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 : 0.677 Fit side-chains REVERT: A 15 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6558 (mt-10) REVERT: A 44 LYS cc_start: 0.5112 (OUTLIER) cc_final: 0.4745 (ptpt) REVERT: A 392 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6747 (pptt) REVERT: A 476 GLN cc_start: 0.7801 (tt0) cc_final: 0.7349 (tt0) REVERT: B 259 GLU cc_start: 0.8400 (mm-30) cc_final: 0.6619 (mp0) REVERT: C 15 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6596 (mt-10) REVERT: C 434 MET cc_start: 0.8295 (mtp) cc_final: 0.8083 (mtm) REVERT: C 480 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6412 (tp30) REVERT: D 259 GLU cc_start: 0.8474 (mm-30) cc_final: 0.6690 (mp0) outliers start: 31 outliers final: 16 residues processed: 205 average time/residue: 0.7842 time to fit residues: 175.9950 Evaluate side-chains 191 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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: 1.9990 chunk 96 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 167 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.098919 restraints weight = 18108.983| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.44 r_work: 0.2989 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.343 16499 Z= 0.262 Angle : 0.725 30.948 22243 Z= 0.342 Chirality : 0.046 0.146 2336 Planarity : 0.005 0.044 2858 Dihedral : 5.718 64.822 2533 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.21 % Allowed : 14.51 % Favored : 83.28 % 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: 0.50 (0.19), residues: 1992 helix: 1.28 (0.17), residues: 1008 sheet: -0.30 (0.38), residues: 190 loop : -0.68 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 210 TYR 0.016 0.002 TYR D 88 PHE 0.013 0.002 PHE B 375 TRP 0.012 0.001 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00516 (16483) covalent geometry : angle 0.72534 (22243) hydrogen bonds : bond 0.05272 ( 777) hydrogen bonds : angle 5.35390 ( 2229) Misc. bond : bond 0.16278 ( 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 221 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.670 Fit side-chains REVERT: A 15 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6620 (mt-10) REVERT: A 44 LYS cc_start: 0.5138 (OUTLIER) cc_final: 0.4779 (ptpt) REVERT: A 120 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: A 392 LYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6738 (pptt) REVERT: A 476 GLN cc_start: 0.7822 (tt0) cc_final: 0.7390 (tt0) REVERT: A 480 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6594 (mt-10) REVERT: B 259 GLU cc_start: 0.8428 (mm-30) cc_final: 0.6623 (mp0) REVERT: C 15 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6628 (mt-10) REVERT: C 391 MET cc_start: 0.7019 (mtm) cc_final: 0.6784 (mtm) REVERT: C 392 LYS cc_start: 0.6885 (pttt) cc_final: 0.6345 (pttt) REVERT: C 434 MET cc_start: 0.8298 (mtp) cc_final: 0.8082 (mtm) REVERT: C 480 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6479 (tp30) REVERT: D 259 GLU cc_start: 0.8519 (mm-30) cc_final: 0.6703 (mp0) outliers start: 38 outliers final: 18 residues processed: 212 average time/residue: 0.7754 time to fit residues: 180.0936 Evaluate side-chains 195 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 480 GLU 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 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 369 LEU Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 507 GLU 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: 0.7980 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.121378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.095601 restraints weight = 21667.890| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.58 r_work: 0.2941 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.356 16499 Z= 0.292 Angle : 0.759 30.973 22243 Z= 0.361 Chirality : 0.048 0.147 2336 Planarity : 0.005 0.047 2858 Dihedral : 5.840 58.179 2533 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.09 % Allowed : 14.92 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 1992 helix: 1.25 (0.17), residues: 1006 sheet: -0.31 (0.38), residues: 190 loop : -0.68 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 210 TYR 0.019 0.002 TYR D 88 PHE 0.021 0.002 PHE B 375 TRP 0.013 0.002 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00591 (16483) covalent geometry : angle 0.75932 (22243) hydrogen bonds : bond 0.05837 ( 777) hydrogen bonds : angle 5.38813 ( 2229) Misc. bond : bond 0.17384 ( 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 212 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.578 Fit side-chains REVERT: A 15 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6555 (mt-10) REVERT: A 44 LYS cc_start: 0.5088 (OUTLIER) cc_final: 0.4683 (ptpt) REVERT: A 120 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7427 (tm-30) REVERT: A 476 GLN cc_start: 0.7886 (tt0) cc_final: 0.7450 (tt0) REVERT: A 480 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6593 (mt-10) REVERT: B 259 GLU cc_start: 0.8475 (mm-30) cc_final: 0.6724 (mp0) REVERT: C 15 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6547 (mt-10) REVERT: C 391 MET cc_start: 0.7023 (mtm) cc_final: 0.6779 (mtm) REVERT: C 392 LYS cc_start: 0.6967 (pttt) cc_final: 0.6418 (pttt) REVERT: C 480 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6500 (tp30) REVERT: D 259 GLU cc_start: 0.8559 (mm-30) cc_final: 0.6796 (mp0) REVERT: D 303 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7851 (ttpt) outliers start: 36 outliers final: 20 residues processed: 202 average