Starting phenix.real_space_refine on Sat Jul 4 10:00:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xeu_33159/07_2026/7xeu_33159.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xeu_33159/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xeu_33159/07_2026/7xeu_33159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xeu_33159/07_2026/7xeu_33159.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xeu_33159/07_2026/7xeu_33159.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xeu_33159/07_2026/7xeu_33159.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xeu_33159/07_2026/7xeu_33159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xeu_33159/07_2026/7xeu_33159.map" } 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-6108/lib/python3.11/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: 4.66, per 1000 atoms: 0.23 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: 1.81 Conformation dependent library (CDL) restraints added in 890.1 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: 0.51 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: 3.15 Time building geometry restraints manager: 2.38 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: 10908 17.62 - 35.23: 975 35.23 - 52.85: 135 52.85 - 70.47: 30 70.47 - 88.08: 12 Dihedral angle restraints: 12060 sinusoidal: 4892 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 12057 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: 1.270 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.120 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 13.228 88.084 7436 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/Z covalent geometry : bond 0.00441 / 0.19 (20608) covalent geometry : angle 0.83236 / 0.49 (27988) hydrogen bonds : bond 0.14628 / 9.38 ( 1014) hydrogen bonds : angle 5.11312 / 3.49 ( 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 : 0.780 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: 0.6096 time to fit residues: 238.8575 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 : 0.802 ------------------------------------------------------------------------------- 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... A 181 ASN B 229 HIS C 181 ASN C 230 GLN D 217 GLN D 408 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.159686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106023 restraints weight = 28874.503| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.93 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: 0.8204 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 20608 Z= 0.137 Angle : 0.659 11.986 27988 Z= 0.329 Chirality : 0.040 0.246 3172 Planarity : 0.006 0.129 3432 Dihedral : 6.258 92.738 2759 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.52 % Favored : 95.23 % Rotamer: Outliers : 2.67 % Allowed : 9.74 % Favored : 87.59 % 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: 1.73 (0.15), residues: 1368 sheet: -0.12 (0.52), residues: 68 loop : -2.20 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 682 TYR 0.020 0.001 TYR B 466 PHE 0.010 0.001 PHE B 467 TRP 0.015 0.001 TRP A 173 HIS 0.004 0.001 HIS D 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (20608) covalent geometry : angle 0.65887 / 0.33 (27988) hydrogen bonds : bond 0.04260 / 2.89 ( 1014) hydrogen bonds : angle 4.03982 / 2.80 ( 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 291 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 233 time to evaluate : 0.800 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: A 155 GLU cc_start: 0.6923 (tp30) cc_final: 0.6414 (tm-30) REVERT: A 272 MET cc_start: 0.8535 (tpp) cc_final: 0.8312 (tpp) REVERT: A 371 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7259 (mm-30) REVERT: B 165 ILE cc_start: 0.8628 (mt) cc_final: 0.8282 (mm) REVERT: B 169 LYS cc_start: 0.8210 (mmpt) cc_final: 0.7872 (mptp) REVERT: B 230 GLN cc_start: 0.7528 (tt0) cc_final: 0.7301 (tt0) REVERT: B 272 MET cc_start: 0.8551 (tpp) cc_final: 0.8342 (tpp) REVERT: B 428 MET cc_start: 0.6924 (mmp) cc_final: 0.6007 (pp-130) REVERT: B 489 THR cc_start: 0.7353 (t) cc_final: 0.7097 (t) REVERT: B 677 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7319 (mmt-90) REVERT: C 155 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6144 (tp30) REVERT: C 250 MET cc_start: 0.8530 (mmm) cc_final: 0.8188 (mmt) REVERT: C 272 MET cc_start: 0.8486 (tpp) cc_final: 0.8277 (tpp) REVERT: D 155 GLU cc_start: 0.6946 (tp30) cc_final: 0.6455 (tm-30) REVERT: D 230 GLN cc_start: 0.7793 (tt0) cc_final: 0.7333 (tt0) REVERT: