Starting phenix.real_space_refine on Sun Aug 24 14:36:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekp_28209/08_2025/8ekp_28209.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekp_28209/08_2025/8ekp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ekp_28209/08_2025/8ekp_28209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekp_28209/08_2025/8ekp_28209.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekp_28209/08_2025/8ekp_28209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekp_28209/08_2025/8ekp_28209.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 4.70, per 1000 atoms: 0.23 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: 1.79 Conformation dependent library (CDL) restraints added in 885.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.62 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: 3.26 Time building geometry restraints manager: 2.20 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 - 30.87: 12052 30.87 - 61.73: 360 61.73 - 92.60: 20 92.60 - 123.47: 0 123.47 - 154.33: 4 Dihedral angle restraints: 12436 sinusoidal: 5164 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 12433 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: 7.000 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: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 17.980 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 14.700 154.331 7732 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 aren 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 covalent geometry : bond 0.00410 (20932) covalent geometry : angle 0.87402 (28312) hydrogen bonds : bond 0.24506 ( 1080) hydrogen bonds : angle 7.48591 ( 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 : 0.595 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: 0.5800 time to fit residues: 249.6887 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 : 0.721 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3484 r_free = 0.3484 target = 0.137365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.112884 restraints weight = 23741.696| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.54 r_work: 0.3078 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2053 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= 0.307 Angle : 0.705 9.130 28312 Z= 0.357 Chirality : 0.047 0.159 3160 Planarity : 0.006 0.063 3492 Dihedral : 11.311 148.255 2960 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.60 % Allowed : 6.78 % Favored : 91.62 % 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 aren not related in a simple way. whole: -0.47 (0.16), residues: 2448 helix: 0.05 (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 B 539 TYR 0.022 0.002 TYR B 515 PHE 0.026 0.002 PHE D 407 TRP 0.012 0.002 TRP C 509 HIS 0.005 0.002 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00726 (20932) covalent geometry : angle 0.70453 (28312) hydrogen bonds : bond 0.05400 ( 1080) hydrogen bonds : angle 4.29345 ( 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 384 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 349 time to evaluate : 0.865 Fit side-chains REVERT: A 197 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7504 (ttm170) REVERT: A 372 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8562 (mtp) REVERT: A 683 HIS cc_start: 0.7494 (t-90) cc_final: 0.7023 (t-90) REVERT: B 197 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7521 (ttm170) REVERT: B 683 HIS cc_start: 0.7486 (t-90) cc_final: 0.7056 (t-90) REVERT: C 197 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7502 (ttm170) REVERT: C 683 HIS cc_start: 0.7493 (t-90) cc_final: 0.7020 (t-90) REVERT: D 197 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7513 (ttm170) REVERT: D 683 HIS cc_start: 0.7507 (t-90) cc_final: 0.7088 (t-90) outliers start: 35 outliers final: 12 residues processed: 361 average time/residue: 0.5880 time to fit residues: 240.8998 Evaluate side-chains 330 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 313 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 372 MET 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: 0.0870 chunk 221 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 235 GLN A 414 GLN A 673 ASN B 186 ASN B 235 GLN B 414 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.143036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.118360 restraints weight = 23448.533| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.55 r_work: 0.3157 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20932 Z= 0.104 Angle : 0.481 8.579 28312 Z= 0.251 Chirality : 0.038 0.156 3160 Planarity : 0.004 0.051 3492 Dihedral : 10.198 141.277 2960 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.06 % Allowed : 10.62 % 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 aren not related in a simple way. whole: 0.55 (0.17), residues: 2448 helix: 1.06 (0.14), residues: 1476 sheet: 1.40 (0.52), residues: 112 loop : -0.95 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 41 TYR 0.011 0.001 TYR B 525 PHE 0.013 0.001 PHE A 540 TRP 0.009 0.001 TRP C 509 HIS 0.002 0.001 HIS B 521 Details of bonding type rmsd covalent geometry : bond 0.00233 (20932) covalent geometry : angle 0.48101 (28312) hydrogen bonds : bond 0.03491 ( 1080) hydrogen bonds : angle 3.68790 ( 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 