Starting phenix.real_space_refine on Thu Feb 5 03:11:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9njc_49479/02_2026/9njc_49479.cif Found real_map, /net/cci-nas-00/data/ceres_data/9njc_49479/02_2026/9njc_49479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9njc_49479/02_2026/9njc_49479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9njc_49479/02_2026/9njc_49479.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9njc_49479/02_2026/9njc_49479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9njc_49479/02_2026/9njc_49479.map" } resolution = 2.36 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= 0.007 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 60 5.16 5 C 9072 2.51 5 N 2449 2.21 5 O 2786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14370 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4788 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain: "B" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4788 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain: "C" Number of atoms: 4779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4779 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 31, 'TRANS': 591} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.60, per 1000 atoms: 0.25 Number of scatterers: 14370 At special positions: 0 Unit cell: (108.655, 108.655, 106.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 3 15.00 O 2786 8.00 N 2449 7.00 C 9072 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: 1.25 Conformation dependent library (CDL) restraints added in 616.0 milliseconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 12 sheets defined 43.4% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 164 through 180 removed outlier: 4.334A pdb=" N LEU A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 237 through 266 removed outlier: 3.798A pdb=" N GLN A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 300 removed outlier: 6.459A pdb=" N GLU A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 328 removed outlier: 3.646A pdb=" N GLU A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 356 removed outlier: 3.560A pdb=" N ILE A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 444 through 459 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 482 through 499 Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 567 through 593 removed outlier: 3.584A pdb=" N LYS A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 625 through 636 removed outlier: 3.531A pdb=" N GLY A 636 " --> pdb=" O GLN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'B' and resid 104 through 111 removed outlier: 3.725A pdb=" N ALA B 107 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA B 109 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.501A pdb=" N GLU B 120 " --> pdb=" O TYR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 164 through 180 removed outlier: 4.286A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 237 through 267 removed outlier: 3.712A pdb=" N GLN B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 300 removed outlier: 5.541A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 328 removed outlier: 3.611A pdb=" N GLN B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 356 removed outlier: 3.721A pdb=" N ILE B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 482 through 498 removed outlier: 3.658A pdb=" N ALA B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 567 through 593 removed outlier: 3.628A pdb=" N THR B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 622 Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 653 through 669 removed outlier: 3.791A pdb=" N PHE B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 Processing helix chain 'C' and resid 115 through 118 Processing helix chain 'C' and resid 124 through 139 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 164 through 180 removed outlier: 4.182A pdb=" N LEU C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.752A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 237 through 267 removed outlier: 3.647A pdb=" N GLN C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 301 removed outlier: 5.890A pdb=" N GLU C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 328 removed outlier: 3.693A pdb=" N GLU C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 356 removed outlier: 3.604A pdb=" N PHE C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 352 " --> pdb=" O PHE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.516A pdb=" N ILE C 406 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 417 removed outlier: 3.565A pdb=" N ASN C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 444 through 459 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 482 through 499 Processing helix chain 'C' and resid 534 through 540 Processing helix chain 'C' and resid 567 through 593 removed outlier: 3.535A pdb=" N VAL C 571 " --> pdb=" O PRO C 567 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 622 Processing helix chain 'C' and resid 625 through 636 removed outlier: 3.644A pdb=" N LYS C 629 " --> pdb=" O GLY C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 668 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51 removed outlier: 6.407A pdb=" N ALA A 79 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 99 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N CYS A 154 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP A 101 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N LEU A 156 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ARG A 103 