Starting phenix.real_space_refine on Sun Aug 9 06:27:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z6t_73857/08_2026/9z6t_73857.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z6t_73857/08_2026/9z6t_73857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z6t_73857/08_2026/9z6t_73857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z6t_73857/08_2026/9z6t_73857.map" model { file = "/net/cci-nas-00/data/ceres_data/9z6t_73857/08_2026/9z6t_73857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z6t_73857/08_2026/9z6t_73857.cif" } resolution = 2.6 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= 0.002 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 132 5.16 5 C 10508 2.51 5 N 2684 2.21 5 O 2864 1.98 5 H 16016 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32208 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 8030 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 16, 'TRANS': 481} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 10.08, per 1000 atoms: 0.31 Number of scatterers: 32208 At special positions: 0 Unit cell: (116.543, 116.543, 125.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 P 4 15.00 O 2864 8.00 N 2684 7.00 C 10508 6.00 H 16016 1.00 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: 2.70 Conformation dependent library (CDL) restraints added in 785.7 milliseconds 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 8 sheets defined 75.9% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 97 through 102 removed outlier: 3.704A pdb=" N LEU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 131 removed outlier: 4.143A pdb=" N GLY A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 167 removed outlier: 3.690A pdb=" N ASP A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.735A pdb=" N ARG A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.551A pdb=" N ARG A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 290 removed outlier: 3.808A pdb=" N MET A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 removed outlier: 3.601A pdb=" N VAL A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix removed outlier: 3.661A pdb=" N GLN A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'A' and resid 368 through 401 removed outlier: 3.511A pdb=" N ASP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 422 removed outlier: 3.574A pdb=" N ARG A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 473 through 478 removed outlier: 4.002A pdb=" N ASN A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.874A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 4.433A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 Processing helix chain 'A' and resid 577 through 593 removed outlier: 4.107A pdb=" N ARG A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 605 Processing helix chain 'B' and resid 97 through 102 removed outlier: 3.703A pdb=" N LEU B 102 " --> pdb=" O PHE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 116 through 131 removed outlier: 4.143A pdb=" N GLY B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 167 removed outlier: 3.691A pdb=" N ASP B 146 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 148 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.734A pdb=" N ARG B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.552A pdb=" N ARG B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 269 Processing helix chain 'B' and resid 270 through 290 removed outlier: 3.808A pdb=" N MET B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B 290 " --> pdb=" O HIS B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 removed outlier: 3.601A pdb=" N VAL B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix removed outlier: 3.661A pdb=" N GLN B 323 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 340 through 358 Processing helix chain 'B' and resid 368 through 401 removed outlier: 3.512A pdb=" N ASP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 422 removed outlier: 3.574A pdb=" N ARG B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN B 413 " --> pdb=" O GLU B 409 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 466 through 473 Processing helix chain 'B' and resid 473 through 478 removed outlier: 4.002A pdb=" N ASN B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 490 removed outlier: 3.875A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 546 removed outlier: 4.433A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 Processing helix chain 'B' and resid 577 through 593 removed outlier: 4.107A pdb=" N ARG B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 605 Processing helix chain 'C' and resid 97 through 102 removed outlier: 3.703A pdb=" N LEU C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 131 removed outlier: 4.143A pdb=" N GLY C 131 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 167 removed outlier: 3.690A pdb=" N ASP C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 196 removed outlier: 3.735A pdb=" N ARG C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.551A pdb=" N ARG C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 269 Processing helix chain 'C' and resid 270 through 290 removed outlier: 3.808A