Starting phenix.real_space_refine on Mon Apr 6 07:57:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mlz_48382/04_2026/9mlz_48382.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mlz_48382/04_2026/9mlz_48382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mlz_48382/04_2026/9mlz_48382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mlz_48382/04_2026/9mlz_48382.map" model { file = "/net/cci-nas-00/data/ceres_data/9mlz_48382/04_2026/9mlz_48382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mlz_48382/04_2026/9mlz_48382.cif" } resolution = 2.19 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= 0.012 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 4161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 17206 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: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 360 Classifications: {'water': 360} Link IDs: {None: 359} Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 224 Classifications: {'water': 224} Link IDs: {None: 223} Chain: "D" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 364 Classifications: {'water': 364} Link IDs: {None: 363} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 26.528 37.571 35.680 1.00 28.05 S ATOM 4552 SG CYS B 95 31.295 54.539 51.260 1.00 16.24 S ATOM 1170 SG CYS A 154 27.312 56.840 48.023 1.00 27.36 S ATOM 465 SG CYS A 62 29.528 51.067 45.660 1.00 20.15 S ATOM 652 SG CYS A 88 33.636 56.617 45.582 1.00 33.89 S ATOM 652 SG CYS A 88 33.636 56.617 45.582 1.00 33.89 S ATOM 5005 SG CYS B 153 30.838 59.959 49.663 1.00 24.09 S ATOM 4372 SG CYS B 70 37.399 57.570 51.174 1.00 18.91 S ATOM 4552 SG CYS B 95 31.295 54.539 51.260 1.00 16.24 S ATOM 10056 SG CYS C 275 104.315 47.620 35.649 1.00 26.03 S ATOM 12516 SG CYS D 95 99.439 30.711 51.223 1.00 15.59 S ATOM 9134 SG CYS C 154 103.537 28.378 47.985 1.00 26.35 S ATOM 8429 SG CYS C 62 101.393 34.133 45.594 1.00 17.75 S ATOM 8616 SG CYS C 88 97.185 28.656 45.590 1.00 27.43 S ATOM 8616 SG CYS C 88 97.185 28.656 45.590 1.00 27.43 S ATOM 12969 SG CYS D 153 100.009 25.292 49.662 1.00 26.27 S ATOM 12336 SG CYS D 70 93.435 27.684 51.179 1.00 16.56 S ATOM 12516 SG CYS D 95 99.439 30.711 51.223 1.00 15.59 S Time building chain proxies: 4.93, per 1000 atoms: 0.29 Number of scatterers: 17206 At special positions: 0 Unit cell: (132.3, 86.73, 95.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mo 2 41.97 Fe 32 26.01 S 139 16.00 O 4161 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: 1.21 Conformation dependent library (CDL) restraints added in 927.0 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 12 sheets defined 58.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 removed outlier: 3.656A pdb=" N GLU A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.128A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.615A 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: 3.568A 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: 3.772A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.893A 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: 4.253A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 3.609A pdb=" N MET A 279 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 317 through 343 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 344 through 347 removed outlier: 4.015A pdb=" N GLU A 347 " --> pdb=" O PRO A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 347' Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.510A pdb=" N HIS A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.986A 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: 4.581A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.637A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.545A pdb=" N LYS A 473 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 31 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 70 through 80 removed outlier: 4.035A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.025A 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: 3.946A 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: 4.292A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.247A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.867A 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: 3.597A 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: 4.426A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 30 removed outlier: 4.140A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.531A 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 removed outlier: 3.592A pdb=" N GLN C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.790A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.782A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.217A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 245 removed outlier: 4.238A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 291 removed outlier: 3.563A pdb=" N MET C 279 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.116A 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 343 removed outlier: 3.502A pdb=" N GLN C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 344 through 347 removed outlier: 3.965A pdb=" N GLU C 347 " --> pdb=" O PRO C 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 344 through 347' Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 370 Processing helix chain 'C' and resid 383 through 391 Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 434 removed outlier: 4.619A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.623A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.565A