Starting phenix.real_space_refine on Mon Jul 28 13:50:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ilr_35543/07_2025/8ilr_35543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ilr_35543/07_2025/8ilr_35543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ilr_35543/07_2025/8ilr_35543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ilr_35543/07_2025/8ilr_35543.map" model { file = "/net/cci-nas-00/data/ceres_data/8ilr_35543/07_2025/8ilr_35543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ilr_35543/07_2025/8ilr_35543.cif" } resolution = 3.05 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= -0.001 sd= 0.105 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 73 5.16 5 C 6603 2.51 5 N 1792 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10374 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7981 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 977, 7981 Classifications: {'peptide': 977} Link IDs: {'PTRANS': 47, 'TRANS': 929} Chain breaks: 5 Chain: "B" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2346 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 4, 'TRANS': 271} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 47 Unusual residues: {'7TZ': 1} Classifications: {'undetermined': 1, 'water': 7} Link IDs: {None: 7} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N BGLU A 950 " occ=0.46 ... (7 atoms not shown) pdb=" OE2BGLU A 950 " occ=0.46 residue: pdb=" N BARG A 951 " occ=0.46 ... (9 atoms not shown) pdb=" NH2BARG A 951 " occ=0.46 residue: pdb=" N BPRO A 953 " occ=0.46 ... (5 atoms not shown) pdb=" CD BPRO A 953 " occ=0.46 residue: pdb=" N BVAL A 955 " occ=0.46 ... (5 atoms not shown) pdb=" CG2BVAL A 955 " occ=0.46 residue: pdb=" N BLEU A 956 " occ=0.50 ... (6 atoms not shown) pdb=" CD2BLEU A 956 " occ=0.50 Time building chain proxies: 6.59, per 1000 atoms: 0.64 Number of scatterers: 10374 At special positions: 0 Unit cell: (86.751, 112.455, 129.591, 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 73 16.00 O 1906 8.00 N 1792 7.00 C 6603 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: 2.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2398 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 11 sheets defined 52.0% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 88 through 93 removed outlier: 4.205A pdb=" N ARG A 93 " --> pdb=" O CYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 122 removed outlier: 3.596A pdb=" N LEU A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.774A pdb=" N ASP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 178 through 184 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.643A pdb=" N ASP A 203 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.811A pdb=" N LYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.529A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 528 through 537 removed outlier: 3.590A pdb=" N ARG A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 removed outlier: 3.805A pdb=" N SER A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 559 removed outlier: 3.828A pdb=" N VAL A 559 " --> pdb=" O HIS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 576 through 589 removed outlier: 3.520A pdb=" N GLN A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 removed outlier: 3.794A pdb=" N ASP A 603 " --> pdb=" O GLU A 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 603' Processing helix chain 'A' and resid 608 through 623 removed outlier: 3.595A pdb=" N LYS A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 639 removed outlier: 3.775A pdb=" N GLN A 630 " --> pdb=" O ASP A 626 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ILE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLN A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 660 through 674 removed outlier: 3.642A pdb=" N GLU A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 697 through 720 removed outlier: 4.182A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 718 " --> pdb=" O ASN A 714 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 720 " --> pdb=" O THR A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 738 removed outlier: 3.763A pdb=" N GLN A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 748 removed outlier: 3.517A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 769 removed outlier: 3.555A pdb=" N CYS A 769 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.562A pdb=" N GLN A 815 " --> pdb=" O MET A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 864 Processing helix chain 'A' and resid 875 through 885 removed outlier: 3.537A