Starting phenix.real_space_refine on Sat Jul 4 11:48:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ekp_28209/07_2026/8ekp_28209.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekp_28209/07_2026/8ekp_28209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ekp_28209/07_2026/8ekp_28209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekp_28209/07_2026/8ekp_28209.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ekp_28209/07_2026/8ekp_28209.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ekp_28209/07_2026/8ekp_28209.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ekp_28209/07_2026/8ekp_28209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekp_28209/07_2026/8ekp_28209.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 112 5.16 5 C 13368 2.51 5 N 3404 2.21 5 O 3556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20448 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5042 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PEX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.45, per 1000 atoms: 0.22 Number of scatterers: 20448 At special positions: 0 Unit cell: (137.97, 137.97, 112.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 8 15.00 O 3556 8.00 N 3404 7.00 C 13368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 772.6 milliseconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 62.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.833A pdb=" N THR A 93 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.644A pdb=" N LEU A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN A 141 " --> pdb=" O MET A 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 142 " --> pdb=" O PRO A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.529A pdb=" N VAL A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.955A pdb=" N VAL A 374 " --> pdb=" O HIS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.217A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 466 through 492 removed outlier: 7.391A pdb=" N PHE A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 510 removed outlier: 3.687A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.691A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 539 through 559 removed outlier: 4.081A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 619 through 649 Processing helix chain 'A' and resid 655 through 672 Processing helix chain 'A' and resid 711 through 718 removed outlier: 3.549A pdb=" N TRP A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.833A pdb=" N THR B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 146 removed outlier: 3.644A pdb=" N LEU B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN B 141 " --> pdb=" O MET B 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 142 " --> pdb=" O PRO B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.529A pdb=" N VAL B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.955A pdb=" N VAL B 374 " --> pdb=" O HIS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.217A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 466 through 492 removed outlier: 7.391A pdb=" N PHE B 472 " --> pdb=" O MET B 468 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 510 removed outlier: 3.687A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 518 removed outlier: 3.691A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 529 Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 539 through 559 removed outlier: 4.081A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 557 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 619 through 649 Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 711 through 718 removed outlier: 3.549A pdb=" N TRP B 715 " --> pdb=" O ASN B 711 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.833A pdb=" N THR C 93 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 146 removed outlier: 3.644A pdb=" N LEU C 140 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN C 141 " --> pdb=" O MET C 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 142 " --> pdb=" O PRO C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.529A pdb=" N VAL C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.955A pdb=" N VAL C 374 " --> pdb=" O HIS C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.217A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 466 through 492 removed outlier: 7.391A pdb=" N PHE C 472 " --> pdb=" O MET C 468 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 510 removed outlier: 3.687A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 518 removed outlier: 3.691A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 529 Processing helix chain 'C' and resid 533 through 538 Processing helix chain 'C' and resid 539 through 559 removed outlier: 4.081A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 557 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 619 through 649 Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 711 through 718 removed outlier: 3.549A pdb=" N TRP C 715 " --> pdb=" O ASN C 711 