pdb=" N LYS C 473 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 31 Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 70 through 80 removed outlier: 4.034A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.999A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.896A 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: 5.348A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.887A 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: 3.585A 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: 4.381A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.627A pdb=" N LEU A 353 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 377 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE A 355 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR A 379 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.300A 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: 6.970A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.235A 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: 7.167A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 225 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.165A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.697A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.530A pdb=" N TYR C 401 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL C 351 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C 376 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.307A 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: 6.982A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.216A 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: 7.334A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.138A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.759A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) 774 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: 2.69 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.84: 16347 1.84 - 2.48: 102 2.48 - 3.11: 20 3.11 - 3.75: 10 3.75 - 4.39: 4 Bond restraints: 16483 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 4.393 -2.193 2.00e-02 2.50e+03 1.20e+04 bond pdb="FE2 CLF B 602 " pdb="FE8 CLF B 602 " ideal model delta sigma weight residual 2.200 4.388 -2.188 2.00e-02 2.50e+03 1.20e+04 bond pdb="FE5 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.941 -1.741 2.00e-02 2.50e+03 7.58e+03 bond pdb="FE5 CLF B 602 " pdb="FE6 CLF B 602 " ideal model delta sigma weight residual 2.200 3.941 -1.741 2.00e-02 2.50e+03 7.57e+03 bond pdb=" S1 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 3.732 -1.532 2.00e-02 2.50e+03 5.87e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.91: 22235 6.91 - 13.81: 2 13.81 - 20.72: 2 20.72 - 27.62: 0 27.62 - 34.53: 4 Bond angle restraints: 22243 Sorted by residual: angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.47 34.53 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 55.48 34.52 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE1 CLF B 602 " ideal model delta sigma weight residual 90.00 60.74 29.26 3.00e+00 1.11e-01 9.51e+01 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 60.76 29.24 3.00e+00 1.11e-01 9.50e+01 angle pdb=" N GLY C 356 " pdb=" CA GLY C 356 " pdb=" C GLY C 356 " ideal model delta sigma weight residual 112.50 122.03 -9.53 1.16e+00 7.43e-01 6.76e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9338 17.86 - 35.72: 608 35.72 - 53.58: 93 53.58 - 71.44: 34 71.44 - 89.30: 28 Dihedral angle restraints: 10101 sinusoidal: 4359 harmonic: 5742 Sorted by residual: dihedral pdb=" CA PHE B 367 " pdb=" C PHE B 367 " pdb=" N ALA B 368 " pdb=" CA ALA B 368 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ARG A 361 " pdb=" C ARG A 361 " pdb=" N HIS A 362 " pdb=" CA HIS A 362 " ideal model delta harmonic sigma weight residual 180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+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 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1655 0.047 - 0.093: 513 0.093 - 0.140: 157 0.140 - 0.186: 10 0.186 - 0.233: 1 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 2.88 -0.23 2.00e-01 2.50e+01 1.35e+00 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 2.60 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILE C 355 " pdb=" N ILE C 355 " pdb=" C ILE C 355 " pdb=" CB ILE C 355 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 444 " 0.018 2.00e-02 2.50e+03 2.52e-02 1.59e+01 pdb=" CG TRP A 444 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP A 444 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A 444 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 444 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 444 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 444 " 0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 444 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 444 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 444 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 446 " 0.028 2.00e-02 2.50e+03 2.05e-02 8.39e+00 pdb=" CG TYR C 446 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR C 446 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 446 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 446 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 446 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 446 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 446 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 6 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.28e+00 pdb=" C ARG A 6 " -0.043 2.00e-02 2.50e+03 pdb=" O ARG A 6 