Starting phenix.real_space_refine on Wed Mar 4 21:27:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dfv_30579/03_2026/7dfv_30579.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dfv_30579/03_2026/7dfv_30579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dfv_30579/03_2026/7dfv_30579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dfv_30579/03_2026/7dfv_30579.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dfv_30579/03_2026/7dfv_30579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dfv_30579/03_2026/7dfv_30579.map" } resolution = 2.99 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= 1.000 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10564 2.51 5 N 2880 2.21 5 O 3040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16580 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4163 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4127 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 14, 'TRANS': 501} Restraints were copied for chains: D, A Time building chain proxies: 5.24, per 1000 atoms: 0.32 Number of scatterers: 16580 At special positions: 0 Unit cell: (106.496, 108.692, 128.454, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3040 8.00 N 2880 7.00 C 10564 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=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 856.3 milliseconds 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 14 sheets defined 59.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 99 through 111 removed outlier: 4.243A pdb=" N HIS B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.518A pdb=" N GLU B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 Processing helix chain 'B' and resid 152 through 170 removed outlier: 4.026A pdb=" N LEU B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 removed outlier: 3.513A pdb=" N LYS B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 200 removed outlier: 3.719A pdb=" N PHE B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.598A pdb=" N GLU B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 231 through 248 removed outlier: 3.770A pdb=" N MET B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 274 removed outlier: 3.643A pdb=" N LEU B 272 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 305 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 316 through 321 removed outlier: 3.507A pdb=" N CYS B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 344 removed outlier: 3.714A pdb=" N ALA B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 375 through 383 removed outlier: 4.152A pdb=" N LEU B 379 " --> pdb=" O GLN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 401 through 408 removed outlier: 3.967A pdb=" N LEU B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 433 Processing helix chain 'B' and resid 442 through 453 Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 471 through 484 Proline residue: B 480 - end of helix Processing helix chain 'B' and resid 487 through 499 removed outlier: 4.323A pdb=" N ILE B 493 " --> pdb=" O LYS B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 515 Processing helix chain 'B' and resid 520 through 528 Processing helix chain 'B' and resid 533 through 544 Processing helix chain 'B' and resid 557 through 568 Processing helix chain 'B' and resid 592 through 596 removed outlier: 3.735A pdb=" N ASP B 596 " --> pdb=" O LEU B 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 99 through 111 removed outlier: 4.090A pdb=" N HIS C 103 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 137 removed outlier: 3.623A pdb=" N ILE C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 231 through 249 Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.751A pdb=" N GLY C 258 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 274 removed outlier: 3.910A pdb=" N HIS C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 272 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 305 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'C' and resid 327 through 344 removed outlier: 3.584A pdb=" N ALA C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 375 through 383 removed outlier: 3.674A pdb=" N LEU C 379 " --> pdb=" O GLN C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 409 removed outlier: 4.153A pdb=" N LEU C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 434 removed outlier: 3.592A pdb=" N GLY C 434 " --> pdb=" O MET C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 453 Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 471 through 485 Proline residue: C 480 - end of helix Processing helix chain 'C' and resid 487 through 499 removed outlier: 4.346A pdb=" N ILE C 493 " --> pdb=" O LYS C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 515 Processing helix chain 'C' and resid 520 through 529 Processing helix chain 'C' and resid 533 through 544 removed outlier: 3.553A pdb=" N HIS C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.974A