Starting phenix.real_space_refine on Sat Oct 24 00:23:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12ri_76708/10_2026/12ri_76708_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/12ri_76708/10_2026/12ri_76708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/12ri_76708/10_2026/12ri_76708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12ri_76708/10_2026/12ri_76708.map" model { file = "/net/cci-nas-00/data/ceres_data/12ri_76708/10_2026/12ri_76708_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12ri_76708/10_2026/12ri_76708_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 7310 2.51 5 N 1898 2.21 5 O 2168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11434 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5717 Classifications: {'peptide': 713} Link IDs: {'PCIS': 5, 'PTRANS': 26, 'TRANS': 681} Chain breaks: 2 Restraints were copied for chains: B Time building chain proxies: 5.44, per 1000 atoms: 0.48 Number of scatterers: 11434 At special positions: 0 Unit cell: (101.32, 139.4, 82.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 2168 8.00 N 1898 7.00 C 7310 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: 0.88 Conformation dependent library (CDL) restraints added in 523.3 milliseconds 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 28 sheets defined 37.4% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 161 through 165 removed outlier: 3.845A pdb=" N SER A 165 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 284 through 309 removed outlier: 3.871A pdb=" N ALA A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.549A pdb=" N ILE A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 removed outlier: 4.613A pdb=" N TYR A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 379 removed outlier: 3.855A pdb=" N GLU A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.579A pdb=" N PHE A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 429 removed outlier: 3.835A pdb=" N ALA A 425 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 443 Processing helix chain 'A' and resid 468 through 489 removed outlier: 3.624A pdb=" N TYR A 476 " --> pdb=" O ASN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 514 Proline residue: A 504 - end of helix Processing helix chain 'A' and resid 545 through 551 Processing helix chain 'A' and resid 554 through 560 removed outlier: 4.200A pdb=" N TYR A 558 " --> pdb=" O PRO A 555 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 577 Processing helix chain 'A' and resid 596 through 604 Proline residue: A 601 - end of helix removed outlier: 3.636A pdb=" N GLU A 604 " --> pdb=" O PRO A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.672A pdb=" N THR A 613 " --> pdb=" O TYR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 617 Processing helix chain 'A' and resid 622 through 635 Processing helix chain 'A' and resid 637 through 653 Processing helix chain 'A' and resid 678 through 682 removed outlier: 3.722A pdb=" N LYS A 681 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 682 " --> pdb=" O PRO A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 678 through 682' Processing helix chain 'A' and resid 689 through 696 removed outlier: 4.138A pdb=" N TYR A 692 " --> pdb=" O TYR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 704 removed outlier: 3.711A pdb=" N SER A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 81 Processing helix chain 'B' and resid 161 through 165 removed outlier: 3.845A pdb=" N SER B 165 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 284 through 309 removed outlier: 3.871A pdb=" N ALA B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.549A pdb=" N ILE B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 359 removed outlier: 4.613A pdb=" N TYR B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 379 removed outlier: 3.856A pdb=" N GLU B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.579A pdb=" N PHE B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 429 removed outlier: 3.835A pdb=" N ALA B 425 " --> pdb=" O ASN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 443 Processing helix chain 'B' and resid 468 through 489 removed outlier: 3.624A pdb=" N TYR B 476 " --> pdb=" O ASN B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 514 Proline residue: B 504 - end of helix Processing helix chain 'B' and resid 545 through 551 Processing helix chain 'B' and resid 554 through 560 removed outlier: 4.200A pdb=" N TYR B 558 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 560 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 577 Processing helix chain 'B' and resid 596 through 604 Proline residue: B 601 - end of helix removed outlier: 3.636A pdb=" N GLU B 604 " --> pdb=" O PRO B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.672A pdb=" N THR B 613 " --> pdb=" O TYR B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 617 