Starting phenix.real_space_refine on Thu Mar 5 06:46:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xeu_33159/03_2026/7xeu_33159.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xeu_33159/03_2026/7xeu_33159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xeu_33159/03_2026/7xeu_33159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xeu_33159/03_2026/7xeu_33159.map" model { file = "/net/cci-nas-00/data/ceres_data/7xeu_33159/03_2026/7xeu_33159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xeu_33159/03_2026/7xeu_33159.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 108 5.16 5 C 13172 2.51 5 N 3372 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s 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: 20092 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "C" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "D" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.76, per 1000 atoms: 0.24 Number of scatterers: 20092 At special positions: 0 Unit cell: (158.184, 157.17, 118.638, 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 108 16.00 O 3440 8.00 N 3372 7.00 C 13172 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: 1.63 Conformation dependent library (CDL) restraints added in 974.1 milliseconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 4 sheets defined 61.4% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 83 through 88 removed outlier: 3.591A pdb=" N GLU A 86 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.755A pdb=" N TYR A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 130 through 139 removed outlier: 3.747A pdb=" N LEU A 134 " --> pdb=" O CYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.544A pdb=" N ILE A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.612A pdb=" N ASN A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 219 through 227 removed outlier: 3.599A pdb=" N TYR A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 251 Processing helix chain 'A' and resid 255 through 277 removed outlier: 3.792A pdb=" N ALA A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.683A pdb=" N ASP A 284 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 302 through 311 removed outlier: 3.571A pdb=" N PHE A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 373 through 408 Proline residue: A 386 - end of helix Processing helix chain 'A' and resid 424 through 454 Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 467 through 486 removed outlier: 4.216A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 507 removed outlier: 4.100A pdb=" N LEU A 495 " --> pdb=" O TRP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 removed outlier: 3.517A pdb=" N ARG A 512 " --> pdb=" O TYR A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 532 removed outlier: 3.531A pdb=" N TYR A 520 " --> pdb=" O HIS A 516 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 553 Processing helix chain 'A' and resid 587 through 597 Processing helix chain 'A' and resid 613 through 629 Processing helix chain 'A' and resid 631 through 647 Processing helix chain 'A' and resid 649 through 668 removed outlier: 4.299A pdb=" N SER A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 712 removed outlier: 3.961A pdb=" N LYS A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 83 through 88 removed outlier: 4.275A pdb=" N THR B 88 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.631A pdb=" N TYR B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B 97 " --> pdb=" O TYR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.584A pdb=" N ILE B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 181 removed outlier: 3.576A pdb=" N VAL B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.796A pdb=" N GLN B 195 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 219 through 227 removed outlier: 3.654A pdb=" N TYR B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 225 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 251 Processing helix chain 'B' and resid 255 through 277 removed outlier: 3.637A pdb=" N ALA B 260 " --> pdb=" O PRO B 256 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 285 removed outlier: 3.672A pdb=" N ASP B 284 " --> pdb=" O GLN B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 301 Processing helix chain 'B' and resid 302 through 311 removed outlier: 3.591A pdb=" N PHE B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 374 through 408 Proline residue: B 386 - end of helix Processing helix chain 'B' and resid 424 through 454 Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 467 through 485 Processing helix chain 'B' and resid 491 through 507 removed outlier: 4.042A pdb=" N LEU B 495 " --> pdb=" O TRP B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 514 through 532 removed outlier: 3.532A pdb=" N TYR B 520 " --> pdb=" O HIS B 516 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 532 " --> pdb=" O ILE B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 553 Processing helix chain 'B' and resid 587 through 597 Processing helix chain 'B' and resid 613 through 629 Processing helix chain 'B' and resid 631 through 647 Processing helix chain 'B' and resid 649 through 668 removed outlier: 4.335A pdb=" N SER B 653 " --> pdb=" O THR B 649 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 712 removed outlier: 3.827A pdb=" N LYS B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 82 Processing helix chain 'C' and resid 83 through 88 removed outlier: 3.528A pdb=" N GLU C 86 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR C 88 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.561A pdb=" N THR C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 130 through 139 removed outlier: 3.662A pdb=" N LEU C 134 " --> pdb=" O CYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.688A pdb=" N ILE C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 181 removed outlier: 3.743A pdb=" N ASN C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 219 through 227 removed outlier: 3.600A pdb=" N TYR C 223 " --> pdb=" O ASP C 219 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 225 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 