pdb=" N PHE C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 594 removed outlier: 3.960A pdb=" N VAL C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 99 through 111 removed outlier: 4.243A pdb=" N HIS D 103 " --> pdb=" O THR D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 126 through 137 removed outlier: 3.517A pdb=" N GLU D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 151 Processing helix chain 'D' and resid 152 through 170 removed outlier: 4.026A pdb=" N LEU D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY D 170 " --> pdb=" O ARG D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 188 removed outlier: 3.512A pdb=" N LYS D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 200 removed outlier: 3.720A pdb=" N PHE D 196 " --> pdb=" O PHE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 220 removed outlier: 3.598A pdb=" N GLU D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 231 through 248 removed outlier: 3.770A pdb=" N MET D 235 " --> pdb=" O ASN D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 274 removed outlier: 3.643A pdb=" N LEU D 272 " --> pdb=" O MET D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 316 through 321 removed outlier: 3.508A pdb=" N CYS D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 344 removed outlier: 3.714A pdb=" N ALA D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 361 Processing helix chain 'D' and resid 375 through 383 removed outlier: 4.151A pdb=" N LEU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 401 through 408 removed outlier: 3.966A pdb=" N LEU D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 433 Processing helix chain 'D' and resid 442 through 453 Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 471 through 484 Proline residue: D 480 - end of helix Processing helix chain 'D' and resid 487 through 499 removed outlier: 4.323A pdb=" N ILE D 493 " --> pdb=" O LYS D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 515 Processing helix chain 'D' and resid 520 through 528 Processing helix chain 'D' and resid 533 through 544 Processing helix chain 'D' and resid 557 through 568 Processing helix chain 'D' and resid 592 through 596 removed outlier: 3.735A pdb=" N ASP D 596 " --> pdb=" O LEU D 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 99 through 111 removed outlier: 4.090A pdb=" N HIS A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.623A pdb=" N ILE A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 189 through 200 Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 231 through 249 Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.751A pdb=" N GLY A 258 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.911A pdb=" N HIS A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 272 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 305 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 327 through 344 removed outlier: 3.584A pdb=" N ALA A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.674A pdb=" N LEU A 379 " --> pdb=" O GLN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 409 removed outlier: 4.153A pdb=" N LEU A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.592A pdb=" N GLY A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 453 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 485 Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 487 through 499 removed outlier: 4.346A pdb=" N ILE A 493 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 515 Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 533 through 544 removed outlier: 3.554A pdb=" N HIS A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.974A pdb=" N PHE A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.960A pdb=" N VAL A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 85 through 90 removed outlier: 6.833A pdb=" N GLN B 86 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS B 139 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N MET B 174 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA B 141 " --> pdb=" O MET B 174 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE B 176 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL B 143 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 310 through 314 Processing sheet with id=AA3, first strand: chain 'B' and resid 548 through 549 Processing sheet with id=AA4, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AA5, first strand: chain 'C' and resid 310 through 314 removed outlier: 6.303A pdb=" N VAL C 366 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE C 396 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU C 368 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR C 398 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU C 370 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 283 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR C 399 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE C 285 " --> pdb=" O THR C 399 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N MET C 282 " --> pdb=" O HIS C 412 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR C 414 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY C 284 " --> pdb=" O TYR C 414 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 548 through 550 Processing sheet with id=AA7, first strand: chain 'C' and resid 573 through 574 Processing sheet with id=AA8, first strand: chain 'D' and resid 85 through 90 removed outlier: 6.833A pdb=" N GLN D 86 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS D 139 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N MET D 174 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA D 141 " --> pdb=" O MET D 174 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE D 176 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL D 143 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 310 through 314 Processing sheet with id=AB1, first strand: chain 'D' and resid 548 through 549 Processing sheet with id=AB2, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AB3, first strand: chain 'A' and resid 310 through 314 removed outlier: 6.303A pdb=" N VAL A 366 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE A 396 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 368 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR A 398 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 370 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 283 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR A 399 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE A 285 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N MET A 282 " --> pdb=" O HIS A 412 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR A 414 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY A 284 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 548 through 550 Processing sheet with id=AB5, first strand: chain 'A' and resid 573 through 574 816 hydrogen bonds defined for protein. 2358 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2776 1.31 - 1.44: 4326 1.44 - 1.56: 9646 1.56 - 1.68: 0 1.68 - 1.81: 156 Bond restraints: 16904 Sorted by residual: bond pdb=" C PRO B 288 " pdb=" O PRO B 288 " ideal model delta sigma weight residual 1.240 1.191 0.050 1.12e-02 7.97e+03 1.98e+01 bond pdb=" C PRO D 288 " pdb=" O PRO D 288 " ideal model delta sigma weight residual 1.240 1.191 0.049 1.12e-02 7.97e+03 1.94e+01 bond pdb=" C LEU B 269 " pdb=" O LEU B 269 " ideal model delta sigma weight residual 1.237 1.194 0.042 1.19e-02 7.06e+03 1.26e+01 bond pdb=" C LEU D 269 " pdb=" O LEU D 269 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.19e-02 7.06e+03 1.23e+01 bond pdb=" C GLY C 287 " pdb=" N PRO C 288 " ideal model delta sigma weight residual 1.329 1.370 -0.040 1.18e-02 7.18e+03 1.18e+01 ... (remaining 16899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 21900 2.08 - 4.15: 753 4.15 - 6.23: 77 6.23 - 8.31: 8 8.31 - 10.38: 6 Bond angle restraints: 22744 Sorted by residual: angle pdb=" N CYS B 590 " pdb=" CA CYS B 590 " pdb=" C CYS B 590 " ideal model delta sigma weight residual 114.75 105.77 8.98 1.26e+00 6.30e-01 5.08e+01 angle pdb=" N CYS D 590 " pdb=" CA CYS D 590 " pdb=" C CYS D 590 " ideal model delta sigma weight residual 114.75 105.77 8.98 1.26e+00 6.30e-01 5.07e+01 angle pdb=" C THR B 398 " pdb=" CA THR B 398 " pdb=" CB THR B 398 " ideal model delta sigma weight residual 109.48 119.86 -10.38 1.68e+00 3.54e-01 3.82e+01 angle pdb=" C THR D 398 " pdb=" CA THR D 398 " pdb=" CB THR D 398 " ideal model delta sigma weight residual 109.48 119.84 -10.36 1.68e+00 3.54e-01 3.80e+01 angle pdb=" CA PRO D 288 " pdb=" C PRO D 288 " pdb=" N PRO D 289 " ideal model delta sigma weight residual 117.93 124.59 -6.66 1.20e+00 6.94e-01 3.08e+01 ... (remaining 22739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 9193 16.97 - 33.94: 833 33.94 - 50.91: 138 50.91 - 67.88: 42 67.88 - 84.85: 14 Dihedral angle restraints: 10220 sinusoidal: 4260 harmonic: 5960 Sorted by residual: dihedral pdb=" C THR B 398 " pdb=" N THR B 398 " pdb=" CA THR B 398 " pdb=" CB THR B 398 " ideal model delta harmonic sigma weight residual -122.00 -133.46 11.46 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" C THR D 398 " pdb=" N THR D 398 " pdb=" CA THR D 398 " pdb=" CB THR D 398 " ideal model delta harmonic sigma weight residual -122.00 -133.42 11.42 0 2.50e+00 1.60e-01 2.09e+01 dihedral pdb=" CA LEU D 370 " pdb=" C LEU D 370 " pdb=" N ASP D 371 " pdb=" CA ASP D 371 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 10217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2084 0.067 - 0.134: 361 0.134 - 0.201: 41 0.201 - 0.268: 10 0.268 - 0.335: 6 Chirality restraints: 2502 Sorted by residual: chirality pdb=" CA PHE C 442 " pdb=" N PHE C 442 " pdb=" C PHE C 442 " pdb=" CB PHE C 442 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.33 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA PHE A 442 " pdb=" N PHE A 442 " pdb=" C PHE A 442 " pdb=" CB PHE A 442 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ASN C 411 " pdb=" N ASN C 411 " pdb=" C ASN C 411 " pdb=" CB ASN C 411 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 2499 not shown) Planarity restraints: 2910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 266 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C MET B 266 " -0.049 2.00e-02 2.50e+03 pdb=" O MET B 266 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP B 267 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 266 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C MET D 266 " -0.049 2.00e-02 2.50e+03 pdb=" O MET D 266 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP D 267 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 530 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C LYS A 530 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS A 530 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE A 531 " -0.015 2.00e-02 2.50e+03 ... (remaining 2907 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1413 2.74 - 3.28: 16178 3.28 - 3.82: 26641 3.82 - 4.36: 33137 4.36 - 4.90: 57304 Nonbonded interactions: 134673 Sorted by model distance: nonbonded pdb=" O GLU B 474 " pdb=" OG1 THR B 478 " model vdw 2.195 3.040 nonbonded pdb=" O GLU D 474 " pdb=" OG1 THR D 478 " model vdw 2.196 3.040 nonbonded pdb=" OG SER B 471 " pdb=" OE1 GLU B 474 " model vdw 2.207 3.040 nonbonded pdb=" OG SER D 471 " pdb=" OE1 GLU D 474 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR B 224 " pdb=" OD2 ASP B 242 " model vdw 2.218 3.040 ... (remaining 134668 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'A' } 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: 0.010 Normalize map: mean=0, sd=1: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.890 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.007 0.055 16904 Z= 0.366 Angle : 0.845 10.381 22744 Z= 0.547 Chirality : 0.055 0.335 2502 Planarity : 0.004 0.045 2910 Dihedral : 13.607 84.855 6380 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.89 % Allowed : 1.44 % Favored : 97.67 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.18), residues: 2064 helix: 0.32 (0.15), residues: 1134 sheet: -0.16 (0.37), residues: 214 loop : -1.51 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 394 TYR 0.018 0.002 TYR C 511 PHE 0.023 0.002 PHE A 442 TRP 0.028 0.002 TRP B 286 HIS 0.010 0.001 HIS D 346 Details of bonding type rmsd covalent geometry : bond 0.00683 (16904) covalent geometry : angle 0.84452 (22744) hydrogen bonds : bond 0.14493 ( 816) hydrogen bonds : angle 6.09658 ( 2358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: B 485 SER cc_start: 0.8498 (t) cc_final: 0.7946 (p) REVERT: C 363 ASP cc_start: 0.7196 (p0) cc_final: 0.6935 (p0) REVERT: D 485 SER cc_start: 0.8563 (t) cc_final: 0.8096 (p) REVERT: A 363 ASP cc_start: 0.7135 (p0) cc_final: 0.6892 (p0) REVERT: A 591 GLU cc_start: 0.7618 (pm20) cc_final: 0.7301 (pm20) outliers start: 16 outliers final: 2 residues processed: 210 average time/residue: 0.7058 time to fit residues: 162.2052 Evaluate side-chains 129 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 439 HIS Chi-restraints excluded: chain A residue 439 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 HIS B 302 ASN B 334 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 HIS D 92 HIS D 302 ASN D 334 GLN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.103186 restraints weight = 23826.263| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.85 r_work: 0.3203 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16904 Z= 0.138 Angle : 0.549 8.094 22744 Z= 0.295 Chirality : 0.044 0.205 2502 Planarity : 0.004 0.036 2910 Dihedral : 4.848 32.823 2232 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.61 % Allowed : 7.59 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.03 (0.19), residues: 2064 helix: 0.80 (0.16), residues: 1156 sheet: 0.01 (0.38), residues: 214 loop : -1.34 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 281 TYR 0.012 0.001 TYR C 498 PHE 0.012 0.001 PHE A 442 TRP 0.015 0.001 TRP B 286 HIS 0.005 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00325 (16904) covalent geometry : angle 0.54917 (22744) hydrogen bonds : bond 0.03520 ( 816) hydrogen bonds : angle 4.53850 ( 2358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.601 Fit side-chains REVERT: B 550 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7442 (tp30) REVERT: C 169 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8565 (mm) REVERT: C 363 ASP cc_start: 0.7793 (p0) cc_final: 0.7423 (p0) REVERT: D 485 SER cc_start: 0.8370 (t) cc_final: 0.7600 (p) REVERT: D 550 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7430 (tp30) REVERT: A 169 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8571 (mm) REVERT: A 363 ASP cc_start: 0.7767 (p0) cc_final: 0.7385 (p0) REVERT: A 591 GLU cc_start: 0.7488 (pm20) cc_final: 0.7256 (pm20) outliers start: 29 outliers final: 14 residues processed: 165 average time/residue: 0.6337 time to fit residues: 115.8486 Evaluate side-chains 134 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 439 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 183 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 154 optimal weight: 0.0020 chunk 153 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN B 334 GLN C 346 HIS D 302 ASN D 334 GLN A 346 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.122565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101634 restraints weight = 24455.528| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.84 r_work: 0.3177 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16904 Z= 0.167 Angle : 0.548 6.701 22744 Z= 0.292 Chirality : 0.044 0.168 2502 Planarity : 0.003 0.037 2910 Dihedral : 4.758 26.953 2232 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.55 % Allowed : 9.97 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.08 (0.19), residues: 2064 helix: 0.93 (0.16), residues: 1154 sheet: -0.04 (0.37), residues: 214 loop : -1.35 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 481 TYR 0.013 0.001 TYR C 498 PHE 0.013 0.001 PHE A 389 TRP 0.017 0.001 TRP A 286 HIS 0.006 0.001 HIS D 346 Details of bonding type rmsd covalent geometry : bond 0.00402 (16904) covalent geometry : angle 0.54785 (22744) hydrogen bonds : bond 0.03568 ( 816) hydrogen bonds : angle 4.38143 ( 2358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: B 362 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7373 (ttm110) REVERT: B 485 SER cc_start: 0.8285 (t) cc_final: 0.7510 (p) REVERT: B 550 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7528 (tp30) REVERT: C 363 ASP cc_start: 0.7834 (p0) cc_final: 0.7513 (p0) REVERT: D 209 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7441 (tp30) REVERT: D 362 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8387 (mtm110) REVERT: D 485 SER cc_start: 0.8353 (t) cc_final: 0.7604 (p) REVERT: D 550 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7491 (tp30) REVERT: A 363 ASP cc_start: 0.7774 (p0) cc_final: 0.7402 (p0) REVERT: A 531 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.6635 (p90) REVERT: A 591 GLU cc_start: 0.7492 (pm20) cc_final: 0.7274 (pm20) outliers start: 46 outliers final: 19 residues processed: 157 average time/residue: 0.6362 time to fit residues: 110.6254 Evaluate side-chains 139 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 362 ARG Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 85 optimal weight: 0.4980 chunk 198 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 87 optimal weight: 0.0370 chunk 188 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN B 334 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 HIS C 408 HIS D 302 ASN D 334 GLN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103858 restraints weight = 23931.131| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.83 r_work: 0.3211 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16904 Z= 0.114 Angle : 0.489 7.045 22744 Z= 0.260 Chirality : 0.042 0.226 2502 Planarity : 0.003 0.032 2910 Dihedral : 4.415 19.962 2228 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.60 % Allowed : 10.69 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.33 (0.19), residues: 2064 helix: 1.19 (0.16), residues: 1154 sheet: 0.00 (0.38), residues: 214 loop : -1.33 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 230 TYR 0.012 0.001 TYR C 498 PHE 0.009 0.001 PHE D 250 TRP 0.012 0.001 TRP A 286 HIS 0.004 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00265 (16904) covalent geometry : angle 0.48910 (22744) hydrogen bonds : bond 0.02928 ( 816) hydrogen bonds : angle 4.19194 ( 2358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7512 (tp30) REVERT: B 262 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7986 (mmm) REVERT: B 398 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8646 (t) REVERT: B 550 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7325 (tp30) REVERT: C 363 ASP cc_start: 0.7823 (p0) cc_final: 0.7490 (p0) REVERT: C 591 GLU cc_start: 0.7323 (pm20) cc_final: 0.7080 (pm20) REVERT: D 209 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: D 398 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.8680 (t) REVERT: D 485 SER cc_start: 0.8037 (t) cc_final: 0.7189 (p) REVERT: D 550 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7343 (tp30) REVERT: A 363 ASP cc_start: 0.7817 (p0) cc_final: 0.7454 (p0) REVERT: A 591 GLU cc_start: 0.7425 (pm20) cc_final: 0.7222 (pm20) outliers start: 47 outliers final: 16 residues processed: 159 average time/residue: 0.6357 time to fit residues: 112.2638 Evaluate side-chains 137 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 120 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 102 optimal weight: 0.0030 chunk 127 optimal weight: 0.0020 chunk 95 