Starting phenix.real_space_refine on Fri Sep 11 20:29:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xsp_33430/09_2026/7xsp_33430.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xsp_33430/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xsp_33430/09_2026/7xsp_33430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xsp_33430/09_2026/7xsp_33430.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xsp_33430/09_2026/7xsp_33430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xsp_33430/09_2026/7xsp_33430.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xsp_33430/09_2026/7xsp_33430.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xsp_33430/09_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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 2.37, per 1000 atoms: 0.21 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: 0.84 Conformation dependent library (CDL) restraints added in 427.5 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: 1.16 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: 2.62 Time building geometry restraints manager: 1.15 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 1.20e-02 6.94e+03 6.93e+01 bond pdb=" O3' A D -1 " pdb=" P C D 0 " ideal model delta sigma weight residual 1.607 1.537 0.070 1.20e-02 6.94e+03 3.42e+01 bond pdb=" O3' C D 15 " pdb=" P G D 16 " ideal model delta sigma weight residual 1.607 1.543 0.064 1.20e-02 6.94e+03 2.82e+01 bond pdb=" O3' G D 16 " pdb=" P G D 17 " ideal model delta sigma weight residual 1.607 1.561 0.046 1.20e-02 6.94e+03 1.46e+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 ... (remaining 11672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 15762 3.36 - 6.72: 199 6.72 - 10.08: 15 10.08 - 13.44: 3 13.44 - 16.80: 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 113.80 97.00 16.80 2.00e+00 2.50e-01 7.06e+01 angle pdb=" O2' A D -1 " pdb=" C2' A D -1 " pdb=" C1' A D -1 " ideal model delta sigma weight residual 108.20 121.65 -13.45 2.00e+00 2.50e-01 4.52e+01 angle pdb=" O2' G D 16 " pdb=" C2' G D 16 " pdb=" C1' G D 16 " ideal model delta sigma weight residual 108.20 96.17 12.03 2.00e+00 2.50e-01 3.62e+01 angle pdb=" C3' A D -1 " pdb=" C2' A D -1 " pdb=" O2' A D -1 " ideal model delta sigma weight residual 109.80 121.29 -11.49 2.00e+00 2.50e-01 3.30e+01 angle pdb=" C4' A D -1 " pdb=" C3' A D -1 " pdb=" O3' A D -1 " ideal model delta sigma weight residual 112.50 101.33 11.17 2.00e+00 2.50e-01 3.12e+01 ... (remaining 15977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5814 17.99 - 35.97: 734 35.97 - 53.95: 221 53.95 - 71.94: 100 71.94 - 89.92: 17 Dihedral angle restraints: 6886 sinusoidal: 3260 harmonic: 3626 Sorted by residual: dihedral pdb=" C4' G D 11 " pdb=" C3' G D 11 " pdb=" C2' G D 11 " pdb=" C1' G D 11 " ideal model delta sinusoidal sigma weight residual 36.34 -37.98 74.33 1 3.10e+00 1.04e-01 7.29e+02 dihedral pdb=" C4' G D -17 " pdb=" C3' G D -17 " pdb=" C2' G D -17 " pdb=" C1' G D -17 " ideal model delta sinusoidal sigma weight residual 36.34 -37.57 73.91 1 3.10e+00 1.04e-01 7.22e+02 dihedral pdb=" C4' G D -4 " pdb=" C3' G D -4 " pdb=" C2' G D -4 " pdb=" C1' G D -4 " ideal model delta sinusoidal sigma weight residual 36.35 -37.43 73.77 1 3.10e+00 1.04e-01 7.20e+02 ... (remaining 6883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 1651 0.215 - 0.429: 74 0.429 - 0.644: 1 0.644 - 0.859: 0 0.859 - 1.073: 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 -2.79 -1.72 -1.07 2.00e-01 2.50e+01 2.88e+01 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 -2.50 -3.07 0.58 2.00e-01 2.50e+01 8.27e+00 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 2.46 2.03 0.42 2.00e-01 2.50e+01 4.47e+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: 1.210 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.460 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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= 0.400 Angle : 1.114 41.158 16003 Z= 0.516 Chirality : 0.082 1.073 1727 Planarity : 0.008 0.084 1884 Dihedral : 18.611 89.922 4566 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/Z covalent geometry : bond 0.00621 / 0.29 (11677) covalent geometry : angle 0.95231 / 0.50 (15982) hydrogen bonds : bond 0.18797 / 12.90 ( 338) hydrogen bonds : angle 6.75997 / 4.91 ( 1020) metal coordination : bond 0.21295 / 11.92 ( 16) metal coordination : angle 