Processing helix chain 'B' and resid 622 through 635 Processing helix chain 'B' and resid 637 through 653 Processing helix chain 'B' and resid 678 through 682 removed outlier: 3.722A pdb=" N LYS B 681 " --> pdb=" O GLU B 678 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 682 " --> pdb=" O PRO B 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 678 through 682' Processing helix chain 'B' and resid 689 through 696 removed outlier: 4.138A pdb=" N TYR B 692 " --> pdb=" O TYR B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 704 removed outlier: 3.710A pdb=" N SER B 701 " --> pdb=" O GLU B 697 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 5.575A pdb=" N PHE A 127 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER A 142 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 129 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 50 removed outlier: 7.555A pdb=" N TYR A 56 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE A 67 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 124 removed outlier: 3.505A pdb=" N LYS A 123 " --> pdb=" O ARG A 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AA5, first strand: chain 'A' and resid 310 through 311 removed outlier: 3.565A pdb=" N ALA A 723 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 726 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU A 734 " --> pdb=" O GLU A 726 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG A 728 " --> pdb=" O ASP A 732 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP A 732 " --> pdb=" O ARG A 728 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER A 733 " --> pdb=" O TYR A 763 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL A 765 " --> pdb=" O SER A 733 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER A 735 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N PHE A 767 " --> pdb=" O SER A 735 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER A 737 " --> pdb=" O PHE A 767 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 331 through 333 Processing sheet with id=AA7, first strand: chain 'A' and resid 444 through 445 Processing sheet with id=AA8, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AA9, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AB1, first strand: chain 'A' and resid 515 through 516 Processing sheet with id=AB2, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB3, first strand: chain 'A' and resid 578 through 581 Processing sheet with id=AB4, first strand: chain 'A' and resid 619 through 621 removed outlier: 6.822A pdb=" N CYS A 620 " --> pdb=" O ASN A 663 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 706 through 707 Processing sheet with id=AB6, first strand: chain 'B' and resid 39 through 40 removed outlier: 5.575A pdb=" N PHE B 127 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER B 142 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS B 129 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 50 removed outlier: 7.555A pdb=" N TYR B 56 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE B 67 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 123 through 124 removed outlier: 3.506A pdb=" N LYS B 123 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 244 through 246 Processing sheet with id=AC1, first strand: chain 'B' and resid 310 through 311 removed outlier: 3.565A pdb=" N ALA B 723 " --> pdb=" O SER B 311 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU B 726 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU B 734 " --> pdb=" O GLU B 726 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG B 728 " --> pdb=" O ASP B 732 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP B 732 " --> pdb=" O ARG B 728 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER B 733 " --> pdb=" O TYR B 763 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL B 765 " --> pdb=" O SER B 733 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER B 735 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE B 767 " --> pdb=" O SER B 735 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER B 737 " --> pdb=" O PHE B 767 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AC3, first strand: chain 'B' and resid 444 through 445 Processing sheet with id=AC4, first strand: chain 'B' and resid 466 through 467 Processing sheet with id=AC5, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC6, first strand: chain 'B' and resid 515 through 516 Processing sheet with id=AC7, first strand: chain 'B' and resid 540 through 541 Processing sheet with id=AC8, first strand: chain 'B' and resid 578 through 581 Processing sheet with id=AC9, first strand: chain 'B' and resid 619 through 621 removed outlier: 6.822A pdb=" N CYS B 620 " --> pdb=" O ASN B 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 706 through 707 508 hydrogen bonds defined for protein. 