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 89 optimal weight: 0.0470 chunk 12 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN B 334 GLN C 336 GLN C 346 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN D 334 GLN D 336 GLN A 336 GLN A 346 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106095 restraints weight = 23989.110| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.84 r_work: 0.3240 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16904 Z= 0.094 Angle : 0.471 7.709 22744 Z= 0.249 Chirality : 0.042 0.217 2502 Planarity : 0.003 0.029 2910 Dihedral : 4.180 19.786 2228 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.16 % Allowed : 12.29 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 2064 helix: 1.45 (0.16), residues: 1142 sheet: 0.00 (0.38), residues: 214 loop : -1.29 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 230 TYR 0.012 0.001 TYR C 498 PHE 0.023 0.001 PHE C 496 TRP 0.009 0.001 TRP A 286 HIS 0.005 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00210 (16904) covalent geometry : angle 0.47082 (22744) hydrogen bonds : bond 0.02636 ( 816) hydrogen bonds : angle 4.05430 ( 2358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7539 (tp30) REVERT: B 262 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7953 (mmm) REVERT: B 398 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8361 (t) REVERT: B 550 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7272 (tp30) REVERT: C 363 ASP cc_start: 0.7816 (p0) cc_final: 0.7483 (p0) REVERT: C 591 GLU cc_start: 0.7242 (pm20) cc_final: 0.7012 (pm20) REVERT: D 209 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7516 (tp30) REVERT: D 262 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8008 (mmm) REVERT: D 398 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8375 (t) REVERT: D 550 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7261 (tp30) REVERT: A 363 ASP cc_start: 0.7756 (p0) cc_final: 0.7380 (p0) outliers start: 39 outliers final: 16 residues processed: 167 average time/residue: 0.6758 time to fit residues: 124.3375 Evaluate side-chains 142 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 204 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C 346 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 346 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.099317 restraints weight = 24395.136| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.85 r_work: 0.3135 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16904 Z= 0.247 Angle : 0.619 8.886 22744 Z= 0.324 Chirality : 0.047 0.243 2502 Planarity : 0.004 0.066 2910 Dihedral : 4.723 24.399 2228 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.94 % Allowed : 14.01 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.11 (0.19), residues: 2064 helix: 1.07 (0.16), residues: 1142 sheet: -0.08 (0.37), residues: 216 loop : -1.50 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 535 TYR 0.014 0.002 TYR C 498 PHE 0.022 0.002 PHE B 496 TRP 0.018 0.002 TRP A 286 HIS 0.007 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00602 (16904) covalent geometry : angle 0.61932 (22744) hydrogen bonds : bond 0.03889 ( 816) hydrogen bonds : angle 4.37109 ( 2358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7585 (tp30) REVERT: B 485 SER cc_start: 0.8391 (t) cc_final: 0.7597 (p) REVERT: B 550 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7667 (tp30) REVERT: C 363 ASP cc_start: 0.8128 (p0) cc_final: 0.7793 (p0) REVERT: C 445 ILE cc_start: 0.8079 (mm) cc_final: 0.7864 (tp) REVERT: C 591 GLU cc_start: 0.7441 (pm20) cc_final: 0.7143 (pm20) REVERT: D 209 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: D 485 SER cc_start: 0.8418 (t) cc_final: 0.7661 (p) REVERT: D 550 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7648 (tp30) REVERT: A 314 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8448 (mtm) REVERT: A 363 ASP cc_start: 0.7987 (p0) cc_final: 0.7582 (p0) REVERT: A 445 ILE cc_start: 0.8080 (mm) cc_final: 0.7868 (tp) outliers start: 35 outliers final: 21 residues processed: 143 average time/residue: 0.6594 time to fit residues: 104.0122 Evaluate side-chains 140 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 88 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 81 optimal weight: 0.1980 chunk 122 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN C 346 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN A 346 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.123214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.102492 restraints weight = 23969.730| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.83 r_work: 0.3189 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16904 Z= 0.123 Angle : 0.522 9.210 22744 Z= 0.274 Chirality : 0.043 0.209 2502 Planarity : 0.003 0.054 2910 Dihedral : 4.433 21.646 2228 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.10 % Allowed : 14.17 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 