Starting phenix.real_space_refine on Mon Apr 6 04:14:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cjc_45627/04_2026/9cjc_45627.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cjc_45627/04_2026/9cjc_45627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cjc_45627/04_2026/9cjc_45627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cjc_45627/04_2026/9cjc_45627.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cjc_45627/04_2026/9cjc_45627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cjc_45627/04_2026/9cjc_45627.map" } resolution = 2.04 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= 0.069 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 134 5.16 5 C 9686 2.51 5 N 2571 2.21 5 O 3524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s 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: 15949 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} 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: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3026 Classifications: {'peptide': 383} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 364} Chain breaks: 3 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: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'ICS': 1} Classifications: {'undetermined': 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: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 264 Classifications: {'water': 264} Link IDs: {None: 263} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "D" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 250 Classifications: {'water': 250} Link IDs: {None: 249} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 50.131 58.526 26.292 1.00 13.57 S ATOM 1170 SG CYS A 154 31.001 46.800 25.387 1.00 6.37 S ATOM 4549 SG CYS B 95 32.655 43.677 29.438 1.00 17.94 S ATOM 465 SG CYS A 62 36.401 49.092 27.932 1.00 4.22 S ATOM 652 SG CYS A 88 30.550 49.187 31.443 1.00 13.23 S ATOM 652 SG CYS A 88 30.550 49.187 31.443 1.00 13.23 S ATOM 5002 SG CYS B 153 27.563 45.490 28.651 1.00 16.74 S ATOM 4369 SG CYS B 70 29.270 43.922 35.429 1.00 10.71 S ATOM 4549 SG CYS B 95 32.655 43.677 29.438 1.00 17.94 S ATOM 9666 SG CYS C 275 33.824 57.864 101.120 1.00 41.89 S ATOM 8747 SG CYS C 154 52.709 45.589 102.490 1.00 10.67 S ATOM 11749 SG CYS D 95 50.900 42.708 98.379 1.00 20.65 S ATOM 8042 SG CYS C 62 47.464 48.212 99.978 1.00 5.08 S ATOM 8229 SG CYS C 88 53.131 48.101 96.449 1.00 5.68 S ATOM 8229 SG CYS C 88 53.131 48.101 96.449 1.00 5.68 S ATOM 12202 SG CYS D 153 56.084 44.196 99.149 1.00 17.66 S ATOM 11569 SG CYS D 70 54.195 42.802 92.383 1.00 19.95 S ATOM 11749 SG CYS D 95 50.900 42.708 98.379 1.00 20.65 S Time building chain proxies: 3.75, per 1000 atoms: 0.24 Number of scatterers: 15949 At special positions: 0 Unit cell: (83.85, 94.9, 125.45, 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 134 16.00 O 3524 8.00 N 2571 7.00 C 9686 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: 1.60 Conformation dependent library (CDL) restraints added in 672.0 milliseconds 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3488 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 12 sheets defined 58.3% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.970A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.600A pdb=" N GLY A 157 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.155A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) 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: 4.009A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 5.779A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 314 removed outlier: 4.230A pdb=" N LYS A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 removed outlier: 3.625A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.589A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.516A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 31 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 81 removed outlier: 3.996A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.168A 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 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.924A 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: 4.017A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.146A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.990A 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: 3.873A 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: 3.978A 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 62 through 68 Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.542A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 206 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.891A 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 280 through 291 Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'C' and resid 317 through 347 Proline residue: C 333 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 