Starting phenix.real_space_refine on Tue May 20 22:41:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekp_28209/05_2025/8ekp_28209.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekp_28209/05_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_28209/05_2025/8ekp_28209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekp_28209/05_2025/8ekp_28209.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekp_28209/05_2025/8ekp_28209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekp_28209/05_2025/8ekp_28209.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1} 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: C, B, D Time building chain proxies: 12.07, per 1000 atoms: 0.59 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: 5.29 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.10 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: 6.30 Time building geometry restraints manager: 6.18 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 44.890 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.920 ------------------------------------------------------------------------------- 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 : 3.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP D 333 HIS 0.005 0.001 HIS C 251 PHE 0.014 0.001 PHE D 161 TYR 0.022 0.001 TYR B 544 ARG 0.017 0.001 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.24506 ( 1080) hydrogen bonds : angle 7.48591 ( 3120) covalent geometry : bond 0.00410 (20932) covalent geometry : angle 0.87402 (28312) *********************** 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 : 2.380 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: 1.2116 time to fit residues: 523.9624 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 : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.137899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.113499 restraints weight = 23566.561| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.53 r_work: 0.3089 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2017 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= 0.294 Angle : 0.690 9.299 28312 Z= 0.350 Chirality : 0.046 0.160 3160 Planarity : 0.006 0.063 3492 Dihedral : 11.246 147.657 2960 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.79 % Allowed : 6.64 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 2448 helix: 0.11 (0.13), residues: 1472 sheet: 1.20 (0.51), residues: 112 loop : -0.94 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 509 HIS 0.005 0.002 HIS D 521 PHE 0.026 0.002 PHE D 407 TYR 0.022 0.002 TYR D 515 ARG 0.004 0.001 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.05159 ( 1080) hydrogen bonds : angle 4.23608 ( 3120) covalent geometry : bond 0.00693 (20932) covalent geometry : angle 0.68993 (28312) *********************** 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 398 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 359 time to evaluate : 2.156 Fit side-chains REVERT: A 197 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7553 (ttm170) REVERT: A 683 HIS cc_start: 0.7491 (t-90) cc_final: 0.7043 (t-90) REVERT: B 197 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7568 (ttm170) REVERT: B 683 HIS cc_start: 0.7491 (t-90) cc_final: 0.7036 (t-90) REVERT: C 197 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7561 (ttm170) REVERT: C 683 HIS cc_start: 0.7496 (t-90) cc_final: 0.7048 (t-90) REVERT: D 197 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7550 (ttm170) REVERT: D 683 HIS cc_start: 0.7505 (t-90) cc_final: 0.7107 (t-90) outliers start: 39 outliers final: 12 residues processed: 373 average time/residue: 1.1787 time to fit residues: 503.2074 Evaluate side-chains 330 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 314 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 101 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 233 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.142674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.117910 restraints weight = 23259.833| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.56 r_work: 0.3221 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20932 Z= 0.106 Angle : 0.489 8.565 28312 Z= 0.254 Chirality : 0.038 0.172 3160 Planarity : 0.004 0.051 3492 Dihedral : 10.244 141.599 2960 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.97 % Allowed : 10.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2448 helix: 1.07 (0.14), residues: 1480 sheet: 1.39 (0.52), residues: 112 loop : -0.96 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 509 HIS 0.002 0.001 HIS D 521 PHE 0.015 0.001 PHE A 540 TYR 0.012 0.001 TYR B 525 ARG 0.005 0.000 ARG D 41 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 1080) hydrogen bonds : angle 3.69267 ( 3120) covalent geometry : bond 0.00236 (20932) covalent geometry : angle 0.48863 (28312) *********************** 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 357 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 314 time to evaluate : 2.212 Fit side-chains outliers start: 43 outliers final: 22 residues processed: 338 average time/residue: 1.1931 time to fit residues: 460.3404 Evaluate side-chains 305 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 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 29 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 146 optimal weight: 0.0370 chunk 109 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 138 optimal weight: 0.4980 chunk 216 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 overall best weight: 1.3662 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.140516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.115699 restraints weight = 23592.196| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.56 r_work: 0.3121 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20932 Z= 0.150 Angle : 0.523 9.274 28312 Z= 0.268 Chirality : 0.040 