pdb=" N MET C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP C 290 " --> pdb=" O HIS C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 removed outlier: 3.601A pdb=" N VAL C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix removed outlier: 3.661A pdb=" N GLN C 323 " --> pdb=" O VAL C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 340 through 358 Processing helix chain 'C' and resid 368 through 401 removed outlier: 3.512A pdb=" N ASP C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 422 removed outlier: 3.574A pdb=" N ARG C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 413 " --> pdb=" O GLU C 409 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 454 through 466 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 473 through 478 removed outlier: 4.002A pdb=" N ASN C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 removed outlier: 3.874A pdb=" N LYS C 490 " --> pdb=" O ALA C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 546 removed outlier: 4.433A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 576 Processing helix chain 'C' and resid 577 through 593 removed outlier: 4.107A pdb=" N ARG C 581 " --> pdb=" O PRO C 577 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 605 Processing helix chain 'D' and resid 97 through 102 removed outlier: 3.703A pdb=" N LEU D 102 " --> pdb=" O PHE D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 131 removed outlier: 4.144A pdb=" N GLY D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 167 removed outlier: 3.691A pdb=" N ASP D 146 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 148 " --> pdb=" O TYR D 144 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 196 removed outlier: 3.734A pdb=" N ARG D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.552A pdb=" N ARG D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 269 Processing helix chain 'D' and resid 270 through 290 removed outlier: 3.808A pdb=" N MET D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR D 288 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 removed outlier: 3.601A pdb=" N VAL D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix removed outlier: 3.661A pdb=" N GLN D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 335 Processing helix chain 'D' and resid 340 through 358 Processing helix chain 'D' and resid 368 through 401 removed outlier: 3.512A pdb=" N ASP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 422 removed outlier: 3.574A pdb=" N ARG D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 Processing helix chain 'D' and resid 454 through 466 Processing helix chain 'D' and resid 466 through 473 Processing helix chain 'D' and resid 473 through 478 removed outlier: 4.002A pdb=" N ASN D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 490 removed outlier: 3.874A pdb=" N LYS D 490 " --> pdb=" O ALA D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 546 removed outlier: 4.433A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 Processing helix chain 'D' and resid 577 through 593 removed outlier: 4.107A pdb=" N ARG D 581 " --> pdb=" O PRO D 577 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 605 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.958A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.638A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.957A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.637A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.957A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.638A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.958A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.637A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3132 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: 6.52 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15984 1.03 - 1.22: 32 1.22 - 1.42: 7068 1.42 - 1.61: 9280 1.61 - 1.81: 236 Bond restraints: 32600 Sorted by residual: bond pdb=" C4' CMP A 901 " pdb=" C5' CMP A 901 " ideal model delta sigma weight residual 1.524 1.498 0.026 2.00e-02 2.50e+03 1.72e+00 bond pdb=" C4' CMP C 901 " pdb=" C5' CMP C 901 " ideal model delta sigma weight residual 1.524 1.498 0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C4' CMP D 901 " pdb=" C5' CMP D 901 " ideal model delta sigma weight residual 1.524 1.498 0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C4' CMP B 901 " pdb=" C5' CMP B 901 " ideal model delta sigma weight residual 1.524 1.498 0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" CB ILE A 160 " pdb=" CG2 ILE A 160 " ideal model delta sigma weight residual 1.521 1.564 -0.043 3.30e-02 9.18e+02 1.68e+00 ... (remaining 32595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 57929 2.08 - 4.15: 729 4.15 - 6.23: 66 6.23 - 8.31: 16 8.31 - 10.38: 16 Bond angle restraints: 58756 Sorted by residual: angle pdb=" C1' CMP B 901 " pdb=" C2' CMP B 901 " pdb=" C3' CMP B 901 " ideal model delta sigma weight residual 111.00 100.62 10.38 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C1' CMP A 901 " pdb=" C2' CMP A 901 " pdb=" C3' CMP A 901 " ideal model delta sigma weight residual 111.00 100.68 10.32 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C1' CMP