Starting phenix.real_space_refine on Wed Mar 4 06:18:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xsp_33430/03_2026/7xsp_33430.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xsp_33430/03_2026/7xsp_33430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xsp_33430/03_2026/7xsp_33430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xsp_33430/03_2026/7xsp_33430.map" model { file = "/net/cci-nas-00/data/ceres_data/7xsp_33430/03_2026/7xsp_33430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xsp_33430/03_2026/7xsp_33430.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.046 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 50 5.49 5 S 33 5.16 5 C 6991 2.51 5 N 1979 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11317 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 10247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1271, 10247 Classifications: {'peptide': 1271} Link IDs: {'PTRANS': 60, 'TRANS': 1210} Chain breaks: 6 Chain: "A" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 331 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 735 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 3, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 15} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 676 SG CYS B 88 77.713 23.479 19.824 1.00 50.66 S ATOM 947 SG CYS B 121 81.097 22.783 17.534 1.00 58.82 S ATOM 993 SG CYS B 127 80.389 26.879 19.183 1.00 46.40 S ATOM 1017 SG CYS B 130 81.082 24.013 21.266 1.00 43.14 S ATOM 3604 SG CYS B 491 55.166 29.174 45.413 1.00 50.01 S ATOM 3672 SG CYS B 501 56.555 28.034 42.294 1.00 44.90 S ATOM 3686 SG CYS B 503 54.360 30.892 41.958 1.00 44.09 S ATOM 3708 SG CYS B 506 58.143 31.814 42.708 1.00 43.59 S ATOM 5679 SG CYS B 750 40.765 34.293 72.491 1.00 55.83 S ATOM 5692 SG CYS B 752 38.920 37.986 71.151 1.00 51.95 S ATOM 5714 SG CYS B 755 42.536 38.002 70.638 1.00 48.48 S ATOM 7692 SG CYS B1018 41.070 58.721 102.197 1.00 40.83 S ATOM 7908 SG CYS B1406 41.835 55.177 100.983 1.00 41.16 S ATOM 7959 SG CYS B1414 37.793 57.007 100.502 1.00 40.43 S ATOM 7976 SG CYS B1417 40.582 57.625 98.336 1.00 36.21 S Time building chain proxies: 2.49, per 1000 atoms: 0.22 Number of scatterers: 11317 At special positions: 0 Unit cell: (111.15, 113.715, 138.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 33 16.00 P 50 15.00 O 2260 8.00 N 1979 7.00 C 6991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 466.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 88 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 130 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 127 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 121 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 506 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 491 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 503 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 501 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" ND1 HIS B 747 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 752 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 755 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 750 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1406 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1018 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1414 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1417 " Number of angles added : 21 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 18 sheets defined 27.6% alpha, 23.4% beta 8 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'B' and resid 32 through 38 removed outlier: 3.805A pdb=" N MET B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 78 removed outlier: 3.746A pdb=" N VAL B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 267 through 287 removed outlier: 3.567A pdb=" N GLN B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 303 removed outlier: 4.247A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 354 through 375 removed outlier: 4.214A pdb=" N LEU B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 375 " --> pdb=" O LYS B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 488 removed outlier: 3.562A pdb=" N LEU B 475 " --> pdb=" O PRO B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 637 removed outlier: 3.787A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU B 636 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 740 removed outlier: 3.696A pdb=" N HIS B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 759 Processing helix chain 'B' and resid 776 through 780 removed outlier: 3.895A pdb=" N PHE B 780 " --> pdb=" O GLY B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 848 Processing helix chain 'B' and resid 855 through 859 Processing helix chain 'B' and resid 873 through 881 Processing helix chain 'B' and resid 999 through 1016 removed outlier: 3.716A pdb=" N LEU B1003 " --> pdb=" O PRO B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1414 through 1420 Processing helix chain 'B' and resid 1486 through 1493 removed outlier: 3.842A pdb=" N ILE B1490 " --> pdb=" O GLY B1486 " (cutoff:3.500A) Processing helix chain 'B' and resid 1493 through 1499 Processing helix chain 'B' and resid 1528 through 1540 Processing helix chain 'B' and resid 1583 through 1603 removed outlier: 3.555A pdb=" N ILE B1587 " --> pdb=" O PRO B1583 " (cutoff:3.500A) Processing helix chain 'B' and resid 1615 through 1618 removed outlier: 3.685A pdb=" N VAL B1618 " --> pdb=" O GLN B1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1615 through 1618' Processing helix chain 'B' and resid 1619 through 1629 Processing helix chain 'B' and resid 1662 through 1667 removed outlier: 3.566A pdb=" N LEU B1666 " --> pdb=" O THR B1662 " (cutoff:3.500A) Processing