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 7 " 0.015 2.00e-02 2.50e+03 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 958 2.71 - 3.26: 18162 3.26 - 3.81: 33402 3.81 - 4.35: 44278 4.35 - 4.90: 66702 Nonbonded interactions: 163502 Sorted by model distance: nonbonded pdb=" OE1 GLU D 109 " pdb="FE FE B 601 " model vdw 2.163 2.260 nonbonded pdb=" OE2 GLU B 109 " pdb="FE FE D 601 " model vdw 2.199 2.260 nonbonded pdb=" O LEU C 353 " pdb=" OH TYR C 401 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR A 450 " pdb=" OD2 ASP A 462 " model vdw 2.209 3.040 nonbonded pdb=" O1 HCA A 501 " pdb=" O7 HCA A 501 " model vdw 2.222 3.040 ... (remaining 163497 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=0.34 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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.860 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 2.193 16499 Z= 2.484 Angle : 0.796 34.525 22243 Z= 0.405 Chirality : 0.047 0.233 2336 Planarity : 0.005 0.052 2858 Dihedral : 13.424 89.303 6433 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.29 % Allowed : 0.35 % Favored : 99.36 % 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: 0.23 (0.18), residues: 1992 helix: 1.19 (0.17), residues: 968 sheet: -0.44 (0.42), residues: 142 loop : -0.88 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 277 TYR 0.049 0.002 TYR C 446 PHE 0.026 0.002 PHE A 118 TRP 0.066 0.002 TRP A 444 HIS 0.008 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.04868 (16483) covalent geometry : angle 0.79632 (22243) hydrogen bonds : bond 0.14282 ( 774) hydrogen bonds : angle 6.81708 ( 2229) Misc. bond : bond 0.16415 ( 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 358 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 353 time to evaluate : 0.473 Fit side-chains REVERT: A 4 MET cc_start: 0.0683 (OUTLIER) cc_final: -0.0137 (mtp) REVERT: A 26 LYS cc_start: 0.7523 (tttp) cc_final: 0.7254 (ttmt) REVERT: A 53 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7918 (mm110) REVERT: A 120 GLU cc_start: 0.8130 (tp30) cc_final: 0.6750 (mp0) REVERT: A 133 LYS cc_start: 0.8143 (tptp) cc_final: 0.7870 (tptp) REVERT: A 173 GLU cc_start: 0.7543 (tt0) cc_final: 0.7331 (tt0) REVERT: A 209 LYS cc_start: 0.7646 (mmtt) cc_final: 0.7324 (mtmt) REVERT: A 322 LYS cc_start: 0.7255 (tttp) cc_final: 0.6399 (tmmt) REVERT: A 473 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7620 (mptt) REVERT: B 4 GLN cc_start: 0.7618 (mt0) cc_final: 0.7253 (mp10) REVERT: B 50 LYS cc_start: 0.7882 (tptp) cc_final: 0.7407 (mttp) REVERT: B 145 ASP cc_start: 0.8550 (m-30) cc_final: 0.8345 (m-30) REVERT: B 334 GLU cc_start: 0.8269 (tt0) cc_final: 0.8056 (tm-30) REVERT: B 417 LYS cc_start: 0.8099 (pttt) cc_final: 0.7793 (mmtm) REVERT: B 503 GLU cc_start: 0.8006 (tt0) cc_final: 0.7613 (mt-10) REVERT: C 112 MET cc_start: 0.9053 (mtp) cc_final: 0.8829 (mtp) REVERT: C 133 LYS cc_start: 0.8149 (tptp) cc_final: 0.7915 (tptp) REVERT: C 218 SER cc_start: 0.8143 (p) cc_final: 0.7784 (m) REVERT: C 284 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7469 (mtm110) REVERT: C 318 GLU cc_start: 0.7326 (pt0) cc_final: 0.6866 (mm-30) REVERT: C 322 LYS cc_start: 0.7640 (tttm) cc_final: 0.6724 (tmmt) REVERT: C 473 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7665 (mptt) REVERT: C 476 GLN cc_start: 0.7756 (tp-100) cc_final: 0.7517 (tt0) REVERT: D 4 GLN cc_start: 0.7628 (mt0) cc_final: 0.7324 (mp10) REVERT: D 145 ASP cc_start: 0.8516 (m-30) cc_final: 0.8275 (m-30) REVERT: D 299 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7632 (mp0) REVERT: D 417 LYS cc_start: 0.7871 (pttm) cc_final: 0.7634 (mmtm) outliers start: 5 outliers final: 1 residues processed: 356 average time/residue: 0.8082 time to fit residues: 311.9623 Evaluate side-chains 229 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain C residue 355 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.4980 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 199 ASN A 280 ASN A 383 HIS A 476 GLN B 106 HIS B 317 ASN C 98 ASN C 107 ASN C 199 ASN C 280 ASN C 362 HIS C 384 ASN D 106 HIS D 518 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.105208 restraints weight = 13582.104| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 0.86 r_work: 0.3102 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.436 16499 Z= 0.315 Angle : 0.816 30.758 22243 Z= 0.401 Chirality : 0.050 0.238 2336 Planarity : 0.005 0.075 2858 Dihedral : 5.436 49.346 2521 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.39 % Allowed : 6.44 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 1992 helix: 1.18 (0.16), residues: 998 sheet: -0.33 (0.37), residues: 170 loop : -0.69 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 277 TYR 0.023 0.002 TYR D 102 PHE 0.044 0.002 PHE C 118 TRP 0.040 0.002 TRP A 444 HIS 0.010 0.002 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00611 (16483) covalent geometry : angle 0.81572 (22243) hydrogen bonds : bond 0.06876 ( 774) hydrogen bonds : angle 5.77366 ( 2229) Misc. bond : bond 0.19541 ( 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 256 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 0.664 Fit side-chains REVERT: A 4 MET cc_start: 0.1484 (OUTLIER) cc_final: 0.0846 (mtp) REVERT: A 129 LYS cc_start: 0.8352 (mmtm) cc_final: 0.8152 (mmmm) REVERT: A 322 LYS cc_start: 0.7603 (tttp) cc_final: 0.7165 (ttpp) REVERT: A 326 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7362 (mt-10) REVERT: A 345 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.6947 (mtp85) REVERT: A 473 