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N ALA A 158 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 202 removed outlier: 4.019A pdb=" N ILE A 195 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU A 214 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 215 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA A 231 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 217 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU A 229 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 219 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 227 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A 561 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 229 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR A 555 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET A 543 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 513 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A 526 " --> pdb=" O LYS A 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 374 removed outlier: 6.236A pdb=" N GLN A 392 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 611 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.323A pdb=" N ALA B 79 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 99 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N CYS B 154 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP B 101 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LEU B 156 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ARG B 103 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N ALA B 158 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 202 removed outlier: 4.066A pdb=" N ILE B 195 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU B 214 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN B 215 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA B 231 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 217 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU B 229 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA B 219 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 227 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE B 561 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 229 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR B 555 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET B 543 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 513 " --> pdb=" O MET B 543 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA B 510 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR B 531 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY B 512 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B 529 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B 514 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR B 527 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS B 516 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 370 through 374 removed outlier: 6.274A pdb=" N GLN B 392 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 606 through 611 Processing sheet with id=AA9, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.441A pdb=" N ALA C 79 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 103 " --> pdb=" O CYS C 154 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU C 156 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 199 through 202 removed outlier: 4.107A pdb=" N ILE C 195 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU C 214 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN C 215 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA C 231 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 217 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU C 229 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA C 219 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL C 227 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE C 561 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 229 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR C 555 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N MET C 543 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU C 513 " --> pdb=" O MET C 543 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP C 526 " --> pdb=" O LYS C 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 370 through 371 removed outlier: 6.343A pdb=" N GLN C 392 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 606 through 611 834 hydrogen bonds defined for protein. 2337 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.66 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: 4785 1.34 - 1.46: 2851 1.46 - 1.58: 6866 1.58 - 1.70: 0 1.70 - 1.82: 99 Bond restraints: 14601 Sorted by residual: bond pdb=" N ASN C 444 " pdb=" CA ASN C 444 " ideal model delta sigma weight residual 1.453 1.481 -0.028 1.27e-02 6.20e+03 4.85e+00 bond pdb=" N ARG B 118 " pdb=" CA ARG B 118 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.25e-02 6.40e+03 4.30e+00 bond pdb=" N ASN A 444 " pdb=" CA ASN A 444 " ideal model delta sigma weight residual 1.462 1.488 -0.026 1.28e-02 6.10e+03 4.19e+00 bond pdb=" C ASN C 444 " pdb=" O ASN C 444 " ideal model delta sigma weight residual 1.234 1.251 -0.016 1.31e-02 5.83e+03 1.53e+00 bond pdb=" C ASN A 444 " pdb=" O ASN A 444 " ideal model delta sigma weight residual 1.235 1.249 -0.014 1.14e-02 7.69e+03 1.52e+00 ... (remaining 14596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 19484 1.62 - 3.25: 251 3.25 - 4.87: 36 4.87 - 6.50: 2 6.50 - 8.12: 1 Bond angle restraints: 19774 Sorted by residual: angle pdb=" N GLY A 442 " pdb=" CA GLY A 442 " pdb=" C GLY A 442 " ideal model delta sigma