D 272 MET cc_start: 0.8618 (tpp) cc_final: 0.8318 (tpp) outliers start: 58 outliers final: 33 residues processed: 271 average time/residue: 0.4847 time to fit residues: 151.7131 Evaluate side-chains 217 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 180 GLU 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 529 LEU Chi-restraints excluded: chain B residue 677 ARG Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 230 GLN 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 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: 9.9990 chunk 166 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 85 optimal weight: 0.0370 chunk 136 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 59 optimal weight: 0.0370 overall best weight: 0.9338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.159762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106082 restraints weight = 28961.074| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.60 r_work: 0.3206 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1634 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= 0.122 Angle : 0.599 10.299 27988 Z= 0.300 Chirality : 0.039 0.252 3172 Planarity : 0.006 0.123 3432 Dihedral : 6.034 90.038 2741 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.56 % Favored : 95.23 % Rotamer: Outliers : 3.12 % Allowed : 11.86 % Favored : 85.02 % 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: 0.47 (0.18), residues: 2432 helix: 1.89 (0.15), residues: 1364 sheet: 0.22 (0.53), residues: 68 loop : -2.07 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 275 TYR 0.020 0.001 TYR C 466 PHE 0.012 0.001 PHE D 76 TRP 0.023 0.001 TRP D 173 HIS 0.004 0.000 HIS D 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (20608) covalent geometry : angle 0.59948 / 0.30 (27988) hydrogen bonds : bond 0.03852 / 2.63 ( 1014) hydrogen bonds : angle 3.83428 / 2.67 ( 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 279 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 211 time to evaluate : 0.786 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: 0.8797 (mmm) cc_final: 0.8432 (mmm) REVERT: A 272 MET cc_start: 0.8591 (tpp) cc_final: 0.8258 (tpp) REVERT: A 371 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: B 165 ILE cc_start: 0.8627 (mt) cc_final: 0.8340 (mm) REVERT: B 230 GLN cc_start: 0.7589 (tt0) cc_final: 0.7326 (tt0) REVERT: B 250 MET cc_start: 0.8706 (mmm) cc_final: 0.8448 (mmt) REVERT: B 272 MET cc_start: 0.8671 (tpp) cc_final: 0.8337 (tpp) REVERT: B 428 MET cc_start: 0.6932 (mmp) cc_final: 0.6009 (pp-130) REVERT: B 489 THR cc_start: 0.7353 (t) cc_final: 0.7042 (t) REVERT: C 155 GLU cc_start: 0.6406 (tm-30) cc_final: 0.5874 (tp30) REVERT: C 167 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8028 (mp) REVERT: C 250 MET cc_start: 0.8686 (mmm) cc_final: 0.8442 (mmt) REVERT: C 272 MET cc_start: 0.8560 (tpp) cc_final: 0.8257 (tpp) REVERT: C 711 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7643 (pt0) REVERT: D 230 GLN cc_start: 0.7682 (tt0) cc_final: 0.7238 (tt0) REVERT: D 257 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: D 272 MET cc_start: 0.8768 (tpp) cc_final: 0.8443 (tpp) outliers start: 68 outliers final: 34 residues processed: 255 average time/residue: 0.5191 time to fit residues: 153.4093 Evaluate side-chains 221 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 185 VAL 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 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 438 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 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 226 GLU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 426 ASP 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 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 180 GLU 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 371 GLU Chi-restraints excluded: chain D residue 438 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 111 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 234 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 144 optimal weight: 0.0270 chunk 201 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN B 181 ASN B 186 HIS D 186 HIS D 634 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.160238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107295 restraints weight = 28972.741| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.54 r_work: 0.3226 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 20608 Z= 0.112 Angle : 0.594 10.148 27988 Z= 0.293 Chirality : 0.038 0.251 3172 Planarity : 0.005 0.119 3432 Dihedral : 5.971 89.694 2741 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer: Outliers : 3.40 % Allowed : 13.42 % Favored : 83.18 % 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: 0.59 (0.18), residues: 2432 helix: 1.95 (0.15), residues: 1368 sheet: 0.40 (0.55), residues: 68 loop : -1.98 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 682 TYR 0.023 0.001 TYR C 466 PHE 0.009 0.001 PHE D 389 TRP 0.016 0.001 TRP D 173 HIS 0.002 0.000 HIS D 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (20608) covalent geometry : angle 0.59352 / 0.29 (27988) hydrogen bonds : bond 0.03552 / 2.43 ( 1014) hydrogen bonds : angle 3.74555 / 2.61 ( 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 275 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 201 time to evaluate : 0.748 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: A 88 THR cc_start: 0.8209 (m) cc_final: 0.7992 (p) REVERT: A 173 TRP cc_start: 0.7421 (t60) cc_final: 0.7166 (t60) REVERT: A 250 MET cc_start: 0.8679 (mmm) cc_final: 0.8306 (mmm) REVERT: A 272 MET cc_start: 0.8588 (tpp) cc_final: 0.8226 (tpp) REVERT: A 371 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: B 165 ILE cc_start: 0.8672 (mt) cc_final: 0.8355 (mm) REVERT: B 230 GLN cc_start: 0.7630 (tt0) cc_final: 0.7342 (tt0) REVERT: B 250 MET cc_start: 0.8716 (mmm) cc_final: 0.8435 (mmm) REVERT: B 272 MET cc_start: 0.8733 (tpp) cc_final: 0.8438 (tpp) REVERT: B 428 MET cc_start: 0.6912 (mmp) cc_final: 0.5989 (pp-130) REVERT: B 489 THR cc_start: 0.7343 (t) cc_final: 0.7010 (t) REVERT: B 677 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7255 (mmt-90) REVERT: C 155 GLU cc_start: 0.6385 (tm-30) cc_final: 0.5839 (tp30) REVERT: C 167 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8083 (mp) REVERT: C 250 MET cc_start: 0.8667 (mmm) cc_final: 0.8412 (mmm) REVERT: C 272 MET cc_start: 0.8543 (tpp) cc_final: 0.7959 (tpp) REVERT: C 276 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7809 (mm) REVERT: C 711 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: D 230 GLN cc_start: 0.7656 (tt0) cc_final: 0.7220 (tt0) REVERT: D 272 MET cc_start: 0.8698 (tpp) cc_final: 0.8402 (tpp) outliers start: 74 outliers final: 34 residues processed: 251 average time/residue: 0.5089 time to fit residues: 148.5243 Evaluate side-chains 221 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 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 511 THR Chi-restraints excluded: chain A residue 529 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 430 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 666 MET 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 276 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 426 ASP 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 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 180 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 159 optimal weight: 4.9990 chunk 187 optimal weight: 0.0040 chunk 75 optimal weight: 3.9990 chunk 239 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 0.0270 chunk 55 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 79 optimal weight: 0.1980 overall best weight: 0.3650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN B 181 ASN B 634 ASN C 186 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.161739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.108989 restraints weight = 28990.718| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.59 r_work: 0.3251 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 20608 Z= 0.106 Angle : 0.573 10.114 27988 Z= 0.284 Chirality : 0.038 0.247 3172 Planarity : 0.005 0.116 3432 Dihedral : 5.611 89.364 2741 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.69 % Favored : 95.15 % Rotamer: Outliers : 3.35 % Allowed : 13.79 % Favored : 82.86 % 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: 0.71 (0.18), residues: 2432 helix: 2.07 (0.15), residues: 1368 sheet: 0.55 (0.56), residues: 68 loop : -1.96 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 682 TYR 0.023 0.001 TYR C 466 PHE 0.008 0.001 PHE C 193 TRP 0.017 0.001 TRP D 173 HIS 0.002 0.000 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (20608) covalent geometry : angle 0.57329 / 0.28 (27988) hydrogen bonds : bond 0.03221 / 2.20 ( 1014) hydrogen bonds : angle 3.66601 / 2.56 ( 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 285 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 212 time to evaluate : 0.694 