413 through 417 removed outlier: 3.508A pdb=" N LYS C 417 " --> pdb=" O VAL C 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 417' Processing helix chain 'C' and resid 428 through 434 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.574A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'D' and resid 4 through 8 removed outlier: 4.224A pdb=" N ILE D 8 " --> pdb=" O VAL D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 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 81 removed outlier: 4.013A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.006A 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 158 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.841A 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 320 through 337 removed outlier: 4.001A pdb=" N TRP D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR D 325 " --> pdb=" O GLY D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.296A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 6.030A 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: 3.650A 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: 4.301A 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: 6.285A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.305A 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: 4.155A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 6.482A pdb=" N VAL A 223 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 251 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.386A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.471A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 178 through 181 removed outlier: 4.218A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 248 through 254 removed outlier: 6.489A pdb=" N VAL C 223 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 251 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 373 through 375 removed outlier: 6.040A pdb=" N VAL C 351 " --> pdb=" O VAL C 375 " (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: 6.344A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.565A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) 755 hydrogen bonds defined for protein. 2154 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: 2.34 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.56: 15378 1.56 - 1.91: 171 1.91 - 2.25: 36 2.25 - 2.60: 82 2.60 - 2.94: 18 Bond restraints: 15685 Sorted by residual: bond pdb="FE2 CLF D 601 " pdb="FE8 CLF D 601 " ideal model delta sigma weight residual 2.200 2.944 -0.744 2.00e-02 2.50e+03 1.38e+03 bond pdb="FE2 CLF B 601 " pdb="FE8 CLF B 601 " ideal model delta sigma weight residual 2.200 2.938 -0.738 2.00e-02 2.50e+03 1.36e+03 bond pdb="FE4 CLF B 601 " pdb="FE5 CLF B 601 " ideal model delta sigma weight residual 2.200 2.880 -0.680 2.00e-02 2.50e+03 1.15e+03 bond pdb="FE4 CLF D 601 " pdb="FE5 CLF D 601 " ideal model delta sigma weight residual 2.200 2.878 -0.678 2.00e-02 2.50e+03 1.15e+03 bond pdb="FE6 CLF D 601 " pdb="FE7 CLF D 601 " ideal model delta sigma weight residual 2.200 2.861 -0.661 2.00e-02 2.50e+03 1.09e+03 ... (remaining 15680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.90: 21152 6.90 - 13.80: 2 13.80 - 20.70: 3 20.70 - 27.60: 0 27.60 - 34.50: 4 Bond angle restraints: 21161 Sorted by residual: angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE4 CLF B 601 " ideal model delta sigma weight residual 90.00 55.50 34.50 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF D 601 " pdb="FE2 CLF D 601 " pdb="FE4 CLF D 601 " ideal model delta sigma weight residual 90.00 55.66 34.34 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S1 CLF D 601 " pdb="FE2 CLF D 601 " pdb="FE1 CLF D 601 " ideal model delta sigma weight residual 90.00 56.82 33.18 3.00e+00 1.11e-01 1.22e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE1 CLF B 601 " ideal model delta sigma weight residual 90.00 56.90 33.10 3.00e+00 1.11e-01 1.22e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE3 CLF B 601 " ideal model delta sigma weight residual 90.00 106.98 -16.98 3.00e+00 1.11e-01 3.20e+01 ... (remaining 21156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 8478 17.79 - 35.58: 813 35.58 - 53.38: 213 53.38 - 71.17: 64 71.17 - 88.96: 26 Dihedral angle restraints: 9594 sinusoidal: 4139 harmonic: 5455 Sorted by residual: dihedral pdb=" CA PHE D 367 " pdb=" C PHE D 367 " pdb=" N ALA D 368 " pdb=" CA ALA D 368 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ILE C 364 " pdb=" C ILE C 364 " pdb=" N GLY C 365 " pdb=" CA GLY C 365 " ideal model delta harmonic sigma weight residual 180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP C 445 " pdb=" C ASP C 445 " pdb=" N TYR C 446 " pdb=" CA TYR C 446 " ideal model delta harmonic sigma weight residual -180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 9591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1122 