362 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 317 time to evaluate : 0.663 Fit side-chains REVERT: C 647 GLU cc_start: 0.7788 (tt0) cc_final: 0.7093 (mp0) outliers start: 45 outliers final: 21 residues processed: 340 average time/residue: 0.5118 time to fit residues: 198.1565 Evaluate side-chains 305 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 284 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 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 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 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: 9.9990 chunk 56 optimal weight: 0.4980 chunk 194 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3486 r_free = 0.3486 target = 0.137368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.112836 restraints weight = 23650.878| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.54 r_work: 0.3140 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 20932 Z= 0.273 Angle : 0.638 9.624 28312 Z= 0.324 Chirality : 0.046 0.216 3160 Planarity : 0.005 0.057 3492 Dihedral : 10.808 146.938 2960 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.98 % Allowed : 11.40 % Favored : 85.62 % 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 aren not related in a simple way. whole: 0.45 (0.17), residues: 2448 helix: 1.00 (0.14), residues: 1476 sheet: 1.58 (0.59), residues: 88 loop : -0.99 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 41 TYR 0.019 0.002 TYR D 515 PHE 0.019 0.002 PHE D 407 TRP 0.012 0.002 TRP A 333 HIS 0.005 0.002 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00650 (20932) covalent geometry : angle 0.63840 (28312) hydrogen bonds : bond 0.04597 ( 1080) hydrogen bonds : angle 4.00315 ( 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 401 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 336 time to evaluate : 0.687 Fit side-chains REVERT: A 197 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7596 (ttm170) REVERT: A 234 HIS cc_start: 0.7460 (m-70) cc_final: 0.7192 (m170) REVERT: A 645 MET cc_start: 0.7879 (mtm) cc_final: 0.7541 (mtm) REVERT: A 681 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7359 (pttp) REVERT: B 197 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7604 (ttm170) REVERT: B 234 HIS cc_start: 0.7460 (m-70) cc_final: 0.7188 (m170) REVERT: B 681 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7338 (pttp) REVERT: C 197 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7585 (ttm170) REVERT: C 234 HIS cc_start: 0.7459 (m-70) cc_final: 0.7188 (m170) REVERT: C 681 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7354 (pttp) REVERT: D 197 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7587 (ttm170) REVERT: D 234 HIS cc_start: 0.7460 (m-70) cc_final: 0.7198 (m170) REVERT: D 681 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7311 (pttp) outliers start: 65 outliers final: 31 residues processed: 361 average time/residue: 0.5703 time to fit residues: 233.2360 Evaluate side-chains 352 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 313 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 492 MET 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 492 MET 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 492 MET 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: 0.9990 chunk 5 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 213 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 235 GLN B 186 ASN B 235 GLN B 452 GLN C 186 ASN C 235 GLN C 452 GLN 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 = 0.3506 r_free = 0.3506 target = 0.139086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.114451 restraints weight = 23469.674| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.54 r_work: 0.3109 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2388 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= 0.184 Angle : 0.556 9.153 28312 Z= 0.285 Chirality : 0.042 0.178 3160 Planarity : 0.004 0.055 3492 Dihedral : 10.478 144.528 2960 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.93 % Allowed : 12.41 % Favored : 84.66 % 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 aren not related in a simple way. whole: 0.64 (0.17), residues: 2448 helix: 1.18 (0.14), residues: 1476 sheet: 1.66 (0.59), residues: 88 loop : -0.95 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 41 TYR 0.014 0.002 TYR B 515 PHE 0.019 0.002 PHE C 540 TRP 0.011 0.001 TRP C 333 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00437 (20932) covalent geometry : angle 0.55627 (28312) hydrogen bonds : bond 0.03991 ( 1080) hydrogen bonds : angle 3.82432 ( 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 395 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 331 time to evaluate : 0.526 Fit side-chains REVERT: A 197 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7579 (ttm170) REVERT: B 197 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7598 (ttm170) REVERT: C 182 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7747 (tt) REVERT: C 197 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7610 (ttm170) REVERT: D 197 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7596 (ttm170) outliers start: 64 outliers final: 29 residues processed: 364 average time/residue: 0.5319 time to fit residues: 219.8373 Evaluate side-chains 350 