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7933 (mptt) REVERT: B 4 GLN cc_start: 0.7913 (mt0) cc_final: 0.7638 (mp10) REVERT: B 7 LYS cc_start: 0.8085 (tptm) cc_final: 0.7638 (mmmm) REVERT: B 50 LYS cc_start: 0.8120 (tptp) cc_final: 0.7783 (mttp) REVERT: B 171 LYS cc_start: 0.7750 (ptpt) cc_final: 0.7053 (pttm) REVERT: B 258 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: B 417 LYS cc_start: 0.8136 (pttt) cc_final: 0.7854 (mmtm) REVERT: C 218 SER cc_start: 0.8314 (p) cc_final: 0.8004 (m) REVERT: C 284 ARG cc_start: 0.8397 (mtt90) cc_final: 0.7719 (mtm110) REVERT: C 318 GLU cc_start: 0.7345 (pt0) cc_final: 0.7079 (mm-30) REVERT: C 322 LYS cc_start: 0.7822 (tttm) cc_final: 0.6962 (tmmt) REVERT: C 473 LYS cc_start: 0.8164 (mmtm) cc_final: 0.7936 (mptt) REVERT: D 4 GLN cc_start: 0.7829 (mt0) cc_final: 0.7545 (mp10) REVERT: D 7 LYS cc_start: 0.8100 (tptm) cc_final: 0.7702 (mmmm) REVERT: D 145 ASP cc_start: 0.8700 (m-30) cc_final: 0.8460 (m-30) REVERT: D 171 LYS cc_start: 0.7827 (ptpt) cc_final: 0.7126 (pttm) REVERT: D 299 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7471 (mp0) REVERT: D 417 LYS cc_start: 0.7936 (pttm) cc_final: 0.7651 (mmtm) outliers start: 24 outliers final: 7 residues processed: 247 average time/residue: 0.8397 time to fit residues: 224.9430 Evaluate side-chains 233 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 222 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain D residue 315 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 23 optimal weight: 0.3980 chunk 164 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 90 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 196 HIS ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS A 384 ASN A 476 GLN C 98 ASN C 196 HIS ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 ASN C 476 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.108956 restraints weight = 19553.454| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.07 r_work: 0.3145 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.322 16499 Z= 0.233 Angle : 0.702 30.756 22243 Z= 0.330 Chirality : 0.044 0.139 2336 Planarity : 0.004 0.041 2858 Dihedral : 5.151 54.525 2521 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.39 % Allowed : 7.78 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.19), residues: 1992 helix: 1.41 (0.17), residues: 1000 sheet: -0.36 (0.38), residues: 170 loop : -0.67 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 277 TYR 0.013 0.001 TYR A 229 PHE 0.022 0.001 PHE C 118 TRP 0.013 0.001 TRP C 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00438 (16483) covalent geometry : angle 0.70176 (22243) hydrogen bonds : bond 0.04828 ( 774) hydrogen bonds : angle 5.47404 ( 2229) Misc. bond : bond 0.14646 ( 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 247 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.546 Fit side-chains REVERT: A 4 MET cc_start: 0.1385 (OUTLIER) cc_final: 0.0649 (mtp) REVERT: A 322 LYS cc_start: 0.7520 (tttp) cc_final: 0.6751 (tmmt) REVERT: A 326 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: A 345 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.6798 (mtp85) REVERT: A 410 GLU cc_start: 0.8390 (tt0) cc_final: 0.8106 (tt0) REVERT: A 473 LYS cc_start: 0.8339 (mmtm) cc_final: 0.7983 (mptt) REVERT: B 4 GLN cc_start: 0.7809 (mt0) cc_final: 0.7525 (mp10) REVERT: B 50 LYS cc_start: 0.8069 (tptp) cc_final: 0.7672 (mttp) REVERT: B 171 LYS cc_start: 0.7655 (ptpt) cc_final: 0.7041 (pttm) REVERT: B 177 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7681 (t70) REVERT: B 389 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7965 (mt-10) REVERT: B 417 LYS cc_start: 0.8127 (pttt) cc_final: 0.7805 (mmtm) REVERT: C 8 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7427 (mt-10) REVERT: C 218 SER cc_start: 0.8295 (p) cc_final: 0.7960 (m) REVERT: C 318 GLU cc_start: 0.7335 (pt0) cc_final: 0.6978 (mm-30) REVERT: C 322 LYS cc_start: 0.7748 (tttm) cc_final: 0.6827 (tmmt) REVERT: C 326 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: C 473 LYS cc_start: 0.8226 (mmtm) cc_final: 0.7926 (mptt) REVERT: D 4 GLN cc_start: 0.7716 (mt0) cc_final: 0.7467 (mp10) REVERT: D 7 LYS cc_start: 0.8047 (tptm) cc_final: 0.7771 (mmmm) REVERT: D 171 LYS cc_start: 0.7808 (ptpt) cc_final: 0.7236 (pttm) REVERT: D 177 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7656 (t70) REVERT: D 299 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7448 (mp0) REVERT: D 417 LYS cc_start: 0.7908 (pttm) cc_final: 0.7590 (mmtm) outliers start: 24 outliers final: 7 residues processed: 236 average time/residue: 0.8270 time to fit residues: 211.8972 Evaluate side-chains 223 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 315 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 87 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 362 HIS A 383 HIS A 469 ASN A 476 GLN C 98 ASN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.124846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.105084 restraints weight = 24037.308| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.22 r_work: 0.3091 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.329 16499 Z= 0.254 Angle : 0.722 30.725 22243 Z= 0.343 Chirality : 0.045 0.137 2336 Planarity : 0.004 0.053 2858 Dihedral : 5.140 54.449 2521 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.22 % Allowed : 9.05 % Favored : 89.73 % 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: 1.43 (0.17), residues: 1000 sheet: -0.31 (0.38), residues: 170 loop : -0.66 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 