helix chain 'B' and resid 1673 through 1681 Processing sheet with id=AA1, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.795A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG B 19 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N TRP B 44 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL B 21 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N TRP B 46 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TRP B 195 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 9.773A pdb=" N GLU B 22 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 13.786A pdb=" N ARG B 193 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG B 180 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR B 191 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 178 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG B 193 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG B 176 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP B 195 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N SER B 174 " --> pdb=" O TRP B 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.864A pdb=" N LEU B 167 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR B 9 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.625A pdb=" N VAL B 85 " --> pdb=" O TRP B 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.075A pdb=" N THR B 110 " --> pdb=" O VAL B 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.698A pdb=" N GLU B 415 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU B 611 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE B 417 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 609 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 419 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 607 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY B 600 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.698A pdb=" N GLU B 415 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU B 611 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE B 417 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 609 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 419 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 607 " --> pdb=" O VAL B 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 431 through 432 removed outlier: 3.944A pdb=" N VAL B 432 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN B 459 " --> pdb=" O VAL B 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AA9, first strand: chain 'B' and resid 526 through 530 Processing sheet with id=AB1, first strand: chain 'B' and resid 533 through 534 removed outlier: 3.740A pdb=" N THR B 539 " --> pdb=" O ASN B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 703 through 704 removed outlier: 6.061A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 703 through 704 removed outlier: 6.061A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 699 through 700 removed outlier: 7.043A pdb=" N ALA B 699 " --> pdb=" O TYR B 808 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 803 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 920 through 921 Processing sheet with id=AB6, first strand: chain 'B' and resid 924 through 927 Processing sheet with id=AB7, first strand: chain 'B' and resid 991 through 992 removed outlier: 6.906A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 991 through 992 removed outlier: 6.906A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL B1517 " --> pdb=" O THR B 960 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N THR B 960 " --> pdb=" O VAL B1517 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N SER B1519 " --> pdb=" O LEU B 958 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU B 958 " --> pdb=" O SER B1519 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASP B1521 " --> pdb=" O CYS B 956 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N CYS B 956 " --> pdb=" O ASP B1521 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ARG B1523 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE B 954 " --> pdb=" O ARG B1523 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLU B1525 " --> pdb=" O GLY B 952 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY B 952 " --> pdb=" O GLU B1525 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS B 957 " --> pdb=" O ILE B1564 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE B1564 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLU B 959 " --> pdb=" O ILE B1562 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE B1562 " --> pdb=" O GLU B 959 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 985 through 986 removed outlier: 6.533A pdb=" N LYS B 985 " --> pdb=" O THR B1508 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N GLU B1510 " --> pdb=" O LYS B 985 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3048 1.33 - 1.45: 2347 1.45 - 1.57: 6143 1.57 - 1.69: 94 1.69 - 1.81: 45 Bond restraints: 11677 Sorted by residual: bond pdb=" O3' U D -2 " pdb=" P A D -1 " ideal model delta sigma weight residual 1.607 1.507 0.100 1.50e-02 4.44e+03 4.43e+01 bond pdb=" O3' A D -1 " pdb=" P C D 0 " ideal model delta sigma weight residual 1.607 1.537 0.070 1.50e-02 4.44e+03 2.19e+01 bond pdb=" O3' C D 15 " pdb=" P G D 16 " ideal model delta sigma weight residual 1.607 1.543 0.064 1.50e-02 4.44e+03 1.80e+01 bond pdb=" P A D -1 " pdb=" OP1 A D -1 " ideal model delta sigma weight residual 1.485 1.424 0.061 2.00e-02 2.50e+03 9.45e+00 bond pdb=" O3' G D 16 " pdb=" P G D 17 " ideal model delta sigma weight residual 1.607 1.561 0.046 1.50e-02 4.44e+03 9.36e+00 ... (remaining 11672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 15722 2.75 - 5.49: 232 5.49 - 8.24: 18 8.24 - 10.99: 7 10.99 - 13.73: 3 Bond angle restraints: 15982 