1326 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: 2.26 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3674 1.34 - 1.46: 2557 1.46 - 1.58: 5437 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 11756 Sorted by residual: bond pdb=" N GLN B 336 " pdb=" CA GLN B 336 " ideal model delta sigma weight residual 1.458 1.477 -0.020 1.42e-02 4.96e+03 1.92e+00 bond pdb=" N GLN A 336 " pdb=" CA GLN A 336 " ideal model delta sigma weight residual 1.458 1.477 -0.020 1.42e-02 4.96e+03 1.92e+00 bond pdb=" C GLY A 584 " pdb=" N ASP A 585 " ideal model delta sigma weight residual 1.331 1.314 0.016 1.23e-02 6.61e+03 1.72e+00 bond pdb=" C GLY B 584 " pdb=" N ASP B 585 " ideal model delta sigma weight residual 1.331 1.314 0.016 1.23e-02 6.61e+03 1.72e+00 bond pdb=" N ASP B 585 " pdb=" CA ASP B 585 " ideal model delta sigma weight residual 1.461 1.478 -0.017 1.38e-02 5.25e+03 1.57e+00 ... (remaining 11751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 15305 1.32 - 2.65: 571 2.65 - 3.97: 70 3.97 - 5.30: 12 5.30 - 6.62: 4 Bond angle restraints: 15962 Sorted by residual: angle pdb=" CA ASP A 585 " pdb=" C ASP A 585 " pdb=" O ASP A 585 " ideal model delta sigma weight residual 122.45 116.94 5.51 1.30e+00 5.92e-01 1.80e+01 angle pdb=" CA ASP B 585 " pdb=" C ASP B 585 " pdb=" O ASP B 585 " ideal model delta sigma weight residual 122.45 117.00 5.45 1.30e+00 5.92e-01 1.75e+01 angle pdb=" C CYS A 432 " pdb=" N LYS A 433 " pdb=" CA LYS A 433 " ideal model delta sigma weight residual 121.54 128.16 -6.62 1.91e+00 2.74e-01 1.20e+01 angle pdb=" C CYS B 432 " pdb=" N LYS B 433 " pdb=" CA LYS B 433 " ideal model delta sigma weight residual 121.54 128.16 -6.62 1.91e+00 2.74e-01 1.20e+01 angle pdb=" CA ASP B 585 " pdb=" C ASP B 585 " pdb=" N TYR B 586 " ideal model delta sigma weight residual 114.17 119.18 -5.01 1.55e+00 4.16e-01 1.05e+01 ... (remaining 15957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 6237 17.54 - 35.07: 487 35.07 - 52.60: 82 52.60 - 70.14: 18 70.14 - 87.67: 8 Dihedral angle restraints: 6832 sinusoidal: 2706 harmonic: 4126 Sorted by residual: dihedral pdb=" CA LYS A 133 " pdb=" C LYS A 133 " pdb=" N MET A 134 " pdb=" CA MET A 134 " ideal model delta harmonic sigma weight residual -180.00 -159.16 -20.84 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA LYS B 133 " pdb=" C LYS B 133 " pdb=" N MET B 134 " pdb=" CA MET B 134 " ideal model delta harmonic sigma weight residual -180.00 -159.16 -20.84 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA GLU B 596 " pdb=" C GLU B 596 " pdb=" N LYS B 597 " pdb=" CA LYS B 597 " ideal model delta harmonic sigma weight residual -180.00 -159.90 -20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 963 0.029 - 0.059: 393 0.059 - 0.088: 174 0.088 - 0.117: 90 0.117 - 0.146: 20 Chirality restraints: 1640 Sorted by residual: chirality pdb=" CA ILE A 214 " pdb=" N ILE A 214 " pdb=" C ILE A 214 " pdb=" CB ILE A 214 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE B 214 " pdb=" N ILE B 214 " pdb=" C ILE B 214 " pdb=" CB ILE B 214 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA TYR B 615 " pdb=" N TYR B 615 " pdb=" C TYR B 615 " pdb=" CB TYR B 615 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 1637 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 433 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LYS A 433 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS A 433 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA A 434 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 433 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LYS B 433 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS B 433 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA B 434 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 72 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO B 73 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 73 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 73 " 0.033 5.00e-02 4.00e+02 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3036 2.81 - 3.33: 9253 3.33 - 3.86: 17893 3.86 - 4.38: 21743 4.38 - 4.90: 38669 Nonbonded interactions: 90594 Sorted by model distance: nonbonded pdb=" OH TYR A 458 " pdb=" OD2 ASP A 543 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR B 458 " pdb=" OD2 ASP B 543 " model vdw 2.288 3.040 nonbonded pdb=" NH1 ARG A 685 " pdb=" O PRO A 687 " model vdw 2.312 3.120 nonbonded pdb=" NH1 ARG B 685 " pdb=" O PRO B 687 " model vdw 2.312 3.120 nonbonded pdb=" OH TYR A 580 " pdb=" OD1 ASP A 585 " model vdw 2.338 3.040 ... (remaining 90589 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 5.