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: 0.8213 (m) cc_final: 0.7999 (p) REVERT: A 173 TRP cc_start: 0.7593 (t60) cc_final: 0.7370 (t60) REVERT: A 185 VAL cc_start: 0.8028 (t) cc_final: 0.7600 (m) REVERT: A 250 MET cc_start: 0.8722 (mmm) cc_final: 0.8441 (mmm) REVERT: A 272 MET cc_start: 0.8582 (tpp) cc_final: 0.8008 (tpp) REVERT: A 276 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7734 (mm) REVERT: A 371 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7190 (mm-30) REVERT: B 94 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7271 (pp) REVERT: B 230 GLN cc_start: 0.7565 (tt0) cc_final: 0.7276 (tt0) REVERT: B 250 MET cc_start: 0.8689 (mmm) cc_final: 0.8405 (mmm) REVERT: B 272 MET cc_start: 0.8685 (tpp) cc_final: 0.8381 (tpp) REVERT: B 428 MET cc_start: 0.6950 (mmp) cc_final: 0.5984 (pp-130) REVERT: B 489 THR cc_start: 0.7298 (t) cc_final: 0.6955 (t) REVERT: B 677 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7227 (mmt-90) REVERT: C 155 GLU cc_start: 0.6446 (tm-30) cc_final: 0.5892 (tp30) REVERT: C 167 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8122 (mp) REVERT: C 250 MET cc_start: 0.8641 (mmm) cc_final: 0.8384 (mmm) REVERT: C 272 MET cc_start: 0.8552 (tpp) cc_final: 0.8033 (tpp) REVERT: C 276 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7826 (mm) REVERT: C 711 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7669 (pt0) REVERT: D 230 GLN cc_start: 0.7641 (tt0) cc_final: 0.7204 (tt0) REVERT: D 257 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7476 (pt0) REVERT: D 272 MET cc_start: 0.8675 (tpp) cc_final: 0.8392 (tpp) outliers start: 73 outliers final: 30 residues processed: 262 average time/residue: 0.4645 time to fit residues: 141.6415 Evaluate side-chains 221 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 371 GLU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 313 GLU 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 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 282 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 426 ASP 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 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 180 GLU Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 281 GLN 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 438 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 67 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN C 181 ASN C 311 GLN D 181 ASN D 217 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.155022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100709 restraints weight = 28759.015| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.58 r_work: 0.3127 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20608 Z= 0.205 Angle : 0.675 10.806 27988 Z= 0.334 Chirality : 0.041 0.261 3172 Planarity : 0.006 0.116 3432 Dihedral : 5.325 88.924 2741 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.14 % Favored : 94.74 % Rotamer: Outliers : 3.68 % Allowed : 14.38 % Favored : 81.94 % 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: 0.45 (0.17), residues: 2432 helix: 1.78 (0.14), residues: 1364 sheet: 0.53 (0.56), residues: 68 loop : -1.93 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 682 TYR 0.025 0.002 TYR C 466 PHE 0.013 0.002 PHE D 389 TRP 0.014 0.001 TRP D 173 HIS 0.005 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.20 (20608) covalent geometry : angle 0.67494 / 0.33 (27988) hydrogen bonds : bond 0.05055 / 3.44 ( 1014) hydrogen bonds : angle 3.86116 / 2.69 ( 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 278 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 198 time to evaluate : 0.744 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: 0.8218 (m) cc_final: 0.8006 (p) REVERT: A 250 MET cc_start: 0.8815 (mmm) cc_final: 0.8504 (mmm) REVERT: A 489 THR cc_start: 0.6112 (m) cc_final: 0.5897 (m) REVERT: B 88 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7982 (p) REVERT: B 94 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7286 (pp) REVERT: B 230 GLN cc_start: 0.7574 (tt0) cc_final: 0.7260 (tt0) REVERT: B 250 MET cc_start: 0.8773 (mmm) cc_final: 0.8458 (mmm) REVERT: B 428 MET cc_start: 0.7002 (mmp) cc_final: 0.5999 (pp-130) REVERT: B 489 THR cc_start: 0.7269 (t) cc_final: 0.6955 (t) REVERT: B 677 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7246 (mmt-90) REVERT: C 155 GLU cc_start: 0.6477 (tm-30) cc_final: 0.5907 (tp30) REVERT: C 167 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8195 (mp) REVERT: C 250 MET cc_start: 0.8747 (mmm) cc_final: 0.8439 (mmm) REVERT: C 452 TRP cc_start: 0.8392 (t-100) cc_final: 0.8112 (t-100) REVERT: C 711 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: D 88 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7946 (p) REVERT: D 230 GLN cc_start: 0.7500 (tt0) cc_final: 0.7092 (tt0) REVERT: D 257 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7533 (pt0) REVERT: D 272 MET cc_start: 0.8747 (tpp) cc_final: 0.8507 (tpp) REVERT: D 371 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7212 (mm-30) outliers start: 80 outliers final: 44 residues processed: 255 average time/residue: 0.5002 time to fit residues: 146.7601 Evaluate side-chains 230 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 187 ILE Chi-restraints excluded: chain A residue 277 CYS 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 B residue 88 THR Chi-restraints excluded: chain B residue 94 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 431 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 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 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 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 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 180 GLU 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 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 674 ARG Chi-restraints excluded: chain D residue 695 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 238 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 228 optimal weight: 0.7980 chunk 211 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.156344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102052 restraints weight = 29021.975| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.59 r_work: 0.3146 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 20608 Z= 0.151 Angle : 0.648 24.914 27988 Z= 0.313 Chirality : 0.039 0.304 3172 Planarity : 0.006 0.193 3432 Dihedral : 5.063 90.341 2735 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.85 % Favored : 95.02 % Rotamer: Outliers : 3.08 % Allowed : 15.81 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2432 helix: 1.88 (0.14), residues: 1364 sheet: 0.53 (0.56), residues: 68 loop : -1.88 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 682 TYR 0.026 0.001 TYR C 466 PHE 0.010 0.001 PHE C 389 TRP 0.008 0.001 TRP B 173 HIS 0.002 0.001 HIS D 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (20608) covalent geometry : angle 0.64764 / 0.31 (27988) hydrogen bonds : bond 0.04334 / 2.95 ( 1014) hydrogen bonds : angle 3.81237 / 2.66 ( 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 263 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 196 time to evaluate : 0.773 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: 0.8759 (mmm) cc_final: 0.8421 (mmm) REVERT: A 272 MET cc_start: 0.8786 (tpp) cc_final: 0.8354 (tpp) REVERT: A 489 THR cc_start: 0.6282 (m) cc_final: 0.6056 (m) REVERT: B 88 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7985 (p) REVERT: B 94 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7309 (pp) REVERT: B 230 GLN cc_start: 0.7529 (tt0) cc_final: 0.7265 (tt0) REVERT: B 250 MET cc_start: 0.8735 (mmm) cc_final: 0.8396 (mmm) REVERT: B 272 MET cc_start: 0.8711 (tpp) cc_final: 0.8400 (tpp) REVERT: B 428 MET cc_start: 0.7016 (mmp) cc_final: 0.5982 (pp-130) REVERT: B 489 THR cc_start: 0.7227 (t) cc_final: 0.6920 (t) REVERT: B 677 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7224 (mmt-90) REVERT: C 155 GLU cc_start: 0.6476 (tm-30) cc_final: 0.5927 (tp30) REVERT: C 167 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8373 (mp) REVERT: C 250 MET cc_start: 0.8708 (mmm) cc_final: 0.8375 (mmm) REVERT: C 272 MET cc_start: 0.8713 (tpp) cc_final: 0.8405 (tpp) REVERT: C 489 THR cc_start: 0.6742 (m) cc_final: 0.6464 (t) REVERT: C 711 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7731 (pt0) REVERT: D 88 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.8034 (p) REVERT: D 230 GLN cc_start: 0.7540 (tt0) cc_final: 0.7080 (tt0) REVERT: D 257 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: D 272 MET cc_start: 0.8725 (tpp) cc_final: 0.8360 (tpp) REVERT: D 612 ARG cc_start: 0.8250 (ttp-170) cc_final: 0.7732 (ttt180) outliers start: 67 outliers final: 37 residues processed: 247 average time/residue: 0.5295 time to fit residues: 151.1183 Evaluate side-chains 227 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 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 B residue 88 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 