Starting phenix.real_space_refine on Fri Jul 3 00:57:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d1v_27138/07_2026/8d1v_27138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1v_27138/07_2026/8d1v_27138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d1v_27138/07_2026/8d1v_27138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1v_27138/07_2026/8d1v_27138.map" model { file = "/net/cci-nas-00/data/ceres_data/8d1v_27138/07_2026/8d1v_27138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1v_27138/07_2026/8d1v_27138.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d1v_27138/07_2026/8d1v_27138.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d1v_27138/07_2026/8d1v_27138.cif" } resolution = 2.82 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= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 51 5.49 5 S 47 5.16 5 C 6729 2.51 5 N 1965 2.21 5 O 2177 1.98 5 H 9 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10982 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1229, 9875 Classifications: {'peptide': 1229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 4, 'PTRANS': 69, 'TRANS': 1155} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 716 Classifications: {'RNA': 34} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 4, 'rna3p_pyr': 11} Link IDs: {'rna2p': 19, 'rna3p': 14} Chain: "N" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 387 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 11} Chain: "A" 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 7389 SG CYS A 965 52.610 79.489 34.405 1.00 16.18 S ATOM 7646 SG CYS A1312 54.788 76.398 34.787 1.00 42.26 S ATOM 7776 SG CYS A1342 56.145 79.835 35.770 1.00 16.46 S ATOM 7794 SG CYS A1345 53.703 78.265 37.918 1.00 42.76 S ATOM 5323 SG CYS A 706 67.274 57.736 63.303 1.00 64.50 S ATOM 5338 SG CYS A 708 66.711 61.546 63.496 1.00 47.76 S ATOM 5360 SG CYS A 711 63.819 58.979 64.304 1.00 40.08 S ATOM 3404 SG CYS A 463 56.018 42.763 85.262 1.00 49.22 S ATOM 3466 SG CYS A 472 56.667 39.772 87.611 1.00 43.87 S ATOM 3480 SG CYS A 474 56.786 43.428 88.933 1.00 31.88 S ATOM 3502 SG CYS A 477 53.532 41.954 87.701 1.00 37.68 S ATOM 704 SG CYS A 86 41.398 20.116 105.052 1.00 54.15 S ATOM 950 SG CYS A 115 39.201 17.399 106.531 1.00 59.03 S ATOM 1012 SG CYS A 123 37.966 21.095 106.260 1.00 59.56 S ATOM 1036 SG CYS A 126 38.414 19.054 103.155 1.00 54.26 S Time building chain proxies: 2.48, per 1000 atoms: 0.23 Number of scatterers: 10982 At special positions: 0 Unit cell: (84.66, 126.99, 124.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 47 16.00 P 51 15.00 O 2177 8.00 N 1965 7.00 C 6729 6.00 H 9 1.00 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: 0.83 Conformation dependent library (CDL) restraints added in 475.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A1312 " pdb="ZN ZN A1701 " - pdb=" SG CYS A1345 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 965 " pdb="ZN ZN A1701 " - pdb=" SG CYS A1342 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 706 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 711 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 708 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 477 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 463 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 474 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 472 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 86 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 126 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 123 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 115 " Number of angles added : 21 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 17 sheets defined 30.8% alpha, 25.1% beta 10 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 57 through 76 Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.990A pdb=" N ILE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 167' Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 260 through 276 removed outlier: 3.678A pdb=" N ALA A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 344 through 366 Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 