D 901 " pdb=" C2' CMP D 901 " pdb=" C3' CMP D 901 " ideal model delta sigma weight residual 111.00 100.68 10.32 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C1' CMP C 901 " pdb=" C2' CMP C 901 " pdb=" C3' CMP C 901 " ideal model delta sigma weight residual 111.00 100.71 10.29 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C2' CMP D 901 " pdb=" C3' CMP D 901 " pdb=" C4' CMP D 901 " ideal model delta sigma weight residual 111.00 101.79 9.21 3.00e+00 1.11e-01 9.42e+00 ... (remaining 58751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 13960 17.23 - 34.46: 1024 34.46 - 51.70: 217 51.70 - 68.93: 107 68.93 - 86.16: 40 Dihedral angle restraints: 15348 sinusoidal: 8148 harmonic: 7200 Sorted by residual: dihedral pdb=" N GLN A 416 " pdb=" CA GLN A 416 " pdb=" CB GLN A 416 " pdb=" CG GLN A 416 " ideal model delta sinusoidal sigma weight residual -60.00 -116.38 56.38 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" N GLN B 416 " pdb=" CA GLN B 416 " pdb=" CB GLN B 416 " pdb=" CG GLN B 416 " ideal model delta sinusoidal sigma weight residual -60.00 -116.38 56.38 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" N GLN C 416 " pdb=" CA GLN C 416 " pdb=" CB GLN C 416 " pdb=" CG GLN C 416 " ideal model delta sinusoidal sigma weight residual -60.00 -116.37 56.37 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 15345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2003 0.049 - 0.098: 404 0.098 - 0.148: 91 0.148 - 0.197: 2 0.197 - 0.246: 4 Chirality restraints: 2504 Sorted by residual: chirality pdb=" C2' CMP A 901 " pdb=" C1' CMP A 901 " pdb=" C3' CMP A 901 " pdb=" O2' CMP A 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C2' CMP B 901 " pdb=" C1' CMP B 901 " pdb=" C3' CMP B 901 " pdb=" O2' CMP B 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C2' CMP D 901 " pdb=" C1' CMP D 901 " pdb=" C3' CMP D 901 " pdb=" O2' CMP D 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2501 not shown) Planarity restraints: 4708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 319 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO C 320 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 320 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 320 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 319 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A 320 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 319 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO D 320 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 320 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 320 " 0.027 5.00e-02 4.00e+02 ... (remaining 4705 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.52: 23223 2.52 - 3.04: 73100 3.04 - 3.56: 78284 3.56 - 4.08: 103657 4.08 - 4.60: 157712 Nonbonded interactions: 435976 Sorted by model distance: nonbonded pdb=" H SER D 220 " pdb=" HG SER D 220 " model vdw 1.999 2.100 nonbonded pdb=" H SER A 220 " pdb=" HG SER A 220 " model vdw 2.000 2.100 nonbonded pdb=" H SER B 220 " pdb=" HG SER B 220 " model vdw 2.000 2.100 nonbonded pdb=" H SER C 220 " pdb=" HG SER C 220 " model vdw 2.000 2.100 nonbonded pdb=" HG SER C 229 " pdb="HH22 ARG C 273 " model vdw 2.011 2.100 ... (remaining 435971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 31.770 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.005 0.052 16584 Z= 0.186 Angle : 0.704 10.383 22456 Z= 0.347 Chirality : 0.042 0.246 2504 Planarity : 0.004 0.048 2792 Dihedral : 10.838 72.399 6048 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 0.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.18), residues: 1968 helix: 1.72 (0.14), residues: 1312 sheet: -1.46 (0.46), residues: 112 loop : -0.25 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 580 TYR 0.008 0.001 TYR C 417 PHE 0.016 0.002 PHE D 569 TRP 0.011 0.001 TRP A 373 HIS 0.005 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (16584) covalent geometry : angle 0.70382 / 0.35 (22456) hydrogen bonds : bond 0.16062 / 10.78 ( 1068) hydrogen bonds : angle 5.87739 / 4.38 ( 3132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Evaluate side-chains 401 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7114 (mtp) cc_final: 0.6375 (ptt) REVERT: A 184 THR cc_start: 0.8297 (m) cc_final: 0.8074 (m) REVERT: A 454 ASN cc_start: 0.8455 (p0) cc_final: 0.8235 (p0) REVERT: A 476 PHE cc_start: 0.8145 (m-10) cc_final: 0.7917 (m-80) REVERT: A 500 ASP cc_start: 0.7730 (m-30) cc_final: 0.7497 (m-30) REVERT: B 101 MET cc_start: 0.7041 (mtp) cc_final: 0.6281 (ptt) REVERT: B 184 THR cc_start: 0.8368 (m) cc_final: 0.8155 (m) REVERT: B 454 ASN cc_start: 0.8375 (p0) cc_final: 0.8150 (p0) REVERT: B 476 PHE cc_start: 0.8149 (m-10) cc_final: 0.7885 (m-80) REVERT: B 500 ASP cc_start: 0.7788 (m-30) cc_final: 0.7580 (m-30) REVERT: C 101 MET cc_start: 0.7123 (mtp) cc_final: 0.6380 (ptt) REVERT: C 184 THR cc_start: 0.8323 (m) cc_final: 0.8106 (m) REVERT: C 454 ASN cc_start: 0.8450 (p0) cc_final: 0.8228 (p0) REVERT: C 476 PHE cc_start: 0.8123 (m-10) cc_final: 0.7895 (m-80) REVERT: D 101 MET cc_start: 0.7044 (mtp) cc_final: 0.6285 (ptt) REVERT: D 454 ASN cc_start: 0.8390 (p0) cc_final: 0.8166 (p0) outliers start: 