time/residue: 0.7986 time to fit residues: 175.8508 Evaluate side-chains 194 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 480 GLU Chi-restraints excluded: chain B residue 7 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 161 optimal weight: 4.9990 chunk 192 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 193 optimal weight: 0.0060 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.097536 restraints weight = 21348.791| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.58 r_work: 0.2963 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.325 16499 Z= 0.260 Angle : 0.728 30.849 22243 Z= 0.343 Chirality : 0.046 0.146 2336 Planarity : 0.004 0.045 2858 Dihedral : 5.554 54.149 2530 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.38 % Allowed : 14.39 % Favored : 83.23 % 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: 0.49 (0.19), residues: 1992 helix: 1.29 (0.17), residues: 1008 sheet: -0.36 (0.38), residues: 190 loop : -0.69 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 210 TYR 0.016 0.002 TYR D 88 PHE 0.014 0.002 PHE A 409 TRP 0.013 0.001 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00516 (16483) covalent geometry : angle 0.72815 (22243) hydrogen bonds : bond 0.05220 ( 777) hydrogen bonds : angle 5.28272 ( 2229) Misc. bond : bond 0.15560 ( 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 219 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.810 Fit side-chains REVERT: A 15 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6621 (mt-10) REVERT: A 44 LYS cc_start: 0.5020 (OUTLIER) cc_final: 0.4660 (ptpt) REVERT: A 120 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: A 392 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6710 (pptt) REVERT: A 476 GLN cc_start: 0.7881 (tt0) cc_final: 0.7455 (tt0) REVERT: B 259 GLU cc_start: 0.8468 (mm-30) cc_final: 0.6687 (mp0) REVERT: C 15 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6535 (mt-10) REVERT: C 322 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7155 (tttm) REVERT: C 392 LYS cc_start: 0.6893 (pttt) cc_final: 0.6337 (pttt) REVERT: C 445 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.6812 (m-30) REVERT: C 480 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6502 (tp30) REVERT: D 259 GLU cc_start: 0.8554 (mm-30) cc_final: 0.6792 (mp0) REVERT: D 303 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7842 (ttpt) outliers start: 41 outliers final: 22 residues processed: 208 average time/residue: 0.8070 time to fit residues: 183.6495 Evaluate side-chains 199 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 322 LYS 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 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 Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 48 optimal weight: 0.0020 chunk 15 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 5 optimal weight: 0.0370 chunk 37 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.5870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 GLN B 518 ASN C 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.102580 restraints weight = 21278.655| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.58 r_work: 0.3037 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.272 16499 Z= 0.217 Angle : 0.684 30.643 22243 Z= 0.317 Chirality : 0.044 0.145 2336 Planarity : 0.004 0.045 2858 Dihedral : 5.381 52.546 2530 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.03 % Allowed : 15.38 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 1992 helix: 1.39 (0.17), residues: 1022 sheet: -0.38 (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 0.023 0.001 PHE B 375 TRP 0.013 0.001 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00421 (16483) covalent geometry : angle 0.68414 (22243) hydrogen bonds : bond 0.04169 ( 777) hydrogen bonds : angle 5.10631 ( 2229) Misc. bond : bond 0.12347 ( 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 232 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.696 Fit side-chains REVERT: A 15 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6456 (mt-10) REVERT: A 44 LYS cc_start: 0.5029 (OUTLIER) cc_final: 0.4691 (ptpt) REVERT: A 362 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7054 (m90) REVERT: A 392 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6277 (pptt) REVERT: A 476 GLN cc_start: 0.7767 (tt0) cc_final: 0.7346 (tt0) REVERT: B 259 GLU cc_start: 0.8392 (mm-30) cc_final: 0.6534 (mp0) REVERT: B 303 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7848 (ttpt) REVERT: C 15 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6578 (mt-10) REVERT: C 322 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7105 (tttm) REVERT: C 392 LYS cc_start: 0.6953 (pttt) cc_final: 0.6385 (pttt) REVERT: C 445 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.6687 (m-30) REVERT: D 259 GLU cc_start: 0.8515 (mm-30) cc_final: 0.6747 (mp0) REVERT: D 303 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7826 (ttpt) outliers start: 35 outliers final: 21 residues processed: 224 average time/residue: 0.7594 time to fit residues: 186.8261 Evaluate side-chains 204 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 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 432 SER Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 322 LYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.099135 restraints weight = 17923.010| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.43 r_work: 0.2998 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.308 16499 Z= 0.262 Angle : 0.728 30.807 22243 Z= 0.343 Chirality : 