15.97633 / 8.79 ( 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 : 0.406 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: 0.5542 time to fit residues: 172.5901 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 : 0.296 ------------------------------------------------------------------------------- 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: 2.9990 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... B 78 ASN B 112 GLN B 114 GLN B 276 GLN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.120425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102320 restraints weight = 15290.793| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.85 r_work: 0.3153 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11693 Z= 0.198 Angle : 0.972 16.534 16003 Z= 0.424 Chirality : 0.099 1.074 1727 Planarity : 0.006 0.053 1884 Dihedral : 13.737 138.955 2001 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 3.69 % Allowed : 18.56 % Favored : 77.75 % 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: -1.61 (0.20), residues: 1257 helix: 0.14 (0.27), residues: 308 sheet: -0.07 (0.34), residues: 192 loop : -1.96 (0.18), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 274 TYR 0.014 0.001 TYR B 149 PHE 0.018 0.002 PHE B1691 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS B 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (11677) covalent geometry : angle 0.96159 / 0.42 (15982) hydrogen bonds : bond 0.05030 / 3.37 ( 338) hydrogen bonds : angle 4.46853 / 3.25 ( 1020) metal coordination : bond 0.01391 / 0.72 ( 16) metal coordination : angle 4.04416 / 2.14 ( 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 268 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8233 (mttm) REVERT: B 131 ILE cc_start: 0.8215 (pt) cc_final: 0.7954 (mt) REVERT: B 159 ASP cc_start: 0.7771 (t0) cc_final: 0.7412 (t0) REVERT: B 201 THR cc_start: 0.8764 (m) cc_final: 0.8467 (p) REVERT: B 310 VAL cc_start: 0.8011 (OUTLIER) cc_final: 0.7741 (t) REVERT: B 357 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8241 (ttmt) REVERT: B 656 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: B 748 GLU cc_start: 0.7657 (tp30) cc_final: 0.7249 (tp30) REVERT: B 821 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8477 (tttt) REVERT: B 830 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: B 1470 ASP cc_start: 0.6686 (t0) cc_final: 0.6296 (OUTLIER) REVERT: B 1472 GLU cc_start: 0.7682 (pm20) cc_final: 0.7322 (pp20) REVERT: B 1474 GLU cc_start: 0.7850 (pm20) cc_final: 0.7636 (pm20) REVERT: B 1493 LYS cc_start: 0.8543 (mtpt) cc_final: 0.8192 (mtmm) REVERT: B 1496 GLU cc_start: 0.6998 (mp0) cc_final: 0.6592 (mp0) REVERT: B 1498 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6868 (mtm110) REVERT: B 1640 GLU cc_start: 0.8029 (pp20) cc_final: 0.7670 (pp20) REVERT: B 1651 GLU cc_start: 0.7223 (tp30) cc_final: 0.6863 (tp30) REVERT: B 1668 ASP cc_start: 0.7538 (m-30) cc_final: 0.7282 (m-30) outliers start: 41 outliers final: 21 residues processed: 246 average time/residue: 0.5641 time to fit residues: 149.2968 Evaluate side-chains 239 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 310 VAL Chi-restraints excluded: chain B residue 357 LYS 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 0.0010 chunk 121 optimal weight: 0.2980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 GLN B 213 ASN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN B 433 GLN B 915 HIS 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 = 0.3569 r_free = 0.3569 target = 0.123112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104921 restraints weight = 15422.204| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.86 r_work: 0.3195 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11693 Z= 0.129 Angle : 0.769 11.932 16003 Z= 0.340 Chirality : 0.073 0.752 1727 Planarity : 0.005 0.051 1884 Dihedral : 13.548 152.318 1989 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.51 % Rotamer: Outliers : 3.42 % Allowed : 19.64 % Favored : 76.94 % 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: -0.88 (0.21), residues: 1257 helix: 1.26 (0.29), residues: 308 sheet: 0.14 (0.35), residues: 192 loop : -1.67 (0.19), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 212 TYR 0.009 0.001 TYR B 149 PHE 0.016 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/Z covalent geometry : bond 0.00289 / 0.13 (11677) covalent geometry : angle 0.76025 / 0.34 (15982) hydrogen bonds : bond 0.03969 / 2.58 ( 338) hydrogen bonds : angle 4.02339 / 2.93 ( 1020) metal coordination : bond 0.00333 / 0.18 ( 16) metal coordination : angle 3.25056 / 1.77 ( 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 264 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.464 Fit side-chains REVERT: B 6 MET cc_start: 0.7937 (mtp) cc_final: 0.7281 (mmt) REVERT: B 26 TRP cc_start: 0.8492 (t60) cc_final: 0.8257 (t60) REVERT: B 81 LYS cc_start: 0.8486 (mtmm) cc_final: 0.8243 (mttp) REVERT: B 131 ILE cc_start: 0.8227 (pt) cc_final: 0.7994 (mt) REVERT: B 159 ASP cc_start: 0.7832 (t0) cc_final: 0.7521 (t0) REVERT: B 201 THR cc_start: 0.8734 (m) cc_final: 0.8443 (p) REVERT: B 627 MET cc_start: 0.8668 (mmm) cc_final: 0.8416 (mmt) REVERT: B 656 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: B 748 GLU cc_start: 0.7635 (tp30) cc_final: 0.7241 (tp30) REVERT: B 754 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8430 (ttm) REVERT: B 821 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8471 (tttt) REVERT: B 830 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.8106 (m-80) REVERT: B 844 ASP cc_start: 0.7769 (m-30) cc_final: 0.7504 (m-30) REVERT: B 1459 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7874 (pp) REVERT: B 1474 GLU cc_start: 0.7860 (pm20) cc_final: 0.7647 (pm20) REVERT: B 1496 GLU cc_start: 0.7003 (mp0) cc_final: 0.6593 (mp0) REVERT: B 1640 GLU cc_start: 0.8076 (pp20) cc_final: 0.7705 (pp20) REVERT: B 1651 GLU cc_start: 0.7295 (tp30) cc_final: 0.6943 (tp30) outliers start: 38 outliers final: 13 residues processed: 241 average time/residue: 0.5921 time to fit residues: 154.3941 Evaluate side-chains 231 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 THR 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 711 ASN Chi-restraints excluded: chain B residue 754 MET 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 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU 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: 0.0770 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.0980 chunk 63 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 GLN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS B 433 GLN B 459 ASN B 534 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.125450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.107141 restraints weight = 15382.896| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.86 r_work: 0.3232 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11693 Z= 0.108 Angle : 0.711 12.140 16003 Z= 0.318 Chirality : 0.066 0.731 1727 Planarity : 0.005 0.052 1884 Dihedral : 13.073 145.868 1981 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.93 % Favored : 94.99 % Rotamer: Outliers : 3.24 % Allowed : 21.53 % Favored : 75.23 % 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: 1.92 (0.30), residues: 303 sheet: 0.22 (0.34), residues: 200 loop : -1.48 (0.19), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 212 TYR 0.008 0.001 TYR B 578 PHE 0.018 0.001 PHE B1570 TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS B 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (11677) covalent geometry : angle 0.70465 / 0.32 (15982) hydrogen bonds : bond 0.03291 / 2.08 ( 338) hydrogen bonds : angle 3.78747 / 2.76 ( 1020) metal coordination : bond 0.00332 / 0.19 ( 16) metal coordination : angle 2.80285 / 1.58 ( 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 254 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.416 Fit side-chains REVERT: B 6 MET cc_start: 0.7878 (mtp) cc_final: 0.7256 (mmt) REVERT: B 26 TRP cc_start: 0.8480 (t60) cc_final: 0.8208 (t60) REVERT: B 159 ASP cc_start: 0.7817 (t0) cc_final: 0.7543 (t0) REVERT: B 201 THR cc_start: 0.8738 (m) cc_final: 0.8451 (p) REVERT: B 357 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8218 (ttmt) REVERT: B 421 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7711 (mtt-85) REVERT: B 498 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7906 (mt0) REVERT: B 528 ARG cc_start: 0.8442 (ttm170) cc_final: 0.8109 (mtt180) REVERT: B 627 MET cc_start: 0.8665 (mmm) cc_final: 0.8428 (mmt) REVERT: B 656 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7558 (pm20) REVERT: B 748 GLU cc_start: 0.7625 (tp30) cc_final: 0.7369 (tp30) REVERT: B 800 LEU cc_start: 0.7945 (tp) cc_final: 0.7731 (tp) REVERT: B 821 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8438 (tttt) REVERT: B 830 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.8015 (m-80) REVERT: B 1459 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7774 (pp) REVERT: B 1472 GLU cc_start: 0.7392 (pp20) cc_final: 0.7150 (pp20) REVERT: B 1496 GLU cc_start: 0.7053 (mp0) cc_final: 0.6680 (mp0) REVERT: B 1498 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7575 (mtm-85) REVERT: B 1511 VAL cc_start: 0.8719 (m) cc_final: 0.8516 (t) REVERT: B 1580 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7511 (mtpp) REVERT: B 1629 LEU cc_start: 0.8709 (mt) cc_final: 0.8502 (mp) REVERT: B 1640 GLU cc_start: 0.8047 (pp20) cc_final: 0.7686 (pp20) REVERT: B 1651 GLU cc_start: 0.7273 (tp30) cc_final: 0.6945 (tp30) outliers start: 36 outliers final: 12 residues processed: 236 average time/residue: 0.6279 time to fit residues: 159.6288 Evaluate side-chains 224 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 498 GLN 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 1007 LEU Chi-restraints excluded: chain B residue 1028 LEU 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 1498 ARG 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: 2.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 118 optimal weight: 0.0030 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 GLN B 434 GLN B 534 ASN B 778 ASN B1485 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103352 restraints weight = 15235.743| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.84 r_work: 0.3168 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11693 Z= 0.167 Angle : 0.774 12.259 16003 Z= 0.347 Chirality : 0.073 0.705 1727 Planarity : 0.005 0.054 1884 Dihedral : 13.255 144.752 1978 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.57 % Favored : 94.35 % Rotamer: Outliers : 4.14 % Allowed : 21.44 % Favored : 74.41 % 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: -0.44 (0.22), residues: 1257 helix: 1.89 (0.30), residues: 308 sheet: 0.28 (0.35), residues: 192 loop : -1.47 (0.19), residues: 757 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 0.020 0.002 PHE B1570 TRP 0.008 0.001 TRP B 82 HIS 0.005 0.001 HIS B 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (11677) covalent geometry : angle 0.76679 / 0.35 (15982) hydrogen bonds : bond 0.04211 / 2.79 ( 338) hydrogen bonds : angle 3.97351 / 2.90 ( 1020) metal coordination : bond 0.00412 / 0.25 ( 16) metal coordination : angle 3.04006 / 1.74 ( 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 258 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: B 6 MET cc_start: 0.7904 (mtp) cc_final: 0.7472 (mmt) REVERT: B 201 THR cc_start: 0.8765 (m) cc_final: 0.8494 (p) REVERT: B 282 GLU cc_start: 0.5872 (OUTLIER) cc_final: 0.5238 (tt0) REVERT: B 421 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7823 (mtt-85) REVERT: B 498 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7781 (mt0) REVERT: B 627 MET cc_start: 0.8726 (mmm) cc_final: 0.8470 (mmt) REVERT: B 630 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8660 (mtpp) REVERT: B 656 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: B 748 GLU cc_start: 0.7710 (tp30) cc_final: 0.7474 (tp30) REVERT: B 821 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8460 (tttt) REVERT: B 830 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: B 947 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7533 (mm-30) REVERT: B 1454 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8189 (mp) REVERT: B 1472 GLU cc_start: 0.7609 (pp20) cc_final: 0.7394 (pp20) REVERT: B 1496 GLU cc_start: 0.7206 (mp0) cc_final: 0.6764 (mp0) REVERT: B 1580 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7569 (mtpp) REVERT: B 1640 GLU cc_start: 0.7996 (pp20) cc_final: 0.7666 (pp20) outliers start: 46 outliers final: 22 residues processed: 237 average time/residue: 0.5855 time to fit residues: 149.8585 Evaluate side-chains 230 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 55 LYS 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 432 VAL Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 518 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 656 GLU 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 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 