277 TYR 0.016 0.002 TYR B 88 PHE 0.025 0.002 PHE C 118 TRP 0.011 0.001 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00488 (16483) covalent geometry : angle 0.72250 (22243) hydrogen bonds : bond 0.05382 ( 774) hydrogen bonds : angle 5.44815 ( 2229) Misc. bond : bond 0.15639 ( 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 241 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 0.619 Fit side-chains REVERT: A 4 MET cc_start: 0.1364 (ttp) cc_final: 0.0669 (mtp) REVERT: A 322 LYS cc_start: 0.7554 (tttp) cc_final: 0.6777 (tmmt) REVERT: A 326 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: A 345 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.6882 (mtp85) REVERT: A 473 LYS cc_start: 0.8368 (mmtm) cc_final: 0.7978 (mptt) REVERT: B 4 GLN cc_start: 0.7847 (mt0) cc_final: 0.7540 (mp10) REVERT: B 50 LYS cc_start: 0.8130 (tptp) cc_final: 0.7706 (mttp) REVERT: B 171 LYS cc_start: 0.7705 (ptpt) cc_final: 0.7080 (pttm) REVERT: B 389 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7959 (mt-10) REVERT: B 417 LYS cc_start: 0.8165 (pttt) cc_final: 0.7794 (mmtm) REVERT: C 8 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7460 (mt-10) REVERT: C 218 SER cc_start: 0.8282 (p) cc_final: 0.7969 (m) REVERT: C 318 GLU cc_start: 0.7347 (pt0) cc_final: 0.6948 (mm-30) REVERT: C 322 LYS cc_start: 0.7779 (tttm) cc_final: 0.6829 (tmmt) REVERT: C 326 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7415 (mt-10) REVERT: C 445 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.7726 (m-30) REVERT: C 473 LYS cc_start: 0.8242 (mmtm) cc_final: 0.7915 (mptt) REVERT: D 4 GLN cc_start: 0.7787 (mt0) cc_final: 0.7511 (mp10) REVERT: D 7 LYS cc_start: 0.8062 (tptm) cc_final: 0.7820 (mmmm) REVERT: D 171 LYS cc_start: 0.7838 (ptpt) cc_final: 0.7236 (pttm) REVERT: D 299 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7448 (mp0) REVERT: D 417 LYS cc_start: 0.7954 (pttm) cc_final: 0.7579 (mmtm) outliers start: 21 outliers final: 9 residues processed: 232 average time/residue: 0.8034 time to fit residues: 202.6879 Evaluate side-chains 225 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 326 GLU 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 467 LEU Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 134 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS A 383 HIS A 476 GLN C 53 GLN C 98 ASN C 476 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.102290 restraints weight = 20243.411| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.09 r_work: 0.3053 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.405 16499 Z= 0.297 Angle : 0.774 30.706 22243 Z= 0.376 Chirality : 0.048 0.143 2336 Planarity : 0.005 0.069 2858 Dihedral : 5.272 55.279 2518 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.74 % Allowed : 8.76 % Favored : 89.50 % 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 (0.18), residues: 1992 helix: 1.29 (0.16), residues: 1000 sheet: -0.36 (0.37), residues: 170 loop : -0.68 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 277 TYR 0.018 0.002 TYR B 88 PHE 0.034 0.002 PHE C 118 TRP 0.010 0.002 TRP C 335 HIS 0.009 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00578 (16483) covalent geometry : angle 0.77433 (22243) hydrogen bonds : bond 0.06472 ( 774) hydrogen bonds : angle 5.58127 ( 2229) Misc. bond : bond 0.18513 ( 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 245 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.504 Fit side-chains REVERT: A 4 MET cc_start: 0.1470 (ttp) cc_final: 0.0707 (mtp) REVERT: A 322 LYS cc_start: 0.7638 (tttp) cc_final: 0.6877 (tmmt) REVERT: A 326 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: A 345 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7039 (mtp85) REVERT: A 445 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: A 473 LYS cc_start: 0.8402 (mmtm) cc_final: 0.8008 (mptt) REVERT: B 4 GLN cc_start: 0.7907 (mt0) cc_final: 0.7585 (mp10) REVERT: B 50 LYS cc_start: 0.8183 (tptp) cc_final: 0.7744 (mttp) REVERT: B 171 LYS cc_start: 0.7825 (ptpt) cc_final: 0.7201 (pttm) REVERT: B 389 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7980 (mt-10) REVERT: B 417 LYS cc_start: 0.8164 (pttt) cc_final: 0.7789 (mmtm) REVERT: C 8 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7528 (mt-10) REVERT: C 218 SER cc_start: 0.8292 (p) cc_final: 0.7959 (m) REVERT: C 318 GLU cc_start: 0.7389 (pt0) cc_final: 0.7012 (mm-30) REVERT: C 322 LYS cc_start: 0.7792 (tttm) cc_final: 0.6872 (tmmt) REVERT: C 445 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: C 473 LYS cc_start: 0.8267 (mmtm) cc_final: 0.7948 (mptt) REVERT: D 4 GLN cc_start: 0.7918 (mt0) cc_final: 0.7600 (mp10) REVERT: D 7 LYS cc_start: 0.8121 (tptm) cc_final: 0.7875 (mmmm) REVERT: D 119 THR cc_start: 0.8102 (p) cc_final: 0.7793 (m) REVERT: D 171 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7271 (pttm) REVERT: D 177 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7735 (t70) REVERT: D 299 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7465 (mp0) REVERT: D 417 LYS cc_start: 0.8047 (pttm) cc_final: 0.7626 (mmtm) outliers start: 30 outliers final: 9 residues processed: 232 average time/residue: 0.7952 time to fit residues: 200.9137 Evaluate side-chains 222 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 19 VAL 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 158 ILE Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 43 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS A 383 HIS A 476 GLN C 83 HIS C 98 ASN C 476 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.101741 