0.030 - 0.060: 685 0.060 - 0.090: 270 0.090 - 0.121: 128 0.121 - 0.151: 18 Chirality restraints: 2223 Sorted by residual: chirality pdb=" CA ILE D 318 " pdb=" N ILE D 318 " pdb=" C ILE D 318 " pdb=" CB ILE D 318 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA ILE B 318 " pdb=" N ILE B 318 " pdb=" C ILE B 318 " pdb=" CB ILE B 318 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE A 226 " pdb=" N ILE A 226 " pdb=" C ILE A 226 " pdb=" CB ILE A 226 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 2220 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 453 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C ARG B 453 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG B 453 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP B 454 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 73 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO C 74 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 453 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ARG D 453 " 0.025 2.00e-02 2.50e+03 pdb=" O ARG D 453 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP D 454 " -0.009 2.00e-02 2.50e+03 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 458 2.65 - 3.21: 15566 3.21 - 3.78: 31096 3.78 - 4.34: 43021 4.34 - 4.90: 64974 Nonbonded interactions: 155115 Sorted by model distance: nonbonded pdb=" OD2 ASP B 357 " pdb="FE FE B 602 " model vdw 2.091 2.260 nonbonded pdb=" OE2 GLU B 109 " pdb="FE FE D 602 " model vdw 2.129 2.260 nonbonded pdb=" O ARG B 108 " pdb="FE FE D 602 " model vdw 2.147 2.260 nonbonded pdb=" O ARG D 108 " pdb="FE FE B 602 " model vdw 2.173 2.260 nonbonded pdb=" OD2 ASP C 117 " pdb=" O HOH C 701 " model vdw 2.177 3.040 ... (remaining 155110 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 '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=1.00 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: 17.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.640 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 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 : 0.024 0.744 15701 Z= 1.206 Angle : 0.793 34.500 21161 Z= 0.375 Chirality : 0.046 0.151 2223 Planarity : 0.005 0.058 2712 Dihedral : 16.087 88.961 6106 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.85 % Allowed : 11.78 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.19), residues: 1890 helix: 1.30 (0.17), residues: 935 sheet: -0.86 (0.37), residues: 164 loop : -0.12 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 96 TYR 0.022 0.003 TYR B 142 PHE 0.019 0.002 PHE A 431 TRP 0.020 0.002 TRP C 444 HIS 0.008 0.002 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.02411 (15685) covalent geometry : angle 0.79320 (21161) hydrogen bonds : bond 0.12871 ( 755) hydrogen bonds : angle 6.70267 ( 2154) Misc. bond : bond 0.03936 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.431 Fit side-chains REVERT: A 391 MET cc_start: 0.7694 (mmm) cc_final: 0.7493 (mmm) REVERT: D 503 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7682 (mp0) outliers start: 14 outliers final: 9 residues processed: 195 average time/residue: 0.7962 time to fit residues: 168.3632 Evaluate side-chains 190 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 503 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 53 GLN A 98 ASN B 518 ASN C 298 ASN C 451 HIS C 476 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108422 restraints weight = 10093.254| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 0.69 r_work: 0.3119 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work: 0.2835 rms_B_bonded: 4.54 restraints_weight: 0.1250 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.0504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.258 15701 Z= 0.203 Angle : 0.749 29.192 21161 Z= 0.361 Chirality : 0.046 0.151 2223 Planarity : 0.005 0.066 2712 Dihedral : 5.958 59.282 2408 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.83 % Allowed : 10.87 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.19), residues: 1890 helix: 1.30 (0.17), residues: 958 sheet: -0.92 (0.35), residues: 169 loop : -0.15 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 96 TYR 0.021 0.002 TYR A 379 PHE 0.017 0.002 PHE A 431 TRP 0.015 0.002 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00393 (15685) covalent geometry : angle 0.74871 (21161) hydrogen bonds : bond 0.05671 ( 755) hydrogen bonds : angle 5.90273 ( 2154) Misc. bond : bond 0.12163 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 168 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8182 (mtpt) REVERT: A 433 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.6604 (mptp) REVERT: B 120 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7477 (mt-10) REVERT: C 53 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7015 (tt0) REVERT: C 318 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7168 (mm-30) REVERT: C 349 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7915 (mttt) REVERT: D 146 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8727 (ttp) REVERT: D 211 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8103 (mmtm) outliers start: 30 outliers final: 15 residues processed: 201 average time/residue: 0.7854 time to fit residues: 171.2285 Evaluate side-chains 198 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 211 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 122 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 53 GLN A 98 ASN C 451 HIS C 476 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.111069 restraints weight = 10265.790| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 0.69 r_work: 0.3157 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work: 0.2874 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.202 15701 Z= 0.155 Angle : 0.696 29.183 21161 Z= 0.328 Chirality : 0.044 0.146 2223 Planarity : 0.004 0.053 2712 Dihedral : 5.493 59.373 2402 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.89 % Allowed : 10.99 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1890 helix: 1.45 (0.17), residues: 960 sheet: -0.90 (0.36), residues: 169 loop : -0.10 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.017 0.002 TYR C 229 PHE 0.013 0.002 PHE A 431 TRP 0.015 0.002 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00294 (15685) covalent geometry : angle 0.69624 (21161) hydrogen bonds : bond 0.04789 ( 755) hydrogen bonds : angle 5.67567 ( 2154) Misc. bond : bond 0.09597 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 401 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.6590 (p90) REVERT: A 433 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.6374 (mptp) REVERT: B 120 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7325 (mt-10) REVERT: B 121 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7460 (p0) REVERT: B 417 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7834 (mmpt) REVERT: C 53 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7010 (tt0) REVERT: C 318 GLU cc_start: 0.7667 (mm-30) cc_final: 0.6854 (mp0) REVERT: D 121 ASP cc_start: 0.7596 (m-30) cc_final: 0.7091 (t70) REVERT: D 146 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8743 (ttp) REVERT: D 503 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8016 (mp0) outliers start: 31 outliers final: 12 residues processed: 203 average time/residue: 0.8059 time to fit residues: 177.4087 Evaluate side-chains 196 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 503 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 75 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 53 GLN A 98 ASN A 321 GLN C 451 HIS C 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.111058 restraints weight = 10217.577| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 0.69 r_work: 0.3156 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work: 0.2874 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.200 15701 Z= 0.154 Angle : 0.697 29.222 21161 Z= 0.328 Chirality : 0.044 0.158 2223 Planarity : 0.004 0.053 2712 Dihedral : 5.428 59.669 2401 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.71 % Allowed : 11.36 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % 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: 0.91 (0.19), residues: 1890 helix: 1.49 (0.17), residues: 960 sheet: -0.86 (0.36), residues: 169 loop : -0.09 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.017 0.002 TYR C 229 PHE 0.014 0.002 PHE A 431 TRP 0.014 0.002 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00295 (15685) covalent geometry : angle 0.69718 (21161) hydrogen bonds : bond 0.04776 ( 755) hydrogen bonds : angle 5.62428 ( 2154) Misc. bond : bond 0.09314 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 168 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8177 (mtpt) REVERT: A 401 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.6792 (p90) REVERT: A 433 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.6369 (mptp) REVERT: B 120 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7404 (mt-10) REVERT: B 121 ASP cc_start: 0.7794 (m-30) cc_final: 0.7442 (p0) REVERT: B 417 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7853 (mmpt) REVERT: C 53 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: C 318 GLU cc_start: 0.7686 (mm-30) cc_final: 0.6858 (mp0) REVERT: C 349 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7839 (mttt) REVERT: D 121 ASP cc_start: 0.7570 (m-30) cc_final: 0.7071 (t70) REVERT: D 146 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8714 (ttp) REVERT: D 503 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8007 (mp0) outliers start: 28 outliers final: 14 residues processed: 200 average time/residue: 0.7895 time to fit residues: 171.1945 Evaluate side-chains 198 