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU 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: 3.9990 chunk 95 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 GLN B 213 ASN B 433 GLN B 534 ASN B 778 ASN B 986 ASN B1485 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104108 restraints weight = 15225.369| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.82 r_work: 0.3180 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3244 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= 0.150 Angle : 0.755 12.047 16003 Z= 0.340 Chirality : 0.071 0.720 1727 Planarity : 0.005 0.055 1884 Dihedral : 13.305 143.926 1978 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.49 % Favored : 94.43 % Rotamer: Outliers : 3.69 % Allowed : 22.25 % Favored : 74.05 % 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: 2.06 (0.30), residues: 308 sheet: 0.33 (0.35), residues: 197 loop : -1.43 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 274 TYR 0.011 0.001 TYR B 149 PHE 0.020 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/Z covalent geometry : bond 0.00352 / 0.15 (11677) covalent geometry : angle 0.74754 / 0.34 (15982) hydrogen bonds : bond 0.03880 / 2.55 ( 338) hydrogen bonds : angle 3.93346 / 2.88 ( 1020) metal coordination : bond 0.00361 / 0.21 ( 16) metal coordination : angle 2.94128 / 1.71 ( 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 248 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.409 Fit side-chains REVERT: B 6 MET cc_start: 0.7836 (mtp) cc_final: 0.7395 (mmt) REVERT: B 159 ASP cc_start: 0.7813 (t0) cc_final: 0.7567 (t0) REVERT: B 201 THR cc_start: 0.8768 (m) cc_final: 0.8492 (p) REVERT: B 282 GLU cc_start: 0.5943 (OUTLIER) cc_final: 0.5317 (tt0) REVERT: B 421 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7867 (mtp85) REVERT: B 498 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: B 567 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8293 (ptpp) REVERT: B 627 MET cc_start: 0.8721 (mmm) cc_final: 0.8057 (mmm) REVERT: B 630 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8636 (mtpp) REVERT: B 748 GLU cc_start: 0.7695 (tp30) cc_final: 0.7449 (tp30) REVERT: B 821 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8447 (tttt) REVERT: B 830 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: B 947 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7505 (mm-30) REVERT: B 1454 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8200 (mp) REVERT: B 1460 GLU cc_start: 0.7327 (pm20) cc_final: 0.7110 (pm20) REVERT: B 1472 GLU cc_start: 0.7650 (pp20) cc_final: 0.7381 (pp20) REVERT: B 1496 GLU cc_start: 0.7245 (mp0) cc_final: 0.6799 (mp0) REVERT: B 1640 GLU cc_start: 0.7990 (pp20) cc_final: 0.7648 (pp20) outliers start: 41 outliers final: 25 residues processed: 225 average time/residue: 0.6090 time to fit residues: 147.9099 Evaluate side-chains 234 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 55 LYS 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 411 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 644 ASP 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 766 LYS 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 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 1495 LEU 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: 0.9980 chunk 118 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN B 534 ASN B 673 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.118856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100454 restraints weight = 15320.554| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.85 r_work: 0.3122 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11693 Z= 0.223 Angle : 0.835 12.823 16003 Z= 0.376 Chirality : 0.079 0.793 1727 Planarity : 0.006 0.046 1884 Dihedral : 13.576 147.737 1978 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 4.23 % Allowed : 22.61 % Favored : 73.15 % 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: 1.91 (0.30), residues: 307 sheet: 0.49 (0.34), residues: 202 loop : -1.54 (0.19), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 212 TYR 0.016 0.002 TYR B 149 PHE 0.022 0.002 PHE B1570 TRP 0.008 0.001 TRP B1530 HIS 0.008 0.001 HIS B 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.22 (11677) covalent geometry : angle 0.82720 / 0.38 (15982) hydrogen bonds : bond 0.04787 / 3.20 ( 338) hydrogen bonds : angle 