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.833A pdb=" N THR D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 146 removed outlier: 3.644A pdb=" N LEU D 140 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN D 141 " --> pdb=" O MET D 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D 142 " --> pdb=" O PRO D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.529A pdb=" N VAL D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.955A pdb=" N VAL D 374 " --> pdb=" O HIS D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.217A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 466 through 492 removed outlier: 7.391A pdb=" N PHE D 472 " --> pdb=" O MET D 468 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 510 removed outlier: 3.687A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 518 removed outlier: 3.691A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 529 Processing helix chain 'D' and resid 533 through 538 Processing helix chain 'D' and resid 539 through 559 removed outlier: 4.080A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 557 " --> pdb=" O VAL D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 619 through 649 Processing helix chain 'D' and resid 655 through 672 Processing helix chain 'D' and resid 711 through 718 removed outlier: 3.549A pdb=" N TRP D 715 " --> pdb=" O ASN D 711 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.986A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP A 700 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.986A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP B 700 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.986A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP C 700 " --> pdb=" O VAL C 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.986A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP D 700 " --> pdb=" O VAL D 691 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 3120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3160 1.31 - 1.43: 5844 1.43 - 1.56: 11736 1.56 - 1.69: 20 1.69 - 1.81: 172 Bond restraints: 20932 Sorted by residual: bond pdb=" C4 PEX D 802 " pdb=" O4 PEX D 802 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 PEX C 802 " pdb=" O4 PEX C 802 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 PEX B 802 " pdb=" O4 PEX B 802 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 PEX A 802 " pdb=" O4 PEX A 802 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 PEX A 801 " pdb=" O4 PEX A 801 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 20927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 27896 3.23 - 6.45: 360 6.45 - 9.68: 44 9.68 - 12.90: 4 12.90 - 16.13: 8 Bond angle restraints: 28312 Sorted by residual: angle pdb=" O3 PEX A 802 " pdb=" P1 PEX A 802 " pdb=" O8 PEX A 802 " ideal model delta sigma weight residual 93.74 109.87 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3 PEX B 802 " pdb=" P1 PEX B 802 " pdb=" O8 PEX B 802 " ideal model delta sigma weight residual 93.74 109.87 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3 PEX C 802 " pdb=" P1 PEX C 802 " pdb=" O8 PEX C 802 " ideal model delta sigma weight residual 93.74 109.87 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3 PEX D 802 " pdb=" P1 PEX D 802 " pdb=" O8 PEX D 802 " ideal model delta sigma weight residual 93.74 109.87 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3 PEX B 801 " pdb=" P1 PEX B 801 " pdb=" O8 PEX B 801 " ideal model delta sigma weight residual 93.74 109.48 -15.74 3.00e+00 1.11e-01 2.75e+01 ... (remaining 28307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 11104 17.78 - 35.56: 1048 35.56 - 53.33: 156 53.33 - 71.11: 52 71.11 - 88.89: 4 Dihedral angle restraints: 12364 sinusoidal: 5092 harmonic: 7272 Sorted by residual: dihedral pdb=" CA ARG A 539 " pdb=" C ARG A 539 " pdb=" N PHE A 540 " pdb=" CA PHE A 540 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ARG B 539 " pdb=" C ARG B 539 " pdb=" N PHE B 540 " pdb=" CA PHE B 540 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ARG C 539 " pdb=" C ARG C 539 " pdb=" N PHE C 540 " pdb=" CA PHE C 540 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 12361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2350 0.045 - 0.090: 646 0.090 - 0.134: 132 0.134 - 0.179: 12 0.179 - 0.224: 20 Chirality restraints: 3160 Sorted by residual: chirality pdb=" CG LEU B 636 " pdb=" CB LEU B 636 " pdb=" CD1 LEU B 636 " pdb=" CD2 LEU B 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU C 636 " pdb=" CB LEU C 636 " pdb=" CD1 LEU C 636 " pdb=" CD2 LEU C 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU A 636 " pdb=" CB LEU A 636 " pdb=" CD1 LEU A 636 " pdb=" CD2 LEU A 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 3157 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 530 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" CD GLN B 530 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLN B 530 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN B 530 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 