0.183 3160 Planarity : 0.004 0.050 3492 Dihedral : 10.245 142.835 2960 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.70 % Allowed : 11.40 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2448 helix: 1.30 (0.14), residues: 1476 sheet: 1.38 (0.52), residues: 112 loop : -0.89 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 333 HIS 0.003 0.001 HIS B 251 PHE 0.015 0.001 PHE D 405 TYR 0.013 0.002 TYR A 515 ARG 0.005 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 1080) hydrogen bonds : angle 3.71626 ( 3120) covalent geometry : bond 0.00355 (20932) covalent geometry : angle 0.52346 (28312) *********************** 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 369 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 310 time to evaluate : 2.315 Fit side-chains REVERT: A 91 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7377 (pt0) REVERT: A 197 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7559 (ttm170) REVERT: B 197 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7590 (ttm170) REVERT: C 91 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7386 (pt0) REVERT: C 197 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7567 (ttm170) REVERT: D 91 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7397 (pt0) REVERT: D 197 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7562 (ttm170) outliers start: 59 outliers final: 25 residues processed: 344 average time/residue: 1.2095 time to fit residues: 473.2525 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 : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain 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 D residue 91 GLU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 105 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 0.0370 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.1464 ------------------------------------------------------------------------------- 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 B 186 ASN B 235 GLN B 414 GLN B 673 ASN C 186 ASN C 235 GLN C 414 GLN D 186 ASN D 235 GLN D 414 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.141259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.116308 restraints weight = 23400.824| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.56 r_work: 0.3185 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20932 Z= 0.132 Angle : 0.508 9.396 28312 Z= 0.260 Chirality : 0.040 0.198 3160 Planarity : 0.004 0.047 3492 Dihedral : 10.058 140.503 2960 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.15 % Allowed : 12.87 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2448 helix: 1.43 (0.14), residues: 1476 sheet: 1.87 (0.61), residues: 88 loop : -0.83 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 333 HIS 0.002 0.001 HIS B 202 PHE 0.018 0.001 PHE C 540 TYR 0.012 0.001 TYR A 515 ARG 0.005 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 1080) hydrogen bonds : angle 3.64877 ( 3120) covalent geometry : bond 0.00310 (20932) covalent geometry : angle 0.50768 (28312) *********************** 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 342 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 295 time to evaluate : 2.172 Fit side-chains REVERT: A 91 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7363 (pt0) REVERT: A 197 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7586 (ttm170) REVERT: B 91 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7361 (pt0) REVERT: B 197 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7587 (ttm170) REVERT: C 91 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7355 (pt0) REVERT: C 197 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7589 (ttm170) REVERT: D 91 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7372 (pt0) REVERT: D 197 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7593 (ttm170) outliers start: 47 outliers final: 24 residues processed: 326 average time/residue: 1.2481 time to fit residues: 461.7936 Evaluate side-chains 321 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 289 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain 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 D residue 91 GLU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 103 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 190 optimal weight: 0.0070 chunk 153 optimal weight: 0.8980 overall best weight: 1.3802 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.140301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115391 restraints weight = 23365.643| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.56 r_work: 0.3120 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20932 Z= 0.150 Angle : 0.525 9.698 28312 Z= 0.267 Chirality : 0.040 0.237 3160 Planarity : 0.004 0.047 3492 Dihedral : 10.005 140.254 2960 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.20 % Allowed : 13.55 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2448 helix: 1.42 (0.14), residues: 1476 sheet: 1.87 (0.61), residues: 88 loop : -0.76 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 333 HIS 0.003 0.001 HIS D 251 PHE 0.018 0.001 PHE D 405 TYR 0.013 0.001 TYR A 515 ARG 0.005 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 1080) hydrogen bonds : angle 3.68573 ( 3120) covalent geometry : bond 0.00357 (20932) covalent geometry : angle 0.52452 (28312) *********************** 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 364 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 316 time to evaluate : 2.285 Fit side-chains REVERT: A 91 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7406 (pt0) REVERT: A 197 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7552 (ttm170) REVERT: B 91 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7395 (pt0) REVERT: B 197 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7577 (ttm170) REVERT: C 91 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7391 (pt0) REVERT: C 197 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7580 (ttm170) REVERT: D 91 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7411 (pt0) REVERT: D 197 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7580 (ttm170) outliers start: 48 outliers final: 28 residues processed: 344 average time/residue: 1.1907 time to fit residues: 468.3977 Evaluate side-chains 339 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 303 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 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 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 D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 184 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 153 optimal weight: 0.0050 chunk 224 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 176 optimal weight: 0.0770 chunk 175 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 208 optimal weight: 0.0980 overall best weight: 0.3352 ------------------------------------------------------------------------------- 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 A 673 ASN B 186 ASN B 235 GLN B 452 GLN B 673 ASN C 186 ASN C 235 GLN C 452 GLN C 673 ASN D 186 ASN D 235 GLN D 452 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 = 0.3571 r_free = 0.3571 target = 0.144880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119380 restraints weight = 22846.525| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.61 r_work: 0.3189 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20932 Z= 0.086 Angle : 0.472 10.730 28312 Z= 0.237 Chirality : 0.037 0.200 3160 Planarity : 0.003 0.042 3492 Dihedral : 9.250 137.052 2960 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.52 % Allowed : 14.10 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.17), residues: 2448 helix: 1.69 (0.14), residues: 1480 sheet: 2.05 (0.61), residues: 88 loop : -0.60 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 333 HIS 0.002 0.001 HIS B 521 PHE 0.017 0.001 PHE D 405 TYR 0.009 0.001 TYR D 525 ARG 0.007 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.02924 ( 1080) hydrogen bonds : angle 3.43802 ( 3120) covalent geometry : bond 0.00185 (20932) covalent geometry : angle 0.47225 (28312) *********************** 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 369 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 314 time to evaluate : 2.284 Fit side-chains REVERT: A 91 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7229 (pt0) REVERT: B 91 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7238 (pt0) REVERT: C 91 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7259 (pt0) REVERT: C 289 GLU cc_start: 0.8168 (mp0) cc_final: 0.7805 (mp0) REVERT: D 91 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7262 (pt0) outliers start: 55 outliers final: 20 residues processed: 351 average time/residue: 1.3313 time to fit residues: 528.0216 Evaluate side-chains 315 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 291 time to evaluate : 2.261 ------------------------------------------------------------------------------- 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 358 GLU Chi-restraints excluded: chain A residue 373 VAL 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 641 LEU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL 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 358 GLU Chi-restraints excluded: chain D residue 373 VAL 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 247 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 0.0040 chunk 210 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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 D 186 ASN D 235 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.141722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.116701 restraints weight = 23409.633| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.57 r_work: 0.3128 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20932 Z= 0.135 Angle : 0.527 9.774 28312 Z= 0.262 Chirality : 0.039 0.206 3160 Planarity : 0.004 0.042 3492 Dihedral : 9.555 138.899 2960 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.83 % Allowed : 15.98 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.17), residues: 2448 helix: 1.68 (0.14), residues: 1476 sheet: 1.97 (0.61), residues: 88 loop : -0.59 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 333 HIS 0.003 0.001 HIS C 251 PHE 0.021 0.001 PHE B 405 TYR 0.014 0.001 TYR C 447 ARG 0.006 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 1080) hydrogen bonds : angle 3.54891 ( 3120) covalent geometry : bond 0.00320 (20932) covalent geometry : angle 0.52724 (28312) *********************** 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 345 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 305 time to evaluate : 2.261 Fit side-chains REVERT: A 197 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7553 (ttm170) REVERT: A 416 SER cc_start: 0.8058 (t) cc_final: 0.7536 (m) REVERT: B 416 SER cc_start: 0.8052 (t) cc_final: 0.7531 (m) REVERT: C 416 SER cc_start: 0.8038 (t) cc_final: 0.7544 (m) outliers start: 40 outliers final: 26 residues processed: 333 average time/residue: 1.1909 time to fit residues: 456.1474 Evaluate side-chains 327 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 300 time to evaluate : 2.281 ------------------------------------------------------------------------------- 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 502 VAL Chi-restraints excluded: chain A residue 641 LEU 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 401 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 153 VAL 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 502 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 153 VAL 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 502 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 645 