restraints weight = 18242.330| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.02 r_work: 0.3047 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.428 16499 Z= 0.316 Angle : 0.802 30.637 22243 Z= 0.393 Chirality : 0.049 0.148 2336 Planarity : 0.005 0.080 2858 Dihedral : 5.386 56.020 2518 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.51 % Allowed : 9.29 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 1992 helix: 1.15 (0.16), residues: 1000 sheet: -0.39 (0.37), residues: 170 loop : -0.70 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 277 TYR 0.018 0.002 TYR A 446 PHE 0.032 0.002 PHE C 118 TRP 0.011 0.002 TRP C 444 HIS 0.009 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00625 (16483) covalent geometry : angle 0.80200 (22243) hydrogen bonds : bond 0.06873 ( 774) hydrogen bonds : angle 5.64163 ( 2229) Misc. bond : bond 0.19053 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.531 Fit side-chains REVERT: A 4 MET cc_start: 0.1287 (ttp) cc_final: 0.0496 (mtp) REVERT: A 322 LYS cc_start: 0.7673 (tttp) cc_final: 0.6874 (tmmt) REVERT: A 326 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: A 345 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7051 (mtp85) REVERT: A 445 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: A 473 LYS cc_start: 0.8349 (mmtm) cc_final: 0.7969 (mptt) REVERT: B 4 GLN cc_start: 0.7967 (mt0) cc_final: 0.7641 (mp10) REVERT: B 50 LYS cc_start: 0.8225 (tptp) cc_final: 0.7774 (mttp) REVERT: B 119 THR cc_start: 0.8238 (p) cc_final: 0.7990 (m) REVERT: B 171 LYS cc_start: 0.7840 (ptpt) cc_final: 0.7229 (pttm) REVERT: B 177 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7770 (t70) REVERT: B 389 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7931 (mt-10) REVERT: B 417 LYS cc_start: 0.8195 (pttt) cc_final: 0.7807 (mmtm) REVERT: C 8 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7518 (mt-10) REVERT: C 218 SER cc_start: 0.8340 (p) cc_final: 0.8032 (m) REVERT: C 318 GLU cc_start: 0.7414 (pt0) cc_final: 0.7027 (mm-30) REVERT: C 322 LYS cc_start: 0.7814 (tttm) cc_final: 0.6906 (tmmt) REVERT: C 445 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: C 473 LYS cc_start: 0.8353 (mmtm) cc_final: 0.7999 (mptt) REVERT: D 4 GLN cc_start: 0.7969 (mt0) cc_final: 0.7641 (mp10) REVERT: D 7 LYS cc_start: 0.8105 (tptm) cc_final: 0.7877 (mmmm) REVERT: D 119 THR cc_start: 0.8121 (p) cc_final: 0.7819 (m) REVERT: D 171 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7308 (pttm) REVERT: D 299 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7496 (mp0) REVERT: D 417 LYS cc_start: 0.8074 (pttm) cc_final: 0.7659 (mmtm) outliers start: 26 outliers final: 7 residues processed: 222 average time/residue: 0.8165 time to fit residues: 197.0679 Evaluate side-chains 222 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 209 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 19 VAL 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 171 LYS Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS A 383 HIS A 476 GLN C 98 ASN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.123041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.104926 restraints weight = 17624.265| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.00 r_work: 0.3093 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.344 16499 Z= 0.264 Angle : 0.740 30.727 22243 Z= 0.355 Chirality : 0.046 0.138 2336 Planarity : 0.004 0.059 2858 Dihedral : 5.243 59.669 2518 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.22 % Allowed : 9.92 % Favored : 88.86 % 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 (0.18), residues: 1992 helix: 1.32 (0.16), residues: 1000 sheet: -0.40 (0.37), residues: 170 loop : -0.69 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 277 TYR 0.015 0.002 TYR C 229 PHE 0.023 0.002 PHE C 118 TRP 0.013 0.002 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00508 (16483) covalent geometry : angle 0.73968 (22243) hydrogen bonds : bond 0.05670 ( 774) hydrogen bonds : angle 5.48054 ( 2229) Misc. bond : bond 0.16331 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.635 Fit side-chains REVERT: A 4 MET cc_start: 0.1230 (ttp) cc_final: 0.0449 (mtp) REVERT: A 322 LYS cc_start: 0.7613 (tttp) cc_final: 0.6801 (tmmt) REVERT: A 326 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7324 (mt-10) REVERT: A 345 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.6985 (mtp85) REVERT: A 445 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.7683 (m-30) REVERT: A 473 LYS cc_start: 0.8346 (mmtm) cc_final: 0.7970 (mptt) REVERT: B 4 GLN cc_start: 0.7938 (mt0) cc_final: 0.7614 (mp10) REVERT: B 50 LYS cc_start: 0.8193 (tptp) cc_final: 0.7735 (mttp) REVERT: B 119 THR cc_start: 0.8201 (p) cc_final: 0.7964 (m) REVERT: B 171 LYS cc_start: 0.7829 (ptpt) cc_final: 0.7224 (pttm) REVERT: B 389 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8001 (mt-10) REVERT: B 417 LYS cc_start: 0.8161 (pttt) cc_final: 0.7785 (mmtm) REVERT: C 8 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7568 (mt-10) REVERT: C 218 SER cc_start: 0.8359 (p) cc_final: 0.8022 (m) REVERT: C 318 GLU cc_start: 0.7342 (pt0) cc_final: 0.6963 (mm-30) REVERT: C 322 LYS cc_start: 0.7783 (tttm) cc_final: 0.6880 (tmmt) REVERT: C 445 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: C 473 LYS cc_start: 0.8353 (mmtm) cc_final: 0.7989 (mptt) REVERT: D 4 GLN cc_start: 0.7910 (mt0) cc_final: 0.7589 (mp10) REVERT: D 7 LYS cc_start: 0.8068 (tptm) cc_final: 0.7867 (mmmm) REVERT: D 119 THR cc_start: 0.8056 (p) cc_final: 0.7765 (m) REVERT: D 171 LYS