542 through 554 removed outlier: 3.585A pdb=" N THR A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 594 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.431A pdb=" N GLU A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU A 605 " --> pdb=" O LYS A 601 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 removed outlier: 3.578A pdb=" N ALA A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 691 removed outlier: 3.839A pdb=" N ILE A 690 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS A 691 " --> pdb=" O VAL A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 715 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 920 through 924 removed outlier: 3.559A pdb=" N ARG A 924 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.712A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1331 through 1336 Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 3.604A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1426 Processing helix chain 'A' and resid 1464 through 1476 Processing helix chain 'A' and resid 1488 through 1492 Processing helix chain 'A' and resid 1518 through 1535 Processing helix chain 'A' and resid 1538 through 1549 Processing helix chain 'A' and resid 1565 through 1569 Processing helix chain 'A' and resid 1575 through 1582 removed outlier: 3.872A pdb=" N ASP A1581 " --> pdb=" O GLU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1594 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.807A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 169 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 107 removed outlier: 6.138A pdb=" N THR A 106 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.992A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.992A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA8, first strand: chain 'A' and resid 497 through 504 removed outlier: 5.593A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 659 through 664 removed outlier: 3.557A pdb=" N GLU A 667 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 659 through 664 removed outlier: 3.557A pdb=" N GLU A 667 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 744 removed outlier: 6.310A pdb=" N LYS A 755 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 836 through 837 removed outlier: 6.943A pdb=" N ALA A 836 " --> pdb=" O TRP A1512 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ASN A1514 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 944 through 945 removed outlier: 5.411A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB6, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AB7, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.284A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 932 through 933 removed outlier: 6.952A pdb=" N LYS A 932 " --> pdb=" O THR A1444 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N GLU A1446 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG A1443 " --> pdb=" O LEU A1388 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 9 1.05 - 1.24: 1339 1.24 - 1.43: 3607 1.43 - 1.62: 6313 1.62 - 1.81: 68 Bond restraints: 11336 Sorted by residual: bond pdb=" CB PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 1.492 1.095 0.397 5.00e-02 4.00e+02 6.31e+01 bond pdb=" N PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 1.473 1.384 0.089 1.40e-02 5.10e+03 4.05e+01 bond pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sigma weight residual 1.533 1.606 -0.073 1.47e-02 4.63e+03 2.46e+01 bond pdb=" CB ASP A1536 " pdb=" CG ASP A1536 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.69e+00 bond pdb=" N LYS A 827 " pdb=" CA LYS A 827 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.62e+00 ... (remaining 11331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.87: 15509 4.87 - 9.75: 10 9.75 - 14.62: 2 14.62 - 19.50: 2 19.50 - 24.37: 3 Bond angle restraints: 15526 Sorted by residual: angle pdb=" CA PRO A 114 " pdb=" N PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 112.00 87.63 24.37 1.40e+00 5.10e-01 3.03e+02 angle pdb=" N PRO A 114 " pdb=" CD PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 103.20 86.02 17.18 1.50e+00 4.44e-01 1.31e+02 angle pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 104.50 84.08 20.42 1.90e+00 2.77e-01 1.16e+02 angle pdb=" C GLU A 877 " pdb=" N GLU A 878 " pdb=" CA GLU A 878 " ideal model delta sigma weight residual 121.70 136.07 -14.37 1.80e+00 3.09e-01 6.37e+01 angle pdb=" CB PRO A 114 " pdb=" CG PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 106.10 88.47 17.63 3.20e+00 9.77e-02 3.04e+01 ... (remaining 15521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6614 35.97 - 71.94: 132 71.94 - 107.90: 17 107.90 - 143.87: 0 143.87 - 179.84: 4 Dihedral angle restraints: 6767 sinusoidal: 3238 harmonic: 3529 Sorted by residual: dihedral pdb=" O4' C J 8 " pdb=" C1' C J 8 " pdb=" N1 C J 8 " pdb=" C2 C J 8 " ideal model delta sinusoidal sigma weight residual -160.00 14.71 -174.71 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C J 10 " pdb=" C1' C J 10 " pdb=" N1 C J 10 " pdb=" C2 C J 10 " ideal model delta sinusoidal sigma weight residual 232.00 70.80 161.20 1 1.70e+01 3.46e-03 6.47e+01 dihedral pdb=" CA GLY A 824 " pdb=" C GLY A 824 " pdb=" N ASP A 825 " pdb=" CA ASP A 825 " ideal model delta harmonic sigma weight residual 180.00 147.16 32.84 0 5.00e+00 4.00e-02 4.31e+01 ... (remaining 6764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1300 0.047 - 0.093: 286 0.093 - 0.140: 83 0.140 - 0.187: 3 0.187 - 0.234: 1 Chirality restraints: 1673 Sorted by residual: chirality pdb=" C3' A N 6 " pdb=" C4' A N 6 " pdb=" O3' A N 6 " pdb=" C2' A N 6 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1' G N 7 " pdb=" O4' G N 7 " pdb=" C2' G N 7 " pdb=" N9 G N 7 " both_signs ideal model delta sigma weight residual False 2.46 2.28 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" C3' C N 8 " pdb=" C4' C N 8 " pdb=" O3' C N 8 " pdb=" C2' C N 8 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.17 2.00e-01 2.50e+01 7.23e-01 ... (remaining 1670 not shown) Planarity restraints: 1829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 113 " -0.062 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 114 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U J 24 " -0.032 2.00e-02 2.50e+03 1.72e-02 6.66e+00 pdb=" N1 U J 24 " 0.036 2.00e-02 2.50e+03 pdb=" C2 U J 24 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U J 24 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U J 24 " 0.009 2.00e-02 2.50e+03 pdb=" C4 U J 24 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U J 24 " -0.013 2.00e-02 2.50e+03 pdb=" C5 U J 24 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U J 24 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 825 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C ASP A 825 " -0.032 2.00e-02 2.50e+03 pdb=" O ASP A 825 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP A 826 " 0.011 2.00e-02 2.50e+03 ... (remaining 1826 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.57: 143 2.57 - 3.08: 7593 3.08 - 3.58: 13373 3.58 - 4.09: 21124 4.09 - 4.60: 30889 Nonbonded interactions: 73122 Sorted by model distance: nonbonded pdb=" O SER A 399 " pdb=" OG SER A 583 " model vdw 2.059 2.800 nonbonded pdb=" OD2 ASP A 193 " pdb=" OG1 THR A 195 " model vdw 2.063 2.800 nonbonded pdb=" OH TYR A 863 " pdb=" OP2 A J 30 " model vdw 2.178 2.800 nonbonded pdb=" NE ARG A 951 " pdb=" OP1 U J 24 " model vdw 2.195 2.950 nonbonded pdb=" O GLY A1486 " pdb=" NZ LYS A1489 " model vdw 2.199 2.950 ... (remaining 73117 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: 1.770 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: 0.070 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.620 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:5.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.006 0.397 11343 Z= 0.233 Angle : 0.752 24.374 15528 Z= 0.403 Chirality : 0.043 0.234 1673 Planarity : 0.005 0.082 1829 Dihedral : 15.502 179.839 4489 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 25.