weight residual 110.90 115.68 -4.78 1.53e+00 4.27e-01 9.75e+00 angle pdb=" CA GLU B 326 " pdb=" CB GLU B 326 " pdb=" CG GLU B 326 " ideal model delta sigma weight residual 114.10 120.03 -5.93 2.00e+00 2.50e-01 8.79e+00 angle pdb=" CA ILE B 412 " pdb=" CB ILE B 412 " pdb=" CG1 ILE B 412 " ideal model delta sigma weight residual 110.40 115.02 -4.62 1.70e+00 3.46e-01 7.40e+00 angle pdb=" CB MET C 485 " pdb=" CG MET C 485 " pdb=" SD MET C 485 " ideal model delta sigma weight residual 112.70 120.82 -8.12 3.00e+00 1.11e-01 7.33e+00 angle pdb=" CB GLN B 104 " pdb=" CG GLN B 104 " pdb=" CD GLN B 104 " ideal model delta sigma weight residual 112.60 117.18 -4.58 1.70e+00 3.46e-01 7.27e+00 ... (remaining 19769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7838 17.90 - 35.80: 830 35.80 - 53.70: 234 53.70 - 71.60: 58 71.60 - 89.49: 30 Dihedral angle restraints: 8990 sinusoidal: 3587 harmonic: 5403 Sorted by residual: dihedral pdb=" CD ARG B 118 " pdb=" NE ARG B 118 " pdb=" CZ ARG B 118 " pdb=" NH1 ARG B 118 " ideal model delta sinusoidal sigma weight residual 0.00 72.86 -72.86 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CA ASP A 420 " pdb=" C ASP A 420 " pdb=" N LYS A 421 " pdb=" CA LYS A 421 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA THR A 441 " pdb=" C THR A 441 " pdb=" N GLY A 442 " pdb=" CA GLY A 442 " ideal model delta harmonic sigma weight residual -180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 8987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1510 0.035 - 0.069: 527 0.069 - 0.104: 182 0.104 - 0.138: 93 0.138 - 0.173: 3 Chirality restraints: 2315 Sorted by residual: chirality pdb=" CB THR C 272 " pdb=" CA THR C 272 " pdb=" OG1 THR C 272 " pdb=" CG2 THR C 272 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CA ARG B 118 " pdb=" N ARG B 118 " pdb=" C ARG B 118 " pdb=" CB ARG B 118 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE A 112 " pdb=" N ILE A 112 " pdb=" C ILE A 112 " pdb=" CB ILE A 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 2312 not shown) Planarity restraints: 2561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 118 " -1.047 9.50e-02 1.11e+02 4.69e-01 1.33e+02 pdb=" NE ARG B 118 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG B 118 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 118 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 118 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 332 " -0.038 5.00e-02 4.00e+02 5.83e-02 5.45e+00 pdb=" N PRO A 333 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 104 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" C GLN B 104 " -0.035 2.00e-02 2.50e+03 pdb=" O GLN B 104 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS B 105 " 0.011 2.00e-02 2.50e+03 ... (remaining 2558 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 5906 2.92 - 3.42: 14114 3.42 - 3.91: 24596 3.91 - 4.41: 28803 4.41 - 4.90: 46596 Nonbonded interactions: 120015 Sorted by model distance: nonbonded pdb=" O GLN B 104 " pdb=" OE1 GLN B 104 " model vdw 2.430 3.040 nonbonded pdb=" O GLU B 322 " pdb=" OE1 GLU B 326 " model vdw 2.554 3.040 nonbonded pdb=" O LYS C 583 " pdb=" NE2 GLN C 587 " model vdw 2.565 3.120 nonbonded pdb=" O THR A 266 " pdb=" OG1 THR A 266 " model vdw 2.566 3.040 nonbonded pdb=" O SER C 408 " pdb=" OG SER C 408 " model vdw 2.602 3.040 ... (remaining 120010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 668 or resid 901)) selection = (chain 'B' and (resid 46 through 668 or resid 901)) selection = chain 'C' } 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: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.610 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 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 0.034 14601 Z= 0.159 Angle : 0.487 8.124 19774 Z= 0.263 Chirality : 0.044 0.173 2315 Planarity : 0.010 0.469 2561 Dihedral : 17.039 89.495 5506 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.83 % Allowed : 20.26 % Favored : 76.90 % 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: 0.77 (0.19), residues: 1865 helix: 0.38 (0.18), residues: 719 sheet: 1.54 (0.25), residues: 427 loop : 0.17 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 446 TYR 0.012 0.001 TYR B 427 PHE 0.026 0.001 PHE C 663 TRP 0.006 0.001 TRP C 184 HIS 0.003 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00358 (14601) covalent geometry : angle 0.48706 (19774) hydrogen bonds : bond 0.21398 ( 834) hydrogen bonds : angle 7.72067 ( 2337) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6969 (mtt180) REVERT: A 239 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7840 (mp-120) REVERT: A 407 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8027 (mmtm) REVERT: A 436 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6474 (mm-30) REVERT: A 443 LEU cc_start: 0.5107 (OUTLIER) cc_final: 0.4562 (tm) REVERT: A 516 LYS cc_start: 0.8919 (tttt) cc_final: 0.8543 (ttmm) REVERT: A 643 ASP cc_start: 0.8202 (t0) cc_final: 0.7814 (t70) REVERT: A 646 THR cc_start: 0.8641 (p) cc_final: 0.8276 (p) REVERT: A 663 PHE cc_start: 0.7575 (m-80) cc_final: 0.7163 (m-10) REVERT: B 126 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8311 (pttm) REVERT: B 387 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8201 (tp40) REVERT: B 523 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7864 (mm-30) REVERT: B 552 LYS cc_start: 0.8746 (pttm) cc_final: 0.8376 (pptt) REVERT: B 632 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7740 (tp40) REVERT: B 664 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7823 (mp) REVERT: B 665 THR cc_start: 0.8504 (m) cc_final: 0.8139 (p) REVERT: C 54 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7596 (mmt90) REVERT: C 230 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: C 375 ASP cc_start: 0.8721 (t0) cc_final: 0.8462 (t70) REVERT: C 617 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.6787 (tmm-80) REVERT: C 629 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8114 (mmmt) REVERT: C 645 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8472 (mm-30) outliers start: 45 outliers final: 23 residues processed: 153 average time/residue: 0.7251 time to fit residues: 120.3361 Evaluate side-chains 154 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 629 LYS Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0010 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN B 104 GLN B 611 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.099427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.078825 restraints weight = 21972.202| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.16 r_work: 0.2868 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14601 Z= 0.207 Angle : 0.542 7.212 19774 Z= 0.302 Chirality : 0.046 0.145 2315 Planarity : 0.004 0.052 2561 Dihedral : 8.142 89.266 2097 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.15 % Allowed : 18.44 % Favored : 77.41 % 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: 1.68 (0.19), residues: 1865 helix: 1.84 (0.18), residues: 722 sheet: 1.64 (0.25), residues: 425 loop : 0.10 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 118 TYR 0.018 0.002 TYR B 334 PHE 0.017 0.001 PHE C 663 TRP 0.005 0.001 TRP A 184 HIS 0.004 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00460 (14601) covalent geometry : angle 0.54234 (19774) hydrogen bonds : bond 0.06542 ( 834) hydrogen bonds : angle 5.38924 ( 2337) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 115 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8384 (mp) REVERT: A 443 LEU cc_start: 0.5209 (OUTLIER) cc_final: 0.4679 (tm) REVERT: A 516 LYS cc_start: 0.8978 (tttt) cc_final: 0.8666 (ttmm) REVERT: A 643 ASP cc_start: 0.8213 (t0) cc_final: 0.7415 (t70) REVERT: A 646 THR cc_start: 0.8740 (p) cc_final: 0.8353 (p) REVERT: A 663 PHE cc_start: 0.7499 (m-80) cc_final: 0.7050 (m-10) REVERT: B 126 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8290 (pttm) REVERT: B 228 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8745 (tmm) REVERT: B 523 GLU cc_start: 0.8146 (tt0) cc_final: 0.7856 (mm-30) REVERT: B 552 LYS cc_start: 0.8723 (pttm) cc_final: 0.8421 (pptt) REVERT: B 658 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7615 (p-80) REVERT: B 663 PHE cc_start: 0.6942 (t80) cc_final: 0.6671 (t80) REVERT: B 664 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7905 (mp) REVERT: B 665 THR cc_start: 0.8515 (m) cc_final: 0.8178 (p) REVERT: C 54 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7056 (mmt90) REVERT: C 375 ASP cc_start: 0.8745 (t0) cc_final: 0.8508 (t70) REVERT: C 642 VAL cc_start: 0.8988 (t) cc_final: 0.8788 (m) REVERT: C 645 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8431 (mt-10) outliers start: 66 outliers final: 23 residues processed: 168 average time/residue: 0.6518 time to fit residues: 119.5324 Evaluate side-chains 143 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 407 LYS Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 587 GLN Chi-restraints excluded: chain C residue 667 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 24 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN B 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.080144 restraints weight = 21852.360| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.22 r_work: 0.2894 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14601 Z= 0.148 Angle : 0.490 5.414 19774 Z= 0.271 Chirality : 0.044 0.137 2315 Planarity : 0.004 0.048 2561 Dihedral : 5.537 59.863 2040 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.52 % Allowed : 19.13 % Favored : 77.34 % 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: 1.95 (0.19), residues: 1865 helix: 2.22 (0.18), residues: 727 sheet: 1.64 (0.25), residues: 425 loop : 0.15 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 118 TYR 0.018 0.001 TYR B 334 PHE 0.012 0.001 PHE A 545 TRP 0.006 0.001 TRP C 184 HIS 0.002 0.000 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00316 (14601) covalent geometry : angle 0.49017 (19774) hydrogen bonds : bond 0.05632 ( 834) hydrogen bonds : angle 5.02408 ( 2337) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 126 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7412 (tmmm) REVERT: A 56 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 57 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: A 94 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7530 (mt0) REVERT: A 443 LEU cc_start: 0.5398 (OUTLIER) cc_final: 0.4914 (tm) REVERT: A 516 LYS cc_start: 0.8972 (tttt) cc_final: 0.8666 (ttmm) REVERT: A 643 ASP cc_start: 0.7823 (t0) cc_final: 0.7492 (t0) REVERT: A 646 THR cc_start: 0.8738 (p) cc_final: 0.8396 (p) REVERT: A 663 PHE cc_start: 0.7554 (m-80) cc_final: 0.7051 (m-10) REVERT: B 126 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8206 (pttm) REVERT: B 523 GLU cc_start: 0.8188 (tt0) cc_final: 0.7940 (pt0) REVERT: B 552 LYS cc_start: 0.8703 (pttm) cc_final: 0.8423 (pptt) REVERT: B 658 HIS cc_start: 0.8012 (OUTLIER) cc_final: 0.7645 (p-80) REVERT: B 664 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7956 (mp) REVERT: B 665 THR cc_start: 0.8575 (m) cc_final: 0.8252 (p) REVERT: C 294 ARG cc_start: 0.8368 (mtm180) cc_final: 