2064 helix: 1.36 (0.16), residues: 1124 sheet: -0.09 (0.37), residues: 216 loop : -1.40 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 535 TYR 0.013 0.001 TYR A 498 PHE 0.017 0.001 PHE B 496 TRP 0.012 0.001 TRP A 286 HIS 0.007 0.001 HIS C 346 Details of bonding type rmsd covalent geometry : bond 0.00290 (16904) covalent geometry : angle 0.52204 (22744) hydrogen bonds : bond 0.03023 ( 816) hydrogen bonds : angle 4.18520 ( 2358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7541 (tp30) REVERT: B 262 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8078 (mmm) REVERT: B 550 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7454 (tp30) REVERT: C 363 ASP cc_start: 0.7994 (p0) cc_final: 0.7626 (p0) REVERT: C 591 GLU cc_start: 0.7391 (pm20) cc_final: 0.7128 (pm20) REVERT: D 187 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7999 (mtmm) REVERT: D 209 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7540 (tp30) REVERT: D 262 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8065 (mmm) REVERT: D 485 SER cc_start: 0.8193 (t) cc_final: 0.7375 (p) REVERT: D 550 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7445 (tp30) REVERT: A 363 ASP cc_start: 0.7949 (p0) cc_final: 0.7529 (p0) outliers start: 38 outliers final: 22 residues processed: 147 average time/residue: 0.7020 time to fit residues: 113.4869 Evaluate side-chains 140 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 142 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 195 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 128 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 150 optimal weight: 0.0040 chunk 100 optimal weight: 0.0970 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN C 336 GLN C 346 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 336 GLN A 336 GLN A 346 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.104964 restraints weight = 23937.681| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.83 r_work: 0.3224 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16904 Z= 0.101 Angle : 0.497 9.381 22744 Z= 0.259 Chirality : 0.042 0.187 2502 Planarity : 0.003 0.074 2910 Dihedral : 4.192 20.010 2228 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.99 % Allowed : 14.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 2064 helix: 1.51 (0.16), residues: 1124 sheet: -0.05 (0.37), residues: 216 loop : -1.31 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 230 TYR 0.011 0.001 TYR A 498 PHE 0.014 0.001 PHE D 496 TRP 0.012 0.001 TRP A 154 HIS 0.007 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00233 (16904) covalent geometry : angle 0.49745 (22744) hydrogen bonds : bond 0.02681 ( 816) hydrogen bonds : angle 4.04540 ( 2358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: B 262 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8087 (mmm) REVERT: B 398 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8543 (t) REVERT: B 550 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7353 (tp30) REVERT: C 250 PHE cc_start: 0.7886 (t80) cc_final: 0.7613 (t80) REVERT: C 363 ASP cc_start: 0.7968 (p0) cc_final: 0.7575 (p0) REVERT: C 591 GLU cc_start: 0.7273 (pm20) cc_final: 0.7008 (pm20) REVERT: D 209 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7569 (tp30) REVERT: D 262 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8080 (mmm) REVERT: D 398 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8549 (t) REVERT: D 550 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7315 (tp30) REVERT: A 250 PHE cc_start: 0.7862 (t80) cc_final: 0.7636 (t80) REVERT: A 363 ASP cc_start: 0.7951 (p0) cc_final: 0.7482 (p0) outliers start: 36 outliers final: 18 residues processed: 147 average time/residue: 0.6377 time to fit residues: 104.1341 Evaluate side-chains 139 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 102 optimal weight: 0.0970 chunk 106 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 190 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN B 358 GLN C 346 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 358 GLN A 346 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103876 restraints weight = 24189.700| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.84 r_work: 0.3208 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16904 Z= 0.117 Angle : 0.505 7.587 22744 Z= 0.265 Chirality : 0.042 0.246 2502 Planarity : 0.003 0.065 2910 Dihedral : 4.194 20.669 2228 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.88 % Allowed : 15.17 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.19), residues: 2064 helix: 1.50 (0.16), residues: 1124 sheet: -0.01 (0.37), residues: 216 loop : -1.33 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 230 TYR 0.012 0.001 TYR C 498 PHE 0.017 0.001 PHE B 496 TRP 0.015 0.001 TRP A 154 HIS 0.008 0.001 HIS C 346 Details of bonding type rmsd covalent geometry : bond 0.00277 (16904) covalent geometry : angle 0.50497 (22744) hydrogen bonds : bond 0.02833 ( 