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.54 (0.24), residues: 1217 helix: -0.15 (0.28), residues: 318 sheet: -0.09 (0.35), residues: 206 loop : -0.47 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 53 TYR 0.015 0.002 TYR A 577 PHE 0.020 0.002 PHE A 757 TRP 0.015 0.001 TRP A 597 HIS 0.010 0.001 HIS A 931 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.23 (11327) covalent geometry : angle 0.74278 / 0.40 (15507) hydrogen bonds : bond 0.23799 / 15.68 ( 364) hydrogen bonds : angle 8.82194 / 6.03 ( 1097) metal coordination : bond 0.00820 / 0.48 ( 16) metal coordination : angle 3.36015 / 1.82 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 155 LEU cc_start: 0.7569 (mt) cc_final: 0.7329 (mp) REVERT: A 188 LYS cc_start: 0.7473 (ptpt) cc_final: 0.7017 (mtmt) REVERT: A 209 LYS cc_start: 0.5970 (pttm) cc_final: 0.5489 (pttp) REVERT: A 294 ARG cc_start: 0.7611 (ptt-90) cc_final: 0.7201 (ptt90) REVERT: A 473 MET cc_start: 0.7444 (mmm) cc_final: 0.7197 (mmt) REVERT: A 507 PHE cc_start: 0.7649 (m-80) cc_final: 0.7398 (m-10) REVERT: A 589 ASN cc_start: 0.7330 (m-40) cc_final: 0.6445 (m-40) REVERT: A 616 GLU cc_start: 0.6167 (tp30) cc_final: 0.5666 (tt0) REVERT: A 786 GLU cc_start: 0.6700 (pm20) cc_final: 0.6488 (pm20) REVERT: A 970 ASP cc_start: 0.6937 (p0) cc_final: 0.6725 (p0) REVERT: A 1566 LYS cc_start: 0.7675 (tttt) cc_final: 0.7301 (tttm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.7888 time to fit residues: 136.7974 Evaluate side-chains 97 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.179127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.154383 restraints weight = 11250.581| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.27 r_work: 0.3624 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 11343 Z= 0.343 Angle : 0.818 15.010 15528 Z= 0.422 Chirality : 0.050 0.179 1673 Planarity : 0.007 0.050 1829 Dihedral : 14.838 177.254 1963 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 29.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.84 % Allowed : 10.49 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.57 (0.24), residues: 1217 helix: 0.28 (0.30), residues: 313 sheet: 0.09 (0.35), residues: 211 loop : -0.81 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1565 TYR 0.023 0.003 TYR A 534 PHE 0.022 0.003 PHE A 757 TRP 0.015 0.003 TRP A1512 HIS 0.011 0.002 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.34 (11327) covalent geometry : angle 0.80209 / 0.42 (15507) hydrogen bonds : bond 0.06717 / 4.41 ( 364) hydrogen bonds : angle 6.23972 / 4.34 ( 1097) metal coordination : bond 0.01126 / 0.68 ( 16) metal coordination : angle 4.40712 / 2.07 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 155 LEU cc_start: 0.7622 (mt) cc_final: 0.7321 (mp) REVERT: A 188 LYS cc_start: 0.7532 (ptpt) cc_final: 0.7258 (mtmt) REVERT: A 209 LYS cc_start: 0.5891 (pttm) cc_final: 0.5426 (pttp) REVERT: A 294 ARG cc_start: 0.7649 (ptt-90) cc_final: 0.7318 (ttp-170) REVERT: A 409 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7470 (mm-30) REVERT: A 473 MET cc_start: 0.7480 (mmm) cc_final: 0.7253 (mmt) REVERT: A 576 LYS cc_start: 0.7849 (mttp) cc_final: 0.7533 (mtpt) REVERT: A 614 LEU cc_start: 0.7618 (tp) cc_final: 0.7326 (tt) REVERT: A 896 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7197 (ttp80) REVERT: A 1310 ARG cc_start: 0.6658 (tpp80) cc_final: 0.6455 (mmm-85) REVERT: A 1369 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: A 1375 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.6083 (ttpt) REVERT: A 1395 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6892 (mmp80) REVERT: A 1478 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: A 1487 MET cc_start: 0.8541 (ptt) cc_final: 0.8104 (ptt) REVERT: A 1592 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7797 (mmtt) outliers start: 30 outliers final: 7 residues processed: 126 average time/residue: 0.7191 time to fit residues: 96.9367 Evaluate side-chains 106 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1478 GLU Chi-restraints excluded: chain A residue 1592 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 107 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A1405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.184421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156455 restraints weight = 11327.927| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.46 r_work: 0.3693 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11343 Z= 0.111 Angle : 0.516 9.021 15528 Z= 0.271 Chirality : 0.039 0.163 1673 Planarity : 0.004 0.049 1829 Dihedral : 14.550 174.022 1963 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 29.