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.680 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.003 0.032 11756 Z= 0.135 Angle : 0.573 6.620 15962 Z= 0.347 Chirality : 0.044 0.146 1640 Planarity : 0.005 0.061 2066 Dihedral : 13.239 87.674 4224 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.22), residues: 1414 helix: 1.15 (0.27), residues: 414 sheet: 1.67 (0.33), residues: 238 loop : -1.34 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 691 TYR 0.016 0.001 TYR A 173 PHE 0.010 0.001 PHE B 245 TRP 0.018 0.001 TRP A 474 HIS 0.003 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (11756) covalent geometry : angle 0.57349 / 0.35 (15962) hydrogen bonds : bond 0.13361 / 8.83 ( 508) hydrogen bonds : angle 5.68749 / 4.00 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.458 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.8656 time to fit residues: 66.0994 Evaluate side-chains 48 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN A 761 ASN B 606 ASN B 761 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.058385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.046032 restraints weight = 29935.237| |-----------------------------------------------------------------------------| r_work (start): 0.2580 rms_B_bonded: 3.46 r_work: 0.2420 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11756 Z= 0.168 Angle : 0.532 5.822 15962 Z= 0.293 Chirality : 0.045 0.139 1640 Planarity : 0.004 0.044 2066 Dihedral : 4.590 21.667 1582 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.33 % Allowed : 5.00 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.22), residues: 1414 helix: 1.60 (0.27), residues: 420 sheet: 1.78 (0.33), residues: 234 loop : -1.15 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 685 TYR 0.019 0.001 TYR B 173 PHE 0.012 0.001 PHE B 245 TRP 0.019 0.001 TRP B 474 HIS 0.002 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (11756) covalent geometry : angle 0.53189 / 0.29 (15962) hydrogen bonds : bond 0.04991 / 3.25 ( 508) hydrogen bonds : angle 4.66810 / 3.23 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.427 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 52 average time/residue: 0.7272 time to fit residues: 40.7552 Evaluate side-chains 50 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [127, 5, 72, 109, 4, 49, 20, 61, 73, 129, 57] chunk 127 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.0370 chunk 73 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.060549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.048189 restraints weight = 29802.781| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 3.48 r_work: 0.2477 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11756 Z= 0.104 Angle : 0.458 5.476 15962 Z= 0.252 Chirality : 0.043 0.132 1640 Planarity : 0.004 0.039 2066 Dihedral : 4.191 20.765 1582 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1414 helix: 1.83 (0.27), residues: 422 sheet: 1.86 (0.33), residues: 234 loop : -1.01 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 685 TYR 0.016 0.001 TYR A 173 PHE 0.008 0.001 PHE B 245 TRP 0.016 0.001 TRP B 474 HIS 0.002 0.000 HIS B 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (11756) covalent geometry : angle 0.45752 / 0.25 (15962) hydrogen bonds : bond 0.03661 / 2.38 ( 508) hydrogen bonds : angle 4.45290 / 3.09 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.441 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.7106 time to fit residues: 36.9276 Evaluate side-chains 48 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [18, 93, 1, 113, 98, 118, 50, 99, 59, 45, 10] chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 118 optimal weight: 0.0970 chunk 50 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.061192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.048870 restraints weight = 29895.186| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 3.48 r_work: 0.2499 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11756 Z= 0.094 Angle : 0.440 5.738 15962 Z= 0.242 Chirality : 0.042 0.131 1640 Planarity : 0.004 0.035 2066 Dihedral : 4.046 20.570 1582 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.33 % Allowed : 7.67 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1414 helix: 1.83 (0.27), residues: 432 sheet: 1.93 (0.34), residues: 234 loop : -0.96 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 685 TYR 0.015 0.001 TYR A 173 PHE 0.008 0.001 PHE A 245 TRP 0.015 0.001 TRP B 474 HIS 0.002 0.000 HIS B 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 (11756) covalent geometry : angle 0.43950 / 0.24 (15962) hydrogen bonds : bond 0.03358 / 2.17 ( 508) hydrogen bonds : angle 4.34492 / 3.02 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.359 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 52 average time/residue: 0.7529 time to fit residues: 42.0903 Evaluate side-chains 43 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [98, 79, 129, 75, 113, 33, 107, 34, 87, 36, 27] chunk 98 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 33 optimal weight: 0.0670 chunk 107 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.058648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.046373 