0.047 0.167 2336 Planarity : 0.005 0.045 2858 Dihedral : 5.459 56.570 2528 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.32 % Allowed : 15.44 % Favored : 82.24 % 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: 0.61 (0.19), residues: 1992 helix: 1.36 (0.17), residues: 1022 sheet: -0.39 (0.37), residues: 190 loop : -0.60 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 461 TYR 0.018 0.002 TYR D 88 PHE 0.012 0.002 PHE A 409 TRP 0.012 0.002 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00526 (16483) covalent geometry : angle 0.72826 (22243) hydrogen bonds : bond 0.05159 ( 777) hydrogen bonds : angle 5.20222 ( 2229) Misc. bond : bond 0.14962 ( 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 219 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.695 Fit side-chains REVERT: A 15 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6529 (mt-10) REVERT: A 44 LYS cc_start: 0.5074 (OUTLIER) cc_final: 0.4718 (ptpt) REVERT: A 300 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7909 (t80) REVERT: A 392 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6414 (pptt) REVERT: A 476 GLN cc_start: 0.7834 (tt0) cc_final: 0.7417 (tt0) REVERT: B 259 GLU cc_start: 0.8477 (mm-30) cc_final: 0.6716 (mp0) REVERT: C 15 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6624 (mt-10) REVERT: C 322 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7114 (tttm) REVERT: C 391 MET cc_start: 0.6954 (mtm) cc_final: 0.6703 (mtm) REVERT: C 392 LYS cc_start: 0.6933 (pttt) cc_final: 0.6399 (pttt) REVERT: C 445 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.6801 (m-30) REVERT: C 480 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6503 (tp30) REVERT: D 259 GLU cc_start: 0.8518 (mm-30) cc_final: 0.6803 (mp0) REVERT: D 303 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7847 (ttpt) outliers start: 40 outliers final: 22 residues processed: 207 average time/residue: 0.7764 time to fit residues: 176.3970 Evaluate side-chains 203 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 300 PHE 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 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 322 LYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 73 optimal weight: 0.0370 chunk 26 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.101172 restraints weight = 23654.035| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.68 r_work: 0.3014 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.278 16499 Z= 0.222 Angle : 0.691 30.654 22243 Z= 0.320 Chirality : 0.044 0.170 2336 Planarity : 0.004 0.044 2858 Dihedral : 5.307 55.799 2528 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.15 % Allowed : 15.84 % Favored : 82.01 % 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: 1.40 (0.17), residues: 1024 sheet: -0.45 (0.37), residues: 190 loop : -0.61 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 187 TYR 0.013 0.001 TYR D 88 PHE 0.023 0.001 PHE B 375 TRP 0.013 0.001 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00431 (16483) covalent geometry : angle 0.69148 (22243) hydrogen bonds : bond 0.04301 ( 777) hydrogen bonds : angle 5.09768 ( 2229) Misc. bond : bond 0.12740 ( 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 220 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.691 Fit side-chains REVERT: A 15 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6434 (mt-10) REVERT: A 44 LYS cc_start: 0.4948 (OUTLIER) cc_final: 0.4630 (ptpt) REVERT: A 362 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7171 (m90) REVERT: A 392 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6313 (pptt) REVERT: A 476 GLN cc_start: 0.7784 (tt0) cc_final: 0.7367 (tt0) REVERT: B 259 GLU cc_start: 0.8421 (mm-30) cc_final: 0.6550 (mp0) REVERT: B 303 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7868 (ttpt) REVERT: C 15 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6527 (mt-10) REVERT: C 300 PHE cc_start: 0.8363 (m-80) cc_final: 0.7794 (t80) REVERT: C 322 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7127 (tttm) REVERT: C 392 LYS cc_start: 0.6915 (pttt) cc_final: 0.6373 (pttt) REVERT: C 480 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6484 (tp30) REVERT: D 259 GLU cc_start: 0.8519 (mm-30) cc_final: 0.6742 (mp0) REVERT: D 303 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7844 (ttpt) outliers start: 37 outliers final: 21 residues processed: 211 average time/residue: 0.7672 time to fit residues: 177.5060 Evaluate side-chains 202 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 475 LEU 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 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 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 322 LYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 47 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.123931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.097173 restraints weight = 26594.531| |-----------------------------------------------------------------------------| r_work (start): 0.3060 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: 4.11 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1217 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 30.804 22243 Z= 0.340 Chirality : 0.046 0.163 2336 Planarity : 0.004 0.046 2858 Dihedral : 5.439 56.614 2528 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.74 % Allowed : 16.13 % 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: 0.62 (0.19), residues: 1992 helix: 1.37 (0.17), residues: 1020 sheet: -0.41 (0.37), residues: 190 loop : -0.60 