pdb=" N ASN A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 912 removed outlier: 4.396A pdb=" N ALA A 892 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.674A pdb=" N LEU A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A 962 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 993 Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.592A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1009 removed outlier: 4.116A pdb=" N GLY A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 3.855A pdb=" N ILE A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR A1021 " --> pdb=" O ASP A1017 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE A1022 " --> pdb=" O ASP A1018 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1048 removed outlier: 3.703A pdb=" N GLU A1037 " --> pdb=" O GLN A1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 339 through 348 removed outlier: 3.511A pdb=" N GLU B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 410 removed outlier: 3.624A pdb=" N ASN B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 removed outlier: 4.319A pdb=" N GLN B 415 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 Processing helix chain 'B' and resid 441 through 505 removed outlier: 3.577A pdb=" N GLU B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 515 removed outlier: 4.205A pdb=" N LYS B 511 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 587 removed outlier: 3.805A pdb=" N ILE B 521 " --> pdb=" O ASN B 517 " (cutoff:3.500A) Proline residue: B 568 - end of helix Processing helix chain 'B' and resid 590 through 598 removed outlier: 4.022A pdb=" N LEU B 594 " --> pdb=" O ARG B 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 37 removed outlier: 3.855A pdb=" N VAL A 32 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS A 36 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE A 20 " --> pdb=" O CYS A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 212 removed outlier: 4.296A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.212A pdb=" N LYS A 325 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 392 removed outlier: 4.488A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.556A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 372 removed outlier: 3.720A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 402 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASN A 426 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 752 Processing sheet with id=AA8, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AB1, first strand: chain 'B' and resid 355 through 358 Processing sheet with id=AB2, first strand: chain 'B' and resid 384 through 386 481 hydrogen bonds defined for protein. 1362 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1825 1.32 - 1.44: 2672 1.44 - 1.57: 5975 1.57 - 1.69: 2 1.69 - 1.81: 114 Bond restraints: 10588 Sorted by residual: bond pdb=" CA ARG A 777 " pdb=" C ARG A 777 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.26e-02 6.30e+03 1.25e+01 bond pdb=" C16 7TZ A1101 " pdb=" N18 7TZ A1101 " ideal model delta sigma weight residual 1.301 1.359 -0.058 2.00e-02 2.50e+03 8.30e+00 bond pdb=" C ARG A 777 " pdb=" O ARG A 777 " ideal model delta sigma weight residual 1.238 1.201 0.037 1.28e-02 6.10e+03 8.21e+00 bond pdb=" C14 7TZ A1101 " pdb=" N13 7TZ A1101 " ideal model delta sigma weight residual 1.302 1.356 -0.054 2.00e-02 2.50e+03 7.24e+00 bond pdb=" C39 7TZ A1101 " pdb=" N40 7TZ A1101 " ideal model delta sigma weight residual 1.302 1.355 -0.053 2.00e-02 2.50e+03 7.12e+00 ... (remaining 10583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 14203 2.49 - 4.99: 66 4.99 - 7.48: 6 7.48 - 9.98: 5 9.98 - 12.47: 2 Bond angle restraints: 14282 Sorted by residual: angle pdb=" C ARG A 777 " pdb=" N PRO A 778 " pdb=" CA PRO A 778 " ideal model delta sigma weight residual 119.85 111.66 8.19 1.01e+00 9.80e-01 6.57e+01 angle pdb=" N ASN B 325 " pdb=" CA ASN B 325 " pdb=" C ASN B 325 " ideal model delta sigma weight residual 107.37 117.92 -10.55 2.07e+00 2.33e-01 2.60e+01 angle pdb=" CA PRO A 97 " pdb=" N PRO A 97 " pdb=" CD PRO A 97 " ideal model delta sigma weight residual 112.00 106.97 5.03 1.40e+00 5.10e-01 1.29e+01 angle pdb=" N ALA A 775 " pdb=" CA ALA A 775 " pdb=" C ALA A 775 " ideal model delta sigma weight residual 110.80 118.00 -7.20 2.13e+00 2.20e-01 1.14e+01 angle pdb=" C ASN B 325 " pdb=" CA ASN B 325 " pdb=" CB ASN B 325 " ideal model delta sigma weight residual 111.82 107.55 4.27 1.38e+00 5.25e-01 9.56e+00 ... (remaining 14277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5560 