cc_start: 0.7851 (ptpt) cc_final: 0.7245 (pttm) REVERT: D 299 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7474 (mp0) REVERT: D 417 LYS cc_start: 0.8015 (pttm) cc_final: 0.7605 (mmtm) outliers start: 21 outliers final: 9 residues processed: 225 average time/residue: 0.8214 time to fit residues: 200.8952 Evaluate side-chains 223 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 86 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 21 optimal weight: 0.0470 chunk 184 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS A 383 HIS A 476 GLN C 98 ASN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.106413 restraints weight = 17726.256| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.01 r_work: 0.3111 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.314 16499 Z= 0.247 Angle : 0.721 30.693 22243 Z= 0.342 Chirality : 0.045 0.134 2336 Planarity : 0.004 0.053 2858 Dihedral : 5.090 56.465 2518 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.33 % Allowed : 10.04 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 1992 helix: 1.35 (0.16), residues: 1014 sheet: -0.43 (0.37), residues: 170 loop : -0.61 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 415 TYR 0.014 0.002 TYR A 229 PHE 0.020 0.002 PHE C 118 TRP 0.013 0.001 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00473 (16483) covalent geometry : angle 0.72061 (22243) hydrogen bonds : bond 0.05236 ( 774) hydrogen bonds : angle 5.40613 ( 2229) Misc. bond : bond 0.15031 ( 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 240 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.688 Fit side-chains REVERT: A 4 MET cc_start: 0.1346 (ttp) cc_final: 0.0591 (mtp) REVERT: A 322 LYS cc_start: 0.7540 (tttp) cc_final: 0.6756 (tmmt) REVERT: A 326 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7314 (mt-10) REVERT: A 345 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.6979 (mtp85) REVERT: A 445 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: A 473 LYS cc_start: 0.8351 (mmtm) cc_final: 0.7977 (mptt) REVERT: B 4 GLN cc_start: 0.7880 (mt0) cc_final: 0.7558 (mp10) REVERT: B 50 LYS cc_start: 0.8183 (tptp) cc_final: 0.7724 (mttp) REVERT: B 119 THR cc_start: 0.8199 (p) cc_final: 0.7973 (m) REVERT: B 171 LYS cc_start: 0.7795 (ptpt) cc_final: 0.7185 (pttm) REVERT: B 389 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7999 (mt-10) REVERT: B 417 LYS cc_start: 0.8182 (pttt) cc_final: 0.7780 (mmtm) REVERT: C 8 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7556 (mt-10) REVERT: C 218 SER cc_start: 0.8352 (p) cc_final: 0.8038 (m) REVERT: C 318 GLU cc_start: 0.7302 (pt0) cc_final: 0.6923 (mm-30) REVERT: C 322 LYS cc_start: 0.7758 (tttm) cc_final: 0.6855 (tmmt) REVERT: C 445 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.7650 (m-30) REVERT: C 473 LYS cc_start: 0.8367 (mmtm) cc_final: 0.8000 (mptt) REVERT: D 4 GLN cc_start: 0.7859 (mt0) cc_final: 0.7541 (mp10) REVERT: D 119 THR cc_start: 0.8038 (p) cc_final: 0.7749 (m) REVERT: D 171 LYS cc_start: 0.7852 (ptpt) cc_final: 0.7241 (pttm) REVERT: D 177 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7721 (t70) REVERT: D 299 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7469 (mp0) REVERT: D 417 LYS cc_start: 0.8002 (pttm) cc_final: 0.7580 (mmtm) outliers start: 23 outliers final: 10 residues processed: 229 average time/residue: 0.8098 time to fit residues: 201.8666 Evaluate side-chains 227 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 71 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS A 383 HIS A 476 GLN C 98 ASN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.123454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.105595 restraints weight = 16638.167| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 0.97 r_work: 0.3102 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.346 16499 Z= 0.263 Angle : 0.735 30.718 22243 Z= 0.353 Chirality : 0.046 0.135 2336 Planarity : 0.004 0.059 2858 Dihedral : 5.159 57.168 2518 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.28 % Allowed : 9.98 % Favored : 88.74 % 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: 0.53 (0.18), residues: 1992 helix: 1.30 (0.16), residues: 1012 sheet: -0.42 (0.37), residues: 170 loop : -0.63 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 277 TYR 0.016 0.002 TYR C 229 PHE 0.021 0.002 PHE C 118 TRP 0.012 0.002 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00507 (16483) covalent geometry : angle 0.73460 (22243) hydrogen bonds : bond 0.05656 ( 774) hydrogen bonds : angle 5.45966 ( 2229) Misc. bond : bond 0.16202 ( 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 234 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.707 Fit side-chains REVERT: A 4 MET cc_start: 0.1274 (ttp) cc_final: 0.0496 (mtp) REVERT: A 322 LYS cc_start: 0.7588 (tttp) cc_final: 0.6793 (tmmt) REVERT: A 326 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: A 345 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.6942 (mtp85) REVERT: A 445 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: A 473 LYS cc_start: 0.8346 (mmtm) cc_final: 0.7976 (mptt) REVERT: B 4 GLN cc_start: 0.7902 (mt0) cc_final: 0.7575 (mp10) REVERT: B 50 LYS cc_start: 0.8201 (tptp) cc_final: 0.7756 (mttp) REVERT: B 119 THR cc_start: 0.8191 (p) cc_final: 0.7967 (m) REVERT: B 171 LYS cc_start: 0.7732 (ptpt) cc_final: 0.7124 (pttm) REVERT: B 177 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7752 (t70) REVERT: B 389 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7978 (mt-10) REVERT: B 417 LYS cc_start: 0.8181 (pttt) cc_final: 