Sorted by residual: angle pdb=" O3' A D -1 " pdb=" C3' A D -1 " pdb=" C2' A D -1 " ideal model delta sigma weight residual 109.50 97.00 12.50 1.50e+00 4.44e-01 6.94e+01 angle pdb=" O2' G D 16 " pdb=" C2' G D 16 " pdb=" C1' G D 16 " ideal model delta sigma weight residual 108.40 96.17 12.23 1.50e+00 4.44e-01 6.65e+01 angle pdb=" O2' A D -1 " pdb=" C2' A D -1 " pdb=" C1' A D -1 " ideal model delta sigma weight residual 111.80 121.65 -9.85 1.50e+00 4.44e-01 4.31e+01 angle pdb=" C4' A D -1 " pdb=" C3' A D -1 " pdb=" O3' A D -1 " ideal model delta sigma weight residual 109.40 101.33 8.07 1.50e+00 4.44e-01 2.89e+01 angle pdb=" C ASP B1470 " pdb=" N ASP B1471 " pdb=" CA ASP B1471 " ideal model delta sigma weight residual 121.54 130.56 -9.02 1.91e+00 2.74e-01 2.23e+01 ... (remaining 15977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 6733 35.56 - 71.13: 303 71.13 - 106.69: 26 106.69 - 142.26: 1 142.26 - 177.82: 3 Dihedral angle restraints: 7066 sinusoidal: 3440 harmonic: 3626 Sorted by residual: dihedral pdb=" O4' C D -7 " pdb=" C1' C D -7 " pdb=" N1 C D -7 " pdb=" C2 C D -7 " ideal model delta sinusoidal sigma weight residual 200.00 40.72 159.28 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' U D -13 " pdb=" C1' U D -13 " pdb=" N1 U D -13 " pdb=" C2 U D -13 " ideal model delta sinusoidal sigma weight residual -160.00 -27.30 -132.70 1 1.50e+01 4.44e-03 7.16e+01 dihedral pdb=" O4' U D -8 " pdb=" C1' U D -8 " pdb=" N1 U D -8 " pdb=" C2 U D -8 " ideal model delta sinusoidal sigma weight residual -128.00 49.82 -177.82 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 7063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 1707 0.160 - 0.321: 17 0.321 - 0.481: 2 0.481 - 0.642: 0 0.642 - 0.802: 1 Chirality restraints: 1727 Sorted by residual: chirality pdb=" C2' A D -1 " pdb=" C3' A D -1 " pdb=" O2' A D -1 " pdb=" C1' A D -1 " both_signs ideal model delta sigma weight residual False -2.52 -1.72 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" C1' A D -1 " pdb=" O4' A D -1 " pdb=" C2' A D -1 " pdb=" N9 A D -1 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" C3' A D -1 " pdb=" C4' A D -1 " pdb=" O3' A D -1 " pdb=" C2' A D -1 " both_signs ideal model delta sigma weight residual False -2.74 -3.07 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 1724 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D -1 " 0.063 2.00e-02 2.50e+03 3.03e-02 2.53e+01 pdb=" N9 A D -1 " -0.073 2.00e-02 2.50e+03 pdb=" C8 A D -1 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A D -1 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A D -1 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A D -1 " 0.012 2.00e-02 2.50e+03 pdb=" N6 A D -1 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A D -1 " 0.015 2.00e-02 2.50e+03 pdb=" C2 A D -1 " -0.007 2.00e-02 2.50e+03 pdb=" N3 A D -1 " -0.016 2.00e-02 2.50e+03 pdb=" C4 A D -1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 962 " -0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO B 963 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 963 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 963 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 426 " 0.050 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO B 427 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 427 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 427 " 0.042 5.00e-02 4.00e+02 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3375 2.82 - 3.34: 8781 3.34 - 3.86: 17973 3.86 - 4.38: 20992 4.38 - 4.90: 36988 Nonbonded interactions: 88109 Sorted by model distance: nonbonded pdb=" OH TYR B1663 " pdb=" OP2 C D 15 " model vdw 2.303 3.040 nonbonded pdb=" O ASN B 179 " pdb=" O2' G D -3 " model vdw 2.308 3.040 nonbonded pdb=" OH TYR B1645 " pdb=" OP1 C D 14 " model vdw 2.313 3.040 nonbonded pdb=" O PHE B 104 " pdb=" O2' G D -9 " model vdw 2.341 3.040 nonbonded pdb=" OG SER B 680 " pdb=" O GLY B 859 " model vdw 2.346 3.040 ... (remaining 88104 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.950 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.010 0.521 11693 Z= 0.394 Angle : 1.030 41.158 16003 Z= 0.502 Chirality : 0.058 0.802 1727 Planarity : 0.008 0.084 1884 Dihedral : 18.785 177.820 4746 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 3.42 % Allowed : 14.59 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.19), residues: 1257 helix: -2.18 (0.21), residues: 300 sheet: -0.15 (0.35), residues: 192 loop : -2.35 (0.17), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1452 TYR 0.018 0.002 TYR B 860 PHE 0.027 0.003 PHE B1691 TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS B 727 Details of bonding type rmsd covalent geometry : bond 0.00613 (11677) covalent geometry : angle 0.85297 (15982) hydrogen bonds : bond 0.18797 ( 338) hydrogen bonds : angle 6.75997 ( 1020) metal coordination : bond 0.21295 ( 16) metal coordination : angle 15.97633 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: B 159 ASP cc_start: 0.7057 (t0) cc_final: 0.6668 (t0) REVERT: B 213 ASN cc_start: 0.7829 (t0) cc_final: 0.7595 (t0) REVERT: B 282 GLU cc_start: 0.5281 (OUTLIER) cc_final: 0.4951 (tm-30) REVERT: B 310 VAL cc_start: 0.7925 (OUTLIER) cc_final: 0.7637 (t) REVERT: B 421 ARG cc_start: 0.7538 (mtp85) cc_final: 0.7223 (mtt-85) REVERT: B 547 ASP cc_start: 0.7924 (p0) cc_final: 0.7712 (p0) REVERT: B 632 LYS cc_start: 0.8052 (tmtt) cc_final: 0.7845 (tttt) REVERT: B 738 ARG cc_start: 0.7692 (mmm-85) cc_final: 0.7346 (tpt170) REVERT: B 748 GLU cc_start: 0.7020 (tp30) cc_final: 0.6774 (tp30) REVERT: B 760 ASN cc_start: 0.8037 (p0) cc_final: 0.7836 (p0) REVERT: B 813 SER cc_start: 0.7531 (m) cc_final: 0.7284 (m) REVERT: B 821 LYS cc_start: 0.8547 (ttmm) cc_final: 0.8298 (tttt) REVERT: B 830 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: B 1459 LEU cc_start: 0.8117 (pt) cc_final: 0.7849 (pp) REVERT: B 1493 LYS cc_start: 0.8289 (mtpt) cc_final: 0.8072 (mtmm) outliers start: 38 outliers final: 14 residues processed: 288 average time/residue: 0.6477 time to fit residues: 200.1071 Evaluate side-chains 229 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 976 LYS Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1509 THR Chi-restraints excluded: chain B residue 1575 ASN Chi-restraints excluded: chain B residue 1670 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN B 112 GLN B 114 GLN B 276 GLN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN B 350 ASN B 365 ASN B 433 GLN B 871 ASN ** B 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1404 HIS B1621 HIS B1649 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098296 restraints weight = 15350.633| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.85 r_work: 0.3090 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11693 Z= 0.170 Angle : 0.609 8.442 16003 Z= 0.315 Chirality : 0.045 0.262 1727 Planarity : 0.006 0.053 1884 Dihedral : 17.678 179.357 2181 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 3.87 % Allowed : 18.20 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.20), residues: 1257 helix: 0.19 (0.27), residues: 308 sheet: -0.05 (0.34), residues: 192 loop : -1.94 (0.18), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 274 TYR 0.014 0.001 TYR B 149 PHE 0.019 0.002 PHE B1691 TRP 0.010 0.001 TRP B1530 HIS 0.004 0.001 HIS B 924 Details of bonding type rmsd covalent geometry : bond 0.00404 (11677) covalent geometry : angle 0.59155 (15982) hydrogen bonds : bond 0.04952 ( 338) hydrogen bonds : angle 4.44075 ( 1020) metal coordination : bond 0.00901 ( 16) metal coordination : angle 4.02910 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8448 (mtmm) cc_final: 0.8226 (mttm) REVERT: B 131 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7992 (mt) REVERT: B 159 ASP cc_start: 0.7798 (t0) cc_final: 0.7440 (t0) REVERT: B 201 THR cc_start: 0.8771 (m) cc_final: 0.8476 (p) REVERT: B 310 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7739 (t) REVERT: B 656 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: B 748 GLU cc_start: 0.7668 (tp30) cc_final: 0.7257 (tp30) REVERT: B 760 ASN cc_start: 0.8111 (p0) cc_final: 0.7903 (p0) REVERT: B 821 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8474 (tttt) REVERT: B 830 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: B 1470 ASP cc_start: 0.6739 (t0) cc_final: 0.6345 (OUTLIER) REVERT: B 1472 GLU cc_start: 0.7688 (pm20) cc_final: 0.7326 (pp20) REVERT: B 1474 GLU cc_start: 0.7844 (pm20) cc_final: 0.7637 (pm20) REVERT: B 1493 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8171 (mtmm) REVERT: B 1496 GLU cc_start: 0.7029 (mp0) cc_final: 0.6614 (mp0) REVERT: B 1498 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.6870 (mtm110) REVERT: B 1640 GLU cc_start: 0.8054 (pp20) cc_final: 0.7549 (pp20) REVERT: B 1651 GLU cc_start: 0.7186 (tp30) cc_final: 0.6834 (tp30) REVERT: B 1668 ASP cc_start: 0.7514 (m-30) cc_final: 0.7263 (m-30) outliers start: 43 outliers final: 23 residues processed: 246 average time/residue: 0.6359 time to fit residues: 167.9481 Evaluate side-chains 234 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 976 LYS Chi-restraints excluded: chain B residue 1401 LYS Chi-restraints excluded: chain B residue 1422 THR Chi-restraints excluded: chain B residue 1498 ARG Chi-restraints excluded: chain B residue 1509 THR Chi-restraints excluded: chain B residue 1592 ASN Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1670 ASP Chi-restraints excluded: chain B residue 1671 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 121 optimal weight: 0.2980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.116306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.097806 restraints weight = 15437.963| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.85 r_work: 0.3079 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11693 Z= 0.153 Angle : 0.570 7.204 16003 Z= 0.295 Chirality : 0.044 0.251 1727 Planarity : 0.005 0.052 1884 Dihedral : 17.469 177.848 2169 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.49 % Favored : 94.43 % Rotamer: Outliers : 3.87 % Allowed : 19.10 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.21), residues: 1257 helix: 1.21 (0.29), residues: 308 sheet: 0.13 (0.34), residues: 192 loop : -1.72 (0.19), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 212 TYR 0.013 0.001 TYR B 149 PHE 0.018 0.002 PHE B1691 TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS B 727 Details of bonding type rmsd covalent geometry : bond 0.00367 (11677) covalent geometry : angle 0.55512 (15982) hydrogen bonds : bond 0.04303 ( 338) hydrogen bonds : angle 4.17026 ( 1020) metal coordination : bond 0.00391 ( 16) metal coordination : angle 3.57980 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: B 6 MET cc_start: 0.7930 (mtp) cc_final: 0.7417 (mmt) REVERT: B 81 LYS cc_start: 0.8520 (mtmm) cc_final: 0.8274 (mttm) REVERT: B 131 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7946 (mt) REVERT: B 159 ASP cc_start: 0.7819 (t0) cc_final: 0.7507 (t0) REVERT: B 201 THR cc_start: 0.8753 (m) cc_final: 0.8461 (p) REVERT: B 357 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8241 (ttmt) REVERT: B 421 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7984 (mtp85) REVERT: B 627 MET cc_start: 0.8674 (mmm) cc_final: 0.8402 (mmt) REVERT: B 630 LYS cc_start: 0.8871 (mtpp) cc_final: 0.8603 (mtpp) REVERT: B 656 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7654 (pm20) REVERT: B 698 ASP cc_start: 0.8016 (m-30) cc_final: 