0 outliers final: 4 residues processed: 401 average time/residue: 1.4032 time to fit residues: 619.4934 Evaluate side-chains 277 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 273 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain D residue 589 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN A 398 GLN A 451 ASN B 398 GLN C 398 GLN D 398 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.156218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.115703 restraints weight = 51512.691| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.82 r_work: 0.3456 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16584 Z= 0.178 Angle : 0.595 9.232 22456 Z= 0.300 Chirality : 0.040 0.139 2504 Planarity : 0.004 0.043 2792 Dihedral : 4.371 27.561 2228 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.83 % Allowed : 10.72 % Favored : 87.44 % 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: 1.65 (0.19), residues: 1968 helix: 1.82 (0.13), residues: 1384 sheet: -0.77 (0.48), residues: 112 loop : -0.56 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 593 TYR 0.011 0.002 TYR D 347 PHE 0.023 0.002 PHE B 132 TRP 0.012 0.001 TRP D 373 HIS 0.004 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (16584) covalent geometry : angle 0.59505 / 0.30 (22456) hydrogen bonds : bond 0.05682 / 3.71 ( 1068) hydrogen bonds : angle 4.65271 / 3.42 ( 3132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 266 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.6987 (mtp) cc_final: 0.5746 (ptt) REVERT: A 184 THR cc_start: 0.8453 (m) cc_final: 0.8209 (m) REVERT: A 492 ARG cc_start: 0.7930 (ttt90) cc_final: 0.7526 (ttp80) REVERT: B 101 MET cc_start: 0.6968 (mtp) cc_final: 0.5729 (ptt) REVERT: B 117 GLN cc_start: 0.6934 (tt0) cc_final: 0.6695 (tt0) REVERT: B 289 TYR cc_start: 0.7754 (m-80) cc_final: 0.7487 (m-80) REVERT: B 492 ARG cc_start: 0.7902 (ttt90) cc_final: 0.7505 (ttp80) REVERT: B 568 ASN cc_start: 0.6776 (OUTLIER) cc_final: 0.6557 (p0) REVERT: C 101 MET cc_start: 0.6981 (mtp) cc_final: 0.5748 (ptt) REVERT: C 492 ARG cc_start: 0.7971 (ttt90) cc_final: 0.7549 (ttp80) REVERT: D 101 MET cc_start: 0.6990 (mtp) cc_final: 0.5746 (ptt) REVERT: D 117 GLN cc_start: 0.6976 (tt0) cc_final: 0.6730 (tt0) REVERT: D 492 ARG cc_start: 0.7937 (ttt90) cc_final: 0.7529 (ttp80) outliers start: 32 outliers final: 15 residues processed: 278 average time/residue: 1.4755 time to fit residues: 452.6088 Evaluate side-chains 263 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 247 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 540 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 23 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 75 optimal weight: 0.0980 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 ASN B 451 ASN C 179 ASN C 451 ASN D 451 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.156380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115237 restraints weight = 52239.123| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.81 r_work: 0.3429 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16584 Z= 0.156 Angle : 0.555 8.724 22456 Z= 0.275 Chirality : 0.039 0.132 2504 Planarity : 0.004 0.043 2792 Dihedral : 4.086 26.853 2220 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.66 % Allowed : 11.93 % Favored : 86.41 % 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: 1.96 (0.19), residues: 1968 helix: 2.07 (0.14), residues: 1388 sheet: -0.33 (0.48), residues: 112 loop : -0.62 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 581 TYR 0.010 0.001 TYR D 347 PHE 0.014 0.001 PHE D 569 TRP 0.011 0.001 TRP A 373 HIS 0.003 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (16584) covalent geometry : angle 0.55509 / 0.28 (22456) hydrogen bonds : bond 0.05487 / 3.60 ( 1068) hydrogen bonds : angle 4.37151 / 3.22 ( 3132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.6959 (mtp) cc_final: 0.5737 (ptt) REVERT: A 492 ARG cc_start: 0.7946 (ttt90) cc_final: 0.7698 (ttp80) REVERT: A 568 ASN cc_start: 0.6697 (OUTLIER) cc_final: 0.6421 (p0) REVERT: B 101 MET cc_start: 0.6956 (mtp) cc_final: 0.5704 (ptt) REVERT: B 117 GLN cc_start: 0.6800 (tt0) cc_final: 0.6582 (tt0) REVERT: B 476 PHE cc_start: 0.8074 (m-80) cc_final: 0.7855 (m-80) REVERT: B 492 ARG cc_start: 0.7955 (ttt90) cc_final: 0.7710 (ttp80) REVERT: B 512 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8502 (ttp) REVERT: B 540 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6894 (pm20) REVERT: C 101 MET cc_start: 0.6925 (mtp) cc_final: 0.5688 (ptt) REVERT: C 492 ARG cc_start: 0.7987 (ttt90) cc_final: 0.7714 (ttp80) REVERT: C 512 MET cc_start: 0.8824 (ttm) cc_final: 0.8539 (ttp) REVERT: C 568 ASN cc_start: 0.6659 (OUTLIER) cc_final: 0.6370 (p0) REVERT: D 101 MET cc_start: 0.6944 (mtp) cc_final: 0.5687 (ptt) REVERT: D 492 ARG cc_start: 0.7963 (ttt90) cc_final: 0.7705 (ttp80) REVERT: D 512 MET cc_start: 0.8821 (ttm) cc_final: 0.8551 (ttp) outliers start: 29 outliers final: 16 residues processed: 267 average time/residue: 1.4703 time to fit residues: 433.0649 Evaluate side-chains 260 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 565 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 