530 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" CD GLN C 530 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLN C 530 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN C 530 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 530 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" CD GLN A 530 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLN A 530 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN A 530 " -0.014 2.00e-02 2.50e+03 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5224 2.80 - 3.32: 17880 3.32 - 3.85: 33952 3.85 - 4.37: 41364 4.37 - 4.90: 69132 Nonbonded interactions: 167552 Sorted by model distance: nonbonded pdb=" O GLY D 131 " pdb=" OG SER D 176 " model vdw 2.269 3.040 nonbonded pdb=" O GLY A 131 " pdb=" OG SER A 176 " model vdw 2.269 3.040 nonbonded pdb=" O GLY B 131 " pdb=" OG SER B 176 " model vdw 2.269 3.040 nonbonded pdb=" O GLY C 131 " pdb=" OG SER C 176 " model vdw 2.269 3.040 nonbonded pdb=" O MET C 468 " pdb=" N1 PEX C 801 " model vdw 2.415 3.120 ... (remaining 167547 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: 0.04 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: 7.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.260 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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:7.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20932 Z= 0.210 Angle : 0.874 16.126 28312 Z= 0.417 Chirality : 0.044 0.224 3160 Planarity : 0.007 0.093 3492 Dihedral : 13.701 88.888 7660 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.94 (0.14), residues: 2448 helix: -2.37 (0.09), residues: 1424 sheet: 1.00 (0.52), residues: 112 loop : -1.28 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 193 TYR 0.022 0.001 TYR B 544 PHE 0.014 0.001 PHE D 161 TRP 0.010 0.001 TRP D 333 HIS 0.005 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 (20932) covalent geometry : angle 0.87402 / 0.42 (28312) hydrogen bonds : bond 0.24506 / 16.38 ( 1080) hydrogen bonds : angle 7.48591 / 5.23 ( 3120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.765 Fit side-chains REVERT: A 76 ASP cc_start: 0.7519 (t0) cc_final: 0.7085 (t0) REVERT: A 617 ARG cc_start: 0.7042 (ttm170) cc_final: 0.6836 (ttm-80) REVERT: A 654 ASP cc_start: 0.6134 (t70) cc_final: 0.5786 (t70) REVERT: A 701 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7385 (mt-10) REVERT: B 76 ASP cc_start: 0.7524 (t0) cc_final: 0.6384 (p0) REVERT: B 617 ARG cc_start: 0.7050 (ttm170) cc_final: 0.6844 (ttm-80) REVERT: B 654 ASP cc_start: 0.6138 (t70) cc_final: 0.5792 (t70) REVERT: B 701 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7399 (mt-10) REVERT: C 76 ASP cc_start: 0.7525 (t0) cc_final: 0.7094 (t0) REVERT: C 617 ARG cc_start: 0.7037 (ttm170) cc_final: 0.6830 (ttm-80) REVERT: C 654 ASP cc_start: 0.6129 (t70) cc_final: 0.5776 (t70) REVERT: C 701 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7397 (mt-10) REVERT: D 76 ASP cc_start: 0.7519 (t0) cc_final: 0.7087 (t0) REVERT: D 617 ARG cc_start: 0.7049 (ttm170) cc_final: 0.6844 (ttm-80) REVERT: D 654 ASP cc_start: 0.6138 (t70) cc_final: 0.5788 (t70) REVERT: D 701 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7402 (mt-10) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.5581 time to fit residues: 241.9130 Evaluate side-chains 311 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 HIS A 186 ASN A 235 GLN A 354 ASN A 487 GLN A 673 ASN B 165 HIS B 186 ASN B 235 GLN B 354 ASN B 487 GLN B 673 ASN C 165 HIS C 186 ASN C 235 GLN C 354 ASN C 487 GLN C 673 ASN D 165 HIS D 186 ASN D 235 GLN D 354 ASN D 487 GLN D 673 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.137575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.113169 restraints weight = 23708.351| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.53 r_work: 0.3085 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 20932 Z= 0.308 Angle : 0.701 9.282 28312 Z= 0.356 Chirality : 0.047 0.161 3160 Planarity : 0.006 0.064 3492 Dihedral : 8.663 59.147 2888 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.65 % Allowed : 6.59 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2448 helix: 0.06 (0.13), residues: 1472 sheet: 1.19 (0.51), residues: 112 loop : -0.96 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 41 TYR 0.022 0.002 TYR B 515 PHE 0.027 0.002 PHE D 407 TRP 0.011 0.002 TRP B 509 HIS 0.005 0.002 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.31 (20932) covalent geometry : angle 0.70113 / 0.36 (28312) hydrogen bonds : bond 0.05424 / 3.64 ( 1080) hydrogen bonds : angle 4.28203 / 2.93 ( 3120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 349 time to evaluate : 0.784 Fit side-chains REVERT: A 197 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7540 (ttm170) REVERT: A 683 HIS cc_start: 0.7497 (t-90) cc_final: 0.7080 (t-90) REVERT: B 197 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7555 (ttm170) REVERT: B 683 HIS cc_start: 0.7487 (t-90) cc_final: 0.7062 (t-90) REVERT: C 197 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7513 (ttm170) REVERT: C 683 HIS cc_start: 0.7503 (t-90) cc_final: 0.7088 (t-90) REVERT: D 197 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7517 (ttm170) REVERT: D 683 HIS cc_start: 0.7506 (t-90) cc_final: 0.7091 (t-90) outliers start: 36 outliers final: 12 residues processed: 361 average time/residue: 0.5962 time to fit residues: 245.7199 Evaluate side-chains 330 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 314 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 111 optimal weight: 8.9990 chunk 17 optimal weight: 0.4980 chunk 221 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 235 GLN A 414 GLN A 673 ASN B 186 ASN B 235 GLN B 414 GLN B 452 GLN B 673 ASN C 186 ASN C 235 GLN C 414 GLN C 673 ASN D 186 ASN D 235 GLN D 414 GLN D 673 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.142609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.117913 restraints weight = 23447.960| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.55 r_work: 0.3219 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20932 Z= 0.109 Angle : 0.487 8.611 28312 Z= 0.254 Chirality : 0.038 0.153 3160 Planarity : 0.004 0.053 3492 Dihedral : 7.381 59.093 2888 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.01 % Allowed : 10.67 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.17), residues: 2448 helix: 1.06 (0.14), residues: 1480 sheet: 1.39 (0.52), residues: 112 loop : -0.96 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 41 TYR 0.011 0.001 TYR C 525 PHE 0.013 0.001 PHE C 540 TRP 0.009 0.001 TRP D 509 HIS 0.002 0.001 HIS D 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (20932) covalent geometry : angle 0.48694 / 0.25 (28312) hydrogen bonds : bond 0.03575 / 2.39 ( 1080) hydrogen bonds : angle 3.69993 / 2.55 ( 3120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 319 time to evaluate : 0.807 Fit side-chains REVERT: A 647 GLU cc_start: 0.7767 (tt0) cc_final: 0.7094 (mp0) REVERT: B 647 GLU cc_start: 0.7767 (tt0) cc_final: 0.7081 (mp0) REVERT: C 647 GLU cc_start: 0.7776 (tt0) cc_final: 0.7092 (mp0) REVERT: D 647 GLU cc_start: 0.7760 (tt0) cc_final: 0.7070 (mp0) outliers start: 44 outliers final: 24 residues processed: 342 average time/residue: 0.5974 time to fit residues: 233.0844 Evaluate side-chains 309 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 285 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 12 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 235 GLN A 673 ASN B 186 ASN B 235 GLN B 673 ASN C 186 ASN C 235 GLN C 673 ASN D 186 ASN D 235 GLN D 673 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.138360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.113768 restraints weight = 23594.357| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.54 r_work: 0.3091 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20932 Z= 0.228 Angle : 0.600 9.606 28312 Z= 0.306 Chirality : 0.044 0.209 3160 Planarity : 0.005 0.055 3492 Dihedral : 7.917 59.243 2888 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.84 % Allowed : 11.13 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.17), residues: 2448 helix: 1.10 (0.14), residues: 1476 sheet: 1.64 (0.60), residues: 88 loop : -0.94 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 41 TYR 0.018 0.002 TYR B 515 PHE 0.017 0.002 PHE D 407 TRP 0.011 0.002 TRP A 333 HIS 0.004 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (20932) covalent geometry : angle 0.60014 / 0.31 (28312) hydrogen bonds : bond 0.04356 / 2.91 ( 1080) hydrogen bonds : angle 3.91452 / 2.68 ( 3120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 328 time to evaluate : 0.908 Fit side-chains REVERT: A 197 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7583 (ttm170) REVERT: A 681 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7294 (pttp) REVERT: B 197 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7607 (ttm170) REVERT: B 234 HIS cc_start: 0.7410 (m-70) cc_final: 0.7117 (m170) REVERT: B 681 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7299 (pttp) REVERT: C 197 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7597 (ttm170) REVERT: C 234 HIS cc_start: 0.7400 (m-70) cc_final: 0.7105 (m170) REVERT: C 681 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7292 (pttp) REVERT: D 197 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7603 (ttm170) REVERT: D 234 HIS cc_start: 0.7434 (m-70) cc_final: 0.7168 (m170) REVERT: D 681 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7290 (pttp) outliers start: 62 outliers final: 28 residues processed: 351 average time/residue: 0.6115 time to fit residues: 244.2662 Evaluate side-chains 347 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 311 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 681 LYS Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 681 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 681 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 139 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 235 