0.7811 (m-30) REVERT: B 748 GLU cc_start: 0.7642 (tp30) cc_final: 0.7411 (tp30) REVERT: B 821 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8470 (tttp) REVERT: B 830 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: B 844 ASP cc_start: 0.7795 (m-30) cc_final: 0.7573 (m-30) REVERT: B 1459 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7908 (pp) REVERT: B 1496 GLU cc_start: 0.7125 (mp0) cc_final: 0.6659 (mp0) REVERT: B 1640 GLU cc_start: 0.8081 (pp20) cc_final: 0.7695 (pp20) REVERT: B 1651 GLU cc_start: 0.7167 (tp30) cc_final: 0.6844 (tp30) REVERT: B 1668 ASP cc_start: 0.7671 (m-30) cc_final: 0.7416 (m-30) outliers start: 43 outliers final: 23 residues processed: 245 average time/residue: 0.5808 time to fit residues: 153.5436 Evaluate side-chains 244 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 976 LYS Chi-restraints excluded: chain B residue 1437 GLU Chi-restraints excluded: chain B residue 1453 SER Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1592 ASN Chi-restraints excluded: chain B residue 1670 ASP Chi-restraints excluded: chain B residue 1671 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 327 HIS B 328 HIS B 433 GLN B 534 ASN B 917 ASN B 986 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.116794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098242 restraints weight = 15381.061| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.86 r_work: 0.3085 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11693 Z= 0.140 Angle : 0.557 8.159 16003 Z= 0.287 Chirality : 0.043 0.253 1727 Planarity : 0.005 0.054 1884 Dihedral : 17.395 177.841 2167 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.17 % Favored : 94.75 % Rotamer: Outliers : 4.32 % Allowed : 20.81 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.22), residues: 1257 helix: 1.67 (0.30), residues: 308 sheet: 0.29 (0.35), residues: 192 loop : -1.59 (0.19), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 212 TYR 0.012 0.001 TYR B 149 PHE 0.019 0.001 PHE B1570 TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS B 727 Details of bonding type rmsd covalent geometry : bond 0.00333 (11677) covalent geometry : angle 0.54489 (15982) hydrogen bonds : bond 0.03945 ( 338) hydrogen bonds : angle 4.06332 ( 1020) metal coordination : bond 0.00383 ( 16) metal coordination : angle 3.21989 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.378 Fit side-chains REVERT: B 6 MET cc_start: 0.7885 (mtp) cc_final: 0.7369 (mmt) REVERT: B 131 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7937 (mt) REVERT: B 159 ASP cc_start: 0.7786 (t0) cc_final: 0.7517 (t0) REVERT: B 201 THR cc_start: 0.8748 (m) cc_final: 0.8468 (p) REVERT: B 282 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5318 (tt0) REVERT: B 498 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7711 (mt0) REVERT: B 627 MET cc_start: 0.8678 (mmm) cc_final: 0.8419 (mmt) REVERT: B 630 LYS cc_start: 0.8879 (mtpp) cc_final: 0.8610 (mtpp) REVERT: B 656 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: B 737 ARG cc_start: 0.8400 (mtp85) cc_final: 0.8152 (mtm180) REVERT: B 748 GLU cc_start: 0.7704 (tp30) cc_final: 0.7460 (tp30) REVERT: B 821 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8474 (tttp) REVERT: B 830 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: B 844 ASP cc_start: 0.7774 (m-30) cc_final: 0.7547 (m-30) REVERT: B 947 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7618 (mm-30) REVERT: B 1454 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8141 (mp) REVERT: B 1459 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7929 (pp) REVERT: B 1460 GLU cc_start: 0.7437 (pm20) cc_final: 0.7235 (pm20) REVERT: B 1472 GLU cc_start: 0.7417 (pp20) cc_final: 0.7171 (pp20) REVERT: B 1496 GLU cc_start: 0.7202 (mp0) cc_final: 0.6730 (mp0) REVERT: B 1640 GLU cc_start: 0.8027 (pp20) cc_final: 0.7673 (pp20) outliers start: 48 outliers final: 24 residues processed: 237 average time/residue: 0.6160 time to fit residues: 156.9319 Evaluate side-chains 240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1437 GLU Chi-restraints excluded: chain B residue 1453 SER Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1592 ASN Chi-restraints excluded: chain B residue 1643 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN B 327 HIS B 433 GLN B 434 GLN B 673 GLN B 778 ASN B 986 ASN B1485 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.097072 restraints weight = 15327.781| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.85 r_work: 0.3066 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11693 Z= 0.187 Angle : 0.593 8.736 16003 Z= 0.306 Chirality : 0.046 0.266 1727 Planarity : 0.006 0.055 1884 Dihedral : 17.351 178.618 2160 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.57 % Favored : 94.35 % Rotamer: Outliers : 5.32 % Allowed : 21.26 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.22), residues: 1257 helix: 1.65 (0.29), residues: 308 sheet: 0.53 (0.34), residues: 197 loop : -1.59 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 274 TYR 0.015 0.001 TYR B 149 PHE 0.023 0.002 PHE B1691 TRP 0.009 0.001 TRP B1530 HIS 0.005 0.001 HIS B 727 Details of bonding type rmsd covalent geometry : bond 0.00456 (11677) covalent geometry : angle 0.58067 (15982) hydrogen bonds : bond 0.04539 ( 338) hydrogen bonds : angle 4.16532 ( 1020) metal coordination : bond 0.00420 ( 16) metal coordination : angle 3.34735 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 219 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: B 6 MET cc_start: 0.7882 (mtp) cc_final: 0.7409 (mmt) REVERT: B 131 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7892 (mt) REVERT: B 159 ASP cc_start: 0.7825 (t0) cc_final: 0.7562 (t0) REVERT: B 201 THR cc_start: 