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 503 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 181 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 156 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 53 GLN A 98 ASN A 321 GLN C 451 HIS C 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106939 restraints weight = 10047.464| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 0.68 r_work: 0.3101 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 1.69 restraints_weight: 0.2500 r_work: 0.2814 rms_B_bonded: 4.52 restraints_weight: 0.1250 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.0574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.266 15701 Z= 0.250 Angle : 0.789 29.594 21161 Z= 0.384 Chirality : 0.049 0.165 2223 Planarity : 0.005 0.080 2712 Dihedral : 5.770 58.957 2401 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.83 % Allowed : 11.23 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.19), residues: 1890 helix: 1.25 (0.16), residues: 961 sheet: -1.04 (0.35), residues: 178 loop : -0.17 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 96 TYR 0.023 0.003 TYR C 229 PHE 0.020 0.003 PHE A 431 TRP 0.016 0.003 TRP B 296 HIS 0.010 0.002 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00505 (15685) covalent geometry : angle 0.78916 (21161) hydrogen bonds : bond 0.06177 ( 755) hydrogen bonds : angle 5.86551 ( 2154) Misc. bond : bond 0.12047 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 168 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8281 (mppt) REVERT: A 401 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.6716 (p90) REVERT: A 433 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.6529 (mptp) REVERT: B 120 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7443 (mt-10) REVERT: B 121 ASP cc_start: 0.7796 (m-30) cc_final: 0.7419 (p0) REVERT: C 318 GLU cc_start: 0.7759 (mm-30) cc_final: 0.6973 (mp0) REVERT: D 503 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7923 (mp0) outliers start: 30 outliers final: 13 residues processed: 204 average time/residue: 0.8087 time to fit residues: 178.6583 Evaluate side-chains 195 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 503 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 73 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 34 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 53 GLN A 98 ASN C 451 HIS C 476 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.129750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.111131 restraints weight = 10082.718| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 0.68 r_work: 0.3158 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work: 0.2875 rms_B_bonded: 4.58 restraints_weight: 0.1250 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.202 15701 Z= 0.153 Angle : 0.703 29.190 21161 Z= 0.331 Chirality : 0.044 0.153 2223 Planarity : 0.004 0.056 2712 Dihedral : 5.393 59.680 2399 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.71 % Allowed : 11.42 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 1890 helix: 1.46 (0.17), residues: 960 sheet: -0.93 (0.36), residues: 169 loop : -0.13 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 359 TYR 0.017 0.002 TYR C 229 PHE 0.015 0.001 PHE A 431 TRP 0.016 0.002 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00291 (15685) covalent geometry : angle 0.70267 (21161) hydrogen bonds : bond 0.04760 ( 755) hydrogen bonds : angle 5.64391 ( 2154) Misc. bond : bond 0.09528 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 168 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8148 (mtpt) REVERT: A 401 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.6647 (p90) REVERT: A 433 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.6358 (mptp) REVERT: B 120 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7400 (mt-10) REVERT: B 121 ASP cc_start: 0.7803 (m-30) cc_final: 0.7447 (p0) REVERT: B 417 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7848 (mmpt) REVERT: C 53 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.6984 (tt0) REVERT: C 318 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6826 (mp0) REVERT: D 121 ASP cc_start: 0.7560 (m-30) cc_final: 0.7065 (t70) REVERT: D 503 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8013 (mp0) outliers start: 28 outliers final: 17 residues processed: 199 average time/residue: 0.7938 time to fit residues: 171.6183 Evaluate side-chains 198 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 503 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 161 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 53 GLN A 98 ASN A 321 GLN C 451 HIS C 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.108614 restraints weight = 10032.866| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 0.69 r_work: 0.3121 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work: 0.2836 rms_B_bonded: 