0.8061 (mmm-85) REVERT: C 375 ASP cc_start: 0.8711 (t0) cc_final: 0.8469 (t70) REVERT: C 583 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8199 (mptm) REVERT: C 617 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.6923 (tmm-80) REVERT: C 645 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8415 (mm-30) outliers start: 56 outliers final: 19 residues processed: 169 average time/residue: 0.6747 time to fit residues: 124.3237 Evaluate side-chains 144 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 407 LYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 587 GLN Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 43 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 7 optimal weight: 0.0270 chunk 103 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN C 341 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.103130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.082027 restraints weight = 21833.165| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.21 r_work: 0.2932 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14601 Z= 0.121 Angle : 0.469 9.451 19774 Z= 0.256 Chirality : 0.044 0.170 2315 Planarity : 0.004 0.047 2561 Dihedral : 5.095 59.230 2030 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.03 % Allowed : 18.94 % Favored : 77.03 % 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: 2.09 (0.20), residues: 1865 helix: 2.41 (0.18), residues: 731 sheet: 1.56 (0.25), residues: 426 loop : 0.23 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 446 TYR 0.016 0.001 TYR B 334 PHE 0.025 0.001 PHE C 663 TRP 0.007 0.001 TRP C 184 HIS 0.002 0.000 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00253 (14601) covalent geometry : angle 0.46900 (19774) hydrogen bonds : bond 0.04834 ( 834) hydrogen bonds : angle 4.75099 ( 2337) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 126 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7355 (tmmm) REVERT: A 56 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8360 (mp) REVERT: A 57 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8381 (mt-10) REVERT: A 443 LEU cc_start: 0.5662 (OUTLIER) cc_final: 0.5266 (tm) REVERT: A 516 LYS cc_start: 0.8941 (tttt) cc_final: 0.8632 (ttmm) REVERT: A 550 THR cc_start: 0.8712 (m) cc_final: 0.8173 (p) REVERT: A 643 ASP cc_start: 0.7878 (t0) cc_final: 0.7482 (t0) REVERT: A 646 THR cc_start: 0.8722 (p) cc_final: 0.8373 (p) REVERT: A 663 PHE cc_start: 0.7509 (m-80) cc_final: 0.6984 (m-10) REVERT: B 103 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7474 (mmp-170) REVERT: B 126 LYS cc_start: 0.8508 (ptpt) cc_final: 0.8155 (pttm) REVERT: B 523 GLU cc_start: 0.8199 (tt0) cc_final: 0.7896 (mm-30) REVERT: B 552 LYS cc_start: 0.8720 (pttm) cc_final: 0.8424 (pptt) REVERT: B 658 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7583 (p-80) REVERT: B 663 PHE cc_start: 0.6809 (t80) cc_final: 0.6594 (t80) REVERT: B 665 THR cc_start: 0.8560 (m) cc_final: 0.8238 (p) REVERT: C 54 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7616 (mmt90) REVERT: C 230 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: C 375 ASP cc_start: 0.8674 (t0) cc_final: 0.8413 (t70) REVERT: C 583 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8257 (mptm) REVERT: C 617 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7224 (tmm-80) REVERT: C 645 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8331 (mt-10) outliers start: 64 outliers final: 26 residues processed: 176 average time/residue: 0.6122 time to fit residues: 118.3370 Evaluate side-chains 152 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 667 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 73 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.103424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.082347 restraints weight = 21828.358| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.21 r_work: 0.2940 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14601 Z= 0.120 Angle : 0.470 7.731 19774 Z= 0.256 Chirality : 0.044 0.194 2315 Planarity : 0.004 0.046 2561 Dihedral : 4.809 58.795 2023 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.08 % Allowed : 20.01 % Favored : 76.90 % 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: 2.17 (0.20), residues: 1865 helix: 2.53 (0.18), residues: 733 sheet: 1.56 (0.25), residues: 427 loop : 0.23 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 446 TYR 0.015 0.001 TYR C 334 PHE 0.012 0.001 PHE B 340 TRP 0.007 0.001 TRP C 184 HIS 0.002 0.000 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00251 (14601) covalent geometry : angle 0.46984 (19774) hydrogen bonds : bond 0.04657 ( 834) hydrogen bonds : angle 4.67319 ( 2337) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7275 (tmmm) REVERT: A 56 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8329 (mp) REVERT: A 94 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7570 (mt0) REVERT: A 443 LEU cc_start: 0.5656 (OUTLIER) cc_final: 0.5344 (tm) REVERT: A 516 LYS cc_start: 0.8935 (tttt) cc_final: 0.8622 (ttmm) REVERT: A 550 THR cc_start: 0.8683 (m) cc_final: 0.8073 (p) REVERT: A 643 ASP cc_start: 0.7878 (t0) cc_final: 0.7531 (t0) REVERT: A 646 THR cc_start: 0.8707 (p) cc_final: 0.8363 (p) REVERT: A 663 PHE cc_start: 0.7487 (m-80) cc_final: 0.6975 (m-10) REVERT: B 103 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7465 (mmp-170) REVERT: B 126 LYS cc_start: 0.8500 (ptpt) cc_final: 0.8142 (pttm) REVERT: B 523 GLU cc_start: 0.8232 (tt0) cc_final: 0.7907 (mm-30) REVERT: B 552 LYS cc_start: 0.8718 (pttm) cc_final: 0.8426 (pptt) REVERT: B 658 