17.73 - 35.47: 724 35.47 - 53.20: 152 53.20 - 70.94: 23 70.94 - 88.67: 10 Dihedral angle restraints: 6469 sinusoidal: 2774 harmonic: 3695 Sorted by residual: dihedral pdb=" C ARG A 777 " pdb=" N ARG A 777 " pdb=" CA ARG A 777 " pdb=" CB ARG A 777 " ideal model delta harmonic sigma weight residual -122.60 -134.69 12.09 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" N ARG A 777 " pdb=" C ARG A 777 " pdb=" CA ARG A 777 " pdb=" CB ARG A 777 " ideal model delta harmonic sigma weight residual 122.80 134.42 -11.62 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" CB GLU A 768 " pdb=" CG GLU A 768 " pdb=" CD GLU A 768 " pdb=" OE1 GLU A 768 " ideal model delta sinusoidal sigma weight residual 0.00 88.67 -88.67 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 6466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1532 0.118 - 0.237: 5 0.237 - 0.355: 0 0.355 - 0.474: 0 0.474 - 0.592: 1 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA ARG A 777 " pdb=" N ARG A 777 " pdb=" C ARG A 777 " pdb=" CB ARG A 777 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.76e+00 chirality pdb=" CA ALA A 775 " pdb=" N ALA A 775 " pdb=" C ALA A 775 " pdb=" CB ALA A 775 " both_signs ideal model delta sigma weight residual False 2.48 2.28 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ASN B 325 " pdb=" N ASN B 325 " pdb=" C ASN B 325 " pdb=" CB ASN B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1535 not shown) Planarity restraints: 1835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 7TZ A1101 " 0.153 2.00e-02 2.50e+03 8.10e-02 1.48e+02 pdb=" C23 7TZ A1101 " 0.008 2.00e-02 2.50e+03 pdb=" C24 7TZ A1101 " -0.055 2.00e-02 2.50e+03 pdb=" C25 7TZ A1101 " -0.056 2.00e-02 2.50e+03 pdb=" C26 7TZ A1101 " -0.051 2.00e-02 2.50e+03 pdb=" C27 7TZ A1101 " -0.095 2.00e-02 2.50e+03 pdb=" C28 7TZ A1101 " -0.053 2.00e-02 2.50e+03 pdb=" C29 7TZ A1101 " 0.030 2.00e-02 2.50e+03 pdb=" C30 7TZ A1101 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C29 7TZ A1101 " -0.149 2.00e-02 2.50e+03 6.54e-02 1.28e+02 pdb=" C30 7TZ A1101 " 0.001 2.00e-02 2.50e+03 pdb=" C31 7TZ A1101 " 0.066 2.00e-02 2.50e+03 pdb=" C32 7TZ A1101 " 0.044 2.00e-02 2.50e+03 pdb=" C33 7TZ A1101 " 0.022 2.00e-02 2.50e+03 pdb=" C34 7TZ A1101 " 0.093 2.00e-02 2.50e+03 pdb=" C35 7TZ A1101 " 0.051 2.00e-02 2.50e+03 pdb=" C36 7TZ A1101 " 0.012 2.00e-02 2.50e+03 pdb=" C38 7TZ A1101 " -0.077 2.00e-02 2.50e+03 pdb=" C39 7TZ A1101 " -0.044 2.00e-02 2.50e+03 pdb=" N37 7TZ A1101 " -0.047 2.00e-02 2.50e+03 pdb=" N40 7TZ A1101 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C08 7TZ A1101 " 0.000 2.00e-02 2.50e+03 4.09e-02 5.43e+01 pdb=" C09 7TZ A1101 " 0.036 2.00e-02 2.50e+03 pdb=" C10 7TZ A1101 " 0.055 2.00e-02 2.50e+03 pdb=" C11 7TZ A1101 " -0.007 2.00e-02 2.50e+03 pdb=" C12 7TZ A1101 " -0.047 2.00e-02 2.50e+03 pdb=" C14 7TZ A1101 " -0.020 2.00e-02 2.50e+03 pdb=" C15 7TZ A1101 " 0.084 2.00e-02 2.50e+03 pdb=" C16 7TZ A1101 " -0.015 2.00e-02 2.50e+03 pdb=" C17 7TZ A1101 " 0.033 2.00e-02 2.50e+03 pdb=" C19 7TZ A1101 " -0.027 2.00e-02 2.50e+03 pdb=" C20 7TZ A1101 " 0.007 2.00e-02 2.50e+03 pdb=" N13 7TZ A1101 " -0.069 2.00e-02 2.50e+03 pdb=" N18 7TZ A1101 " -0.031 2.00e-02 2.50e+03 ... (remaining 1832 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 89 2.55 - 3.14: 8480 3.14 - 3.73: 15653 3.73 - 4.31: 22460 4.31 - 4.90: 37705 Nonbonded interactions: 84387 Sorted by model distance: nonbonded pdb=" OD2 ASP A 431 " pdb=" OG1 THR A 433 " model vdw 1.967 3.040 nonbonded pdb=" O GLU A 970 " pdb=" OG1 THR A 974 " model vdw 1.984 3.040 nonbonded pdb=" OG SER B 399 " pdb=" OE1 GLU B 403 " model vdw 2.116 3.040 nonbonded pdb=" OD1 ASN A 428 " pdb=" NE2 GLN A 643 " model vdw 2.130 3.120 nonbonded pdb=" OE1 GLU A 642 " pdb=" O HOH A1201 " model vdw 2.134 3.040 ... (remaining 84382 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.46 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: 0.860 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.850 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 0.076 10588 Z= 0.128 Angle : 0.447 12.469 14282 Z= 0.231 Chirality : 0.039 0.592 1538 Planarity : 0.005 0.133 1835 Dihedral : 15.946 88.671 4071 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 27.