426 ASP 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 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 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 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 180 GLU Chi-restraints excluded: chain D residue 257 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 438 LEU Chi-restraints excluded: chain D residue 492 TYR 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: 1.9990 chunk 119 optimal weight: 20.0000 chunk 198 optimal weight: 7.9990 chunk 86 optimal weight: 0.0770 chunk 75 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 216 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 192 optimal weight: 4.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN C 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.158011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.104025 restraints weight = 28987.629| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.61 r_work: 0.3175 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 20608 Z= 0.122 Angle : 0.647 27.427 27988 Z= 0.307 Chirality : 0.039 0.315 3172 Planarity : 0.006 0.199 3432 Dihedral : 4.471 50.668 2732 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.89 % Favored : 94.98 % Rotamer: Outliers : 3.22 % Allowed : 15.90 % Favored : 80.88 % 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: 0.64 (0.18), residues: 2432 helix: 1.94 (0.14), residues: 1364 sheet: 0.57 (0.56), residues: 68 loop : -1.87 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 275 TYR 0.026 0.001 TYR C 466 PHE 0.014 0.001 PHE B 424 TRP 0.007 0.001 TRP B 173 HIS 0.002 0.000 HIS D 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (20608) covalent geometry : angle 0.64717 / 0.31 (27988) hydrogen bonds : bond 0.03824 / 2.60 ( 1014) hydrogen bonds : angle 3.75605 / 2.62 ( 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 255 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 185 time to evaluate : 0.782 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: 0.8743 (mmm) cc_final: 0.8413 (mmm) REVERT: A 272 MET cc_start: 0.8777 (tpp) cc_final: 0.8096 (tpp) REVERT: A 276 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7823 (mm) REVERT: A 463 MET cc_start: 0.6780 (tmt) cc_final: 0.6541 (tmm) REVERT: A 677 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7184 (mmt-90) REVERT: A 701 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.7977 (ttm-80) REVERT: B 88 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7982 (p) REVERT: B 94 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7300 (pp) REVERT: B 230 GLN cc_start: 0.7500 (tt0) cc_final: 0.7203 (tt0) REVERT: B 250 MET cc_start: 0.8684 (mmm) cc_final: 0.8441 (mmm) REVERT: B 272 MET cc_start: 0.8618 (tpp) cc_final: 0.8285 (tpp) REVERT: B 428 MET cc_start: 0.7064 (mmp) cc_final: 0.6062 (pp-130) REVERT: B 489 THR cc_start: 0.7244 (t) cc_final: 0.6953 (t) REVERT: B 677 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7192 (mmt-90) REVERT: C 155 GLU cc_start: 0.6449 (tm-30) cc_final: 0.5860 (tp30) REVERT: C 250 MET cc_start: 0.8660 (mmm) cc_final: 0.8428 (mmm) REVERT: C 272 MET cc_start: 0.8676 (tpp) cc_final: 0.8080 (tpp) REVERT: C 276 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7887 (mm) REVERT: C 711 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7719 (pt0) REVERT: D 88 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.8039 (p) REVERT: D 230 GLN cc_start: 0.7575 (tt0) cc_final: 0.7116 (tt0) REVERT: D 272 MET cc_start: 0.8729 (tpp) cc_final: 0.8405 (tpp) REVERT: D 371 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7378 (mm-30) REVERT: D 612 ARG cc_start: 0.8202 (ttp-170) cc_final: 0.7640 (ttt180) outliers start: 70 outliers final: 31 residues processed: 234 average time/residue: 0.5830 time to fit residues: 156.4861 Evaluate side-chains 217 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 321 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 511 THR 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 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 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 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 180 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 438 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 674 ARG 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: 9.9990 chunk 241 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 156 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 214 