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.80 % Allowed : 12.95 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.02 (0.24), residues: 1217 helix: 1.21 (0.30), residues: 319 sheet: 0.17 (0.34), residues: 214 loop : -0.65 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1346 TYR 0.010 0.001 TYR A 930 PHE 0.011 0.001 PHE A 15 TRP 0.006 0.001 TRP A1466 HIS 0.003 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (11327) covalent geometry : angle 0.50785 / 0.27 (15507) hydrogen bonds : bond 0.04411 / 2.93 ( 364) hydrogen bonds : angle 5.13374 / 3.58 ( 1097) metal coordination : bond 0.00503 / 0.31 ( 16) metal coordination : angle 2.49533 / 1.14 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 155 LEU cc_start: 0.7571 (mt) cc_final: 0.7360 (mp) REVERT: A 209 LYS cc_start: 0.5766 (pttm) cc_final: 0.5289 (pttp) REVERT: A 401 LEU cc_start: 0.6589 (tp) cc_final: 0.6359 (tp) REVERT: A 473 MET cc_start: 0.7475 (mmm) cc_final: 0.7180 (mmt) REVERT: A 576 LYS cc_start: 0.7718 (mttp) cc_final: 0.7417 (mtpt) REVERT: A 600 GLU cc_start: 0.6138 (tp30) cc_final: 0.5899 (tp30) REVERT: A 614 LEU cc_start: 0.7548 (tp) cc_final: 0.7220 (tt) REVERT: A 627 GLU cc_start: 0.8094 (tt0) cc_final: 0.7763 (tt0) REVERT: A 664 GLU cc_start: 0.6114 (tp30) cc_final: 0.5813 (tp30) REVERT: A 735 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5022 (pp20) REVERT: A 970 ASP cc_start: 0.7158 (p0) cc_final: 0.6769 (p0) REVERT: A 1363 SER cc_start: 0.8414 (m) cc_final: 0.8195 (m) REVERT: A 1369 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: A 1395 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6733 (mmp80) REVERT: A 1487 MET cc_start: 0.8430 (ptt) cc_final: 0.7979 (ptt) outliers start: 19 outliers final: 4 residues processed: 119 average time/residue: 0.7659 time to fit residues: 97.0664 Evaluate side-chains 103 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 718 TYR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1395 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 4 optimal weight: 0.0040 chunk 13 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 0.2980 overall best weight: 2.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.182395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.156662 restraints weight = 11366.674| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.22 r_work: 0.3665 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11343 Z= 0.201 Angle : 0.618 10.471 15528 Z= 0.320 Chirality : 0.043 0.159 1673 Planarity : 0.005 0.049 1829 Dihedral : 14.608 175.674 1963 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 30.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.65 % Allowed : 15.12 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.19 (0.24), residues: 1217 helix: 1.05 (0.30), residues: 319 sheet: 0.13 (0.35), residues: 214 loop : -0.76 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1565 TYR 0.018 0.002 TYR A 534 PHE 0.016 0.002 PHE A 757 TRP 0.008 0.002 TRP A1466 HIS 0.007 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (11327) covalent geometry : angle 0.60763 / 0.32 (15507) hydrogen bonds : bond 0.05020 / 3.33 ( 364) hydrogen bonds : angle 5.33569 / 3.72 ( 1097) metal coordination : bond 0.00569 / 0.32 ( 16) metal coordination : angle 3.08249 / 1.45 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.294 Fit side-chains REVERT: A 46 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.7065 (tptm) REVERT: A 155 LEU cc_start: 0.7591 (mt) cc_final: 0.7337 (mp) REVERT: A 209 LYS cc_start: 0.5771 (pttm) cc_final: 0.5315 (pttp) REVERT: A 294 ARG cc_start: 0.7597 (ptt-90) cc_final: 0.7242 (ttp-170) REVERT: A 395 VAL cc_start: 0.6449 (OUTLIER) cc_final: 0.6064 (m) REVERT: A 473 MET cc_start: 0.7563 (mmm) cc_final: 0.7178 (mmt) REVERT: A 576 LYS cc_start: 0.7717 (mttp) cc_final: 0.7469 (mtpt) REVERT: A 585 GLU cc_start: 0.6442 (tm-30) cc_final: 0.6224 (tm-30) REVERT: A 664 GLU cc_start: 0.6120 (tp30) cc_final: 