4.14954 / 3.03 ( 1020) metal coordination : bond 0.00438 / 0.22 ( 16) metal coordination : angle 3.30592 / 1.92 ( 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 263 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: B 159 ASP cc_start: 0.7785 (t0) cc_final: 0.7527 (t0) REVERT: B 201 THR cc_start: 0.8769 (m) cc_final: 0.8495 (p) REVERT: B 282 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5388 (tt0) REVERT: B 421 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7930 (mtp85) REVERT: B 498 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7871 (mt0) REVERT: B 596 SER cc_start: 0.8472 (t) cc_final: 0.8271 (p) REVERT: B 627 MET cc_start: 0.8749 (mmm) cc_final: 0.8484 (mmt) REVERT: B 630 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8647 (mtpp) REVERT: B 748 GLU cc_start: 0.7656 (tp30) cc_final: 0.7425 (tp30) REVERT: B 766 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8198 (mttt) REVERT: B 821 LYS cc_start: 0.8728 (ttmm) cc_final: 0.8509 (tttp) REVERT: B 830 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8166 (m-80) REVERT: B 1454 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8295 (mp) REVERT: B 1472 GLU cc_start: 0.7652 (pp20) cc_final: 0.7382 (pp20) REVERT: B 1496 GLU cc_start: 0.7313 (mp0) cc_final: 0.6885 (mp0) REVERT: B 1640 GLU cc_start: 0.8042 (pp20) cc_final: 0.7685 (pp20) REVERT: B 1660 ASP cc_start: 0.7524 (p0) cc_final: 0.7227 (p0) outliers start: 47 outliers final: 28 residues processed: 237 average time/residue: 0.5906 time to fit residues: 150.9889 Evaluate side-chains 247 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU 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 401 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 556 THR 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 711 ASN Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 766 LYS 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 976 LYS Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1453 SER Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1495 LEU 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: 2.9990 chunk 125 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN B 534 ASN B 778 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100643 restraints weight = 15255.624| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.83 r_work: 0.3124 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11693 Z= 0.221 Angle : 0.834 12.962 16003 Z= 0.376 Chirality : 0.079 0.788 1727 Planarity : 0.006 0.047 1884 Dihedral : 13.565 147.299 1976 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.19 % Rotamer: Outliers : 3.87 % Allowed : 23.78 % 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: -0.47 (0.22), residues: 1257 helix: 1.82 (0.30), residues: 307 sheet: 0.57 (0.35), residues: 197 loop : -1.57 (0.19), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 212 TYR 0.016 0.002 TYR B 149 PHE 0.024 0.002 PHE B1691 TRP 0.008 0.001 TRP B1530 HIS 0.005 0.001 HIS B 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.22 (11677) covalent geometry : angle 0.82695 / 0.38 (15982) hydrogen bonds : bond 0.04691 / 3.14 ( 338) hydrogen bonds : angle 4.14304 / 3.03 ( 1020) metal coordination : bond 0.00448 / 0.22 ( 16) metal coordination : angle 3.18604 / 1.89 ( 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 260 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: B 159 ASP cc_start: 0.7756 (t0) cc_final: 0.7266 (p0) REVERT: B 201 THR cc_start: 0.8773 (m) cc_final: 0.8498 (p) REVERT: B 282 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5430 (tt0) REVERT: B 355 TRP cc_start: 0.8312 (t-100) cc_final: 0.7861 (t-100) REVERT: B 421 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7928 (mtp85) REVERT: B 498 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: B 627 MET cc_start: 0.8749 (mmm) cc_final: 0.8470 (mmt) REVERT: B 630 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8600 (mtpp) REVERT: B 748 GLU cc_start: 0.7643 (tp30) cc_final: 0.7412 (tp30) REVERT: B 766 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8195 (mttt) REVERT: B 830 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: B 1454 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8304 (mp) REVERT: B 1472 GLU cc_start: 0.7660 (pp20) cc_final: 0.7395 (pp20) REVERT: B 1496 GLU cc_start: 0.7389 (mp0) cc_final: 0.6972 (mp0) REVERT: B 1640 GLU