117 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 ASN B 451 ASN C 451 ASN D 451 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.156996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.115971 restraints weight = 51906.042| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.81 r_work: 0.3439 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16584 Z= 0.123 Angle : 0.525 8.752 22456 Z= 0.257 Chirality : 0.038 0.136 2504 Planarity : 0.004 0.039 2792 Dihedral : 3.985 25.599 2220 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.75 % Allowed : 13.65 % Favored : 85.61 % 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: 2.28 (0.19), residues: 1968 helix: 2.34 (0.14), residues: 1384 sheet: -0.17 (0.47), residues: 112 loop : -0.60 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 581 TYR 0.008 0.001 TYR D 347 PHE 0.011 0.001 PHE B 569 TRP 0.010 0.001 TRP D 373 HIS 0.003 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (16584) covalent geometry : angle 0.52470 / 0.26 (22456) hydrogen bonds : bond 0.04683 / 3.07 ( 1068) hydrogen bonds : angle 4.17011 / 3.06 ( 3132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 265 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.6882 (mtp) cc_final: 0.5655 (ptt) REVERT: A 492 ARG cc_start: 0.7945 (ttt90) cc_final: 0.7698 (ttp80) REVERT: B 101 MET cc_start: 0.6930 (mtp) cc_final: 0.5690 (ptt) REVERT: B 492 ARG cc_start: 0.7928 (ttt90) cc_final: 0.7680 (ttp80) REVERT: B 512 MET cc_start: 0.8828 (ttm) cc_final: 0.8443 (ttp) REVERT: B 540 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: C 101 MET cc_start: 0.6906 (mtp) cc_final: 0.5676 (ptt) REVERT: C 492 ARG cc_start: 0.7962 (ttt90) cc_final: 0.7703 (ttp80) REVERT: C 512 MET cc_start: 0.8873 (ttm) cc_final: 0.8585 (ttp) REVERT: C 540 GLU cc_start: 0.7398 (pt0) cc_final: 0.7014 (pm20) REVERT: D 101 MET cc_start: 0.6905 (mtp) cc_final: 0.5686 (ptt) REVERT: D 492 ARG cc_start: 0.7926 (ttt90) cc_final: 0.7675 (ttp80) REVERT: D 512 MET cc_start: 0.8861 (ttm) cc_final: 0.8487 (ttp) outliers start: 13 outliers final: 7 residues processed: 271 average time/residue: 1.3878 time to fit residues: 414.7281 Evaluate side-chains 244 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 236 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 142 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 3 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 170 optimal weight: 0.0770 chunk 187 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN A 451 ASN B 398 GLN B 451 ASN C 398 GLN C 451 ASN D 398 GLN D 451 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.154874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.113797 restraints weight = 52463.579| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.81 r_work: 0.3414 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16584 Z= 0.151 Angle : 0.551 8.811 22456 Z= 0.272 Chirality : 0.038 0.135 2504 Planarity : 0.004 0.040 2792 Dihedral : 4.023 27.375 2220 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.66 % Allowed : 12.73 % Favored : 85.61 % 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: 2.36 (0.19), residues: 1968 helix: 2.40 (0.14), residues: 1360 sheet: -0.02 (0.47), residues: 112 loop : -0.44 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 581 TYR 0.009 0.001 TYR B 347 PHE 0.014 0.001 PHE A 569 TRP 0.011 0.001 TRP D 373 HIS 0.003 0.001 HIS C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (16584) covalent geometry : angle 0.55118 / 0.27 (22456) hydrogen bonds : bond 0.05182 / 3.39 ( 1068) hydrogen bonds : angle 4.16239 / 3.05 ( 3132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 247 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.6893 (mtp) cc_final: 0.5691 (ptt) REVERT: A 285 PHE cc_start: 0.8023 (m-10) cc_final: 0.7708 (m-80) REVERT: A 492 ARG cc_start: 0.7931 (ttt90) cc_final: 0.7689 (ttp80) REVERT: A 512 MET cc_start: 0.8807 (ttm) cc_final: 0.8492 (ttp) REVERT: B 101 MET cc_start: 0.6849 (mtp) cc_final: 0.5609 (ptt) REVERT: B 492 ARG cc_start: 0.7939 (ttt90) cc_final: 0.7686 (ttp80) REVERT: B 512 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8518 (ttp) REVERT: B 540 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6961 (pm20) REVERT: C 101 MET cc_start: 0.6845 (mtp) cc_final: 0.5621 (ptt) REVERT: C 492 ARG cc_start: 0.7977 (ttt90) cc_final: 0.7707 (ttp80) REVERT: C 512 MET cc_start: 0.8867 (ttm) cc_final: 0.8488 (ttp) REVERT: C 540 GLU cc_start: 0.7424 (pt0) cc_final: 0.7050 (pm20) REVERT: D 101 MET cc_start: 0.6848 (mtp) cc_final: 0.5609 (ptt) REVERT: D 285 PHE cc_start: 0.8066 (m-10) cc_final: 0.7768 (m-80) REVERT: D 492 ARG cc_start: 0.7945 (ttt90) cc_final: 0.7679 (ttp80) REVERT: D 512 MET cc_start: 0.8854 (ttm) cc_final: 0.8472 (ttp) outliers start: 29 outliers final: 11 residues processed: 268 average time/residue: 1.4810 time to fit residues: 438.2106 Evaluate side-chains 244 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 231 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 142 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 144 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 ASN B 179 ASN B 451 ASN C 