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7567 (p-80) REVERT: C 54 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7420 (mmt90) REVERT: C 294 ARG cc_start: 0.8327 (mtm180) cc_final: 0.8035 (mmm-85) REVERT: C 375 ASP cc_start: 0.8682 (t0) cc_final: 0.8407 (t70) REVERT: C 583 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8286 (mptm) REVERT: C 617 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7297 (tmm-80) REVERT: C 645 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8344 (mt-10) outliers start: 49 outliers final: 25 residues processed: 162 average time/residue: 0.6338 time to fit residues: 112.8102 Evaluate side-chains 148 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 667 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 32 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 98 optimal weight: 0.0870 chunk 119 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.103514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.082375 restraints weight = 21874.572| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.23 r_work: 0.2942 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14601 Z= 0.119 Angle : 0.468 8.044 19774 Z= 0.255 Chirality : 0.044 0.191 2315 Planarity : 0.004 0.046 2561 Dihedral : 4.760 58.649 2023 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.77 % Favored : 98.18 % Rotamer: Outliers : 3.02 % Allowed : 20.20 % Favored : 76.78 % 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: 2.20 (0.20), residues: 1865 helix: 2.55 (0.18), residues: 736 sheet: 1.55 (0.25), residues: 427 loop : 0.25 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 118 TYR 0.014 0.001 TYR C 334 PHE 0.022 0.001 PHE C 663 TRP 0.006 0.001 TRP C 184 HIS 0.002 0.000 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00250 (14601) covalent geometry : angle 0.46784 (19774) hydrogen bonds : bond 0.04546 ( 834) hydrogen bonds : angle 4.62236 ( 2337) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 121 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7379 (tmmm) REVERT: A 56 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8332 (mp) REVERT: A 57 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: A 94 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7558 (mt0) REVERT: A 443 LEU cc_start: 0.5649 (OUTLIER) cc_final: 0.5370 (tm) REVERT: A 516 LYS cc_start: 0.8943 (tttt) cc_final: 0.8591 (ttmm) REVERT: A 550 THR cc_start: 0.8676 (m) cc_final: 0.8047 (p) REVERT: A 643 ASP cc_start: 0.7868 (t0) cc_final: 0.7534 (t0) REVERT: A 646 THR cc_start: 0.8713 (p) cc_final: 0.8321 (p) REVERT: A 663 PHE cc_start: 0.7481 (m-80) cc_final: 0.6958 (m-10) REVERT: B 103 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7469 (mmp-170) REVERT: B 126 LYS cc_start: 0.8488 (ptpt) cc_final: 0.8115 (pttm) REVERT: B 616 LYS cc_start: 0.8794 (mttt) cc_final: 0.8594 (ttmt) REVERT: B 658 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.7538 (p-80) REVERT: B 663 PHE cc_start: 0.6704 (t80) cc_final: 0.6468 (t80) REVERT: C 54 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7521 (mmt90) REVERT: C 230 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: C 375 ASP cc_start: 0.8687 (t0) cc_final: 0.8404 (t70) REVERT: C 583 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8310 (mptm) REVERT: C 617 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7305 (tmm-80) REVERT: C 645 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8326 (mt-10) outliers start: 48 outliers final: 25 residues processed: 159 average time/residue: 0.5719 time to fit residues: 99.2945 Evaluate side-chains 149 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 667 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 137 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.101139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.080446 restraints weight = 21972.962| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.18 r_work: 0.2904 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14601 Z= 0.168 Angle : 0.507 7.296 19774 Z= 0.276 Chirality : 0.045 0.161 2315 Planarity : 0.004 0.049 2561 Dihedral : 4.904 58.567 2023 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.93 % Favored : 98.02 % Rotamer: Outliers : 3.59 % Allowed : 19.70 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.20), residues: 1865 helix: 2.61 (0.18), residues: 725 sheet: 1.59 (0.25), residues: 430 loop : 0.23 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 118 TYR 0.015 0.002 TYR B 427 PHE 0.013 0.001 PHE B 545 TRP 0.004 0.001 TRP A 184 HIS 0.004 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00373 (14601) covalent geometry : angle 0.50748 (19774) hydrogen bonds : bond 0.05184 ( 834) hydrogen bonds : angle 4.76998 ( 2337) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 115 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7307 (tmmm) REVERT: A 56 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8326 (mp) REVERT: A 57 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: A 94 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7537 (mt0) REVERT: A 149 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8314 (t0) REVERT: A 443 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.5382 (tm) REVERT: A 516 LYS cc_start: 0.8950 (tttt) cc_final: 0.8653 (ttmm) REVERT: A 643 ASP cc_start: 0.7883 (t0) cc_final: 0.7505 (t0) REVERT: A 646 THR cc_start: 0.8754 (p) cc_final: 0.8437 (p) REVERT: A 663 PHE cc_start: 0.7475 (m-80) cc_final: 0.6976 (m-10) REVERT: B 87 LYS cc_start: 0.8588 (mttm) cc_final: 0.8355 (mmpt) REVERT: B 103 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7465 (mmp-170) REVERT: B 126 LYS cc_start: 0.8508 (ptpt) cc_final: 0.8170 (pttm) REVERT: B 523 GLU cc_start: 0.8218 (tt0) cc_final: 0.7897 (mm-30) REVERT: B 533 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.9032 (pt) REVERT: B 658 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7523 (p-80) REVERT: C 54 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7664 (mmt90) REVERT: C 230 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: C 375 ASP cc_start: 0.8721 (t0) cc_final: 0.8459 (t70) REVERT: C 583 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8271 (mptm) REVERT: C 617 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7362 (tmm-80) REVERT: C 645 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8314 (mt-10) outliers start: 57 outliers final: 24 residues processed: 165 average time/residue: 0.6633 time to fit residues: 119.7227 Evaluate side-chains 151 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 667 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 2.9990 chunk 57 optimal weight: 0.0570 chunk 165 optimal weight: 0.0970 chunk 81 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.2300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 632 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.101638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.080534 restraints weight = 21732.667| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.21 r_work: 0.2908 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14601 Z= 0.154 Angle : 0.506 7.135 19774 Z= 0.275 Chirality : 0.045 0.281 2315 Planarity : 0.004 0.048 2561 Dihedral : 4.746 58.019 2021 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.88 % Favored : 98.07 % Rotamer: Outliers : 3.21 % Allowed : 20.33 % Favored : 76.46 % 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: 2.16 (0.20), residues: 1865 helix: 2.55 (0.18), residues: 731 sheet: 1.57 (0.25), residues: 426 loop : 0.19 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 118 TYR 0.014 0.001 TYR C 334 PHE 0.024 0.001 PHE C 663 TRP 0.004 0.001 TRP A 184 HIS 0.002 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00339 (14601) covalent geometry : angle 0.50636 (19774) hydrogen bonds : bond 0.05069 ( 834) hydrogen bonds : angle 4.75990 ( 2337) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7312 (tmmm) REVERT: A 56 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8335 (mp) REVERT: A 57 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: A 94 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7574 (mt0) REVERT: A 443 LEU cc_start: 0.5606 (OUTLIER) cc_final: 0.5355 (tm) REVERT: A 516 LYS cc_start: 0.8946 (tttt) cc_final: 0.8641 (ttmm) REVERT: A 643 ASP cc_start: 0.7860 (t0) cc_final: 0.7497 (t0) REVERT: A 646 THR cc_start: 0.8734 (p) cc_final: 0.8419 (p) REVERT: A 663 PHE cc_start: 0.7469 (m-80) cc_final: 0.6961 (m-10) REVERT: B 87 LYS cc_start: 0.8592 (mttm) cc_final: 0.8358 (mmpt) REVERT: B 103 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7483 (mmp-170) REVERT: B 126 LYS cc_start: 0.8499 (ptpt) cc_final: 0.8173 (pttm) REVERT: B 523 GLU cc_start: 0.8227 (tt0) cc_final: 0.7905 (mm-30) REVERT: B 533 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.9022 (pt) REVERT: B 632 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7583 (tp40) REVERT: B 658 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.7504 (p-80) REVERT: C 54 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7686 (mmt90) REVERT: C 65 ARG cc_start: 0.9256 (OUTLIER) cc_final: 0.8561 (mtp180) REVERT: C 230 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: C 375 ASP cc_start: 0.8716 (t0) cc_final: 0.8459 (t70) REVERT: C 583 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8264 (mptm) REVERT: C 617 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7352 (tmm-80) REVERT: C 645 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8312 (mt-10) outliers start: 51 outliers final: 26 residues processed: 164 average time/residue: 0.6603 time to fit residues: 118.1006 Evaluate side-chains 154 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 667 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 180 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.080851 restraints weight = 21883.996| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.23 r_work: 0.2913 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14601 Z= 0.144 Angle : 0.506 7.016 19774 Z= 0.275 Chirality : 0.044 0.180 2315 Planarity : 0.004 0.048 2561 Dihedral : 4.716 57.880 2021 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.88 % Favored : 98.07 % Rotamer: Outliers : 2.96 % Allowed : 20.58 % Favored : 76.46 % 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: 2.18 (0.20), residues: 1865 helix: 2.56 (0.18), residues: 731 sheet: 1.56 (0.25), residues: 426 loop : 0.21 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 118 TYR 0.015 0.001 TYR C 334 PHE 0.017 0.001 PHE B 663 TRP 0.004 0.001 TRP C 184 HIS 0.002 0.000 HIS C 304 Details of bonding type rmsd covalent geometry : bond 0.00316 (14601) covalent geometry : angle 0.50625 (19774) hydrogen bonds : bond 0.04969 ( 834) hydrogen bonds : angle 4.72915 ( 2337) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 114 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7313 (tmmm) REVERT: A 56 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8320 (mp) REVERT: A 57 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: A 149 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8352 (t0) REVERT: A 443 LEU cc_start: 0.5673 (OUTLIER) cc_final: 0.5433 (tm) REVERT: A 516 LYS cc_start: 0.8945 (tttt) cc_final: 