4.57 restraints_weight: 0.1250 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.236 15701 Z= 0.201 Angle : 0.746 29.434 21161 Z= 0.358 Chirality : 0.046 0.157 2223 Planarity : 0.005 0.069 2712 Dihedral : 5.541 59.169 2399 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.89 % Allowed : 11.23 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 1890 helix: 1.35 (0.17), residues: 962 sheet: -1.04 (0.35), residues: 178 loop : -0.15 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.021 0.002 TYR C 229 PHE 0.019 0.002 PHE A 431 TRP 0.015 0.002 TRP B 296 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00398 (15685) covalent geometry : angle 0.74634 (21161) hydrogen bonds : bond 0.05524 ( 755) hydrogen bonds : angle 5.73562 ( 2154) Misc. bond : bond 0.10780 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 168 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8280 (mppt) REVERT: A 401 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.6694 (p90) REVERT: A 433 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.6359 (mptp) REVERT: B 120 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7442 (mt-10) REVERT: B 121 ASP cc_start: 0.7784 (m-30) cc_final: 0.7424 (p0) REVERT: B 417 LYS cc_start: 0.8225 (mmtm) cc_final: 0.7847 (mmpt) REVERT: C 53 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7004 (tt0) REVERT: C 318 GLU cc_start: 0.7720 (mm-30) cc_final: 0.6906 (mp0) REVERT: D 503 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7988 (mp0) outliers start: 31 outliers final: 17 residues processed: 205 average time/residue: 0.8128 time to fit residues: 180.7957 Evaluate side-chains 201 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 503 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 96 optimal weight: 5.9990 chunk 136 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 53 GLN A 98 ASN A 321 GLN C 451 HIS C 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.109912 restraints weight = 10099.439| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 0.69 r_work: 0.3140 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work: 0.2856 rms_B_bonded: 4.59 restraints_weight: 0.1250 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 15701 Z= 0.173 Angle : 0.723 29.268 21161 Z= 0.343 Chirality : 0.045 0.154 2223 Planarity : 0.004 0.062 2712 Dihedral : 5.462 59.397 2399 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.71 % Allowed : 11.54 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % 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: 0.77 (0.19), residues: 1890 helix: 1.39 (0.17), residues: 962 sheet: -0.97 (0.36), residues: 169 loop : -0.16 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.020 0.002 TYR C 229 PHE 0.017 0.002 PHE A 431 TRP 0.015 0.002 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00336 (15685) covalent geometry : angle 0.72262 (21161) hydrogen bonds : bond 0.05100 ( 755) hydrogen bonds : angle 5.67770 ( 2154) Misc. bond : bond 0.09979 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 168 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8164 (mtpt) REVERT: A 401 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.6687 (p90) REVERT: A 433 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.6363 (mptp) REVERT: B 120 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7442 (mt-10) REVERT: B 121 ASP cc_start: 0.7802 (m-30) cc_final: 0.7441 (p0) REVERT: B 417 LYS cc_start: 0.8222 (mmtm) cc_final: 0.7857 (mmpt) REVERT: C 53 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7002 (tt0) REVERT: C 318 GLU cc_start: 0.7683 (mm-30) cc_final: 0.6870 (mp0) REVERT: D 121 ASP cc_start: 0.7526 (m-30) cc_final: 0.7082 (t70) REVERT: D 503 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7996 (mp0) outliers start: 28 outliers final: 17 residues processed: 201 average time/residue: 0.7830 time to fit residues: 170.8108 Evaluate side-chains 201 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 503 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 184 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 53 GLN A 98 ASN A 321 GLN C 451 HIS C 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111781 restraints weight = 10179.807| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 0.69 r_work: 0.3166 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 1.72 restraints_weight: 0.2500 r_work: 0.2884 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 15701 Z= 0.148 Angle : 0.698 29.162 21161 Z= 0.327 Chirality : 0.044 0.163 2223 Planarity : 0.004 0.054 2712 Dihedral : 5.320 59.807 2399 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.53 % Allowed : 11.78 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.19), residues: 1890 helix: 1.49 (0.17), residues: 960 sheet: -0.92 (0.36), residues: 169 loop : -0.11 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 359 TYR 0.019 0.002 TYR