451 ASN D 451 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.154812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.113980 restraints weight = 52772.316| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.79 r_work: 0.3410 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16584 Z= 0.149 Angle : 0.544 8.773 22456 Z= 0.268 Chirality : 0.038 0.129 2504 Planarity : 0.004 0.040 2792 Dihedral : 4.030 26.784 2220 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.61 % Allowed : 12.79 % Favored : 85.61 % 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: 2.37 (0.19), residues: 1968 helix: 2.41 (0.14), residues: 1356 sheet: 0.03 (0.46), residues: 112 loop : -0.44 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 581 TYR 0.009 0.001 TYR C 347 PHE 0.015 0.001 PHE D 132 TRP 0.011 0.001 TRP C 373 HIS 0.003 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (16584) covalent geometry : angle 0.54440 / 0.27 (22456) hydrogen bonds : bond 0.05103 / 3.34 ( 1068) hydrogen bonds : angle 4.11306 / 3.01 ( 3132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.6880 (mtp) cc_final: 0.5688 (ptt) REVERT: A 285 PHE cc_start: 0.8020 (m-10) cc_final: 0.7703 (m-80) REVERT: A 492 ARG cc_start: 0.7952 (ttt90) cc_final: 0.7699 (ttp80) REVERT: A 512 MET cc_start: 0.8888 (ttm) cc_final: 0.8515 (ttp) REVERT: A 540 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6896 (pm20) REVERT: B 101 MET cc_start: 0.6857 (mtp) cc_final: 0.5632 (ptt) REVERT: B 285 PHE cc_start: 0.8020 (m-10) cc_final: 0.7675 (m-80) REVERT: B 492 ARG cc_start: 0.7942 (ttt90) cc_final: 0.7691 (ttp80) REVERT: B 512 MET cc_start: 0.8803 (ttm) cc_final: 0.8478 (ttp) REVERT: B 540 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6897 (pm20) REVERT: C 101 MET cc_start: 0.6843 (mtp) cc_final: 0.5635 (ptt) REVERT: C 285 PHE cc_start: 0.8022 (m-10) cc_final: 0.7678 (m-80) REVERT: C 492 ARG cc_start: 0.7972 (ttt90) cc_final: 0.7701 (ttp80) REVERT: C 512 MET cc_start: 0.8868 (ttm) cc_final: 0.8531 (ttp) REVERT: C 540 GLU cc_start: 0.7401 (pt0) cc_final: 0.7040 (pm20) REVERT: D 101 MET cc_start: 0.6857 (mtp) cc_final: 0.5633 (ptt) REVERT: D 285 PHE cc_start: 0.8089 (m-10) cc_final: 0.7798 (m-80) REVERT: D 492 ARG cc_start: 0.7928 (ttt90) cc_final: 0.7670 (ttp80) REVERT: D 512 MET cc_start: 0.8858 (ttm) cc_final: 0.8475 (ttp) REVERT: D 540 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7039 (pm20) outliers start: 28 outliers final: 19 residues processed: 264 average time/residue: 1.4903 time to fit residues: 433.2137 Evaluate side-chains 252 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 565 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 158 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 ASN B 451 ASN C 451 ASN D 451 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.155007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.114056 restraints weight = 52620.256| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.81 r_work: 0.3418 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16584 Z= 0.136 Angle : 0.537 8.743 22456 Z= 0.263 Chirality : 0.038 0.131 2504 Planarity : 0.004 0.040 2792 Dihedral : 4.011 26.903 2220 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.38 % Allowed : 13.25 % Favored : 85.38 % 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: 2.42 (0.19), residues: 1968 helix: 2.46 (0.14), residues: 1356 sheet: 0.10 (0.46), residues: 112 loop : -0.47 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 581 TYR 0.009 0.001 TYR C 347 PHE 0.012 0.001 PHE C 569 TRP 0.011 0.001 TRP B 373 HIS 0.003 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (16584) covalent geometry : angle 0.53697 / 0.26 (22456) hydrogen bonds : bond 0.04872 / 3.19 ( 1068) hydrogen bonds : angle 4.06552 / 2.97 ( 3132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.6847 (mtp) cc_final: 0.5630 (ptt) REVERT: A 285 PHE cc_start: 0.7942 (m-10) cc_final: 0.7635 (m-80) REVERT: A 492 ARG cc_start: 0.7948 (ttt90) cc_final: 0.7679 (ttp80) REVERT: A 512 MET cc_start: 0.8834 (ttm) cc_final: 0.8490 (ttp) REVERT: A 540 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: B 101 MET cc_start: 0.6821 (mtp) cc_final: 0.5654 (ptt) REVERT: B 285 PHE cc_start: 0.8020 (m-10) cc_final: 0.7682 (m-80) REVERT: B 492 ARG cc_start: 0.7932 (ttt90) cc_final: 0.7671 (ttp80) REVERT: B 512 MET cc_start: 0.8780 (ttm) cc_final: 0.8413 (ttp) REVERT: B 540 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: C 101 MET cc_start: 0.6823 (mtp) cc_final: 0.5611 (ptt) REVERT: C 285 PHE cc_start: 0.7960 (m-10) cc_final: 0.7632 (m-80) REVERT: C 492 ARG cc_start: 0.7957 (ttt90) cc_final: 0.7682 (ttp80) REVERT: C 512 MET cc_start: 0.8822 (ttm) cc_final: 0.8476 (ttp) REVERT: C 540 GLU cc_start: 0.7406 (pt0) cc_final: 0.7013 (pm20) REVERT: D 101 MET cc_start: 0.6838 (mtp) cc_final: 0.5618 (ptt) REVERT: D 285 PHE cc_start: 0.8054 (m-10) cc_final: 0.7764 (m-80) REVERT: D 492 ARG cc_start: 0.7922 (ttt90) cc_final: 0.7661 (ttp80) REVERT: D 512 MET cc_start: 0.8804 (ttm) cc_final: 0.8413 (ttp) REVERT: D 540 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7030 (pm20) outliers start: 24 outliers final: 18 residues processed: 256 