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 316 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 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 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 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 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 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 641 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 31 optimal weight: 0.8980 chunk 197 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 235 GLN A 452 GLN B 186 ASN B 235 GLN C 186 ASN C 235 GLN D 186 ASN D 235 GLN D 452 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.141705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.117039 restraints weight = 23271.656| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.55 r_work: 0.3149 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20932 Z= 0.109 Angle : 0.489 10.026 28312 Z= 0.252 Chirality : 0.038 0.179 3160 Planarity : 0.004 0.050 3492 Dihedral : 9.845 140.033 2960 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.88 % Allowed : 14.24 % Favored : 83.88 % 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 aren not related in a simple way. whole: 1.06 (0.17), residues: 2448 helix: 1.54 (0.14), residues: 1468 sheet: 1.84 (0.59), residues: 88 loop : -0.82 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 41 TYR 0.010 0.001 TYR B 525 PHE 0.015 0.001 PHE D 405 TRP 0.009 0.001 TRP D 333 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00249 (20932) covalent geometry : angle 0.48889 (28312) hydrogen bonds : bond 0.03334 ( 1080) hydrogen bonds : angle 3.59085 ( 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 353 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 312 time to evaluate : 0.721 Fit side-chains REVERT: A 91 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7399 (pt0) REVERT: B 91 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7389 (pt0) REVERT: C 91 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7414 (pt0) REVERT: C 182 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7727 (tt) REVERT: C 645 MET cc_start: 0.7731 (mtm) cc_final: 0.7503 (mtp) REVERT: D 91 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7408 (pt0) REVERT: D 645 MET cc_start: 0.7773 (mtm) cc_final: 0.7543 (ttm) outliers start: 41 outliers final: 23 residues processed: 337 average time/residue: 0.5586 time to fit residues: 215.0087 Evaluate side-chains 338 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 310 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 358 GLU 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 224 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 401 LEU 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 401 LEU 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: 1.9990 chunk 206 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 188 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 235 GLN B 186 ASN B 235 GLN C 186 ASN C 235 GLN D 186 ASN D 235 GLN D 673 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.140624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.115871 restraints weight = 23192.021| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.54 r_work: 0.3120 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20932 Z= 0.132 Angle : 0.511 9.798 28312 Z= 0.260 Chirality : 0.040 0.229 3160 Planarity : 0.004 0.047 3492 Dihedral : 9.891 140.843 2960 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.20 % Allowed : 14.29 % Favored : 83.52 % 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 aren not related in a simple way. whole: 1.10 (0.17), residues: 2448 helix: 1.56 (0.14), residues: 1468 sheet: 1.86 (0.60), residues: 88 loop : -0.79 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 41 TYR 0.011 0.001 TYR B 515 PHE 0.019 0.001 PHE A 540 TRP 0.009 0.001 TRP B 333 HIS 0.003 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00311 (20932) covalent geometry : angle 0.51111 (28312) hydrogen bonds : bond 0.03551 ( 1080) hydrogen bonds : angle 3.63675 ( 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 365 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 317 time to evaluate : 0.835 Fit side-chains REVERT: A 91 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7355 (pt0) REVERT: A 197 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7554 (ttm170) REVERT: A 416 SER cc_start: 0.8038 (t) cc_final: 0.7526 (m) REVERT: A 645 MET cc_start: 0.7726 (mtm) cc_final: 0.7311 (mtm) REVERT: B 91 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7358 (pt0) REVERT: B 197 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7558 (ttm170) REVERT: B 416 SER cc_start: 0.8038 (t) cc_final: 0.7525 (m) REVERT: C 91 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7380 (pt0) REVERT: C 182 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7729 (tt) REVERT: C 197 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7596 (ttm170) REVERT: C 416 SER cc_start: 0.8028 (t) cc_final: 0.7513 (m) REVERT: D 91 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7388 (pt0) REVERT: D 197 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7586 (ttm170) REVERT: D 416 SER cc_start: 0.8036 (t) cc_final: 0.7515 (m) outliers start: 48 outliers final: 23 residues processed: 352 average time/residue: 0.5694 