0.8638 (ttmm) REVERT: A 643 ASP cc_start: 0.7851 (t0) cc_final: 0.7486 (t0) REVERT: A 646 THR cc_start: 0.8730 (p) cc_final: 0.8411 (p) REVERT: A 663 PHE cc_start: 0.7454 (m-80) cc_final: 0.6938 (m-10) REVERT: B 87 LYS cc_start: 0.8592 (mttm) cc_final: 0.8357 (mmpt) REVERT: B 126 LYS cc_start: 0.8493 (ptpt) cc_final: 0.8167 (pttm) REVERT: B 533 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9021 (pt) REVERT: B 658 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7531 (p-80) REVERT: C 54 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7659 (mmt90) REVERT: C 65 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8556 (mtp180) REVERT: C 230 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8102 (tm-30) REVERT: C 375 ASP cc_start: 0.8711 (t0) cc_final: 0.8439 (t70) REVERT: C 583 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8328 (mptm) REVERT: C 617 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7356 (tmm-80) REVERT: C 645 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8305 (mt-10) outliers start: 47 outliers final: 26 residues processed: 154 average time/residue: 0.6407 time to fit residues: 107.6776 Evaluate side-chains 150 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 667 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 65 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 0.0070 chunk 111 optimal weight: 5.9990 chunk 56 optimal weight: 0.0980 chunk 69 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.6204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.100981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.079903 restraints weight = 21786.267| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.21 r_work: 0.2891 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14601 Z= 0.182 Angle : 0.533 7.154 19774 Z= 0.289 Chirality : 0.045 0.171 2315 Planarity : 0.004 0.050 2561 Dihedral : 4.836 57.832 2021 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.20 % Favored : 97.75 % Rotamer: Outliers : 2.77 % Allowed : 20.70 % Favored : 76.53 % 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: 2.16 (0.20), residues: 1865 helix: 2.56 (0.18), residues: 726 sheet: 1.56 (0.25), residues: 431 loop : 0.18 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 118 TYR 0.015 0.002 TYR B 427 PHE 0.025 0.001 PHE C 663 TRP 0.004 0.001 TRP A 184 HIS 0.002 0.001 HIS C 304 Details of bonding type rmsd covalent geometry : bond 0.00410 (14601) covalent geometry : angle 0.53308 (19774) hydrogen bonds : bond 0.05366 ( 834) hydrogen bonds : angle 4.82579 ( 2337) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7308 (tmmm) REVERT: A 56 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8333 (mp) REVERT: A 57 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: A 94 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7562 (mt0) REVERT: A 149 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8337 (t0) REVERT: A 443 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5415 (tm) REVERT: A 516 LYS cc_start: 0.8948 (tttt) cc_final: 0.8642 (ttmm) REVERT: A 643 ASP cc_start: 0.7895 (t0) cc_final: 0.7526 (t0) REVERT: A 646 THR cc_start: 0.8772 (p) cc_final: 0.8443 (p) REVERT: A 663 PHE cc_start: 0.7480 (m-80) cc_final: 0.6973 (m-10) REVERT: B 87 LYS cc_start: 0.8559 (mttm) cc_final: 0.8310 (mmpt) REVERT: B 103 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8251 (mmt90) REVERT: B 126 LYS cc_start: 0.8516 (ptpt) cc_final: 0.8195 (pttm) REVERT: B 523 GLU cc_start: 0.8235 (tt0) cc_final: 0.7917 (mm-30) REVERT: B 533 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.9040 (pt) REVERT: B 658 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.7549 (p-80) REVERT: C 54 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7713 (mmt90) REVERT: C 65 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8557 (mtp180) REVERT: C 230 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8128 (tm-30) REVERT: C 375 ASP cc_start: 0.8728 (t0) cc_final: 0.8469 (t70) REVERT: C 583 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8186 (mptm) REVERT: C 617 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7374 (tmm-80) REVERT: C 645 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8316 (mt-10) outliers start: 44 outliers final: 27 residues processed: 154 average time/residue: 0.6448 time to fit residues: 108.5762 Evaluate side-chains 153 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 407 LYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 667 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.081179 restraints weight = 21949.858| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.19 r_work: 0.2919 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14601 Z= 0.141 Angle : 0.507 7.701 19774 Z= 0.275 Chirality : 0.044 0.154 2315 Planarity : 0.004 0.047 2561 Dihedral : 4.712 57.635 2021 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 2.77 % Allowed : 20.77 % Favored : 76.46 % 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: 2.18 (0.20), residues: 1865 helix: 2.57 (0.18), residues: 731 sheet: 1.52 (0.25), residues: 427 loop : 0.23 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 118 TYR 0.015 0.001 TYR C 334 PHE 0.014 0.001 PHE B 663 TRP 0.005 0.001 TRP C 184 HIS 0.002 0.000 HIS C 304 Details of bonding type rmsd covalent geometry : bond 0.00309 (14601) covalent geometry : angle 0.50716 (19774) hydrogen bonds : bond 0.04936 ( 834) hydrogen bonds : angle 4.72607 ( 2337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4824.28 seconds wall clock time: 83 minutes 8.57 seconds (4988.57 seconds total)