average time/residue: 1.5053 time to fit residues: 424.8870 Evaluate side-chains 254 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 233 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 540 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 193 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 ASN B 451 ASN C 451 ASN D 451 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.155007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114139 restraints weight = 52655.846| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.80 r_work: 0.3419 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16584 Z= 0.133 Angle : 0.536 8.738 22456 Z= 0.262 Chirality : 0.038 0.138 2504 Planarity : 0.004 0.051 2792 Dihedral : 3.999 26.883 2220 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.49 % Allowed : 13.42 % Favored : 85.09 % 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: 2.48 (0.19), residues: 1968 helix: 2.49 (0.14), residues: 1356 sheet: 0.45 (0.54), residues: 88 loop : -0.43 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 580 TYR 0.009 0.001 TYR D 347 PHE 0.012 0.001 PHE C 569 TRP 0.011 0.001 TRP C 373 HIS 0.004 0.001 HIS C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (16584) covalent geometry : angle 0.53629 / 0.26 (22456) hydrogen bonds : bond 0.04801 / 3.15 ( 1068) hydrogen bonds : angle 4.03438 / 2.95 ( 3132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.891 Fit side-chains REVERT: A 101 MET cc_start: 0.6851 (mtp) cc_final: 0.5634 (ptt) REVERT: A 112 ARG cc_start: 0.7581 (ttp-170) cc_final: 0.7310 (ttt180) REVERT: A 285 PHE cc_start: 0.7952 (m-10) cc_final: 0.7640 (m-80) REVERT: A 492 ARG cc_start: 0.7929 (ttt90) cc_final: 0.7667 (ttp80) REVERT: A 512 MET cc_start: 0.8828 (ttm) cc_final: 0.8533 (ttp) REVERT: A 540 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6955 (pm20) REVERT: B 101 MET cc_start: 0.6839 (mtp) cc_final: 0.5619 (ptt) REVERT: B 285 PHE cc_start: 0.7971 (m-10) cc_final: 0.7647 (m-80) REVERT: B 492 ARG cc_start: 0.7921 (ttt90) cc_final: 0.7666 (ttp80) REVERT: B 512 MET cc_start: 0.8774 (ttm) cc_final: 0.8444 (ttp) REVERT: B 540 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6860 (pm20) REVERT: C 101 MET cc_start: 0.6822 (mtp) cc_final: 0.5611 (ptt) REVERT: C 285 PHE cc_start: 0.7959 (m-10) cc_final: 0.7632 (m-80) REVERT: C 492 ARG cc_start: 0.7948 (ttt90) cc_final: 0.7680 (ttp80) REVERT: C 512 MET cc_start: 0.8826 (ttm) cc_final: 0.8483 (ttp) REVERT: C 540 GLU cc_start: 0.7412 (pt0) cc_final: 0.7039 (pm20) REVERT: D 101 MET cc_start: 0.6836 (mtp) cc_final: 0.5615 (ptt) REVERT: D 285 PHE cc_start: 0.8062 (m-10) cc_final: 0.7776 (m-80) REVERT: D 492 ARG cc_start: 0.7923 (ttt90) cc_final: 0.7660 (ttp80) REVERT: D 512 MET cc_start: 0.8799 (ttm) cc_final: 0.8410 (ttp) REVERT: D 540 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7016 (pm20) outliers start: 26 outliers final: 19 residues processed: 257 average time/residue: 1.4872 time to fit residues: 421.1848 Evaluate side-chains 254 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 565 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 ASN B 451 ASN C 451 ASN D 179 ASN D 451 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.154162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113407 restraints weight = 52634.211| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.79 r_work: 0.3404 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16584 Z= 0.151 Angle : 0.551 8.772 22456 Z= 0.272 Chirality : 0.039 0.127 2504 Planarity : 0.004 0.047 2792 Dihedral : 4.028 27.175 2220 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.49 % Allowed : 13.53 % Favored : 84.98 % 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: 2.38 (0.19), residues: 1968 helix: 2.42 (0.14), residues: 1352 sheet: 0.47 (0.54), residues: 88 loop : -0.49 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 580 TYR 0.010 0.001 TYR C 347 PHE 0.012 0.001 PHE A 569 TRP 0.011 0.001 TRP A 373 HIS 0.003 0.001 HIS A 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (16584) covalent geometry : angle 0.55122 / 0.27 (22456) hydrogen bonds : bond 0.05119 / 3.35 ( 1068) hydrogen bonds : angle 4.07304 / 2.97 ( 3132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Evaluate side-chains 274 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 0.871 Fit side-chains REVERT: A 101 MET cc_start: 0.6886 (mtp) cc_final: 0.5660 (ptt) REVERT: A 112 ARG cc_start: 0.7655 (ttp-170) cc_final: 0.7439 (ttt180) REVERT: A 285 PHE cc_start: 0.7994 (m-10) cc_final: 0.7683 (m-80) REVERT: A 492 ARG cc_start: 0.7954 (ttt90) cc_final: 0.7691 (ttp80) REVERT: A 512 MET cc_start: 0.8826 (ttm) cc_final: 0.8532 (ttp) REVERT: A 540 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6975 (pm20) REVERT: B 101 MET cc_start: 0.6880 (mtp) cc_final: 0.5647 (ptt) REVERT: B 112 ARG cc_start: 0.7663 (ttp-170) cc_final: 0.7392 (ttt180) REVERT: B 285 PHE cc_start: 0.8020 (m-10) cc_final: 0.7691 (m-80) REVERT: B 492 ARG cc_start: 0.7934 (ttt90) cc_final: 0.7690 (ttp80) REVERT: B 512 MET cc_start: 0.8796 (ttm) cc_final: 0.8460 (ttp) REVERT: B 540 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6927 (pm20) REVERT: C 101 MET cc_start: 0.6856 (mtp) cc_final: 0.5632 (ptt) REVERT: C 112 ARG cc_start: 0.7660 (ttp-170) cc_final: 0.7435 (ttt180) REVERT: C 285 PHE cc_start: 0.8034 (m-10) cc_final: 0.7718 (m-80) REVERT: C 492 ARG cc_start: 0.7986 (ttt90) cc_final: 0.7718 (ttp80) REVERT: C 512 MET cc_start: 0.8836 (ttm) cc_final: 0.8496 (ttp) REVERT: C 540 GLU cc_start: 0.7433 (pt0) cc_final: 0.7007 (pm20) REVERT: D 101 MET cc_start: 0.6870 (mtp) cc_final: 0.5641 (ptt) REVERT: D 112 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7471 (ttt180) REVERT: D 285 PHE cc_start: 0.8046 (m-10) cc_final: 0.7759 (m-80) REVERT: D 492 ARG cc_start: 0.7924 (ttt90) cc_final: 0.7666 (ttp80) REVERT: D 512 MET cc_start: 0.8828 (ttm) cc_final: 0.8436 (ttp) REVERT: D 540 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7067 (pm20) outliers start: 26 outliers final: 19 residues processed: 263 average time/residue: 1.4960 time to fit residues: 433.8259 Evaluate side-chains 258 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 236 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 565 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 145 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 ASN A 451 ASN B 448 ASN B 451 ASN C 451 ASN D 448 ASN D 451 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.153748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.112928 restraints weight = 52773.773| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.81 r_work: 0.3409 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16584 Z= 0.148 Angle : 0.551 8.753 22456 Z= 0.270 Chirality : 0.038 0.128 2504 Planarity : 0.004 0.040 2792 Dihedral : 4.039 27.151 2220 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.43 % Allowed : 13.82 % Favored : 84.75 % 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: 2.40 (0.19), residues: 1968 helix: 2.44 (0.14), residues: 1352 sheet: 0.52 (0.54), residues: 88 loop : -0.50 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 580 TYR 0.009 0.001 TYR C 347 PHE 0.012 0.001 PHE C 569 TRP 0.011 0.001 TRP C 373 HIS 0.003 0.001 HIS A 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (16584) covalent geometry : angle 0.55067 / 0.27 (22456) hydrogen bonds : bond 0.05051 / 3.31 ( 1068) hydrogen bonds : angle 4.06310 / 2.97 ( 3132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue LEU 602 is missing expected H atoms. Skipping. Residue LYS 604 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.6871 (mtp) cc_final: 0.5642 (ptt) REVERT: A 285 PHE cc_start: 0.7975 (m-10) cc_final: 0.7672 (m-80) REVERT: A 492 ARG cc_start: 0.7936 (ttt90) cc_final: 0.7668 (ttp80) REVERT: A 512 MET cc_start: 0.8818 (ttm) cc_final: 0.8447 (ttp) REVERT: A 540 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: B 101 MET cc_start: 0.6868 (mtp) cc_final: 0.5629 (ptt) REVERT: B 285 PHE cc_start: 0.7985 (m-10) cc_final: 0.7666 (m-80) REVERT: B 492 ARG cc_start: 0.7930 (ttt90) cc_final: 0.7672 (ttp80) REVERT: B 512 MET cc_start: 0.8783 (ttm) cc_final: 0.8440 (ttp) REVERT: B 540 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6927 (pm20) REVERT: C 101 MET cc_start: 0.6846 (mtp) cc_final: 0.5608 (ptt) REVERT: C 285 PHE cc_start: 0.8015 (m-10) cc_final: 0.7698 (m-80) REVERT: C 492 ARG cc_start: 0.7975 (ttt90) cc_final: 0.7699 (ttp80) REVERT: C 512 MET cc_start: 0.8813 (ttm) cc_final: 0.8463 (ttp) REVERT: C 540 GLU cc_start: 0.7415 (pt0) cc_final: 0.6986 (pm20) REVERT: D 101 MET cc_start: 0.6850 (mtp) cc_final: 0.5610 (ptt) REVERT: D 285 PHE cc_start: 0.8039 (m-10) cc_final: 0.7760 (m-80) REVERT: D 492 ARG cc_start: 0.7909 (ttt90) cc_final: 0.7647 (ttp80) REVERT: D 512 MET cc_start: 0.8818 (ttm) cc_final: 0.8416 (ttp) outliers start: 25 outliers final: 20 residues processed: 255 average time/residue: 1.3024 time to fit residues: 366.2879 Evaluate side-chains 254 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 565 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 192 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 ASN B 451 ASN C 451 ASN D 451 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.155828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.115196 restraints weight = 52538.536| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.80 r_work: 0.3436 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16584 Z= 0.108 Angle : 0.519 8.630 22456 Z= 0.251 Chirality : 0.037 0.138 2504 Planarity : 0.004 0.039 2792 Dihedral : 3.939 25.763 2220 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.97 % Allowed : 14.16 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.19), residues: 1968 helix: 2.64 (0.14), residues: 1352 sheet: 0.58 (0.53), residues: 88 loop : -0.50 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 580 TYR 0.009 0.001 TYR C 347 PHE 0.012 0.001 PHE A 569 TRP 0.011 0.001 TRP C 373 HIS 0.003 0.001 HIS A 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (16584) covalent geometry : angle 0.51924 / 0.25 (22456) hydrogen bonds : bond 0.04239 / 2.78 ( 1068) hydrogen bonds : angle 3.94321 / 2.88 ( 3132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12543.06 seconds wall clock time: 212 minutes 35.67 seconds (12755.67 seconds total)