Starting phenix.real_space_refine on Wed Jun 18 00:33:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekp_28209/06_2025/8ekp_28209.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekp_28209/06_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_28209/06_2025/8ekp_28209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekp_28209/06_2025/8ekp_28209.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekp_28209/06_2025/8ekp_28209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekp_28209/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.49, per 1000 atoms: 0.66 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: 5.02 Conformation dependent library (CDL) restraints added in 2.6 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: 1.98 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: 6.40 Time building geometry restraints manager: 6.03 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: 0.15 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: 4.390 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: 0.900 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 47.720 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.280 ------------------------------------------------------------------------------- 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 : 2.323 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: 1.2191 time to fit residues: 527.3800 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 : 2.270 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.113500 restraints weight = 23566.565| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.53 r_work: 0.3091 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- 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 : 2.179 Fit side-chains REVERT: A 197 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7552 (ttm170) REVERT: A 683 HIS cc_start: 0.7491 (t-90) cc_final: 0.7042 (t-90) REVERT: B 197 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7567 (ttm170) REVERT: B 683 HIS cc_start: 0.7490 (t-90) cc_final: 0.7034 (t-90) REVERT: C 197 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7557 (ttm170) REVERT: C 683 HIS cc_start: 0.7496 (t-90) cc_final: 0.7047 (t-90) REVERT: D 197 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7549 (ttm170) REVERT: D 683 HIS cc_start: 0.7507 (t-90) cc_final: 0.7109 (t-90) outliers start: 39 outliers final: 12 residues processed: 373 average time/residue: 1.2647 time to fit residues: 539.8276 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 : 2.234 ------------------------------------------------------------------------------- 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: 0.2980 chunk 118 optimal weight: 0.6980 chunk 152 optimal weight: 0.5980 chunk 233 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 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: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.142947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.118182 restraints weight = 23271.219| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.56 r_work: 0.3225 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20932 Z= 0.102 Angle : 0.485 8.443 28312 Z= 0.252 Chirality : 0.038 0.173 3160 Planarity : 0.004 0.051 3492 Dihedral : 10.192 141.208 2960 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.01 % Allowed : 10.67 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.17), residues: 2448 helix: 1.08 (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 0.010 0.001 TRP A 509 HIS 0.002 0.001 HIS D 521 PHE 0.015 0.001 PHE A 540 TYR 0.011 0.001 TYR A 525 ARG 0.005 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 1080) hydrogen bonds : angle 3.67543 ( 3120) covalent geometry : bond 0.00225 (20932) covalent geometry : angle 0.48535 (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 359 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 315 time to evaluate : 3.227 Fit side-chains outliers start: 44 outliers final: 20 residues processed: 340 average time/residue: 1.4954 time to fit residues: 580.8960 Evaluate side-chains 302 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 282 time to evaluate : 2.544 ------------------------------------------------------------------------------- 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 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 29 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 138 optimal weight: 0.0370 chunk 216 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.140016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115274 restraints weight = 23616.240| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.55 r_work: 0.3170 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20932 Z= 0.168 Angle : 0.542 9.364 28312 Z= 0.277 Chirality : 0.041 0.197 3160 Planarity : 0.004 0.051 3492 Dihedral : 10.333 143.482 2960 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.47 % Allowed : 11.63 % 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: 0.77 (0.17), residues: 2448 helix: 1.28 (0.14), residues: 1476 sheet: 1.75 (0.60), residues: 88 loop : -0.91 (0.20), residues: 884 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 0.016 0.001 PHE C 405 TYR 0.015 0.002 TYR C 515 ARG 0.005 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 1080) hydrogen bonds : angle 3.75565 ( 3120) covalent geometry : bond 0.00399 (20932) covalent geometry : angle 0.54199 (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 370 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 316 time to evaluate : 4.203 Fit side-chains REVERT: A 197 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7584 (ttm170) REVERT: B 197 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7594 (ttm170) REVERT: C 197 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7563 (ttm170) REVERT: D 197 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7566 (ttm170) outliers start: 54 outliers final: 28 residues processed: 341 average time/residue: 1.5373 time to fit residues: 597.4480 Evaluate side-chains 330 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 2.444 ------------------------------------------------------------------------------- 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: 1.9990 chunk 157 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 91 optimal weight: 0.8980 chunk 88 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 452 GLN C 186 ASN C 235 GLN C 414 GLN C 452 GLN D 186 ASN D 235 GLN D 414 GLN D 452 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.141435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.116506 restraints weight = 23407.671| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.56 r_work: 0.3136 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20932 Z= 0.125 Angle : 0.502 9.284 28312 Z= 0.257 Chirality : 0.039 0.196 3160 Planarity : 0.004 0.048 3492 Dihedral : 10.049 140.367 2960 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.11 % Allowed : 12.87 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.44 (0.14), residues: 1476 sheet: 1.81 (0.61), residues: 88 loop : -0.84 (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 C 313 PHE 0.018 0.001 PHE A 540 TYR 0.011 0.001 TYR A 515 ARG 0.005 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 1080) hydrogen bonds : angle 3.64534 ( 3120) covalent geometry : bond 0.00294 (20932) covalent geometry : angle 0.50211 (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 344 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 298 time to evaluate : 3.943 Fit side-chains REVERT: A 91 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7362 (pt0) REVERT: A 197 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7582 (ttm170) REVERT: B 91 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7353 (pt0) REVERT: B 197 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7588 (ttm170) REVERT: C 91 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7377 (pt0) REVERT: D 91 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7372 (pt0) REVERT: D 197 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7562 (ttm170) outliers start: 46 outliers final: 24 residues processed: 332 average time/residue: 1.8710 time to fit residues: 712.1840 Evaluate side-chains 323 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 292 time to evaluate : 2.277 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 108 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 190 optimal weight: 0.5980 chunk 153 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 235 GLN A 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 = 0.142385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117458 restraints weight = 23293.826| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.57 r_work: 0.3137 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20932 Z= 0.107 Angle : 0.480 9.518 28312 Z= 0.245 Chirality : 0.038 0.219 3160 Planarity : 0.003 0.045 3492 Dihedral : 9.717 138.825 2960 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.29 % Allowed : 13.14 % Favored : 84.57 % 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: 1.13 (0.17), residues: 2448 helix: 1.55 (0.14), residues: 1480 sheet: 1.90 (0.61), residues: 88 loop : -0.74 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 333 HIS 0.002 0.001 HIS C 521 PHE 0.017 0.001 PHE D 405 TYR 0.009 0.001 TYR A 515 ARG 0.007 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 1080) hydrogen bonds : angle 3.54636 ( 3120) covalent geometry : bond 0.00247 (20932) covalent geometry : angle 0.47960 (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 369 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 319 time to evaluate : 2.401 Fit side-chains REVERT: A 91 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7335 (pt0) REVERT: A 681 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7331 (pttp) REVERT: B 91 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7326 (pt0) REVERT: B 681 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7344 (pttp) REVERT: C 91 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7350 (pt0) REVERT: C 197 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7566 (ttm170) REVERT: C 681 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7327 (pttp) REVERT: D 91 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7351 (pt0) REVERT: D 681 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7324 (pttp) outliers start: 50 outliers final: 29 residues processed: 350 average time/residue: 1.4283 time to fit residues: 570.3002 Evaluate side-chains 340 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 302 time to evaluate : 2.334 ------------------------------------------------------------------------------- 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 401 LEU Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 681 LYS Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 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 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 681 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 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 C residue 681 LYS Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 681 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 184 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 224 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 176 optimal weight: 0.4980 chunk 175 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 414 GLN B 673 ASN C 186 ASN C 235 GLN D 186 ASN D 235 GLN D 414 GLN D 673 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.140509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.115585 restraints weight = 23276.270| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.56 r_work: 0.3114 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20932 Z= 0.155 Angle : 0.536 9.999 28312 Z= 0.269 Chirality : 0.041 0.233 3160 Planarity : 0.004 0.045 3492 Dihedral : 9.842 140.338 2960 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.43 % Allowed : 14.01 % Favored : 83.56 % 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: 1.09 (0.17), residues: 2448 helix: 1.51 (0.14), residues: 1480 sheet: 1.85 (0.61), residues: 88 loop : -0.74 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 333 HIS 0.003 0.001 HIS D 251 PHE 0.018 0.001 PHE D 405 TYR 0.013 0.001 TYR C 515 ARG 0.006 0.000 ARG D 41 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 1080) hydrogen bonds : angle 3.66488 ( 3120) covalent geometry : bond 0.00368 (20932) covalent geometry : angle 0.53595 (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 372 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 319 time to evaluate : 2.619 Fit side-chains REVERT: A 91 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: A 197 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7544 (ttm170) REVERT: B 91 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7366 (pt0) REVERT: B 197 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7545 (ttm170) REVERT: C 91 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: C 197 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7594 (ttm170) REVERT: D 91 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: D 197 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7579 (ttm170) outliers start: 53 outliers final: 28 residues processed: 350 average time/residue: 1.4792 time to fit residues: 596.5230 Evaluate side-chains 342 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 306 time to evaluate : 3.468 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 247 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 203 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.138389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.113684 restraints weight = 23489.171| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.54 r_work: 0.3087 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.005 0.056 20932 Z= 0.227 Angle : 0.607 10.014 28312 Z= 0.305 Chirality : 0.044 0.289 3160 Planarity : 0.004 0.047 3492 Dihedral : 10.312 142.424 2960 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.43 % Allowed : 14.61 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.17), residues: 2448 helix: 1.34 (0.14), residues: 1468 sheet: 1.70 (0.60), residues: 88 loop : -0.78 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 333 HIS 0.004 0.001 HIS C 363 PHE 0.018 0.002 PHE D 405 TYR 0.017 0.002 TYR A 515 ARG 0.005 0.001 ARG D 41 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 1080) hydrogen bonds : angle 3.87255 ( 3120) covalent geometry : bond 0.00542 (20932) covalent geometry : angle 0.60694 (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 373 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 320 time to evaluate : 2.302 Fit side-chains REVERT: A 197 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7534 (ttm170) REVERT: B 197 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7547 (ttm170) REVERT: B 535 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.5948 (pmt-80) REVERT: C 197 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7584 (ttm170) REVERT: D 197 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7566 (ttm170) outliers start: 53 outliers final: 26 residues processed: 353 average time/residue: 1.2311 time to fit residues: 496.4911 Evaluate side-chains 353 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 322 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain 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 153 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 100 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 233 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 170 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 235 GLN B 186 ASN B 235 GLN C 186 ASN C 235 GLN D 186 ASN D 235 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.142642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.117840 restraints weight = 23236.078| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.56 r_work: 0.3158 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2461 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= 0.100 Angle : 0.493 9.621 28312 Z= 0.250 Chirality : 0.038 0.228 3160 Planarity : 0.004 0.044 3492 Dihedral : 9.574 137.926 2960 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.60 % Allowed : 15.38 % Favored : 83.01 % 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: 1.62 (0.14), residues: 1480 sheet: 1.92 (0.61), residues: 88 loop : -0.66 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 333 HIS 0.002 0.001 HIS C 370 PHE 0.017 0.001 PHE D 405 TYR 0.009 0.001 TYR C 525 ARG 0.006 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 1080) hydrogen bonds : angle 3.53011 ( 3120) covalent geometry : bond 0.00229 (20932) covalent geometry : angle 0.49345 (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 363 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 328 time to evaluate : 2.313 Fit side-chains REVERT: A 197 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7549 (ttm170) REVERT: A 372 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8373 (mtm) REVERT: B 197 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7566 (ttm170) REVERT: B 372 MET cc_start: 0.8705 (mtp) cc_final: 0.8392 (mtm) REVERT: C 197 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7589 (ttm170) REVERT: C 289 GLU cc_start: 0.8177 (mp0) cc_final: 0.7833 (mp0) REVERT: D 197 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7587 (ttm170) outliers start: 35 outliers final: 18 residues processed: 349 average time/residue: 1.2780 time to fit residues: 508.4530 Evaluate side-chains 329 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 306 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 198 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 128 optimal weight: 0.3980 chunk 64 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 D 673 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.141022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.116191 restraints weight = 23238.823| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.55 r_work: 0.3118 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2494 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= 0.143 Angle : 0.538 10.003 28312 Z= 0.269 Chirality : 0.040 0.247 3160 Planarity : 0.004 0.045 3492 Dihedral : 9.668 138.866 2960 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.51 % Allowed : 16.35 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.20 (0.17), residues: 2448 helix: 1.60 (0.14), residues: 1476 sheet: 1.82 (0.61), residues: 88 loop : -0.68 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 333 HIS 0.003 0.001 HIS B 251 PHE 0.020 0.001 PHE D 405 TYR 0.012 0.001 TYR C 515 ARG 0.006 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 1080) hydrogen bonds : angle 3.62094 ( 3120) covalent geometry : bond 0.00341 (20932) covalent geometry : angle 0.53764 (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 348 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 315 time to evaluate : 2.334 Fit side-chains REVERT: A 197 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7536 (ttm170) REVERT: A 372 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8381 (mtm) REVERT: A 416 SER cc_start: 0.8028 (t) cc_final: 0.7506 (m) REVERT: B 197 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7545 (ttm170) REVERT: B 372 MET cc_start: 0.8784 (mtp) cc_final: 0.8389 (mtm) REVERT: B 416 SER cc_start: 0.8024 (t) cc_final: 0.7499 (m) REVERT: C 197 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7563 (ttm170) REVERT: C 416 SER cc_start: 0.8040 (t) cc_final: 0.7516 (m) REVERT: D 197 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7570 (ttm170) REVERT: D 416 SER cc_start: 0.8060 (t) cc_final: 0.7519 (m) outliers start: 33 outliers final: 22 residues processed: 334 average time/residue: 1.2091 time to fit residues: 461.4299 Evaluate side-chains 336 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 309 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 12 optimal weight: 7.9990 chunk 197 optimal weight: 0.0370 chunk 188 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 121 optimal weight: 0.0170 chunk 95 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 overall best weight: 2.0102 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.138425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113110 restraints weight = 23188.750| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.59 r_work: 0.3094 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20932 Z= 0.202 Angle : 0.595 10.061 28312 Z= 0.296 Chirality : 0.043 0.281 3160 Planarity : 0.004 0.047 3492 Dihedral : 10.051 141.066 2960 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.51 % Allowed : 16.21 % Favored : 82.28 % 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: 1472 sheet: 1.71 (0.60), residues: 88 loop : -0.73 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 333 HIS 0.003 0.001 HIS D 363 PHE 0.020 0.002 PHE C 405 TYR 0.016 0.002 TYR C 515 ARG 0.006 0.001 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 1080) hydrogen bonds : angle 3.79578 ( 3120) covalent geometry : bond 0.00483 (20932) covalent geometry : angle 0.59492 (28312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17213.22 seconds wall clock time: 308 minutes 17.88 seconds (18497.88 seconds total)