255 through 277 removed outlier: 3.692A pdb=" N ALA C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 285 removed outlier: 3.798A pdb=" N ASP C 284 " --> pdb=" O GLN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 301 Processing helix chain 'C' and resid 302 through 311 removed outlier: 3.550A pdb=" N PHE C 306 " --> pdb=" O LYS C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 370 through 408 Proline residue: C 386 - end of helix Processing helix chain 'C' and resid 424 through 454 Processing helix chain 'C' and resid 456 through 461 removed outlier: 4.029A pdb=" N ILE C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 485 Processing helix chain 'C' and resid 491 through 507 removed outlier: 4.108A pdb=" N LEU C 495 " --> pdb=" O TRP C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 512 removed outlier: 3.564A pdb=" N ARG C 512 " --> pdb=" O TYR C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 532 removed outlier: 3.517A pdb=" N TYR C 520 " --> pdb=" O HIS C 516 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU C 532 " --> pdb=" O ILE C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 553 Processing helix chain 'C' and resid 587 through 597 Processing helix chain 'C' and resid 613 through 629 Processing helix chain 'C' and resid 631 through 647 Processing helix chain 'C' and resid 649 through 668 removed outlier: 4.345A pdb=" N SER C 653 " --> pdb=" O THR C 649 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 712 Processing helix chain 'D' and resid 71 through 82 Processing helix chain 'D' and resid 83 through 88 removed outlier: 3.505A pdb=" N GLU D 86 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.588A pdb=" N TYR D 93 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR D 97 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 130 through 139 removed outlier: 3.572A pdb=" N LEU D 134 " --> pdb=" O CYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 169 Processing helix chain 'D' and resid 171 through 181 removed outlier: 3.508A pdb=" N VAL D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 Processing helix chain 'D' and resid 219 through 227 removed outlier: 3.575A pdb=" N TYR D 223 " --> pdb=" O ASP D 219 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU D 225 " --> pdb=" O VAL D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 255 through 277 removed outlier: 3.649A pdb=" N ALA D 260 " --> pdb=" O PRO D 256 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 276 " --> pdb=" O MET D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 285 removed outlier: 3.517A pdb=" N ILE D 285 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 301 Processing helix chain 'D' and resid 302 through 311 removed outlier: 3.617A pdb=" N PHE D 306 " --> pdb=" O LYS D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 358 Processing helix chain 'D' and resid 374 through 408 Proline residue: D 386 - end of helix Processing helix chain 'D' and resid 424 through 454 Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 467 through 485 Processing helix chain 'D' and resid 491 through 507 removed outlier: 4.127A pdb=" N LEU D 495 " --> pdb=" O TRP D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 510 No H-bonds generated for 'chain 'D' and resid 508 through 510' Processing helix chain 'D' and resid 514 through 532 removed outlier: 3.535A pdb=" N TYR D 520 " --> pdb=" O HIS D 516 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D 532 " --> pdb=" O ILE D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 553 Processing helix chain 'D' and resid 587 through 597 Processing helix chain 'D' and resid 613 through 629 Processing helix chain 'D' and resid 631 through 647 Processing helix chain 'D' and resid 649 through 668 removed outlier: 4.298A pdb=" N SER D 653 " --> pdb=" O THR D 649 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 712 Processing sheet with id=AA1, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA2, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA3, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AA4, first strand: chain 'D' and resid 324 through 326 1014 hydrogen bonds defined for protein. 2988 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: 3.29 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6235 1.34 - 1.46: 3735 1.46 - 1.58: 10476 1.58 - 1.69: 2 1.69 - 1.81: 160 Bond restraints: 20608 Sorted by residual: bond pdb=" CG PRO B 146 " pdb=" CD PRO B 146 " ideal model delta sigma weight residual 1.503 1.243 0.260 3.40e-02 8.65e+02 5.83e+01 bond pdb=" CG PRO C 146 " pdb=" CD PRO C 146 " ideal model delta sigma weight residual 1.503 1.248 0.255 3.40e-02 8.65e+02 5.62e+01 bond pdb=" CB PRO B 146 " pdb=" CG PRO B 146 " ideal model delta sigma weight residual 1.492 1.667 -0.175 5.00e-02 4.00e+02 1.22e+01 bond pdb=" CB PRO C 146 " pdb=" CG PRO C 146 " ideal model delta sigma weight residual 1.492 1.662 -0.170 5.00e-02 4.00e+02 1.15e+01 bond pdb=" N PRO C 146 " pdb=" CD PRO C 146 " ideal model delta sigma weight residual 1.473 1.516 -0.043 1.40e-02 5.10e+03 9.38e+00 ... (remaining 20603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 27736 3.33 - 6.66: 203 6.66 - 9.98: 32 9.98 - 13.31: 9 13.31 - 16.64: 8 Bond angle restraints: 27988 Sorted by residual: angle pdb=" N ASN C 143 " pdb=" CA ASN C 143 " pdb=" C ASN C 143 " ideal model delta sigma weight residual 110.13 94.61 15.52 1.15e+00 7.56e-01 1.82e+02 angle pdb=" N ASN A 143 " pdb=" CA ASN A 143 " pdb=" C ASN A 143 " ideal model delta sigma weight residual 110.13 94.68 15.45 1.15e+00 7.56e-01 1.80e+02 angle pdb=" N PRO B 146 " pdb=" CD PRO B 146 " pdb=" CG PRO B 146 " ideal model delta sigma weight residual 103.20 86.56 16.64 1.50e+00 4.44e-01 1.23e+02 angle pdb=" CA PRO C 146 " pdb=" N PRO C 146 " pdb=" CD PRO C 146 " ideal model delta sigma weight residual 112.00 96.74 15.26 1.40e+00 5.10e-01 1.19e+02 angle pdb=" N PRO C 146 " pdb=" CD PRO C 146 " pdb=" CG PRO C 146 " ideal model delta sigma weight residual 103.20 87.27 15.93 1.50e+00 4.44e-01 1.13e+02 ... (remaining 27983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 11104 17.62 - 35.23: 979 