GLN B 186 ASN B 235 GLN C 186 ASN C 234 HIS C 235 GLN D 186 ASN D 235 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.137138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.112636 restraints weight = 23538.031| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.53 r_work: 0.3070 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20932 Z= 0.266 Angle : 0.633 9.137 28312 Z= 0.322 Chirality : 0.046 0.246 3160 Planarity : 0.005 0.058 3492 Dihedral : 8.237 55.669 2888 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.79 % Allowed : 12.27 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.17), residues: 2448 helix: 1.00 (0.14), residues: 1476 sheet: 1.46 (0.58), residues: 88 loop : -0.99 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 41 TYR 0.018 0.002 TYR B 515 PHE 0.020 0.002 PHE C 540 TRP 0.013 0.002 TRP B 333 HIS 0.004 0.002 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.27 (20932) covalent geometry : angle 0.63295 / 0.32 (28312) hydrogen bonds : bond 0.04509 / 3.02 ( 1080) hydrogen bonds : angle 4.01380 / 2.74 ( 3120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 328 time to evaluate : 0.817 Fit side-chains REVERT: A 197 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7601 (ttm170) REVERT: A 535 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.5823 (pmt-80) REVERT: A 681 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7414 (pttp) REVERT: B 197 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7621 (ttm170) REVERT: B 535 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.5855 (pmt-80) REVERT: B 645 MET cc_start: 0.7912 (mtm) cc_final: 0.7588 (mtm) REVERT: B 681 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7420 (pttp) REVERT: C 197 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7610 (ttm170) REVERT: C 535 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.5842 (pmt-80) REVERT: C 681 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7433 (pttp) REVERT: D 197 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7598 (ttm170) REVERT: D 535 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5825 (pmt-80) REVERT: D 645 MET cc_start: 0.7902 (mtm) cc_final: 0.7617 (mtm) REVERT: D 681 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7412 (pttp) outliers start: 61 outliers final: 28 residues processed: 362 average time/residue: 0.5995 time to fit residues: 247.8647 Evaluate side-chains 359 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 319 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 681 LYS Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 681 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 681 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 31 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 234 HIS A 235 GLN A 452 GLN B 186 ASN B 235 GLN C 186 ASN C 235 GLN C 452 GLN D 186 ASN D 234 HIS D 235 GLN D 452 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.141063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.116297 restraints weight = 23293.450| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.55 r_work: 0.3128 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20932 Z= 0.114 Angle : 0.491 9.518 28312 Z= 0.255 Chirality : 0.039 0.183 3160 Planarity : 0.004 0.053 3492 Dihedral : 7.241 49.393 2888 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.47 % Allowed : 13.60 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2448 helix: 1.46 (0.14), residues: 1468 sheet: 1.82 (0.60), residues: 88 loop : -0.85 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 41 TYR 0.010 0.001 TYR D 525 PHE 0.014 0.001 PHE B 405 TRP 0.010 0.001 TRP D 333 HIS 0.002 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (20932) covalent geometry : angle 0.49097 / 0.26 (28312) hydrogen bonds : bond 0.03420 / 2.29 ( 1080) hydrogen bonds : angle 3.63353 / 2.50 ( 3120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 329 time to evaluate : 0.819 Fit side-chains REVERT: A 91 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7382 (pt0) REVERT: B 91 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7366 (pt0) REVERT: B 645 MET cc_start: 0.7797 (mtm) cc_final: 0.7443 (mtm) REVERT: C 91 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7395 (pt0) REVERT: D 91 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7391 (pt0) REVERT: D 645 MET cc_start: 0.7797 (mtm) cc_final: 0.7467 (mtm) outliers start: 54 outliers final: 24 residues processed: 359 average time/residue: 0.5788 time to fit residues: 237.1447 Evaluate side-chains 346 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 318 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 143 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 188 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 245 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 235 GLN A 673 ASN B 186 ASN B 235 GLN B 673 ASN C 186 ASN C 235 GLN D 186 ASN D 235 GLN D 673 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.141892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.117119 