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 0.35 % Allowed : 15.20 % Favored : 84.45 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.25), residues: 1239 helix: 1.22 (0.24), residues: 547 sheet: -1.07 (0.42), residues: 159 loop : -0.73 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 780 HIS 0.002 0.000 HIS A 665 PHE 0.006 0.001 PHE A1039 TYR 0.006 0.001 TYR A 68 ARG 0.003 0.000 ARG B 503 Details of bonding type rmsd hydrogen bonds : bond 0.26077 ( 481) hydrogen bonds : angle 7.68832 ( 1362) covalent geometry : bond 0.00255 (10588) covalent geometry : angle 0.44693 (14282) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: A 93 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7797 (mtm-85) REVERT: B 503 ARG cc_start: 0.6996 (tmm160) cc_final: 0.6700 (tmm160) outliers start: 4 outliers final: 1 residues processed: 146 average time/residue: 0.2542 time to fit residues: 52.8869 Evaluate side-chains 142 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 GLN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.195484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144088 restraints weight = 11538.749| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.35 r_work: 0.3391 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10588 Z= 0.188 Angle : 0.614 7.002 14282 Z= 0.318 Chirality : 0.044 0.191 1538 Planarity : 0.005 0.080 1835 Dihedral : 4.149 31.878 1390 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 2.52 % Allowed : 13.99 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.00 (0.24), residues: 1239 helix: 1.27 (0.22), residues: 569 sheet: -1.14 (0.40), residues: 143 loop : -1.05 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 552 HIS 0.006 0.001 HIS A 665 PHE 0.016 0.002 PHE A 667 TYR 0.012 0.001 TYR B 334 ARG 0.004 0.001 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.06538 ( 481) hydrogen bonds : angle 4.90721 ( 1362) covalent geometry : bond 0.00446 (10588) covalent geometry : angle 0.61387 (14282) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 1.446 Fit side-chains REVERT: A 93 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7351 (mtm-85) REVERT: A 148 LYS cc_start: 0.7855 (tppt) cc_final: 0.7183 (ttpp) REVERT: A 179 LYS cc_start: 0.7868 (tppt) cc_final: 0.7540 (mtmm) REVERT: A 734 PHE cc_start: 0.8199 (t80) cc_final: 0.7946 (t80) REVERT: A 796 ASN cc_start: 0.8288 (m-40) cc_final: 0.7995 (m-40) REVERT: A 798 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7578 (mt-10) REVERT: A 1033 GLN cc_start: 0.7894 (tp-100) cc_final: 0.7059 (tt0) REVERT: A 1034 GLU cc_start: 0.8016 (tp30) cc_final: 0.7714 (tp30) REVERT: A 1037 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: B 417 ASN cc_start: 0.6677 (t0) cc_final: 0.6268 (t0) REVERT: B 461 ARG cc_start: 0.7316 (tpt90) cc_final: 0.6848 (tpt90) REVERT: B 475 GLN cc_start: 0.7466 (tm-30) cc_final: 0.7261 (tm-30) REVERT: B 479 MET cc_start: 0.7519 (mtt) cc_final: 0.7248 (mtt) outliers start: 29 outliers final: 11 residues processed: 173 average time/residue: 0.3027 time to fit residues: 75.3994 Evaluate side-chains 155 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 343 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.192954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140439 restraints weight = 11593.672| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.29 r_work: 0.3447 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10588 Z= 0.143 Angle : 0.544 7.770 14282 Z= 0.281 Chirality : 0.041 0.157 1538 Planarity : 0.004 0.058 1835 Dihedral : 3.937 32.401 1388 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.26 % Allowed : 15.20 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.24), residues: 1239 helix: 1.50 (0.22), residues: 576 sheet: -1.25 (0.38), residues: 155 loop : -0.97 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 583 HIS 0.005 0.001 HIS A 665 PHE 0.015 0.001 PHE A 667 TYR 0.012 0.001 TYR A 904 ARG 0.005 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.05440 ( 481) hydrogen bonds : angle 4.39457 ( 1362) covalent geometry : bond 0.00328 (10588) covalent geometry : angle 0.54366 (14282) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.132 Fit side-chains REVERT: A 146 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8330 (p) REVERT: A 148 LYS cc_start: 0.7994 (tppt) cc_final: 0.7300 (ttpp) REVERT: A 179 LYS cc_start: 0.7942 (tppt) cc_final: 0.7678 (mttt) REVERT: A 282 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7579 (ptt) REVERT: A 732 MET cc_start: 0.7308 (tpt) cc_final: 0.6702 (mmm) REVERT: A 739 MET cc_start: 0.8292 (mtt) cc_final: 0.7847 (mtt) REVERT: A 765 ARG cc_start: 0.7790 (mtm-85) cc_final: 0.7566 (ttm170) REVERT: A 796 ASN cc_start: 0.8172 (m-40) cc_final: 0.7844 (m-40) REVERT: A 825 GLN cc_start: 0.7827 (tp-100) cc_final: 0.7493 (tp-100) REVERT: A 954 PHE cc_start: 0.5345 (OUTLIER) cc_final: 0.4972 (m-80) REVERT: A 1034 GLU cc_start: 0.7967 (tp30) cc_final: 