35.23 - 52.85: 151 52.85 - 70.47: 38 70.47 - 88.08: 12 Dihedral angle restraints: 12284 sinusoidal: 5116 harmonic: 7168 Sorted by residual: dihedral pdb=" CA ASN A 143 " pdb=" C ASN A 143 " pdb=" N PRO A 144 " pdb=" CA PRO A 144 " ideal model delta harmonic sigma weight residual -180.00 -157.11 -22.89 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" C ILE A 693 " pdb=" N ILE A 693 " pdb=" CA ILE A 693 " pdb=" CB ILE A 693 " ideal model delta harmonic sigma weight residual -122.00 -133.26 11.26 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" CA ASN C 143 " pdb=" C ASN C 143 " pdb=" N PRO C 144 " pdb=" CA PRO C 144 " ideal model delta harmonic sigma weight residual -180.00 -160.16 -19.84 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 12281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2720 0.059 - 0.118: 394 0.118 - 0.177: 35 0.177 - 0.236: 16 0.236 - 0.295: 7 Chirality restraints: 3172 Sorted by residual: chirality pdb=" C13 CLR A 801 " pdb=" C12 CLR A 801 " pdb=" C14 CLR A 801 " pdb=" C17 CLR A 801 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C13 CLR D 801 " pdb=" C12 CLR D 801 " pdb=" C14 CLR D 801 " pdb=" C17 CLR D 801 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C13 CLR C 801 " pdb=" C12 CLR C 801 " pdb=" C14 CLR C 801 " pdb=" C17 CLR C 801 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 3169 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 371 " -0.099 5.00e-02 4.00e+02 1.50e-01 3.60e+01 pdb=" N PRO D 372 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO D 372 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO D 372 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 371 " -0.099 5.00e-02 4.00e+02 1.50e-01 3.58e+01 pdb=" N PRO B 372 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO B 372 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO B 372 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 371 " -0.099 5.00e-02 4.00e+02 1.50e-01 3.58e+01 pdb=" N PRO A 372 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO A 372 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO A 372 " -0.070 5.00e-02 4.00e+02 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 853 2.72 - 3.27: 20375 3.27 - 3.81: 32743 3.81 - 4.36: 38624 4.36 - 4.90: 66734 Nonbonded interactions: 159329 Sorted by model distance: nonbonded pdb=" OH TYR C 539 " pdb=" OG1 THR C 599 " model vdw 2.180 3.040 nonbonded pdb=" OH TYR D 539 " pdb=" OG1 THR D 599 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR B 539 " pdb=" OG1 THR B 599 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR A 539 " pdb=" OG1 THR A 599 " model vdw 2.207 3.040 nonbonded pdb=" N ASN A 143 " pdb=" O ASN A 143 " model vdw 2.234 2.496 ... (remaining 159324 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.030 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.930 Find NCS groups from input model: 0.370 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.004 0.260 20608 Z= 0.191 Angle : 0.832 16.638 27988 Z= 0.488 Chirality : 0.045 0.295 3172 Planarity : 0.006 0.150 3432 Dihedral : 13.449 88.084 7660 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.24 % Favored : 95.35 % Rotamer: Outliers : 0.51 % Allowed : 0.55 % Favored : 98.94 % Cbeta Deviations : 0.09 % 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: -0.12 (0.17), residues: 2432 helix: 1.62 (0.15), residues: 1324 sheet: -1.21 (0.63), residues: 44 loop : -2.40 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.033 0.001 TYR D 466 PHE 0.010 0.001 PHE C 76 TRP 0.029 0.001 TRP A 173 HIS 0.009 0.001 HIS C 408 Details of bonding type rmsd covalent geometry : bond 0.00441 (20608) covalent geometry : angle 0.83236 (27988) hydrogen bonds : bond 0.14628 ( 1014) hydrogen bonds : angle 5.11312 ( 2988) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 339 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: B 165 ILE cc_start: 0.8679 (mt) cc_final: 0.8255 (mm) REVERT: B 169 LYS cc_start: 0.8188 (mmpt) cc_final: 0.7832 (mptp) REVERT: B 230 GLN cc_start: 0.7614 (tt0) cc_final: 0.7397 (tt0) REVERT: B 428 MET cc_start: 0.6660 (mmp) cc_final: 0.6240 (pp-130) REVERT: C 155 GLU cc_start: 0.6868 (tm-30) cc_final: 0.6499 (tp30) REVERT: D 165 ILE cc_start: 0.8533 (mt) cc_final: 0.8286 (mp) REVERT: D 230 GLN cc_start: 0.7828 (tt0) cc_final: 0.7518 (tt0) outliers start: 11 outliers final: 11 residues processed: 347 average time/residue: 0.6168 time to fit residues: 240.7998 Evaluate side-chains 216 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 469 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN B 217 GLN B 229 HIS C 181 ASN D 181 ASN D 217 GLN D 408 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.159857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105944 restraints weight = 28915.555| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.95 r_work: 0.3193 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 20608 Z= 0.135 Angle : 0.655 11.881 27988 Z= 0.328 Chirality : 0.040 0.251 3172 Planarity : 0.006 0.128 3432 Dihedral : 6.937 93.969 2983 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.61 % Favored : 95.15 % Rotamer: Outliers : 2.80 % Allowed : 9.74 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.25 (0.17), residues: 2432 helix: 1.71 (0.15), residues: 1372 sheet: -0.13 (0.52), residues: 68 loop : -2.18 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 682 TYR 0.019 0.001 TYR B 466 PHE 0.011 0.001 PHE B 467 TRP 0.016 0.001 TRP A 173 HIS 0.004 0.001 HIS D 408 Details of bonding type rmsd covalent geometry : bond 0.00325 (20608) covalent geometry : angle 0.65518 (27988) hydrogen bonds : bond 0.04251 ( 1014) hydrogen bonds : angle 4.02145 ( 2988) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 239 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.6959 (tp30) cc_final: 0.6429 (tm-30) REVERT: A 250 MET cc_start: 0.8730 (mmm) cc_final: 0.8409 (mmt) REVERT: A 272 MET cc_start: 0.8538 (tpp) cc_final: 0.8298 (tpp) REVERT: A 371 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7253 (mm-30) REVERT: B 165 ILE cc_start: 0.8630 (mt) cc_final: 0.8376 (mm) REVERT: B 230 GLN cc_start: 0.7542 (tt0) cc_final: 