restraints weight = 29880.018| |-----------------------------------------------------------------------------| r_work (start): 0.2597 rms_B_bonded: 3.46 r_work: 0.2437 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11756 Z= 0.145 Angle : 0.494 5.993 15962 Z= 0.273 Chirality : 0.044 0.139 1640 Planarity : 0.004 0.033 2066 Dihedral : 4.233 20.977 1582 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.50 % Allowed : 8.75 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1414 helix: 1.93 (0.27), residues: 428 sheet: 1.92 (0.34), residues: 234 loop : -1.01 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 685 TYR 0.016 0.001 TYR B 173 PHE 0.012 0.001 PHE A 245 TRP 0.014 0.001 TRP B 474 HIS 0.003 0.001 HIS B 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (11756) covalent geometry : angle 0.49443 / 0.27 (15962) hydrogen bonds : bond 0.04365 / 2.82 ( 508) hydrogen bonds : angle 4.42993 / 3.07 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.436 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 46 average time/residue: 0.7216 time to fit residues: 35.8936 Evaluate side-chains 42 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [106, 41, 58, 25, 18, 101, 34, 80, 42, 107, 17] chunk 106 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 80 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.059443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.047156 restraints weight = 30029.091| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 3.48 r_work: 0.2458 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11756 Z= 0.119 Angle : 0.467 6.660 15962 Z= 0.257 Chirality : 0.043 0.133 1640 Planarity : 0.004 0.033 2066 Dihedral : 4.135 20.698 1582 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.50 % Allowed : 8.17 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1414 helix: 1.97 (0.27), residues: 428 sheet: 1.97 (0.34), residues: 234 loop : -0.98 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 685 TYR 0.016 0.001 TYR B 173 PHE 0.010 0.001 PHE A 245 TRP 0.015 0.001 TRP B 474 HIS 0.002 0.000 HIS B 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (11756) covalent geometry : angle 0.46672 / 0.26 (15962) hydrogen bonds : bond 0.03806 / 2.46 ( 508) hydrogen bonds : angle 4.39052 / 3.05 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.362 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 44 average time/residue: 0.7220 time to fit residues: 34.3892 Evaluate side-chains 44 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain B residue 497 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [139, 97, 16, 83, 100, 63, 51, 53, 18, 131, 117] chunk 139 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 16 optimal weight: 0.0870 chunk 83 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 131 optimal weight: 0.0470 chunk 117 optimal weight: 5.9990 overall best weight: 1.1058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.059714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.047390 restraints weight = 29911.306| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 3.49 r_work: 0.2469 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11756 Z= 0.112 Angle : 0.457 6.655 15962 Z= 0.252 Chirality : 0.043 0.133 1640 Planarity : 0.004 0.034 2066 Dihedral : 4.075 20.680 1582 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.58 % Allowed : 8.58 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.23), residues: 1414 helix: 2.00 (0.27), residues: 430 sheet: 2.00 (0.34), residues: 234 loop : -0.92 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 685 TYR 0.015 0.001 TYR B 173 PHE 0.010 0.001 PHE B 245 TRP 0.015 0.001 TRP B 474 HIS 0.002 0.000 HIS B 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (11756) covalent geometry : angle 0.45661 / 0.25 (15962) hydrogen bonds : bond 0.03698 / 2.39 ( 508) hydrogen bonds : angle 4.34646 / 3.02 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.486 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 47 average time/residue: 0.7013 time to fit residues: 35.8439 Evaluate side-chains 43 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [77, 17, 68, 1, 35, 71, 124, 84, 21, 70, 94] chunk 77 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 84 optimal weight: 0.0470 chunk 21 optimal weight: 0.2980 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.8684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS A 307 HIS B 307 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.057761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.045517 restraints weight = 30238.492| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 3.47 r_work: 0.2419 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11756 Z= 0.162 Angle : 0.501 6.804 15962 Z= 0.277 Chirality : 0.044 0.141 1640 Planarity : 0.004 0.035 2066 Dihedral : 4.308 21.202 1582 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.25 % Allowed : 8.92 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.23), residues: 1414 helix: 1.91 (0.27), residues: 428 sheet: 1.97 (0.33), residues: 234 loop : -0.98 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 634 TYR 0.017 0.001 TYR B 173 PHE 0.012 0.001 PHE B 245 TRP 0.014 0.001 TRP B 474 HIS 0.003 0.001 HIS B 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (11756) covalent geometry : angle 0.50071 / 0.28 (15962) hydrogen bonds : bond 0.04640 / 3.00 ( 508) hydrogen bonds : angle 4.49243 / 3.12 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.457 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 0.7016 time to fit residues: 34.1770 Evaluate side-chains 43 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 633 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [106, 19, 75, 76, 98, 4, 108, 0, 39, 28, 125] chunk 106 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 28 optimal weight: 0.0010 chunk 125 optimal weight: 2.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.056918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.044692 restraints weight = 30119.258| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 3.47 r_work: 0.2393 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11756 Z= 0.198 Angle : 0.528 6.837 15962 Z= 0.291 Chirality : 0.046 0.146 1640 Planarity : 0.004 0.039 2066 Dihedral : 4.460 21.569 1582 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.33 % Allowed : 9.08 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.23), residues: 1414 helix: 1.84 (0.27), residues: 428 sheet: 1.94 (0.34), residues: 234 loop : -1.06 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 691 TYR 0.018 0.001 TYR B 173 PHE 0.014 0.001 PHE A 245 TRP 0.014 0.001 TRP A 474 HIS 0.003 0.001 HIS B 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (11756) covalent geometry : angle 0.52757 / 0.29 (15962) hydrogen bonds : bond 0.05065 / 3.27 ( 508) hydrogen bonds : angle 4.57283 / 3.17 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.433 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 46 average time/residue: 0.7112 time to fit residues: 35.5192 Evaluate side-chains 42 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [56, 28, 25, 14, 88, 84, 113, 17, 131, 47, 141] chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 141 optimal weight: 0.0000 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS B 270 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.058586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.046360 restraints weight = 30057.512| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 3.48 r_work: 0.2441 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11756 Z= 0.126 Angle : 0.478 7.212 15962 Z= 0.263 Chirality : 0.043 0.134 1640 Planarity : 0.004 0.038 2066 Dihedral : 4.241 20.955 1582 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.08 % Allowed : 9.42 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.23), residues: 1414 helix: 1.93 (0.27), residues: 428 sheet: 1.95 (0.34), residues: 234 loop : -1.00 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 685 TYR 0.016 0.001 TYR A 173 PHE 0.010 0.001 PHE B 245 TRP 0.016 0.001 TRP B 474 HIS 0.002 0.000 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (11756) covalent geometry : angle 0.47816 / 0.26 (15962) hydrogen bonds : bond 0.03979 / 2.57 ( 508) hydrogen bonds : angle 4.43893 / 3.08 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.448 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.7333 time to fit residues: 34.1543 Evaluate side-chains 43 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 633 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [27, 136, 74, 99, 6, 125, 75, 47, 1, 137, 98] chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.058032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.045731 restraints weight = 30107.264| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 3.50 r_work: 0.2425 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11756 Z= 0.151 Angle : 0.493 7.141 15962 Z= 0.271 Chirality : 0.044 0.137 1640 Planarity : 0.004 0.038 2066 Dihedral : 4.287 21.262 1582 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.08 % Allowed : 9.58 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.23), residues: 1414 helix: 1.92 (0.27), residues: 428 sheet: 1.95 (0.34), residues: 234 loop : -0.99 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 691 TYR 0.016 0.001 TYR B 173 PHE 0.012 0.001 PHE B 245 TRP 0.015 0.001 TRP A 474 HIS 0.003 0.000 HIS B 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (11756) covalent geometry : angle 0.49333 / 0.27 (15962) hydrogen bonds : bond 0.04390 / 2.83 ( 508) hydrogen bonds : angle 4.46090 / 3.10 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2663.13 seconds wall clock time: 46 minutes 24.19 seconds (2784.19 seconds total)