time to fit residues: 227.9412 Evaluate side-chains 333 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 301 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 358 GLU 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 401 LEU 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 401 LEU 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: 0.9980 chunk 164 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 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: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3528 r_free = 0.3528 target = 0.140965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.116201 restraints weight = 23258.053| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.55 r_work: 0.3120 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20932 Z= 0.127 Angle : 0.512 9.968 28312 Z= 0.260 Chirality : 0.039 0.245 3160 Planarity : 0.004 0.046 3492 Dihedral : 9.787 141.014 2960 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.20 % Allowed : 14.51 % Favored : 83.29 % 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 aren not related in a simple way. whole: 1.13 (0.17), residues: 2448 helix: 1.58 (0.14), residues: 1472 sheet: 1.92 (0.60), residues: 88 loop : -0.76 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 41 TYR 0.011 0.001 TYR B 515 PHE 0.018 0.001 PHE D 540 TRP 0.009 0.001 TRP B 333 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00300 (20932) covalent geometry : angle 0.51191 (28312) hydrogen bonds : bond 0.03467 ( 1080) hydrogen bonds : angle 3.61430 ( 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 349 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 301 time to evaluate : 0.605 Fit side-chains REVERT: A 197 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7541 (ttm170) REVERT: A 372 MET cc_start: 0.8769 (mtp) cc_final: 0.8381 (mtm) REVERT: A 416 SER cc_start: 0.8046 (t) cc_final: 0.7526 (m) REVERT: A 681 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7390 (pttp) REVERT: B 197 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7547 (ttm170) REVERT: B 681 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7385 (pttp) REVERT: C 182 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7711 (tt) REVERT: C 197 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7592 (ttm170) REVERT: C 416 SER cc_start: 0.8047 (t) cc_final: 0.7525 (m) REVERT: C 681 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7362 (pttp) REVERT: D 91 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7364 (pt0) REVERT: D 182 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7708 (tt) REVERT: D 197 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7585 (ttm170) REVERT: D 681 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7351 (pttp) outliers start: 48 outliers final: 28 residues processed: 331 average time/residue: 0.5364 time to fit residues: 202.8544 Evaluate side-chains 336 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 401 LEU 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 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 401 LEU 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 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 401 LEU 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 153 VAL Chi-restraints excluded: chain D residue 182 LEU 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 401 LEU 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=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: 3.9990 chunk 141 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 234 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3508 r_free = 0.3508 target = 0.139232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.114493 restraints weight = 23292.076| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.54 r_work: 0.3100 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20932 Z= 0.177 Angle : 0.558 9.986 28312 Z= 0.282 Chirality : 0.042 0.292 3160 Planarity : 0.004 0.048 3492 Dihedral : 10.093 143.356 2960 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.06 % Allowed : 15.20 % Favored : 82.74 % 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 aren not related in a simple way. whole: 0.99 (0.17), residues: 2448 helix: 1.45 (0.14), residues: 1468 sheet: 1.80 (0.60), residues: 88 loop : -0.78 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 41 TYR 0.014 0.002 TYR B 515 PHE 0.019 0.002 PHE C 405 TRP 0.010 0.001 TRP B 333 HIS 0.003 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00424 (20932) covalent geometry : angle 0.55788 (28312) hydrogen bonds : bond 0.03870 ( 1080) hydrogen bonds : angle 3.75781 ( 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 360 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 315 time to evaluate : 0.909 Fit side-chains REVERT: A 182 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7660 (tt) REVERT: A 197 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7554 (ttm170) REVERT: A 372 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8632 (mtp) REVERT: A 416 SER cc_start: 0.8046 (t) cc_final: 0.7532 (m) REVERT: B 197 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7563 (ttm170) REVERT: B 372 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8635 (mtp) REVERT: B 416 SER cc_start: 0.8050 (t) cc_final: 0.7530 (m) REVERT: C 182 