0.7322 (tt0) REVERT: B 250 MET cc_start: 0.8589 (mmm) cc_final: 0.8269 (mmt) REVERT: B 272 MET cc_start: 0.8561 (tpp) cc_final: 0.8343 (tpp) REVERT: B 428 MET cc_start: 0.6959 (mmp) cc_final: 0.6050 (pp-130) REVERT: B 489 THR cc_start: 0.7347 (t) cc_final: 0.7105 (t) REVERT: B 677 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7317 (mmt-90) REVERT: C 155 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6134 (tp30) REVERT: C 250 MET cc_start: 0.8569 (mmm) cc_final: 0.8241 (mmt) REVERT: C 272 MET cc_start: 0.8488 (tpp) cc_final: 0.8262 (tpp) REVERT: D 155 GLU cc_start: 0.6956 (tp30) cc_final: 0.6464 (tm-30) REVERT: D 230 GLN cc_start: 0.7751 (tt0) cc_final: 0.7298 (tt0) REVERT: D 272 MET cc_start: 0.8605 (tpp) cc_final: 0.8299 (tpp) outliers start: 61 outliers final: 34 residues processed: 282 average time/residue: 0.5093 time to fit residues: 165.5866 Evaluate side-chains 223 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 677 ARG Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 127 optimal weight: 30.0000 chunk 189 optimal weight: 20.0000 chunk 166 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 ASN D 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.156867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.102647 restraints weight = 28936.923| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.59 r_work: 0.3156 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20608 Z= 0.161 Angle : 0.635 10.139 27988 Z= 0.318 Chirality : 0.040 0.260 3172 Planarity : 0.006 0.124 3432 Dihedral : 6.363 89.217 2965 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.77 % Favored : 95.02 % Rotamer: Outliers : 3.54 % Allowed : 12.32 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.34 (0.17), residues: 2432 helix: 1.75 (0.14), residues: 1368 sheet: 0.07 (0.52), residues: 68 loop : -2.08 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 275 TYR 0.020 0.002 TYR C 466 PHE 0.013 0.001 PHE A 389 TRP 0.025 0.001 TRP D 173 HIS 0.003 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00391 (20608) covalent geometry : angle 0.63479 (27988) hydrogen bonds : bond 0.04581 ( 1014) hydrogen bonds : angle 3.91617 ( 2988) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 196 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.8754 (mmm) cc_final: 0.8414 (mmm) REVERT: A 272 MET cc_start: 0.8589 (tpp) cc_final: 0.8253 (tpp) REVERT: A 371 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7375 (mm-30) REVERT: B 165 ILE cc_start: 0.8657 (mt) cc_final: 0.8371 (mm) REVERT: B 230 GLN cc_start: 0.7575 (tt0) cc_final: 0.7313 (tt0) REVERT: B 250 MET cc_start: 0.8725 (mmm) cc_final: 0.8466 (mmt) REVERT: B 272 MET cc_start: 0.8677 (tpp) cc_final: 0.8395 (tpp) REVERT: B 428 MET cc_start: 0.6927 (mmp) cc_final: 0.5979 (pp-130) REVERT: B 488 GLU cc_start: 0.7987 (mm-30) cc_final: 0.6958 (tm-30) REVERT: B 489 THR cc_start: 0.7341 (t) cc_final: 0.7001 (t) REVERT: B 677 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7291 (mmt-90) REVERT: C 155 GLU cc_start: 0.6448 (tm-30) cc_final: 0.5909 (tp30) REVERT: C 167 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8079 (mp) REVERT: C 250 MET cc_start: 0.8729 (mmm) cc_final: 0.8459 (mmt) REVERT: C 272 MET cc_start: 0.8587 (tpp) cc_final: 0.8285 (tpp) REVERT: C 456 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7778 (pt) REVERT: C 711 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: D 230 GLN cc_start: 0.7675 (tt0) cc_final: 0.7248 (tt0) REVERT: D 257 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7517 (pt0) REVERT: D 272 MET cc_start: 0.8702 (tpp) cc_final: 0.8427 (tpp) REVERT: D 383 ARG cc_start: 0.8691 (ttt-90) cc_final: 0.8487 (ttm110) outliers start: 77 outliers final: 41 residues processed: 251 average time/residue: 0.4969 time to fit residues: 144.1374 Evaluate side-chains 226 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 372 PRO Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 677 ARG Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 711 GLU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 372 PRO Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 695 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 111 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN B 181 ASN B 186 HIS B 217 GLN B 634 ASN D 186 HIS D 634 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.158067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104022 restraints weight = 28916.090| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.60 r_work: 0.3178 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 20608 Z= 0.123 Angle : 0.587 10.083 27988 Z= 0.293 Chirality : 0.039 0.251 3172 Planarity : 0.006 0.120 3432 Dihedral : 6.081 90.059 2965 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.56 % Favored : 95.27 % Rotamer: Outliers : 3.77 % Allowed : 13.56 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 2432 helix: 1.88 (0.14), residues: 1372 sheet: 0.27 (0.53), residues: 68 loop : -1.97 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 275 TYR 0.023 0.001 TYR C 466 PHE 0.010 0.001 PHE D 389 TRP 0.014 0.001 TRP D 173 HIS 0.002 0.000 HIS D 308 Details of bonding type rmsd covalent geometry : bond 0.00293 (20608) covalent geometry : angle 0.58734 (27988) hydrogen bonds : bond 0.03943 ( 1014) hydrogen bonds : angle 3.77410 ( 2988) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 201 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TRP cc_start: 0.7503 (t60) cc_final: 0.7232 (t60) REVERT: A 250 MET cc_start: 0.8770 (mmm) cc_final: 0.8491 (mmm) REVERT: A 272 MET cc_start: 0.8599 (tpp) cc_final: 0.8297 (tpp) REVERT: A 371 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: B 165 ILE cc_start: 0.8656 (mt) cc_final: 0.8337 (mm) REVERT: B 230 GLN cc_start: 0.7620 (tt0) cc_final: 0.7336 (tt0) REVERT: B 250 MET cc_start: 0.8726 (mmm) cc_final: 0.8449 (mmm) REVERT: B 272 MET cc_start: 0.8652 (tpp) cc_final: 0.8407 (tpp) REVERT: B 428 MET cc_start: 0.6941 (mmp) cc_final: 0.5996 (pp-130) REVERT: B 488 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7006 (tm-30) REVERT: B 489 THR cc_start: 0.7305 (t) cc_final: 0.6934 (t) REVERT: C 155 