0.8769 (m) cc_final: 0.8504 (p) REVERT: B 282 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5376 (tt0) REVERT: B 310 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7691 (t) REVERT: B 627 MET cc_start: 0.8724 (mmm) cc_final: 0.8427 (mmt) REVERT: B 630 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8692 (mtpp) REVERT: B 737 ARG cc_start: 0.8423 (mtp85) cc_final: 0.8180 (mtm180) REVERT: B 748 GLU cc_start: 0.7710 (tp30) cc_final: 0.7467 (tp30) REVERT: B 821 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8492 (tttp) REVERT: B 830 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: B 876 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: B 1454 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8283 (mp) REVERT: B 1460 GLU cc_start: 0.7345 (pm20) cc_final: 0.7121 (pm20) REVERT: B 1472 GLU cc_start: 0.7677 (pp20) cc_final: 0.7382 (pp20) REVERT: B 1491 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8007 (ttt180) REVERT: B 1496 GLU cc_start: 0.7371 (mp0) cc_final: 0.6930 (mp0) REVERT: B 1640 GLU cc_start: 0.7971 (pp20) cc_final: 0.7618 (pp20) outliers start: 59 outliers final: 27 residues processed: 251 average time/residue: 0.6015 time to fit residues: 162.8710 Evaluate side-chains 249 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 876 PHE Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 976 LYS Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1437 GLU Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1592 ASN Chi-restraints excluded: chain B residue 1643 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 52 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 46 optimal weight: 0.8980 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN B 327 HIS B 433 GLN B 498 GLN B 534 ASN B 986 ASN B1485 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098463 restraints weight = 15294.005| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.84 r_work: 0.3088 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11693 Z= 0.140 Angle : 0.564 8.082 16003 Z= 0.291 Chirality : 0.044 0.253 1727 Planarity : 0.005 0.049 1884 Dihedral : 17.337 178.047 2160 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 4.86 % Allowed : 22.34 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.22), residues: 1257 helix: 1.84 (0.30), residues: 308 sheet: 0.47 (0.35), residues: 191 loop : -1.53 (0.19), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 212 TYR 0.012 0.001 TYR B 149 PHE 0.021 0.001 PHE B1691 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS B 727 Details of bonding type rmsd covalent geometry : bond 0.00331 (11677) covalent geometry : angle 0.55330 (15982) hydrogen bonds : bond 0.03910 ( 338) hydrogen bonds : angle 4.04758 ( 1020) metal coordination : bond 0.00373 ( 16) metal coordination : angle 3.02580 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 208 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: B 6 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7338 (mmt) REVERT: B 131 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7893 (mt) REVERT: B 159 ASP cc_start: 0.7820 (t0) cc_final: 0.7294 (p0) REVERT: B 201 THR cc_start: 0.8767 (m) cc_final: 0.8504 (p) REVERT: B 282 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5362 (tt0) REVERT: B 498 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: B 627 MET cc_start: 0.8718 (mmm) cc_final: 0.8439 (mmt) REVERT: B 630 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8705 (mtpp) REVERT: B 737 ARG cc_start: 0.8400 (mtp85) cc_final: 0.8178 (mtm180) REVERT: B 748 GLU cc_start: 0.7718 (tp30) cc_final: 0.7471 (tp30) REVERT: B 821 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8488 (tttt) REVERT: B 830 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: B 1454 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 1472 GLU cc_start: 0.7690 (pp20) cc_final: 0.7393 (pp20) REVERT: B 1496 GLU cc_start: 0.7352 (mp0) cc_final: 0.6911 (mp0) REVERT: B 1640 GLU cc_start: 0.7930 (pp20) cc_final: 0.7600 (pp20) outliers start: 54 outliers final: 28 residues processed: 235 average time/residue: 0.5977 time to fit residues: 150.9153 Evaluate side-chains 241 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 976 LYS Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1437 GLU Chi-restraints excluded: chain B residue 1453 SER Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1592 ASN Chi-restraints excluded: chain B residue 1643 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 1 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN B 327 HIS B 433 GLN B 498 GLN B 778 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.097832 restraints weight = 15477.984| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.85 r_work: 0.3074 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11693 Z= 0.172 Angle : 0.586 8.508 16003 Z= 0.303 Chirality : 0.045 0.260 1727 Planarity : 0.005 0.049 1884 Dihedral : 17.317 178.359 2160 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.19 % Rotamer: Outliers : 4.59 % Allowed : 22.52 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.22), residues: 1257 helix: 1.82 (0.30), residues: 308 sheet: 0.60 (0.35), residues: 197 loop : -1.53 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 212 TYR 0.014 0.001 TYR B 149 PHE 0.023 0.002 PHE B1691 TRP 0.008 0.001 TRP B1530 HIS 0.005 0.001 HIS B 727 Details of bonding type rmsd covalent geometry : bond 0.00416 (11677) covalent geometry : angle 0.57507 (15982) hydrogen bonds : bond 0.04263 ( 338) hydrogen bonds : angle 4.09790 ( 1020) metal coordination : bond 0.00408 ( 16) metal coordination : angle 3.20914 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 211 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: B 