restraints weight = 23206.508| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.56 r_work: 0.3135 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20932 Z= 0.107 Angle : 0.490 10.337 28312 Z= 0.249 Chirality : 0.038 0.214 3160 Planarity : 0.004 0.049 3492 Dihedral : 6.820 48.334 2888 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.97 % Allowed : 14.33 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.18 (0.17), residues: 2448 helix: 1.63 (0.14), residues: 1472 sheet: 1.95 (0.60), residues: 88 loop : -0.78 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 41 TYR 0.009 0.001 TYR C 525 PHE 0.021 0.001 PHE A 540 TRP 0.008 0.001 TRP C 333 HIS 0.002 0.001 HIS D 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (20932) covalent geometry : angle 0.48965 / 0.25 (28312) hydrogen bonds : bond 0.03305 / 2.22 ( 1080) hydrogen bonds : angle 3.53656 / 2.44 ( 3120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 320 time to evaluate : 0.841 Fit side-chains REVERT: A 91 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: A 197 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7581 (ttm170) REVERT: B 91 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7379 (pt0) REVERT: B 197 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7599 (ttm170) REVERT: B 289 GLU cc_start: 0.8184 (mp0) cc_final: 0.7824 (mp0) REVERT: C 91 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7399 (pt0) REVERT: C 182 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7713 (tt) REVERT: C 197 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7621 (ttm170) REVERT: C 289 GLU cc_start: 0.8172 (mp0) cc_final: 0.7809 (mp0) REVERT: D 91 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7385 (pt0) REVERT: D 197 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7592 (ttm170) REVERT: D 645 MET cc_start: 0.7755 (mtm) cc_final: 0.7547 (ttm) outliers start: 43 outliers final: 26 residues processed: 346 average time/residue: 0.5720 time to fit residues: 227.0589 Evaluate side-chains 335 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 300 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 167 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 235 GLN A 673 ASN B 186 ASN B 235 GLN C 186 ASN C 235 GLN C 673 ASN D 186 ASN D 235 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.139268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.114449 restraints weight = 23328.191| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.55 r_work: 0.3099 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20932 Z= 0.174 Angle : 0.550 10.051 28312 Z= 0.278 Chirality : 0.042 0.246 3160 Planarity : 0.004 0.050 3492 Dihedral : 7.441 54.021 2888 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.29 % Allowed : 14.65 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.01 (0.17), residues: 2448 helix: 1.47 (0.14), residues: 1472 sheet: 1.81 (0.60), residues: 88 loop : -0.80 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 41 TYR 0.014 0.002 TYR C 515 PHE 0.019 0.002 PHE A 405 TRP 0.010 0.001 TRP C 333 HIS 0.003 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (20932) covalent geometry : angle 0.55030 / 0.28 (28312) hydrogen bonds : bond 0.03855 / 2.58 ( 1080) hydrogen bonds : angle 3.72238 / 2.55 ( 3120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 314 time to evaluate : 0.795 Fit side-chains REVERT: A 197 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7560 (ttm170) REVERT: A 416 SER cc_start: 0.7996 (t) cc_final: 0.7485 (m) REVERT: B 197 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7543 (ttm170) REVERT: B 416 SER cc_start: 0.8002 (t) cc_final: 0.7490 (m) REVERT: C 182 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7699 (tt) REVERT: C 197 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7594 (ttm170) REVERT: C 416 SER cc_start: 0.7994 (t) cc_final: 0.7483 (m) REVERT: D 197 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7583 (ttm170) REVERT: D 416 SER cc_start: 0.7992 (t) cc_final: 0.7482 (m) REVERT: D 645 MET cc_start: 0.7765 (mtm) cc_final: 0.7404 (mtm) outliers start: 50 outliers final: 24 residues processed: 345 average time/residue: 0.5935 time to fit residues: 234.2891 Evaluate side-chains 340 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 311 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 129 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 200 optimal weight: 0.3980 chunk 141 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 0.0970 chunk 225 optimal weight: 10.0000 chunk 234 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 235 GLN B 186 ASN B 235 GLN C 186 ASN C 235 GLN D 186 ASN D 235 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.142415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.117620 restraints weight = 23206.368| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.56 r_work: 0.3165 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20932 Z= 0.102 Angle : 0.488 9.624 28312 Z= 0.248 Chirality : 0.038 0.231 3160 Planarity : 0.004 0.047 3492 Dihedral : 6.787 49.186 2888 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.60 % Allowed : 15.43 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.23 (0.17), residues: 2448 helix: 1.66 (0.14), residues: 1472 sheet: 1.94 (0.60), residues: 88 loop : -0.75 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 41 TYR 0.012 0.001 TYR C 471 PHE 0.018 0.001 PHE C 405 TRP 0.008 0.001 TRP C 333 HIS 0.002 0.001 HIS A 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (20932) covalent geometry : angle 0.48776 / 0.25 (28312) hydrogen bonds : bond 0.03215 / 2.16 ( 1080) hydrogen bonds : angle 3.52824 / 2.43 ( 3120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 320 time to evaluate : 0.806 Fit side-chains REVERT: A 197 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7590 (ttm170) REVERT: B 197 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7595 (ttm170) REVERT: C 197 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7564 (ttm170) REVERT: C 289 GLU cc_start: 0.8174 (mp0) cc_final: 0.7809 (mp0) REVERT: D 197 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7588 (ttm170) REVERT: D 645 MET cc_start: 0.7747 (mtm) cc_final: 0.7512 (ttm) outliers start: 35 outliers final: 20 residues processed: 345 average time/residue: 0.5750 time to fit residues: 227.8737 Evaluate side-chains 328 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 304 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 198 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 242 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 235 GLN A 673 ASN B 186 ASN B 235 GLN B 673 ASN C 186 ASN C 235 GLN C 673 ASN D 186 ASN D 235 GLN D 673 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.140466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115543 restraints weight = 23234.881| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.56 r_work: 0.3109 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20932 Z= 0.147 Angle : 0.533 10.071 28312 Z= 0.269 Chirality : 0.040 0.259 3160 Planarity : 0.004 0.048 3492 Dihedral : 7.132 52.052 2888 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.51 % Allowed : 16.35 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.17 (0.17), residues: 2448 helix: 1.61 (0.14), residues: 1472 sheet: 1.83 (0.60), residues: 88 loop : -0.73 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 41 TYR 0.012 0.001 TYR C 471 PHE 0.022 0.001 PHE B 405 TRP 0.009 0.001 TRP B 333 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (20932) covalent geometry : angle 0.53263 / 0.27 (28312) hydrogen bonds : bond 0.03634 / 2.43 ( 1080) hydrogen bonds : angle 3.65844 / 2.51 ( 3120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 303 time to evaluate : 0.710 Fit side-chains REVERT: A 197 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7549 (ttm170) REVERT: A 372 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8440 (mtm) REVERT: B 182 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7741 (tt) REVERT: B 197 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7590 (ttm170) REVERT: C 182 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7712 (tt) REVERT: C 197 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7585 (ttm170) REVERT: D 197 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7577 (ttm170) outliers start: 33 outliers final: 20 residues processed: 327 average time/residue: 0.5832 time to fit residues: 218.6458 Evaluate side-chains 326 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 299 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 237 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 197 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 46 optimal weight: 0.0060 chunk 65 optimal weight: 8.9990 chunk 209 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 235 GLN A 673 ASN B 186 ASN C 186 ASN C 234 HIS C 235 GLN C 673 ASN D 186 ASN D 673 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.143596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118711 restraints weight = 23179.790| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.57 r_work: 0.3158 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20932 Z= 0.094 Angle : 0.479 9.858 28312 Z= 0.242 Chirality : 0.038 0.212 3160 Planarity : 0.004 0.046 3492 Dihedral : 6.491 49.468 2888 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.69 % Allowed : 16.12 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.40 (0.17), residues: 2448 helix: 1.79 (0.14), residues: 1472 sheet: 1.97 (0.61), residues: 88 loop : -0.65 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 41 TYR 0.012 0.001 TYR C 471 PHE 0.020 0.001 PHE B 405 TRP 0.007 0.001 TRP A 509 HIS 0.002 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 (20932) covalent geometry : angle 0.47945 / 0.24 (28312) hydrogen bonds : bond 0.03039 / 2.04 ( 1080) hydrogen bonds : angle 3.45874 / 2.39 ( 3120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7217.14 seconds wall clock time: 124 minutes 2.23 seconds (7442.23 seconds total)