C 276 PHE 0.015 0.001 PHE A 431 TRP 0.016 0.002 TRP A 253 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00286 (15685) covalent geometry : angle 0.69767 (21161) hydrogen bonds : bond 0.04599 ( 755) hydrogen bonds : angle 5.58569 ( 2154) Misc. bond : bond 0.08923 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8164 (mtpt) REVERT: A 401 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.6789 (p90) REVERT: A 433 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.6366 (mptp) REVERT: B 120 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7388 (mt-10) REVERT: B 121 ASP cc_start: 0.7807 (m-30) cc_final: 0.7460 (p0) REVERT: B 417 LYS cc_start: 0.8215 (mmtm) cc_final: 0.7865 (mmpt) REVERT: C 53 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: C 318 GLU cc_start: 0.7642 (mm-30) cc_final: 0.6801 (mp0) REVERT: D 121 ASP cc_start: 0.7482 (m-30) cc_final: 0.6969 (t70) outliers start: 25 outliers final: 17 residues processed: 199 average time/residue: 0.8084 time to fit residues: 174.6097 Evaluate side-chains 196 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 503 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 2 optimal weight: 8.9990 chunk 188 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 53 GLN A 98 ASN A 321 GLN C 476 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.109090 restraints weight = 10084.349| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 0.69 r_work: 0.3128 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work: 0.2843 rms_B_bonded: 4.59 restraints_weight: 0.1250 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 15701 Z= 0.194 Angle : 0.746 29.382 21161 Z= 0.357 Chirality : 0.046 0.175 2223 Planarity : 0.004 0.065 2712 Dihedral : 5.506 59.001 2399 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.53 % Allowed : 11.90 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % 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: 0.76 (0.19), residues: 1890 helix: 1.37 (0.17), residues: 962 sheet: -0.94 (0.35), residues: 169 loop : -0.16 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.020 0.002 TYR C 229 PHE 0.018 0.002 PHE A 431 TRP 0.015 0.002 TRP B 296 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00384 (15685) covalent geometry : angle 0.74596 (21161) hydrogen bonds : bond 0.05419 ( 755) hydrogen bonds : angle 5.72066 ( 2154) Misc. bond : bond 0.10554 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 168 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8153 (mtpt) REVERT: A 401 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.6806 (p90) REVERT: A 433 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.6370 (mptp) REVERT: B 120 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7442 (mt-10) REVERT: B 121 ASP cc_start: 0.7779 (m-30) cc_final: 0.7421 (p0) REVERT: B 417 LYS cc_start: 0.8214 (mmtm) cc_final: 0.7833 (mmpt) REVERT: C 53 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: C 318 GLU cc_start: 0.7709 (mm-30) cc_final: 0.6881 (mp0) REVERT: D 121 ASP cc_start: 0.7515 (m-30) cc_final: 0.7030 (t70) REVERT: D 503 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7983 (mp0) outliers start: 25 outliers final: 18 residues processed: 198 average time/residue: 0.7920 time to fit residues: 170.2211 Evaluate side-chains 200 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 503 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 70 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 151 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 53 GLN A 98 ASN A 321 GLN C 476 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.129027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110344 restraints weight = 10132.976| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 0.69 r_work: 0.3153 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 1.72 restraints_weight: 0.2500 r_work: 0.2870 rms_B_bonded: 4.61 restraints_weight: 0.1250 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 15701 Z= 0.161 Angle : 0.714 29.224 21161 Z= 0.337 Chirality : 0.045 0.168 2223 Planarity : 0.004 0.058 2712 Dihedral : 5.388 59.413 2399 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.53 % Allowed : 11.90 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % 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: 0.84 (0.19), residues: 1890 helix: 1.45 (0.17), residues: 960 sheet: -0.93 (0.36), residues: 169 loop : -0.13 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 359 TYR 0.019 0.002 TYR C 276 PHE 0.017 0.002 PHE A 431 TRP 0.015 0.002 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00313 (15685) covalent geometry : angle 0.71425 (21161) hydrogen bonds : bond 0.04859 ( 755) hydrogen bonds : angle 5.64022 ( 2154) Misc. bond : bond 0.09460 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7767.01 seconds wall clock time: 133 minutes 3.34 seconds (7983.34 seconds total)