GLU cc_start: 0.6381 (tm-30) cc_final: 0.5837 (tp30) REVERT: C 167 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8144 (mp) REVERT: C 250 MET cc_start: 0.8712 (mmm) cc_final: 0.8415 (mmm) REVERT: C 272 MET cc_start: 0.8577 (tpp) cc_final: 0.8316 (tpp) REVERT: C 682 ARG cc_start: 0.7475 (ptm160) cc_final: 0.7192 (ptt-90) REVERT: C 711 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7719 (pt0) REVERT: D 230 GLN cc_start: 0.7620 (tt0) cc_final: 0.7241 (tt0) REVERT: D 257 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7512 (pt0) REVERT: D 272 MET cc_start: 0.8757 (tpp) cc_final: 0.8445 (tpp) outliers start: 82 outliers final: 38 residues processed: 258 average time/residue: 0.5025 time to fit residues: 149.8579 Evaluate side-chains 226 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 711 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 695 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 159 optimal weight: 3.9990 chunk 187 optimal weight: 0.0370 chunk 75 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 ASN C 186 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.159325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.105989 restraints weight = 28939.224| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.58 r_work: 0.3204 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 20608 Z= 0.111 Angle : 0.580 10.091 27988 Z= 0.289 Chirality : 0.038 0.249 3172 Planarity : 0.005 0.117 3432 Dihedral : 5.821 90.285 2965 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.77 % Favored : 95.07 % Rotamer: Outliers : 3.45 % Allowed : 14.25 % Favored : 82.31 % 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: 0.64 (0.18), residues: 2432 helix: 1.99 (0.15), residues: 1368 sheet: 0.40 (0.55), residues: 68 loop : -1.96 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 682 TYR 0.024 0.001 TYR C 466 PHE 0.009 0.001 PHE C 389 TRP 0.017 0.001 TRP D 173 HIS 0.002 0.000 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00261 (20608) covalent geometry : angle 0.57965 (27988) hydrogen bonds : bond 0.03566 ( 1014) hydrogen bonds : angle 3.71920 ( 2988) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 191 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 THR cc_start: 0.8206 (m) cc_final: 0.7994 (p) REVERT: A 173 TRP cc_start: 0.7621 (t60) cc_final: 0.7372 (t60) REVERT: A 185 VAL cc_start: 0.7991 (t) cc_final: 0.7651 (m) REVERT: A 250 MET cc_start: 0.8766 (mmm) cc_final: 0.8479 (mmm) REVERT: A 272 MET cc_start: 0.8603 (tpp) cc_final: 0.8052 (tpp) REVERT: A 276 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7790 (mm) REVERT: A 371 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7262 (mm-30) REVERT: B 88 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7957 (p) REVERT: B 94 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7264 (pp) REVERT: B 165 ILE cc_start: 0.8651 (mt) cc_final: 0.8339 (mm) REVERT: B 230 GLN cc_start: 0.7536 (tt0) cc_final: 0.7238 (tt0) REVERT: B 250 MET cc_start: 0.8674 (mmm) cc_final: 0.8402 (mmm) REVERT: B 272 MET cc_start: 0.8728 (tpp) cc_final: 0.8470 (tpp) REVERT: B 383 ARG cc_start: 0.8671 (ttt-90) cc_final: 0.8458 (ttm110) REVERT: B 428 MET cc_start: 0.6968 (mmp) cc_final: 0.5985 (pp-130) REVERT: B 488 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7010 (tm-30) REVERT: B 489 THR cc_start: 0.7292 (t) cc_final: 0.6929 (t) REVERT: B 677 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7233 (mmt-90) REVERT: C 155 GLU cc_start: 0.6486 (tm-30) cc_final: 0.5937 (tp30) REVERT: C 167 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8130 (mp) REVERT: C 250 MET cc_start: 0.8657 (mmm) cc_final: 0.8360 (mmm) REVERT: C 272 MET cc_start: 0.8596 (tpp) cc_final: 0.8129 (tpp) REVERT: C 276 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7851 (mm) REVERT: C 711 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7753 (pt0) REVERT: D 230 GLN cc_start: 0.7602 (tt0) cc_final: 0.7157 (tt0) REVERT: D 257 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7499 (pt0) REVERT: D 272 MET cc_start: 0.8677 (tpp) cc_final: 0.8377 (tpp) outliers start: 75 outliers final: 35 residues processed: 244 average time/residue: 0.5079 time to fit residues: 143.3660 Evaluate side-chains 221 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 674 ARG Chi-restraints excluded: chain B residue 677 ARG Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 711 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 674 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 67 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.156575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102511 restraints weight = 28761.290| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.58 r_work: 0.3153 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20608 Z= 0.153 Angle : 0.617 11.176 27988 Z= 0.304 Chirality : 0.039 0.253 3172 Planarity : 0.006 0.116 3432 Dihedral : 5.530 91.216 2965 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.90 % Rotamer: Outliers : 3.63 % Allowed : 14.61 % Favored : 81.76 % 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: 0.61 (0.18), residues: 2432 helix: 1.95 (0.14), residues: 1364 sheet: 0.43 (0.55), residues: 68 loop : -1.93 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 682 TYR 0.026 0.002 TYR C 466 PHE 0.015 0.001 PHE B 76 TRP 0.012 0.001 TRP D 173 HIS 0.003 0.001 HIS D 308 Details of bonding type rmsd covalent geometry : bond 0.00371 (20608) covalent geometry : angle 0.61679 (27988) hydrogen bonds : bond 0.04279 ( 1014) hydrogen bonds : angle 3.74024 ( 2988) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 189 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 THR cc_start: 0.8250 (m) cc_final: 0.8048 (p) REVERT: A 250 MET cc_start: 0.8775 (mmm) cc_final: 0.8474 (mmm) REVERT: A 677 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7251 (mmt-90) REVERT: B 88 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7935 (p) REVERT: B 94 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7326 (pp) REVERT: B 165 ILE cc_start: 0.8671 (mt) cc_final: 0.8350 (mm) REVERT: B 230 GLN cc_start: 0.7554 (tt0) cc_final: 0.7283 (tt0) REVERT: B 250 MET cc_start: 0.8712 (mmm) cc_final: 0.8427 (mmm) REVERT: B 428 MET cc_start: 0.6970 (mmp) cc_final: 0.5981 (pp-130) REVERT: B 488 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7077 (tm-30) REVERT: B 489 THR cc_start: 0.7250 (t) cc_final: 0.6890 (t) REVERT: B 677 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7258 (mmt-90) REVERT: C 155 GLU cc_start: 0.6451 (tm-30) cc_final: 0.5883 (tp30) REVERT: C 167 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8122 (mp) REVERT: C 250 MET cc_start: 0.8697 (mmm) cc_final: 0.8396 (mmm) REVERT: C 512 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7924 (ptp-170) REVERT: C 711 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7744 (pt0) REVERT: D 88 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7954 (p) REVERT: D 230 GLN cc_start: 0.7557 (tt0) cc_final: 0.7097 (tt0) REVERT: D 257 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: D 272 MET cc_start: 0.8734 (tpp) cc_final: 0.8418 (tpp) REVERT: D 371 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: D 383 ARG cc_start: 0.8686 (ttt-90) cc_final: 0.8471 (ttm110) outliers start: 79 outliers final: 44 residues processed: 249 average time/residue: 0.5641 time to fit residues: 160.0412 Evaluate side-chains 232 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 178 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 674 ARG Chi-restraints excluded: chain B residue 677 ARG Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 711 GLU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 674 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 238 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 228 optimal weight: 0.9990 chunk 211 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 433 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.156368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.102302 restraints weight = 29051.042| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.59 r_work: 0.3150 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20608 Z= 0.150 Angle : 0.618 11.954 27988 Z= 0.307 Chirality : 0.039 0.248 3172 Planarity : 0.006 0.116 3432 Dihedral : 5.267 92.703 2962 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.89 % Favored : 94.98 % Rotamer: Outliers : 3.63 % Allowed : 14.75 % Favored : 81.62 % 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: 0.63 (0.18), residues: 2432 helix: 1.96 (0.14), residues: 1364 sheet: 0.50 (0.56), residues: 68 loop : -1.91 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 682 TYR 0.026 0.001 TYR C 466 PHE 0.012 0.001 PHE D 389 TRP 0.008 0.001 TRP A 504 HIS 0.002 0.001 HIS D 308 Details of bonding type rmsd covalent geometry : bond 0.00367 (20608) covalent geometry : angle 0.61805 (27988) hydrogen bonds : bond 0.04229 ( 1014) hydrogen bonds : angle 3.76009 ( 2988) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 194 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 THR cc_start: 0.8164 (m) cc_final: 0.7959 (p) REVERT: A 250 MET cc_start: 0.8763 (mmm) cc_final: 0.8449 (mmm) REVERT: A 272 MET cc_start: 0.8714 (tpp) cc_final: 0.8159 (tpp) REVERT: A 276 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7936 (mm) REVERT: A 371 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7157 (mm-30) REVERT: A 512 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7909 (ptp-170) REVERT: A 677 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7250 (mmt-90) REVERT: A 701 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.7976 (ttm-80) REVERT: B 88 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7953 (p) REVERT: B 94 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7282 (pp) REVERT: B 165 ILE cc_start: 0.8640 (mt) cc_final: 0.8338 (mm) REVERT: B 230 GLN cc_start: 0.7545 (tt0) cc_final: 0.7244 (tt0) REVERT: B 250 MET cc_start: 0.8719 (mmm) cc_final: 0.8408 (mmm) REVERT: B 272 MET cc_start: 0.8712 (tpp) cc_final: 0.8399 (tpp) REVERT: B 428 MET cc_start: 0.7001 (mmp) cc_final: 0.5974 (pp-130) REVERT: B 489 THR cc_start: 0.7230 (t) cc_final: 0.6936 (t) REVERT: B 677 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7238 (mmt-90) REVERT: C 155 GLU cc_start: 0.6471 (tm-30) cc_final: 0.5923 (tp30) REVERT: C 167 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8232 (mp) REVERT: C 250 MET cc_start: 0.8706 (mmm) cc_final: 0.8474 (mmm) REVERT: C 272 MET cc_start: 0.8674 (tpp) cc_final: 0.8166 (tpp) REVERT: C 276 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7937 (mm) REVERT: C 489 THR cc_start: 0.6750 (m) cc_final: 0.6365 (t) REVERT: C 490 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7458 (pp20) REVERT: C 512 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7921 (ptp-170) REVERT: C 711 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7731 (pt0) REVERT: D 88 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.8022 (p) REVERT: D 177 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8499 (tt) REVERT: D 230 GLN cc_start: 0.7554 (tt0) cc_final: 0.7105 (tt0) REVERT: D 272 MET cc_start: 0.8727 (tpp) cc_final: 0.8432 (tpp) REVERT: D 383 ARG cc_start: 0.8683 (ttt-90) cc_final: 0.8471 (ttm110) REVERT: D 612 ARG cc_start: 0.8197 (ttp-170) cc_final: 0.7800 (ttt180) outliers start: 79 outliers final: 44 residues processed: 254 average time/residue: 0.5487 time to fit residues: 159.4677 Evaluate side-chains 239 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 181 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 674 ARG Chi-restraints excluded: chain B residue 677 ARG Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 711 GLU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 674 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 114 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 198 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 160 optimal weight: 0.0050 chunk 105 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 216 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 192 optimal weight: 7.