0.7756 (tp30) REVERT: B 417 ASN cc_start: 0.6746 (t0) cc_final: 0.6309 (t0) REVERT: B 461 ARG cc_start: 0.7398 (tpt90) cc_final: 0.6861 (tpt90) REVERT: B 475 GLN cc_start: 0.7500 (tm-30) cc_final: 0.6829 (tm-30) REVERT: B 476 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7354 (mp0) REVERT: B 479 MET cc_start: 0.7591 (mtt) cc_final: 0.7292 (mtt) REVERT: B 582 MET cc_start: 0.7581 (ptt) cc_final: 0.7343 (mtm) outliers start: 26 outliers final: 16 residues processed: 183 average time/residue: 0.2725 time to fit residues: 70.7782 Evaluate side-chains 164 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 356 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.192933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.142999 restraints weight = 11501.584| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.01 r_work: 0.3423 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10588 Z= 0.137 Angle : 0.534 7.831 14282 Z= 0.273 Chirality : 0.041 0.145 1538 Planarity : 0.004 0.060 1835 Dihedral : 3.910 32.293 1388 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.52 % Allowed : 15.64 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.24), residues: 1239 helix: 1.64 (0.22), residues: 575 sheet: -1.16 (0.40), residues: 133 loop : -0.96 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.005 0.001 HIS A 665 PHE 0.015 0.001 PHE A 667 TYR 0.010 0.001 TYR B 470 ARG 0.005 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.04953 ( 481) hydrogen bonds : angle 4.16716 ( 1362) covalent geometry : bond 0.00318 (10588) covalent geometry : angle 0.53361 (14282) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7457 (mmp) cc_final: 0.7190 (mmp) REVERT: A 148 LYS cc_start: 0.7960 (tppt) cc_final: 0.7301 (ttpp) REVERT: A 179 LYS cc_start: 0.7954 (tppt) cc_final: 0.7675 (mttt) REVERT: A 282 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7400 (mtm) REVERT: A 431 ASP cc_start: 0.8586 (p0) cc_final: 0.8270 (p0) REVERT: A 732 MET cc_start: 0.7124 (tpt) cc_final: 0.6613 (mmm) REVERT: A 765 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7471 (ttm170) REVERT: A 796 ASN cc_start: 0.8205 (m-40) cc_final: 0.7880 (m-40) REVERT: A 954 PHE cc_start: 0.5508 (OUTLIER) cc_final: 0.5213 (m-80) REVERT: A 1034 GLU cc_start: 0.8073 (tp30) cc_final: 0.7806 (tp30) REVERT: B 417 ASN cc_start: 0.6778 (t0) cc_final: 0.6323 (t0) REVERT: B 461 ARG cc_start: 0.7378 (tpt90) cc_final: 0.6817 (tpt90) REVERT: B 475 GLN cc_start: 0.7475 (tm-30) cc_final: 0.6889 (tm-30) REVERT: B 476 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7199 (mp0) REVERT: B 582 MET cc_start: 0.7568 (ptt) cc_final: 0.6800 (mmt) outliers start: 29 outliers final: 15 residues processed: 177 average time/residue: 0.2323 time to fit residues: 59.3963 Evaluate side-chains 166 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 343 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 122 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 29 optimal weight: 0.0030 chunk 76 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.197870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.147392 restraints weight = 11465.757| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.19 r_work: 0.3401 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10588 Z= 0.119 Angle : 0.505 8.463 14282 Z= 0.261 Chirality : 0.040 0.146 1538 Planarity : 0.004 0.060 1835 Dihedral : 3.840 32.741 1388 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.09 % Allowed : 17.12 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.24), residues: 1239 helix: 1.75 (0.22), residues: 577 sheet: -1.18 (0.38), residues: 150 loop : -0.82 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.004 0.001 HIS A 665 PHE 0.016 0.001 PHE A 667 TYR 0.010 0.001 TYR A 904 ARG 0.005 0.000 ARG B 503 Details of bonding type rmsd hydrogen bonds : bond 0.04562 ( 481) hydrogen bonds : angle 3.96952 ( 1362) covalent geometry : bond 0.00266 (10588) covalent geometry : angle 0.50545 (14282) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.7437 (mmp) cc_final: 0.7000 (mmp) REVERT: A 78 GLU cc_start: 0.7465 (tp30) cc_final: 0.7033 (tt0) REVERT: A 148 LYS cc_start: 0.8033 (tppt) cc_final: 0.7426 (ttpp) REVERT: A 179 LYS cc_start: 0.7966 (tppt) cc_final: 0.7716 (mttt) REVERT: A 282 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7364 (mtm) REVERT: A 431 ASP cc_start: 0.8328 (p0) cc_final: 0.7909 (p0) REVERT: A 732 MET cc_start: 0.7193 (tpt) cc_final: 0.6554 (mmm) REVERT: A 765 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.7422 (ttm170) REVERT: A 796 ASN cc_start: 0.8068 (m-40) cc_final: 0.7814 (m-40) REVERT: A 1034 GLU cc_start: 0.7945 (tp30) cc_final: 0.7638 (tp30) REVERT: A 1037 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: B 406 ASN cc_start: 0.7973 (m-40) cc_final: 0.7722 (m-40) REVERT: B 417 ASN cc_start: 0.6735 (t0) cc_final: 0.6396 (t0) REVERT: B 461 ARG cc_start: 0.7390 (tpt90) cc_final: 0.6848 (tpt90) REVERT: B 475 GLN cc_start: 0.7350 (tm-30) cc_final: 0.6859 (tm-30) REVERT: B 476 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7005 (mp0) REVERT: B 496 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6615 (pt0) REVERT: B 582 MET cc_start: 0.7626 (ptt) cc_final: 0.6872 (mmt) outliers start: 24 outliers final: 17 residues processed: 178 average time/residue: 0.2185 time to fit residues: 56.0924 Evaluate side-chains 168 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 343 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 931 HIS B 385 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.196010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138215 restraints weight = 11567.001| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.82 r_work: 0.3351 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10588 Z= 0.161 Angle : 0.537 8.913 14282 Z= 0.275 Chirality : 0.041 0.143 1538 Planarity : 0.004 0.060 1835 Dihedral : 3.893 30.657 1388 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.17 % Allowed : 17.64 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.24), residues: 1239 helix: 1.67 (0.22), residues: 577 sheet: -1.02 (0.40), residues: 129 loop : -0.95 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 386 HIS 0.006 0.001 HIS A 665 PHE 0.015 0.002 PHE A 667 TYR 0.012 0.001 TYR B 470 ARG 0.003 0.000 ARG A 662 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 481) hydrogen bonds : angle 3.98392 ( 1362) covalent geometry : bond 0.00383 (10588) covalent geometry : angle 0.53731 (14282) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7552 (tp30) cc_final: 0.7095 (tt0) REVERT: A 148 LYS cc_start: 0.7918 (tppt) cc_final: 0.7249 (ttpp) REVERT: A 282 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7342 (mtm) REVERT: A 431 ASP cc_start: 0.8432 (p0) cc_final: 0.7997 (p0) REVERT: A 732 MET cc_start: 0.7128 (tpt) cc_final: 0.6716 (mmm) REVERT: A 765 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7343 (mtt180) REVERT: A 1034 GLU cc_start: 0.7993 (tp30) cc_final: 0.7745 (tp30) REVERT: B 417 ASN cc_start: 0.6808 (t0) cc_final: 0.6413 (t0) REVERT: B 461 ARG cc_start: 0.7379 (tpt90) cc_final: 0.7028 (tpt90) REVERT: B 475 GLN cc_start: 0.7230 (tm-30) cc_final: 0.6729 (tm-30) REVERT: B 476 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7025 (mp0) REVERT: B 496 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6474 (pt0) REVERT: B 525 MET cc_start: 0.7393 (mmm) cc_final: 0.7189 (mmm) outliers start: 25 outliers final: 20 residues processed: 170 average time/residue: 0.2207 time to fit residues: 55.6053 Evaluate side-chains 167 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 343 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.197040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138443 restraints weight = 11698.673| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.82 r_work: 0.3380 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10588 Z= 0.135 Angle : 0.525 9.256 14282 Z= 0.269 Chirality : 0.041 0.146 1538 Planarity : 0.004 0.060 1835 Dihedral : 3.870 30.063 1388 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.09 % Allowed : 18.07 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.24), residues: 1239 helix: 1.69 (0.22), residues: 580 sheet: -1.14 (0.38), residues: 146 loop : -0.85 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.005 0.001 HIS A 665 PHE 0.015 0.001 PHE A 667 TYR 0.011 0.001 TYR B 470 ARG 0.003 0.000 ARG A 662 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 481) hydrogen bonds : angle 3.91859 ( 1362) covalent geometry : bond 0.00316 (10588) covalent geometry : angle 0.52502 (14282) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7583 (tp30) cc_final: 0.7028 (tt0) REVERT: A 81 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7794 (mm-30) REVERT: A 148 LYS cc_start: 0.7899 (tppt) cc_final: 0.7213 (ttpp) REVERT: A 179 LYS cc_start: 0.7908 (tppt) cc_final: 0.7573 (mttt) REVERT: A 282 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7239 (mtm) REVERT: A 431 ASP cc_start: 0.8372 (p0) cc_final: 0.7979 (p0) REVERT: A 732 MET cc_start: 0.7090 (tpt) cc_final: 0.6537 (mmm) REVERT: A 745 MET cc_start: 0.8075 (mmp) cc_final: 0.7840 (mmm) REVERT: A 765 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.7265 (mtt180) REVERT: A 1034 GLU cc_start: 0.7965 (tp30) cc_final: 0.7719 (tp30) REVERT: B 417 ASN cc_start: 0.6818 (t0) cc_final: 0.6342 (t0) REVERT: B 461 ARG cc_start: 0.7391 (tpt90) cc_final: 0.7055 (tpt90) REVERT: B 496 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6468 (pt0) REVERT: B 560 ASP cc_start: 0.7660 (t0) cc_final: 0.7179 (t0) REVERT: B 582 MET cc_start: 0.7326 (ptt) cc_final: 0.6672 (mmp) outliers start: 24 outliers final: 18 residues processed: 172 average time/residue: 0.2098 time to fit residues: 52.0134 Evaluate side-chains 162 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 343 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 96 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 106 optimal weight: 0.1980 chunk 38 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.197553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.151148 restraints weight = 11518.593| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.80 r_work: 0.3358 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10588 Z= 0.124 Angle : 0.525 9.407 14282 Z= 0.269 Chirality : 0.040 0.143 1538 Planarity : 0.004 0.059 1835 Dihedral : 3.830 30.390 1388 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.82 % Allowed : 18.51 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.24), residues: 1239 helix: 1.74 (0.22), residues: 580 sheet: -1.13 (0.38), residues: 146 loop : -0.86 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.005 0.001 HIS A 665 PHE 0.015 0.001 PHE A 667 TYR 0.011 0.001 TYR B 470 ARG 0.002 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 481) hydrogen bonds : angle 3.85984 ( 1362) covalent geometry : bond 0.00289 (10588) covalent geometry : angle 0.52521 (14282) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7681 (tp30) cc_final: 0.7166 (tt0) REVERT: A 148 LYS cc_start: 0.7960 (tppt) cc_final: 0.7324 (ttpp) REVERT: A 179 LYS cc_start: 0.7957 (tppt) cc_final: 0.7675 (mttt) REVERT: A 282 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7256 (mtm) REVERT: A 431 ASP cc_start: 0.8382 (p0) cc_final: 0.7968 (p0) REVERT: A 675 MET cc_start: 0.8397 (mtp) cc_final: 0.8054 (mtp) REVERT: A 732 MET cc_start: 0.7192 (tpt) cc_final: 0.6637 (mmm) REVERT: A 745 MET cc_start: 0.8025 (mmp) cc_final: 0.7816 (mmm) REVERT: A 765 ARG cc_start: 0.7645 (mtm-85) cc_final: 0.7324 (mtt180) REVERT: A 1034 GLU cc_start: 0.7979 (tp30) cc_final: 0.7712 (tp30) REVERT: A 1037 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: B 417 ASN cc_start: 0.6672 (t0) cc_final: 0.6253 (t0) REVERT: B 461 ARG cc_start: 0.7327 (tpt90) cc_final: 0.7088 (tpt90) REVERT: B 475 GLN cc_start: 0.7364 (tm-30) cc_final: 0.6495 (mt0) REVERT: B 476 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7226 (mp0) REVERT: B 496 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6501 (pt0) REVERT: B 560 ASP cc_start: 0.7684 (t0) cc_final: 0.7170 (t0) REVERT: B 582 MET cc_start: 0.7365 (ptt) cc_final: 0.6735 (mmp) outliers start: 21 outliers final: 18 residues processed: 165 average time/residue: 0.2089 time to fit residues: 50.8831 Evaluate side-chains 165 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 341 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.195170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141033 restraints weight = 11598.163| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.41 r_work: 0.3357 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10588 Z= 0.196 Angle : 0.583 7.638 14282 Z= 0.294 Chirality : 0.043 0.153 1538 Planarity : 0.004 0.060 1835 Dihedral : 4.002 27.638 1388 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.09 % Allowed : 18.51 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.24), residues: 1239 helix: 1.53 (0.22), residues: 579 sheet: -1.13 (0.38), residues: 132 loop : -1.06 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 11 HIS 0.006 0.001 HIS A 665 PHE 0.015 0.002 PHE A 930 TYR 0.013 0.001 TYR B 470 ARG 0.003 0.000 ARG A 662 Details of bonding type rmsd hydrogen bonds : bond 0.04976 ( 481) hydrogen bonds : angle 3.98188 ( 1362) covalent geometry : bond 0.00478 (10588) covalent geometry : angle 0.58282 (14282) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7731 (tp30) cc_final: 0.7093 (tt0) REVERT: A 148 LYS cc_start: 0.8009 (tppt) cc_final: 0.7394 (ttpp) REVERT: A 179 LYS cc_start: 0.7937 (tppt) cc_final: 0.7589 (mttt) REVERT: A 282 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7259 (mtm) REVERT: A 431 ASP cc_start: 0.8463 (p0) cc_final: 0.8034 (p0) REVERT: A 732 MET cc_start: 0.7194 (tpt) cc_final: 0.6619 (mmm) REVERT: A 765 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7410 (mtt180) REVERT: A 1034 GLU cc_start: 0.7967 (tp30) cc_final: 0.7759 (tp30) REVERT: B 461 ARG cc_start: 0.7415 (tpt90) cc_final: 0.7092 (tpt90) REVERT: B 476 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7093 (mp0) REVERT: B 479 MET cc_start: 0.7495 (mtt) cc_final: 0.7175 (mtt) REVERT: B 496 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6506 (pt0) REVERT: B 560 ASP cc_start: 0.7665 (t0) cc_final: 0.7379 (t0) REVERT: B 582 MET cc_start: 0.7286 (ptt) cc_final: 0.6703 (mmp) outliers start: 24 outliers final: 21 residues processed: 160 average time/residue: 0.2079 time to fit residues: 49.2658 Evaluate side-chains 164 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 0.7980 chunk 93 optimal weight: 0.0870 chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 107 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 121 optimal weight: 0.4980 chunk 31 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.197874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.138795 restraints weight = 11549.201| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.40 r_work: 0.3388 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10588 Z= 0.115 Angle : 0.535 8.030 14282 Z= 0.272 Chirality : 0.040 0.171 1538 Planarity : 0.004 0.060 1835 Dihedral : 3.853 28.691 1388 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.91 % Allowed : 18.85 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.24), residues: 1239 helix: 1.75 (0.22), residues: 580 sheet: -1.15 (0.38), residues: 149 loop : -0.93 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.004 0.001 HIS A 665 PHE 0.015 0.001 PHE A 667 TYR 0.022 0.001 TYR B 426 ARG 0.002 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 481) hydrogen bonds : angle 3.82811 ( 1362) covalent geometry : bond 0.00260 (10588) covalent geometry : angle 0.53456 (14282) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.7313 (mmp) cc_final: 0.6948 (mmp) REVERT: A 78 GLU cc_start: 0.7757 (tp30) cc_final: 0.7089 (tt0) REVERT: A 148 LYS cc_start: 0.7941 (tppt) cc_final: 0.7318 (ttpp) REVERT: A 179 LYS cc_start: 0.7945 (tppt) cc_final: 0.7650 (mttt) REVERT: A 282 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7245 (mtm) REVERT: A 431 ASP cc_start: 0.8353 (p0) cc_final: 0.7929 (p0) REVERT: A 675 MET cc_start: 0.8326 (mtp) cc_final: 0.7941 (mtp) REVERT: A 732 MET cc_start: 0.7225 (tpt) cc_final: 0.6649 (mmm) REVERT: A 765 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7311 (mtt180) REVERT: A 1034 GLU cc_start: 0.7924 (tp30) cc_final: 0.7678 (tp30) REVERT: A 1037 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: B 461 ARG cc_start: 0.7310 (tpt90) cc_final: 0.7085 (tpt90) REVERT: B 475 GLN cc_start: 0.7381 (tm-30) cc_final: 0.6634 (mt0) REVERT: B 476 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7320 (mp0) REVERT: B 496 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6500 (pt0) REVERT: B 560 ASP cc_start: 0.7655 (t0) cc_final: 0.7130 (t0) REVERT: B 582 MET cc_start: 0.7204 (ptt) cc_final: 0.6688 (mmp) outliers start: 22 outliers final: 18 residues processed: 163 average time/residue: 0.2020 time to fit residues: 48.6486 Evaluate side-chains 166 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1037 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 9 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 6 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.196371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.138221 restraints weight = 11413.207| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.76 r_work: 0.3364 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10588 Z= 0.162 Angle : 0.560 7.904 14282 Z= 0.285 Chirality : 0.042 0.167 1538 Planarity : 0.004 0.059 1835 Dihedral : 3.916 27.485 1388 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.74 % Allowed : 18.85 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.24), residues: 1239 helix: 1.64 (0.22), residues: 582 sheet: -1.07 (0.40), residues: 131 loop : -1.02 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 11 HIS 0.006 0.001 HIS A 665 PHE 0.015 0.002 PHE A 734 TYR 0.018 0.001 TYR A 985 ARG 0.003 0.000 ARG A 662 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 481) hydrogen bonds : angle 3.87239 ( 1362) covalent geometry : bond 0.00390 (10588) covalent geometry : angle 0.55994 (14282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6486.62 seconds wall clock time: 114 minutes 8.26 seconds (6848.26 seconds total)