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.158903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105411 restraints weight = 28797.426| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.58 r_work: 0.3196 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20608 Z= 0.118 Angle : 0.629 19.555 27988 Z= 0.303 Chirality : 0.038 0.271 3172 Planarity : 0.006 0.174 3432 Dihedral : 4.331 46.573 2732 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.69 % Favored : 95.19 % Rotamer: Outliers : 2.30 % Allowed : 16.73 % Favored : 80.97 % 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: 0.76 (0.18), residues: 2432 helix: 2.06 (0.15), residues: 1360 sheet: 0.65 (0.57), residues: 68 loop : -1.85 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 682 TYR 0.027 0.001 TYR B 466 PHE 0.013 0.001 PHE D 462 TRP 0.007 0.001 TRP A 504 HIS 0.002 0.000 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (20608) covalent geometry : angle 0.62931 / 0.30 (27988) hydrogen bonds : bond 0.03567 / 2.42 ( 1014) hydrogen bonds : angle 3.70829 / 2.59 ( 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 239 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 0.806 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: 0.8694 (mmm) cc_final: 0.8470 (mmm) REVERT: A 272 MET cc_start: 0.8786 (tpp) cc_final: 0.8130 (tpp) REVERT: A 276 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7833 (mm) REVERT: A 371 GLU cc_start: 0.7236 (mm-30) cc_final: 0.7033 (mm-30) REVERT: A 463 MET cc_start: 0.6724 (tmt) cc_final: 0.6488 (tmm) REVERT: A 677 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7172 (mmt-90) REVERT: A 701 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7990 (ttm-80) REVERT: B 88 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7990 (p) REVERT: B 94 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7295 (pp) REVERT: B 250 MET cc_start: 0.8667 (mmm) cc_final: 0.8430 (mmm) REVERT: B 272 MET cc_start: 0.8686 (tpp) cc_final: 0.8327 (tpp) REVERT: B 428 MET cc_start: 0.6935 (mmp) cc_final: 0.6014 (pp-130) REVERT: B 488 GLU cc_start: 0.8110 (mm-30) cc_final: 0.6938 (tm-30) REVERT: B 489 THR cc_start: 0.7187 (t) cc_final: 0.6786 (t) REVERT: B 677 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7184 (mmt-90) REVERT: C 155 GLU cc_start: 0.6372 (tm-30) cc_final: 0.5803 (tp30) REVERT: C 250 MET cc_start: 0.8624 (mmm) cc_final: 0.8398 (mmm) REVERT: C 272 MET cc_start: 0.8670 (tpp) cc_final: 0.8070 (tpp) REVERT: C 276 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7837 (mm) REVERT: C 489 THR cc_start: 0.7061 (m) cc_final: 0.6781 (t) REVERT: C 512 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7926 (ptp-170) REVERT: C 711 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7792 (pt0) REVERT: D 88 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.8026 (p) REVERT: D 230 GLN cc_start: 0.7556 (tt0) cc_final: 0.7087 (tt0) REVERT: D 272 MET cc_start: 0.8657 (tpp) cc_final: 0.8326 (tpp) REVERT: D 371 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7217 (mm-30) REVERT: D 612 ARG cc_start: 0.8181 (ttp-170) cc_final: 0.7697 (ttt180) outliers start: 50 outliers final: 29 residues processed: 228 average time/residue: 0.5376 time to fit residues: 141.0459 Evaluate side-chains 219 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 321 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 511 THR 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 321 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 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 512 ARG 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 180 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL 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 511 THR 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: 3.9990 chunk 176 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 228 optimal weight: 0.6980 chunk 119 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN C 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.158616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104904 restraints weight = 28974.392| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.59 r_work: 0.3189 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20608 Z= 0.124 Angle : 0.641 16.198 27988 Z= 0.307 Chirality : 0.039 0.272 3172 Planarity : 0.006 0.161 3432 Dihedral : 4.279 42.324 2732 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.48 % Favored : 95.39 % Rotamer: Outliers : 1.88 % Allowed : 17.05 % Favored : 81.07 % 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: 0.77 (0.18), residues: 2432 helix: 2.05 (0.15), residues: 1364 sheet: 0.70 (0.57), residues: 68 loop : -1.82 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 275 TYR 0.029 0.001 TYR C 466 PHE 0.010 0.001 PHE A 389 TRP 0.007 0.001 TRP A 218 HIS 0.002 0.000 HIS B 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (20608) covalent geometry : angle 0.64139 / 0.31 (27988) hydrogen bonds : bond 0.03719 / 2.53 ( 1014) hydrogen bonds : angle 3.75141 / 2.62 ( 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 231 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.783 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: 0.8674 (mmm) cc_final: 0.8449 (mmm) REVERT: A 272 MET cc_start: 0.8793 (tpp) cc_final: 0.8120 (tpp) REVERT: A 276 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7826 (mm) REVERT: A 612 ARG cc_start: 0.8198 (ttp-170) cc_final: 0.7887 (ttt180) REVERT: A 677 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7195 (mmt-90) REVERT: A 701 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7963 (ttm-80) REVERT: B 88 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7995 (p) REVERT: B 94 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7268 (pp) REVERT: B 250 MET cc_start: 0.8670 (mmm) cc_final: 0.8442 (mmm) REVERT: B 272 MET cc_start: 0.8670 (tpp) cc_final: 0.8317 (tpp) REVERT: B 428 MET cc_start: 0.7093 (mmp) cc_final: 0.5995 (pp-130) REVERT: B 488 GLU cc_start: 0.8097 (mm-30) cc_final: 0.6944 (tm-30) REVERT: B 489 THR cc_start: 0.7231 (t) cc_final: 0.6822 (t) REVERT: B 677 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7171 (mmt-90) REVERT: C 155 GLU cc_start: 0.6415 (tm-30) cc_final: 0.5844 (tp30) REVERT: C 250 MET cc_start: 0.8641 (mmm) cc_final: 0.8416 (mmm) REVERT: C 272 MET cc_start: 0.8627 (tpp) cc_final: 0.8029 (tpp) REVERT: C 276 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7857 (mm) REVERT: C 489 THR cc_start: 0.7027 (m) cc_final: 0.6752 (t) REVERT: C 512 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7914 (ptp-170) REVERT: C 711 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7754 (pt0) REVERT: D 88 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.8033 (p) REVERT: D 230 GLN cc_start: 0.7511 (tt0) cc_final: 0.6994 (tt0) REVERT: D 272 MET cc_start: 0.8663 (tpp) cc_final: 0.8336 (tpp) REVERT: D 371 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7144 (mm-30) REVERT: D 612 ARG cc_start: 0.8179 (ttp-170) cc_final: 0.7650 (ttt180) outliers start: 41 outliers final: 29 residues processed: 223 average time/residue: 0.5879 time to fit residues: 149.8460 Evaluate side-chains 219 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 321 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 511 THR 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 321 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 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 512 ARG 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 180 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL 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 511 THR 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 180 optimal weight: 20.0000 chunk 34 optimal weight: 0.0270 chunk 70 optimal weight: 8.9990 chunk 196 optimal weight: 9.9990 chunk 234 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 218 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.158796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105127 restraints weight = 28959.887| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.59 r_work: 0.3192 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 20608 Z= 0.123 Angle : 0.635 13.869 27988 Z= 0.305 Chirality : 0.039 0.253 3172 Planarity : 0.006 0.151 3432 Dihedral : 4.221 40.991 2732 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.52 % Favored : 95.35 % Rotamer: Outliers : 2.11 % Allowed : 16.73 % Favored : 81.16 % 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: 0.78 (0.18), residues: 2432 helix: 2.04 (0.15), residues: 1368 sheet: 0.74 (0.57), residues: 68 loop : -1.80 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 275 TYR 0.029 0.001 TYR C 466 PHE 0.011 0.001 PHE C 193 TRP 0.006 0.001 TRP A 218 HIS 0.006 0.000 HIS D 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (20608) covalent geometry : angle 0.63532 / 0.30 (27988) hydrogen bonds : bond 0.03713 / 2.53 ( 1014) hydrogen bonds : angle 3.75550 / 2.63 ( 2988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8310.94 seconds wall clock time: 142 minutes 7.57 seconds (8527.57 seconds total)