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.157610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.103703 restraints weight = 29018.434| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.61 r_work: 0.3172 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 20608 Z= 0.126 Angle : 0.655 27.070 27988 Z= 0.306 Chirality : 0.039 0.316 3172 Planarity : 0.007 0.199 3432 Dihedral : 4.628 34.137 2956 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.69 % Favored : 95.19 % Rotamer: Outliers : 3.31 % Allowed : 15.90 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: 0.70 (0.18), residues: 2432 helix: 2.02 (0.14), residues: 1364 sheet: 0.52 (0.56), residues: 68 loop : -1.89 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 275 TYR 0.027 0.001 TYR A 466 PHE 0.010 0.001 PHE A 389 TRP 0.008 0.001 TRP D 504 HIS 0.002 0.000 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00306 (20608) covalent geometry : angle 0.65468 (27988) hydrogen bonds : bond 0.03791 ( 1014) hydrogen bonds : angle 3.70518 ( 2988) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 187 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 THR cc_start: 0.8169 (m) cc_final: 0.7960 (p) REVERT: A 250 MET cc_start: 0.8747 (mmm) cc_final: 0.8431 (mmm) REVERT: A 272 MET cc_start: 0.8709 (tpp) cc_final: 0.8109 (tpp) REVERT: A 276 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7926 (mm) REVERT: A 463 MET cc_start: 0.6707 (tmt) cc_final: 0.6496 (tmm) REVERT: A 512 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7895 (ptp-170) REVERT: A 677 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7244 (mmt-90) REVERT: A 701 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7997 (ttm-80) REVERT: B 94 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7297 (pp) REVERT: B 230 GLN cc_start: 0.7555 (tt0) cc_final: 0.7244 (tt0) REVERT: B 250 MET cc_start: 0.8671 (mmm) cc_final: 0.8453 (mmm) REVERT: B 272 MET cc_start: 0.8613 (tpp) cc_final: 0.8284 (tpp) REVERT: B 428 MET cc_start: 0.6983 (mmp) cc_final: 0.5926 (pp-130) REVERT: B 488 GLU cc_start: 0.7906 (mm-30) cc_final: 0.6748 (tm-30) REVERT: B 489 THR cc_start: 0.7172 (t) cc_final: 0.6782 (t) REVERT: B 677 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7207 (mmt-90) REVERT: C 155 GLU cc_start: 0.6376 (tm-30) cc_final: 0.5827 (tp30) REVERT: C 167 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8265 (mp) REVERT: C 250 MET cc_start: 0.8651 (mmm) cc_final: 0.8412 (mmm) REVERT: C 272 MET cc_start: 0.8664 (tpp) cc_final: 0.8109 (tpp) REVERT: C 276 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7976 (mm) REVERT: C 489 THR cc_start: 0.6958 (m) cc_final: 0.6650 (t) REVERT: C 490 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7511 (pp20) REVERT: C 512 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7934 (ptp-170) REVERT: C 711 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7733 (pt0) REVERT: D 88 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.8011 (p) REVERT: D 230 GLN cc_start: 0.7511 (tt0) cc_final: 0.6994 (tt0) REVERT: D 272 MET cc_start: 0.8734 (tpp) cc_final: 0.8410 (tpp) REVERT: D 371 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7379 (mm-30) REVERT: D 383 ARG cc_start: 0.8682 (ttt-90) cc_final: 0.8472 (ttm110) REVERT: D 612 ARG cc_start: 0.8162 (ttp-170) cc_final: 0.7691 (ttt180) outliers start: 72 outliers final: 39 residues processed: 243 average time/residue: 0.5547 time to fit residues: 154.2477 Evaluate side-chains 230 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 179 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 674 ARG Chi-restraints excluded: chain B residue 677 ARG Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 711 GLU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 674 ARG Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 239 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 241 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 156 optimal weight: 0.0050 chunk 79 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 214 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.159359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.105955 restraints weight = 28857.058| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.59 r_work: 0.3204 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20608 Z= 0.111 Angle : 0.615 19.154 27988 Z= 0.295 Chirality : 0.038 0.268 3172 Planarity : 0.006 0.173 3432 Dihedral : 4.519 37.607 2956 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.81 % Favored : 95.07 % Rotamer: Outliers : 2.71 % Allowed : 16.27 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: 0.83 (0.18), residues: 2432 helix: 2.18 (0.15), residues: 1360 sheet: 0.59 (0.57), residues: 68 loop : -1.89 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 682 TYR 0.029 0.001 TYR D 466 PHE 0.013 0.001 PHE D 462 TRP 0.009 0.001 TRP A 218 HIS 0.002 0.000 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00259 (20608) covalent geometry : angle 0.61532 (27988) hydrogen bonds : bond 0.03367 ( 1014) hydrogen bonds : angle 3.64059 ( 2988) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 192 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.8647 (mmm) cc_final: 0.8433 (mmm) REVERT: A 272 MET cc_start: 0.8696 (tpp) cc_final: 0.8106 (tpp) REVERT: A 276 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7862 (mm) REVERT: A 512 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7861 (ptp-170) REVERT: A 677 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7232 (mmt-90) REVERT: A 701 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8015 (ttm-80) REVERT: B 88 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7988 (p) REVERT: B 94 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7295 (pp) REVERT: B 272 MET cc_start: 0.8665 (tpp) cc_final: 0.8319 (tpp) REVERT: B 428 MET cc_start: 0.6974 (mmp) cc_final: 0.5907 (pp-130) REVERT: B 488 GLU cc_start: 0.8123 (mm-30) cc_final: 0.6955 (tm-30) REVERT: B 489 THR cc_start: 0.7202 (t) cc_final: 0.6768 (t) REVERT: B 556 GLU cc_start: 0.8140 (mp0) cc_final: 0.7899 (mp0) REVERT: B 677 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7176 (mmt-90) REVERT: C 155 GLU cc_start: 0.6399 (tm-30) cc_final: 0.5827 (tp30) REVERT: C 250 MET cc_start: 0.8603 (mmm) cc_final: 0.8381 (mmm) REVERT: C 272 MET cc_start: 0.8629 (tpp) cc_final: 0.8002 (tpp) REVERT: C 276 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7808 (mm) REVERT: C 489 THR cc_start: 0.7092 (m) cc_final: 0.6847 (t) REVERT: C 490 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7441 (pp20) REVERT: C 711 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7735 (pt0) REVERT: D 88 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.8025 (p) REVERT: D 230 GLN cc_start: 0.7524 (tt0) cc_final: 0.6990 (tt0) REVERT: D 272 MET cc_start: 0.8671 (tpp) cc_final: 0.8356 (tpp) REVERT: D 383 ARG cc_start: 0.8662 (ttt-90) cc_final: 0.8459 (ttm110) REVERT: D 612 ARG cc_start: 0.8160 (ttp-170) cc_final: 0.7862 (ttt180) outliers start: 59 outliers final: 27 residues processed: 236 average time/residue: 0.5336 time to fit residues: 144.4540 Evaluate side-chains 218 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 674 ARG Chi-restraints excluded: chain B residue 677 ARG Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 711 GLU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 674 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 150 optimal weight: 0.9990 chunk 176 optimal weight: 0.3980 chunk 12 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.159149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.105727 restraints weight = 28963.376| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.58 r_work: 0.3202 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 20608 Z= 0.117 Angle : 0.651 29.481 27988 Z= 0.302 Chirality : 0.038 0.354 3172 Planarity : 0.007 0.206 3432 Dihedral : 4.522 40.274 2956 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.52 % Favored : 95.35 % Rotamer: Outliers : 1.98 % Allowed : 16.91 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % 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: 0.82 (0.18), residues: 2432 helix: 2.14 (0.15), residues: 1368 sheet: 0.68 (0.57), residues: 68 loop : -1.88 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 275 TYR 0.030 0.001 TYR A 466 PHE 0.009 0.001 PHE A 389 TRP 0.007 0.001 TRP C 218 HIS 0.002 0.000 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00276 (20608) covalent geometry : angle 0.65125 (27988) hydrogen bonds : bond 0.03492 ( 1014) hydrogen bonds : angle 3.66456 ( 2988) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.8655 (mmm) cc_final: 0.8453 (mmm) REVERT: A 272 MET cc_start: 0.8669 (tpp) cc_final: 0.8062 (tpp) REVERT: A 276 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7862 (mm) REVERT: A 512 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7860 (ptp-170) REVERT: A 677 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7209 (mmt-90) REVERT: A 682 ARG cc_start: 0.7379 (ttp-110) cc_final: 0.6722 (ptm-80) REVERT: A 701 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.7989 (ttm-80) REVERT: B 88 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7992 (p) REVERT: B 94 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7262 (pp) REVERT: B 272 MET cc_start: 0.8657 (tpp) cc_final: 0.8322 (tpp) REVERT: B 428 MET cc_start: 0.7001 (mmp) cc_final: 0.5918 (pp-130) REVERT: B 488 GLU cc_start: 0.8102 (mm-30) cc_final: 0.6949 (tm-30) REVERT: B 489 THR cc_start: 0.7205 (t) cc_final: 0.6799 (t) REVERT: B 556 GLU cc_start: 0.8104 (mp0) cc_final: 0.7711 (mp0) REVERT: B 677 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7171 (mmt-90) REVERT: C 155 GLU cc_start: 0.6415 (tm-30) cc_final: 0.5841 (tp30) REVERT: C 250 MET cc_start: 0.8607 (mmm) cc_final: 0.8387 (mmm) REVERT: C 272 MET cc_start: 0.8640 (tpp) cc_final: 0.8092 (tpp) REVERT: C 276 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7872 (mm) REVERT: C 452 TRP cc_start: 0.8378 (t-100) cc_final: 0.8072 (t-100) REVERT: C 489 THR cc_start: 0.7015 (m) cc_final: 0.6795 (t) REVERT: C 490 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7298 (pt0) REVERT: C 512 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7900 (ptp-170) REVERT: C 711 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7744 (pt0) REVERT: D 88 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.8022 (p) REVERT: D 165 ILE cc_start: 0.8361 (mp) cc_final: 0.8137 (mp) REVERT: D 230 GLN cc_start: 0.7530 (tt0) cc_final: 0.6998 (tt0) REVERT: D 272 MET cc_start: 0.8669 (tpp) cc_final: 0.8349 (tpp) REVERT: D 371 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6952 (mm-30) REVERT: D 612 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7679 (ttt180) outliers start: 43 outliers final: 30 residues processed: 223 average time/residue: 0.5554 time to fit residues: 141.5812 Evaluate side-chains 224 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 674 ARG Chi-restraints excluded: chain B residue 677 ARG Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 711 GLU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 674 ARG Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 180 optimal weight: 20.0000 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 203 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 218 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.155800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.101314 restraints weight = 29019.616| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.59 r_work: 0.3138 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 20608 Z= 0.175 Angle : 0.680 24.964 27988 Z= 0.324 Chirality : 0.040 0.270 3172 Planarity : 0.007 0.189 3432 Dihedral : 4.695 42.256 2956 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.89 % Favored : 94.98 % Rotamer: Outliers : 2.25 % Allowed : 16.96 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2432 helix: 1.95 (0.14), residues: 1364 sheet: 0.56 (0.56), residues: 68 loop : -1.87 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 275 TYR 0.031 0.002 TYR C 466 PHE 0.016 0.001 PHE A 389 TRP 0.009 0.001 TRP A 504 HIS 0.003 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00432 (20608) covalent geometry : angle 0.67981 (27988) hydrogen bonds : bond 0.04524 ( 1014) hydrogen bonds : angle 3.80067 ( 2988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8346.29 seconds wall clock time: 142 minutes 12.17 seconds (8532.17 seconds total)