cc_start: 0.8048 (pp20) cc_final: 0.7681 (pp20) REVERT: B 1660 ASP cc_start: 0.7555 (p0) cc_final: 0.7246 (p0) REVERT: B 1672 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7781 (tm) outliers start: 43 outliers final: 26 residues processed: 237 average time/residue: 0.5817 time to fit residues: 148.8055 Evaluate side-chains 244 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU 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 401 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 556 THR 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 766 LYS 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 976 LYS Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1446 ARG Chi-restraints excluded: chain B residue 1453 SER Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1672 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 39 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 0.0270 chunk 96 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN B 534 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.118627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.100392 restraints weight = 15134.139| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.83 r_work: 0.3117 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11693 Z= 0.225 Angle : 0.842 13.168 16003 Z= 0.380 Chirality : 0.080 0.800 1727 Planarity : 0.006 0.047 1884 Dihedral : 13.574 147.209 1975 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.11 % Rotamer: Outliers : 3.78 % Allowed : 24.14 % Favored : 72.07 % 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: -0.48 (0.22), residues: 1257 helix: 1.79 (0.30), residues: 307 sheet: 0.54 (0.35), residues: 202 loop : -1.58 (0.19), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 212 TYR 0.016 0.002 TYR B 149 PHE 0.029 0.002 PHE B1691 TRP 0.008 0.001 TRP B1530 HIS 0.006 0.001 HIS B 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.23 (11677) covalent geometry : angle 0.83472 / 0.38 (15982) hydrogen bonds : bond 0.04760 / 3.17 ( 338) hydrogen bonds : angle 4.18165 / 3.07 ( 1020) metal coordination : bond 0.00452 / 0.22 ( 16) metal coordination : angle 3.20574 / 1.89 ( 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 261 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 0.431 Fit side-chains REVERT: B 159 ASP cc_start: 0.7753 (t0) cc_final: 0.7335 (p0) REVERT: B 201 THR cc_start: 0.8773 (m) cc_final: 0.8493 (p) REVERT: B 282 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5429 (tt0) REVERT: B 355 TRP cc_start: 0.8308 (t-100) cc_final: 0.7853 (t-100) REVERT: B 421 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7937 (mtp85) REVERT: B 498 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: B 596 SER cc_start: 0.8457 (t) cc_final: 0.8247 (p) REVERT: B 630 LYS cc_start: 0.8838 (mtpp) cc_final: 0.8620 (mtpp) REVERT: B 632 LYS cc_start: 0.8531 (tttt) cc_final: 0.8290 (tttt) REVERT: B 766 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8203 (mttt) REVERT: B 830 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: B 976 LYS cc_start: 0.5751 (OUTLIER) cc_final: 0.5173 (mmtm) REVERT: B 1454 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8319 (mp) REVERT: B 1472 GLU cc_start: 0.7746 (pp20) cc_final: 0.7448 (pp20) REVERT: B 1491 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8012 (ttt180) REVERT: B 1496 GLU cc_start: 0.7384 (mp0) cc_final: 0.6979 (mp0) REVERT: B 1640 GLU cc_start: 0.8066 (pp20) cc_final: 0.7668 (pp20) REVERT: B 1660 ASP cc_start: 0.7536 (p0) cc_final: 0.7207 (p0) outliers start: 42 outliers final: 25 residues processed: 241 average time/residue: 0.5955 time to fit residues: 154.9574 Evaluate side-chains 250 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU 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 401 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 612 TRP 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 766 LYS 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 976 LYS 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 1491 ARG Chi-restraints excluded: chain B residue 1512 MET Chi-restraints excluded: chain B residue 1592 ASN 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: 2.9990 chunk 75 optimal weight: 0.0970 chunk 106 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN B 433 GLN B 534 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101948 