0.7801 (mmtm) REVERT: C 8 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7549 (mt-10) REVERT: C 26 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7461 (mmtt) REVERT: C 218 SER cc_start: 0.8347 (p) cc_final: 0.8032 (m) REVERT: C 318 GLU cc_start: 0.7315 (pt0) cc_final: 0.6941 (mm-30) REVERT: C 322 LYS cc_start: 0.7759 (tttm) cc_final: 0.6886 (tmmt) REVERT: C 445 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: C 473 LYS cc_start: 0.8346 (mmtm) cc_final: 0.8000 (mptt) REVERT: D 4 GLN cc_start: 0.7856 (mt0) cc_final: 0.7519 (mp10) REVERT: D 119 THR cc_start: 0.8044 (p) cc_final: 0.7762 (m) REVERT: D 171 LYS cc_start: 0.7853 (ptpt) cc_final: 0.7245 (pttm) REVERT: D 177 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7721 (t70) REVERT: D 299 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7466 (mp0) REVERT: D 417 LYS cc_start: 0.8011 (pttm) cc_final: 0.7605 (mmtm) outliers start: 22 outliers final: 10 residues processed: 224 average time/residue: 0.8102 time to fit residues: 197.0881 Evaluate side-chains 226 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 41 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS A 383 HIS A 476 GLN C 98 ASN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.107813 restraints weight = 16449.089| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 0.96 r_work: 0.3132 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.305 16499 Z= 0.240 Angle : 0.706 30.706 22243 Z= 0.335 Chirality : 0.045 0.133 2336 Planarity : 0.004 0.050 2858 Dihedral : 5.016 53.709 2518 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.16 % Allowed : 10.21 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 1992 helix: 1.38 (0.17), residues: 1014 sheet: -0.43 (0.37), residues: 170 loop : -0.59 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 415 TYR 0.014 0.001 TYR C 229 PHE 0.019 0.001 PHE C 118 TRP 0.014 0.001 TRP C 335 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00459 (16483) covalent geometry : angle 0.70629 (22243) hydrogen bonds : bond 0.05031 ( 774) hydrogen bonds : angle 5.37828 ( 2229) Misc. bond : bond 0.14485 ( 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 232 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.642 Fit side-chains REVERT: A 4 MET cc_start: 0.1266 (ttp) cc_final: 0.0597 (mtp) REVERT: A 26 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7450 (mmtt) REVERT: A 322 LYS cc_start: 0.7503 (tttp) cc_final: 0.6753 (tmmt) REVERT: A 326 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7314 (mt-10) REVERT: A 345 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.6893 (mtp85) REVERT: A 445 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: A 473 LYS cc_start: 0.8339 (mmtm) cc_final: 0.7970 (mptt) REVERT: B 4 GLN cc_start: 0.7835 (mt0) cc_final: 0.7526 (mp10) REVERT: B 50 LYS cc_start: 0.8170 (tptp) cc_final: 0.7721 (mttp) REVERT: B 119 THR cc_start: 0.8167 (p) cc_final: 0.7954 (m) REVERT: B 171 LYS cc_start: 0.7732 (ptpt) cc_final: 0.7117 (pttm) REVERT: B 177 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7712 (t70) REVERT: B 389 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7986 (mt-10) REVERT: B 417 LYS cc_start: 0.8161 (pttt) cc_final: 0.7766 (mmtm) REVERT: C 8 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7550 (mt-10) REVERT: C 26 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7444 (mmtt) REVERT: C 218 SER cc_start: 0.8353 (p) cc_final: 0.8054 (m) REVERT: C 318 GLU cc_start: 0.7253 (pt0) cc_final: 0.6919 (mm-30) REVERT: C 322 LYS cc_start: 0.7737 (tttm) cc_final: 0.6869 (tmmt) REVERT: C 445 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: C 473 LYS cc_start: 0.8350 (mmtm) cc_final: 0.8003 (mptt) REVERT: D 4 GLN cc_start: 0.7819 (mt0) cc_final: 0.7505 (mp10) REVERT: D 119 THR cc_start: 0.8018 (p) cc_final: 0.7754 (m) REVERT: D 171 LYS cc_start: 0.7836 (ptpt) cc_final: 0.7231 (pttm) REVERT: D 177 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7710 (t70) REVERT: D 299 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7474 (mp0) REVERT: D 417 LYS cc_start: 0.7994 (pttm) cc_final: 0.7582 (mmtm) outliers start: 20 outliers final: 10 residues processed: 223 average time/residue: 0.7847 time to fit residues: 190.7329 Evaluate side-chains 223 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 145 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS A 383 HIS A 476 GLN C 98 ASN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.124235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.105548 restraints weight = 19791.103| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.07 r_work: 0.3100 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2289 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= 0.253 Angle : 0.722 30.693 22243 Z= 0.345 Chirality : 0.045 0.134 2336 Planarity : 0.004 0.055 2858 Dihedral : 5.066 54.354 2518 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.22 % Allowed : 10.21 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.18), residues: 1992 helix: 1.34 (0.16), residues: 1016 sheet: -0.42 (0.37), residues: 170 loop : -0.58 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 415 TYR 0.015 0.002 TYR A 229 PHE 0.020 0.002 PHE C 118 TRP 0.013 0.001 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00487 (16483) covalent geometry : angle 0.72190 (22243) hydrogen bonds : bond 0.05389 ( 774) hydrogen bonds : angle 5.40871 ( 2229) Misc. bond : bond 0.15404 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7257.46 seconds wall clock time: 124 minutes 8.56 seconds (7448.56 seconds total)