816) hydrogen bonds : angle 4.04213 ( 2358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7564 (tp30) REVERT: B 262 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8137 (mmm) REVERT: B 358 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8316 (tp-100) REVERT: B 398 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8699 (t) REVERT: B 550 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7437 (tp30) REVERT: C 363 ASP cc_start: 0.8009 (p0) cc_final: 0.7614 (p0) REVERT: C 591 GLU cc_start: 0.7306 (pm20) cc_final: 0.7037 (pm20) REVERT: D 209 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7587 (tp30) REVERT: D 262 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8148 (mmm) REVERT: D 358 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.7844 (tp-100) REVERT: D 398 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8712 (t) REVERT: D 550 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7383 (tp30) REVERT: A 363 ASP cc_start: 0.7895 (p0) cc_final: 0.7444 (p0) outliers start: 34 outliers final: 19 residues processed: 143 average time/residue: 0.6272 time to fit residues: 99.6916 Evaluate side-chains 141 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 358 GLN Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 85 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 196 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: B 334 GLN ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 GLN C 346 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN A 346 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.123002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102197 restraints weight = 24024.347| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.85 r_work: 0.3183 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16904 Z= 0.155 Angle : 0.557 12.371 22744 Z= 0.288 Chirality : 0.043 0.223 2502 Planarity : 0.004 0.075 2910 Dihedral : 4.342 22.080 2228 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.77 % Allowed : 15.50 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 2064 helix: 1.37 (0.16), residues: 1124 sheet: -0.04 (0.37), residues: 216 loop : -1.38 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 230 TYR 0.013 0.001 TYR C 498 PHE 0.017 0.001 PHE D 496 TRP 0.018 0.001 TRP C 154 HIS 0.008 0.001 HIS C 346 Details of bonding type rmsd covalent geometry : bond 0.00376 (16904) covalent geometry : angle 0.55691 (22744) hydrogen bonds : bond 0.03150 ( 816) hydrogen bonds : angle 4.12490 ( 2358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7554 (tp30) REVERT: B 262 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8136 (mmm) REVERT: B 358 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8263 (tp-100) REVERT: B 550 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: C 363 ASP cc_start: 0.7962 (p0) cc_final: 0.7567 (p0) REVERT: C 591 GLU cc_start: 0.7308 (pm20) cc_final: 0.7016 (pm20) REVERT: D 209 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7556 (tp30) REVERT: D 262 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8139 (mmm) REVERT: D 358 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8243 (tp-100) REVERT: D 550 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7491 (tp30) REVERT: A 363 ASP cc_start: 0.7916 (p0) cc_final: 0.7450 (p0) outliers start: 32 outliers final: 22 residues processed: 136 average time/residue: 0.6406 time to fit residues: 96.6366 Evaluate side-chains 142 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 358 GLN Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 502 CYS Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 36 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 100 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN B 358 GLN C 346 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 358 GLN A 346 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.123651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103050 restraints weight = 23853.609| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.82 r_work: 0.3198 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16904 Z= 0.132 Angle : 0.527 9.844 22744 Z= 0.276 Chirality : 0.043 0.196 2502 Planarity : 0.003 0.069 2910 Dihedral : 4.322 21.734 2228 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.99 % Allowed : 15.50 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.42 (0.19), residues: 2064 helix: 1.38 (0.16), residues: 1124 sheet: -0.06 (0.37), residues: 216 loop : -1.38 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 230 TYR 0.012 0.001 TYR C 498 PHE 0.018 0.001 PHE B 496 TRP 0.019 0.001 TRP C 154 HIS 0.008 0.001 HIS C 346 Details of bonding type rmsd covalent geometry : bond 0.00317 (16904) covalent geometry : angle 0.52702 (22744) hydrogen bonds : bond 0.03023 ( 816) hydrogen bonds : angle 4.11488 ( 2358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4642.82 seconds wall clock time: 79 minutes 59.27 seconds (4799.27 seconds total)