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.141603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.116593 restraints weight = 23307.497| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.57 r_work: 0.3126 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20932 Z= 0.133 Angle : 0.531 9.962 28312 Z= 0.264 Chirality : 0.040 0.218 3160 Planarity : 0.004 0.043 3492 Dihedral : 9.503 139.199 2960 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.65 % Allowed : 16.76 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.17), residues: 2448 helix: 1.67 (0.14), residues: 1472 sheet: 1.86 (0.61), residues: 88 loop : -0.56 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 333 HIS 0.002 0.001 HIS C 251 PHE 0.019 0.001 PHE D 405 TYR 0.014 0.001 TYR D 447 ARG 0.006 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 1080) hydrogen bonds : angle 3.56877 ( 3120) covalent geometry : bond 0.00317 (20932) covalent geometry : angle 0.53076 (28312) *********************** 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 340 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 304 time to evaluate : 2.467 Fit side-chains REVERT: A 197 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7552 (ttm170) REVERT: A 416 SER cc_start: 0.8103 (t) cc_final: 0.7566 (m) REVERT: B 197 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7528 (ttm170) REVERT: C 197 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7545 (ttm170) REVERT: C 289 GLU cc_start: 0.8173 (mp0) cc_final: 0.7854 (mp0) REVERT: C 416 SER cc_start: 0.8100 (t) cc_final: 0.7565 (m) REVERT: D 289 GLU cc_start: 0.8176 (mp0) cc_final: 0.7855 (mp0) outliers start: 36 outliers final: 21 residues processed: 331 average time/residue: 1.1777 time to fit residues: 445.5769 Evaluate side-chains 325 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 301 time to evaluate : 2.135 ------------------------------------------------------------------------------- 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 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 401 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 645 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 198 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 128 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.140532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.115753 restraints weight = 23213.750| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.55 r_work: 0.3116 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20932 Z= 0.159 Angle : 0.561 10.012 28312 Z= 0.278 Chirality : 0.041 0.234 3160 Planarity : 0.004 0.043 3492 Dihedral : 9.684 139.542 2960 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.28 % Allowed : 17.03 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 2448 helix: 1.59 (0.14), residues: 1472 sheet: 1.82 (0.61), residues: 88 loop : -0.58 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 333 HIS 0.003 0.001 HIS C 251 PHE 0.023 0.001 PHE B 405 TYR 0.014 0.002 TYR C 447 ARG 0.006 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 1080) hydrogen bonds : angle 3.65473 ( 3120) covalent geometry : bond 0.00381 (20932) covalent geometry : angle 0.56113 (28312) ********************** 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 334 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 306 time to evaluate : 2.471 Fit side-chains REVERT: A 197 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7563 (ttm170) REVERT: A 416 SER cc_start: 0.8108 (t) cc_final: 0.7579 (m) REVERT: B 197 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7536 (ttm170) REVERT: B 416 SER cc_start: 0.8130 (t) cc_final: 0.7593 (m) REVERT: C 416 SER cc_start: 0.8094 (t) cc_final: 0.7563 (m) REVERT: D 197 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7573 (ttm170) REVERT: D 416 SER cc_start: 0.8125 (t) cc_final: 0.7595 (m) outliers start: 28 outliers final: 25 residues processed: 322 average time/residue: 1.2918 time to fit residues: 473.1565 Evaluate side-chains 331 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 303 time to evaluate : 2.167 ------------------------------------------------------------------------------- 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 492 MET Chi-restraints excluded: chain A residue 502 VAL 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 401 LEU Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 502 VAL 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 358 GLU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 645 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 12 optimal weight: 6.9990 chunk 197 optimal weight: 0.4980 chunk 188 optimal weight: 4.9990 chunk 184 optimal weight: 0.3980 chunk 80 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 121 optimal weight: 0.0470 chunk 95 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.142547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.117572 restraints weight = 23374.715| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.58 r_work: 0.3142 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20932 Z= 0.111 Angle : 0.515 9.954 28312 Z= 0.255 Chirality : 0.038 0.195 3160 Planarity : 0.004 0.041 3492 Dihedral : 9.396 137.590 2960 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.74 % Allowed : 16.39 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.17), residues: 2448 helix: 1.68 (0.14), residues: 1476 sheet: 1.88 (0.61), residues: 88 loop : -0.50 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 333 HIS 0.002 0.001 HIS C 251 PHE 0.024 0.001 PHE B 405 TYR 0.014 0.001 TYR D 447 ARG 0.006 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 1080) hydrogen bonds : angle 3.50989 ( 3120) covalent geometry : bond 0.00258 (20932) covalent geometry : angle 0.51457 (28312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14005.64 seconds wall clock time: 242 minutes 15.77 seconds (14535.77 seconds total)