restraints weight = 15184.848| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.84 r_work: 0.3145 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3473 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= 0.167 Angle : 0.787 12.578 16003 Z= 0.355 Chirality : 0.074 0.798 1727 Planarity : 0.005 0.043 1884 Dihedral : 13.426 144.954 1975 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.89 % Favored : 94.03 % Rotamer: Outliers : 2.88 % Allowed : 25.23 % Favored : 71.89 % 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: -0.38 (0.22), residues: 1257 helix: 1.97 (0.30), residues: 307 sheet: 0.53 (0.35), residues: 202 loop : -1.54 (0.19), residues: 748 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 0.024 0.002 PHE B1691 TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS B 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (11677) covalent geometry : angle 0.78011 / 0.36 (15982) hydrogen bonds : bond 0.04164 / 2.75 ( 338) hydrogen bonds : angle 4.06015 / 2.99 ( 1020) metal coordination : bond 0.00362 / 0.18 ( 16) metal coordination : angle 2.94996 / 1.75 ( 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 242 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: B 159 ASP cc_start: 0.7741 (t0) cc_final: 0.7387 (p0) REVERT: B 201 THR cc_start: 0.8759 (m) cc_final: 0.8487 (p) REVERT: B 282 GLU cc_start: 0.6040 (OUTLIER) cc_final: 0.5433 (tt0) REVERT: B 327 HIS cc_start: 0.7625 (t-90) cc_final: 0.7382 (t70) REVERT: B 421 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7937 (mtp85) REVERT: B 498 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7821 (mt0) REVERT: B 627 MET cc_start: 0.8732 (mmm) cc_final: 0.8465 (mmt) REVERT: B 630 LYS cc_start: 0.8881 (mtpp) cc_final: 0.8658 (mtpp) REVERT: B 632 LYS cc_start: 0.8548 (tttt) cc_final: 0.8310 (tttt) REVERT: B 830 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: B 1454 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8273 (mp) REVERT: B 1460 GLU cc_start: 0.7446 (pm20) cc_final: 0.7223 (pm20) REVERT: B 1472 GLU cc_start: 0.7778 (pp20) cc_final: 0.7506 (pp20) REVERT: B 1496 GLU cc_start: 0.7363 (mp0) cc_final: 0.6969 (mp0) REVERT: B 1640 GLU cc_start: 0.8018 (pp20) cc_final: 0.7561 (pp20) REVERT: B 1642 ASP cc_start: 0.7625 (t0) cc_final: 0.7374 (t0) REVERT: B 1644 ARG cc_start: 0.8519 (ptp90) cc_final: 0.8304 (ptp90) REVERT: B 1660 ASP cc_start: 0.7515 (p0) cc_final: 0.7194 (p0) outliers start: 32 outliers final: 24 residues processed: 226 average time/residue: 0.6156 time to fit residues: 150.0869 Evaluate side-chains 238 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU 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 498 GLN Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 556 THR 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 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 976 LYS Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1453 SER Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1459 LEU 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: 3.9990 chunk 84 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN B 433 GLN B 534 ASN B 673 GLN B 786 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103488 restraints weight = 15299.778| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.85 r_work: 0.3170 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11693 Z= 0.139 Angle : 0.744 11.943 16003 Z= 0.337 Chirality : 0.069 0.770 1727 Planarity : 0.005 0.042 1884 Dihedral : 13.270 143.243 1975 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.19 % Rotamer: Outliers : 3.06 % Allowed : 25.05 % Favored : 71.89 % 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: -0.28 (0.22), residues: 1257 helix: 2.07 (0.30), residues: 310 sheet: 0.48 (0.36), residues: 201 loop : -1.47 (0.19), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 212 TYR 0.011 0.001 TYR B 149 PHE 0.023 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/Z covalent geometry : bond 0.00321 / 0.14 (11677) covalent geometry : angle 0.73721 / 0.34 (15982) hydrogen bonds : bond 0.03774 / 2.47 ( 338) hydrogen bonds : angle 3.94486 / 2.92 ( 1020) metal coordination : bond 0.00322 / 0.15 ( 16) metal coordination : angle 2.82188 / 1.66 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4334.79 seconds wall clock time: 74 minutes 34.53 seconds (4474.53 seconds total)