131 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7891 (mt) REVERT: B 159 ASP cc_start: 0.7828 (t0) cc_final: 0.7297 (p0) REVERT: B 201 THR cc_start: 0.8775 (m) cc_final: 0.8517 (p) REVERT: B 282 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5361 (tt0) REVERT: B 310 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7696 (t) REVERT: B 498 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: B 627 MET cc_start: 0.8730 (mmm) cc_final: 0.8444 (mmt) REVERT: B 630 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8708 (mtpp) REVERT: B 727 HIS cc_start: 0.6758 (OUTLIER) cc_final: 0.5291 (p90) REVERT: B 737 ARG cc_start: 0.8406 (mtp85) cc_final: 0.8175 (mtm180) REVERT: B 748 GLU cc_start: 0.7716 (tp30) cc_final: 0.7477 (tp30) REVERT: B 821 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8494 (tttt) REVERT: B 830 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8138 (m-80) REVERT: B 1454 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8250 (mp) REVERT: B 1472 GLU cc_start: 0.7735 (pp20) cc_final: 0.7428 (pp20) REVERT: B 1491 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8006 (ttt180) REVERT: B 1496 GLU cc_start: 0.7398 (mp0) cc_final: 0.6968 (mp0) REVERT: B 1640 GLU cc_start: 0.7936 (pp20) cc_final: 0.7594 (pp20) REVERT: B 1642 ASP cc_start: 0.7633 (t0) cc_final: 0.7428 (t0) REVERT: B 1644 ARG cc_start: 0.8606 (ptp90) cc_final: 0.8383 (ptp90) outliers start: 51 outliers final: 27 residues processed: 239 average time/residue: 0.6032 time to fit residues: 154.8184 Evaluate side-chains 247 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 976 LYS Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1437 GLU Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1579 ILE Chi-restraints excluded: chain B residue 1592 ASN Chi-restraints excluded: chain B residue 1643 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 20 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN B 327 HIS B 433 GLN B 498 GLN B 534 ASN B 986 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.117095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.098939 restraints weight = 15307.643| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.84 r_work: 0.3090 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11693 Z= 0.135 Angle : 0.559 7.951 16003 Z= 0.289 Chirality : 0.043 0.244 1727 Planarity : 0.005 0.043 1884 Dihedral : 17.274 177.370 2160 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 4.32 % Allowed : 23.06 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.22), residues: 1257 helix: 1.93 (0.30), residues: 310 sheet: 0.53 (0.36), residues: 192 loop : -1.48 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 212 TYR 0.011 0.001 TYR B 149 PHE 0.022 0.001 PHE B1570 TRP 0.007 0.001 TRP B 82 HIS 0.005 0.001 HIS B 727 Details of bonding type rmsd covalent geometry : bond 0.00319 (11677) covalent geometry : angle 0.54846 (15982) hydrogen bonds : bond 0.03783 ( 338) hydrogen bonds : angle 4.01438 ( 1020) metal coordination : bond 0.00370 ( 16) metal coordination : angle 3.03510 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 210 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: B 26 TRP cc_start: 0.8528 (t60) cc_final: 0.8326 (t60) REVERT: B 131 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7885 (mt) REVERT: B 159 ASP cc_start: 0.7789 (t0) cc_final: 0.7354 (p0) REVERT: B 201 THR cc_start: 0.8775 (m) cc_final: 0.8523 (p) REVERT: B 282 GLU cc_start: 0.5981 (OUTLIER) cc_final: 0.5335 (tt0) REVERT: B 310 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7666 (t) REVERT: B 627 MET cc_start: 0.8725 (mmm) cc_final: 0.8436 (mmt) REVERT: B 630 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8709 (mtpp) REVERT: B 737 ARG cc_start: 0.8392 (mtp85) cc_final: 0.8141 (mtm180) REVERT: B 748 GLU cc_start: 0.7741 (tp30) cc_final: 0.7495 (tp30) REVERT: B 821 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8481 (tttt) REVERT: B 830 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: B 1454 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8278 (mp) REVERT: B 1472 GLU cc_start: 0.7758 (pp20) cc_final: 0.7440 (pp20) REVERT: B 1496 GLU cc_start: 0.7368 (mp0) cc_final: 0.6941 (mp0) REVERT: B 1640 GLU cc_start: 0.7927 (pp20) cc_final: 0.7572 (pp20) outliers start: 48 outliers final: 29 residues processed: 234 average time/residue: 0.6222 time to fit residues: 156.3694 Evaluate side-chains 240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 976 LYS Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1592 ASN Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1662 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 39 optimal weight: 0.0050 chunk 129 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN B 327 HIS B 433 GLN B 778 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098311 restraints weight = 15211.536| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.84 r_work: 0.3084 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11693 Z= 0.154 Angle : 0.579 8.324 16003 Z= 0.299 Chirality : 0.044 0.251 1727 Planarity : 0.005 0.046 1884 Dihedral : 17.231 177.773 2160 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.19 % Rotamer: Outliers : 4.05 % Allowed : 23.60 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1257 helix: 1.92 (0.30), residues: 309 sheet: 0.63 (0.35), residues: 197 loop : -1.47 (0.19), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 212 TYR 0.013 0.001 TYR B 149 PHE 0.023 0.002 PHE B1570 TRP 0.007 0.001 TRP B1530 HIS 0.005 0.001 HIS B 727 Details of bonding type rmsd covalent geometry : bond 0.00370 (11677) covalent geometry : angle 0.56841 (15982) hydrogen bonds : bond 0.04099 ( 338) hydrogen bonds : angle 4.06710 ( 1020) metal coordination : bond 0.00387 ( 16) metal coordination : angle 3.03296 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 213 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: B 26 TRP cc_start: 0.8523 (t60) cc_final: 0.8312 (t60) REVERT: B 131 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7897 (mt) REVERT: B 159 ASP cc_start: 0.7789 (t0) cc_final: 0.7352 (p0) REVERT: B 201 THR cc_start: 0.8765 (m) cc_final: 0.8503 (p) REVERT: B 282 GLU cc_start: 0.5980 (OUTLIER) cc_final: 0.5329 (tt0) REVERT: B 310 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7693 (t) REVERT: B 627 MET cc_start: 0.8733 (mmm) cc_final: 0.8446 (mmt) REVERT: B 630 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8668 (mtpp) REVERT: B 727 HIS cc_start: 0.6722 (OUTLIER) cc_final: 0.5245 (p90) REVERT: B 737 ARG cc_start: 0.8408 (mtp85) cc_final: 0.8198 (mtm180) REVERT: B 830 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: B 1454 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8336 (mp) REVERT: B 1472 GLU cc_start: 0.7770 (pp20) cc_final: 0.7464 (pp20) REVERT: B 1496 GLU cc_start: 0.7430 (mp0) cc_final: 0.7007 (mp0) REVERT: B 1640 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7547 (pp20) REVERT: B 1642 ASP cc_start: 0.7667 (t0) cc_final: 0.7272 (t0) outliers start: 45 outliers final: 29 residues processed: 238 average time/residue: 0.6224 time to fit residues: 158.9995 Evaluate side-chains 249 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 976 LYS Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1395 LEU Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1592 ASN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1643 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 83 optimal weight: 0.0020 chunk 96 optimal weight: 3.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN B 327 HIS B 534 ASN B 673 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.097926 restraints weight = 15240.510| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.84 r_work: 0.3079 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11693 Z= 0.155 Angle : 0.581 8.247 16003 Z= 0.300 Chirality : 0.044 0.243 1727 Planarity : 0.005 0.041 1884 Dihedral : 17.223 177.764 2160 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.17 % Favored : 94.75 % Rotamer: Outliers : 3.24 % Allowed : 25.41 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.22), residues: 1257 helix: 1.93 (0.30), residues: 310 sheet: 0.61 (0.36), residues: 197 loop : -1.44 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 212 TYR 0.013 0.001 TYR B 149 PHE 0.023 0.002 PHE B1570 TRP 0.007 0.001 TRP B1530 HIS 0.005 0.001 HIS B 727 Details of bonding type rmsd covalent geometry : bond 0.00374 (11677) covalent geometry : angle 0.57113 (15982) hydrogen bonds : bond 0.04016 ( 338) hydrogen bonds : angle 4.03636 ( 1020) metal coordination : bond 0.00383 ( 16) metal coordination : angle 2.98486 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: B 26 TRP cc_start: 0.8523 (t60) cc_final: 0.8306 (t60) REVERT: B 131 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7892 (mt) REVERT: B 159 ASP cc_start: 0.7744 (t0) cc_final: 0.7371 (p0) REVERT: B 201 THR cc_start: 0.8759 (m) cc_final: 0.8505 (p) REVERT: B 282 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5344 (tt0) REVERT: B 310 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7633 (t) REVERT: B 627 MET cc_start: 0.8717 (mmm) cc_final: 0.8450 (mmt) REVERT: B 630 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8670 (mtpp) REVERT: B 632 LYS cc_start: 0.8529 (tttt) cc_final: 0.8295 (tttt) REVERT: B 737 ARG cc_start: 0.8372 (mtp85) cc_final: 0.8163 (mtm180) REVERT: B 751 THR cc_start: 0.8505 (m) cc_final: 0.8289 (t) REVERT: B 830 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8056 (m-80) REVERT: B 1454 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8257 (mp) REVERT: B 1472 GLU cc_start: 0.7744 (pp20) cc_final: 0.7458 (pp20) REVERT: B 1496 GLU cc_start: 0.7397 (mp0) cc_final: 0.6965 (mp0) REVERT: B 1640 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7523 (pp20) REVERT: B 1642 ASP cc_start: 0.7639 (t0) cc_final: 0.7367 (t0) outliers start: 36 outliers final: 26 residues processed: 231 average time/residue: 0.6192 time to fit residues: 153.7477 Evaluate side-chains 240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 976 LYS Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1592 ASN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1643 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 45 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 213 ASN B 327 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097476 restraints weight = 15382.636| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.85 r_work: 0.3072 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11693 Z= 0.163 Angle : 0.588 8.433 16003 Z= 0.304 Chirality : 0.044 0.247 1727 Planarity : 0.005 0.042 1884 Dihedral : 17.229 178.387 2160 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 3.33 % Allowed : 25.32 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.22), residues: 1257 helix: 1.91 (0.30), residues: 309 sheet: 0.64 (0.35), residues: 197 loop : -1.45 (0.19), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 212 TYR 0.013 0.001 TYR B 149 PHE 0.023 0.002 PHE B1570 TRP 0.007 0.001 TRP B1530 HIS 0.005 0.001 HIS B 727 Details of bonding type rmsd covalent geometry : bond 0.00394 (11677) covalent geometry : angle 0.57847 (15982) hydrogen bonds : bond 0.04157 ( 338) hydrogen bonds : angle 4.06214 ( 1020) metal coordination : bond 0.00389 ( 16) metal coordination : angle 3.04149 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4424.05 seconds wall clock time: 75 minutes 58.75 seconds (4558.75 seconds total)