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 187 TYR 0.018 0.002 TYR D 88 PHE 0.013 0.002 PHE A 409 TRP 0.016 0.002 TRP A 253 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00506 (16483) covalent geometry : angle 0.72508 (22243) hydrogen bonds : bond 0.05047 ( 777) hydrogen bonds : angle 5.18169 ( 2229) Misc. bond : bond 0.14748 ( 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 208 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.709 Fit side-chains REVERT: A 15 GLU cc_start: 0.6655 (mt-10) cc_final: 0.6451 (mt-10) REVERT: A 44 LYS cc_start: 0.5009 (OUTLIER) cc_final: 0.4676 (ptpt) REVERT: A 120 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: A 392 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6365 (pptt) REVERT: A 476 GLN cc_start: 0.7867 (tt0) cc_final: 0.7450 (tt0) REVERT: B 259 GLU cc_start: 0.8514 (mm-30) cc_final: 0.6726 (mp0) REVERT: C 15 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6603 (mt-10) REVERT: C 322 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7197 (tttm) REVERT: C 391 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6852 (mtm) REVERT: C 392 LYS cc_start: 0.6951 (pttt) cc_final: 0.6366 (pttt) REVERT: C 480 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6514 (tp30) REVERT: D 259 GLU cc_start: 0.8559 (mm-30) cc_final: 0.6805 (mp0) REVERT: D 303 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7898 (ttpt) outliers start: 30 outliers final: 21 residues processed: 199 average time/residue: 0.7743 time to fit residues: 168.8580 Evaluate side-chains 205 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 322 LYS 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 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: 0.0270 chunk 163 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.101843 restraints weight = 22477.078| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.63 r_work: 0.3024 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.274 16499 Z= 0.220 Angle : 0.693 30.665 22243 Z= 0.321 Chirality : 0.044 0.166 2336 Planarity : 0.004 0.044 2858 Dihedral : 5.291 56.019 2528 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.92 % Allowed : 16.08 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 1992 helix: 1.39 (0.17), residues: 1024 sheet: -0.46 (0.37), residues: 190 loop : -0.62 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 187 TYR 0.013 0.001 TYR B 88 PHE 0.022 0.001 PHE B 375 TRP 0.014 0.001 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00427 (16483) covalent geometry : angle 0.69321 (22243) hydrogen bonds : bond 0.04260 ( 777) hydrogen bonds : angle 5.08800 ( 2229) Misc. bond : bond 0.12584 ( 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 217 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.590 Fit side-chains REVERT: A 44 LYS cc_start: 0.4926 (OUTLIER) cc_final: 0.4626 (ptpt) REVERT: A 120 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: A 362 HIS cc_start: 0.8016 (OUTLIER) cc_final: 0.7280 (m90) REVERT: A 392 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6304 (pptt) REVERT: A 476 GLN cc_start: 0.7816 (tt0) cc_final: 0.7456 (tt0) REVERT: B 259 GLU cc_start: 0.8459 (mm-30) cc_final: 0.6613 (mp0) REVERT: B 303 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7907 (ttpt) REVERT: C 15 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6566 (mt-10) REVERT: C 300 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7863 (t80) REVERT: C 391 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6876 (mtm) REVERT: C 392 LYS cc_start: 0.6972 (pttt) cc_final: 0.6393 (pttt) REVERT: C 475 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8124 (mp) REVERT: C 480 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6512 (tp30) REVERT: D 259 GLU cc_start: 0.8540 (mm-30) cc_final: 0.6812 (mp0) REVERT: D 303 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7882 (ttpt) outliers start: 33 outliers final: 20 residues processed: 207 average time/residue: 0.7791 time to fit residues: 177.0078 Evaluate side-chains 206 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 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 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 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 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 194 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 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: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN D 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.127250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.101146 restraints weight = 23661.544| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.68 r_work: 0.3012 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.273 16499 Z= 0.223 Angle : 0.696 30.660 22243 Z= 0.322 Chirality : 0.044 0.166 2336 Planarity : 0.004 0.044 2858 Dihedral : 5.268 56.349 2528 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.68 % Allowed : 16.42 % 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: 1.42 (0.17), residues: 1022 sheet: -0.44 (0.37), residues: 190 loop : -0.61 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 187 TYR 0.015 0.001 TYR D 88 PHE 0.015 0.001 PHE A 409 TRP 0.015 0.001 TRP A 253 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00436 (16483) covalent geometry : angle 0.69610 (22243) hydrogen bonds : bond 0.04354 ( 777) hydrogen bonds : angle 5.08295 ( 2229) Misc. bond : bond 0.12653 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7048.41 seconds wall clock time: 120 minutes 47.99 seconds (7247.99 seconds total)