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7719 (tt) REVERT: C 197 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7602 (ttm170) REVERT: C 372 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8631 (mtp) REVERT: C 416 SER cc_start: 0.8058 (t) cc_final: 0.7540 (m) REVERT: D 197 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7586 (ttm170) REVERT: D 372 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8634 (mtp) REVERT: D 416 SER cc_start: 0.8052 (t) cc_final: 0.7533 (m) outliers start: 45 outliers final: 23 residues processed: 338 average time/residue: 0.5896 time to fit residues: 227.9933 Evaluate side-chains 351 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 318 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 182 LEU 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 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 372 MET 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 372 MET Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 492 MET 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 372 MET 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: 5.9990 chunk 236 optimal weight: 4.9990 chunk 150 optimal weight: 0.2980 chunk 242 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 17 optimal weight: 0.4980 chunk 165 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3502 r_free = 0.3502 target = 0.138729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.114311 restraints weight = 23478.074| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.55 r_work: 0.3103 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20932 Z= 0.181 Angle : 0.563 9.853 28312 Z= 0.284 Chirality : 0.042 0.281 3160 Planarity : 0.004 0.049 3492 Dihedral : 10.116 143.546 2960 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.79 % Allowed : 15.61 % Favored : 82.60 % 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 aren not related in a simple way. whole: 0.92 (0.17), residues: 2448 helix: 1.41 (0.14), residues: 1468 sheet: 1.77 (0.60), residues: 88 loop : -0.83 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 41 TYR 0.014 0.002 TYR A 515 PHE 0.020 0.002 PHE C 405 TRP 0.010 0.001 TRP D 333 HIS 0.003 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00433 (20932) covalent geometry : angle 0.56253 (28312) hydrogen bonds : bond 0.03904 ( 1080) hydrogen bonds : angle 3.77338 ( 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 349 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 310 time to evaluate : 0.841 Fit side-chains REVERT: A 182 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7700 (tt) REVERT: A 197 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7590 (ttm170) REVERT: A 372 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8642 (mtp) REVERT: A 416 SER cc_start: 0.8056 (t) cc_final: 0.7540 (m) REVERT: B 197 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7566 (ttm170) REVERT: B 416 SER cc_start: 0.8049 (t) cc_final: 0.7530 (m) REVERT: C 182 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7756 (tt) REVERT: C 197 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7636 (ttm170) REVERT: C 372 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8642 (mtp) REVERT: C 416 SER cc_start: 0.8036 (t) cc_final: 0.7520 (m) REVERT: D 197 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7592 (ttm170) REVERT: D 372 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8649 (mtp) REVERT: D 416 SER cc_start: 0.8041 (t) cc_final: 0.7517 (m) outliers start: 39 outliers final: 21 residues processed: 330 average time/residue: 0.5665 time to fit residues: 213.7392 Evaluate side-chains 342 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 312 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 182 LEU 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 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 372 MET Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 401 LEU 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 372 MET 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: 7.9990 chunk 23 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 209 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3539 r_free = 0.3539 target = 0.142004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.117168 restraints weight = 23200.214| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.56 r_work: 0.3137 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20932 Z= 0.105 Angle : 0.494 9.737 28312 Z= 0.250 Chirality : 0.039 0.242 3160 Planarity : 0.004 0.045 3492 Dihedral : 9.580 140.276 2960 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.83 % Allowed : 15.66 % Favored : 82.51 % 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 aren not related in a simple way. whole: 1.17 (0.17), residues: 2448 helix: 1.62 (0.14), residues: 1472 sheet: 1.97 (0.61), residues: 88 loop : -0.78 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 41 TYR 0.009 0.001 TYR B 525 PHE 0.019 0.001 PHE C 405 TRP 0.009 0.001 TRP C 333 HIS 0.002 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00242 (20932) covalent geometry : angle 0.49387 (28312) hydrogen bonds : bond 0.03247 ( 1080) hydrogen bonds : angle 3.55909 ( 3120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6571.19 seconds wall clock time: 112 minutes 51.44 seconds (6771.44 seconds total)