0.5679 (pt0) REVERT: A 667 GLU cc_start: 0.5356 (OUTLIER) cc_final: 0.5098 (pt0) REVERT: A 735 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5234 (pp20) REVERT: A 896 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7158 (ttp80) REVERT: A 1369 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: A 1375 LYS cc_start: 0.6501 (OUTLIER) cc_final: 0.5984 (ttpt) REVERT: A 1395 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7022 (mmp80) REVERT: A 1478 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: A 1487 MET cc_start: 0.8501 (ptt) cc_final: 0.8133 (ptt) outliers start: 28 outliers final: 9 residues processed: 123 average time/residue: 0.6781 time to fit residues: 89.1785 Evaluate side-chains 115 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1478 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 9.9990 chunk 53 optimal weight: 0.0030 chunk 2 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 overall best weight: 3.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 ASN A1555 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.181723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.156697 restraints weight = 11341.389| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.16 r_work: 0.3667 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11343 Z= 0.226 Angle : 0.653 11.339 15528 Z= 0.338 Chirality : 0.044 0.164 1673 Planarity : 0.005 0.053 1829 Dihedral : 14.599 175.259 1963 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 32.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.50 % Allowed : 16.07 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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 (0.24), residues: 1217 helix: 0.82 (0.30), residues: 319 sheet: 0.10 (0.35), residues: 211 loop : -0.88 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1565 TYR 0.018 0.002 TYR A 534 PHE 0.017 0.002 PHE A 757 TRP 0.010 0.002 TRP A1466 HIS 0.008 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 (11327) covalent geometry : angle 0.64166 / 0.34 (15507) hydrogen bonds : bond 0.05188 / 3.42 ( 364) hydrogen bonds : angle 5.41783 / 3.79 ( 1097) metal coordination : bond 0.00625 / 0.36 ( 16) metal coordination : angle 3.38968 / 1.61 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.402 Fit side-chains REVERT: A 155 LEU cc_start: 0.7629 (mt) cc_final: 0.7404 (mp) REVERT: A 173 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8051 (mt) REVERT: A 209 LYS cc_start: 0.5699 (pttm) cc_final: 0.5222 (pttp) REVERT: A 293 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7336 (ptm-80) REVERT: A 294 ARG cc_start: 0.7565 (ptt-90) cc_final: 0.7224 (ttp-170) REVERT: A 395 VAL cc_start: 0.6326 (OUTLIER) cc_final: 0.5889 (m) REVERT: A 409 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7410 (mm-30) REVERT: A 473 MET cc_start: 0.7620 (mmm) cc_final: 0.7264 (mmt) REVERT: A 524 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: A 576 LYS cc_start: 0.7771 (mttp) cc_final: 0.7503 (mtpt) REVERT: A 664 GLU cc_start: 0.6172 (tp30) cc_final: 0.5700 (pt0) REVERT: A 667 GLU cc_start: 0.5492 (OUTLIER) cc_final: 0.5089 (pt0) REVERT: A 707 GLU cc_start: 0.6075 (OUTLIER) cc_final: 0.5496 (tt0) REVERT: A 735 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5347 (pp20) REVERT: A 896 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7016 (ttp80) REVERT: A 1369 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: A 1375 LYS cc_start: 0.6513 (OUTLIER) cc_final: 0.5977 (ttpt) REVERT: A 1395 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7049 (mmp80) REVERT: A 1405 ASN cc_start: 0.6373 (m-40) cc_final: 0.6068 (m-40) REVERT: A 1478 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7372 (mt-10) REVERT: A 1487 MET cc_start: 0.8489 (ptt) cc_final: 0.8169 (ptt) outliers start: 37 outliers final: 15 residues processed: 134 average time/residue: 0.6612 time to fit residues: 94.6209 Evaluate side-chains 129 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 930 TYR Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1478 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.180875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155368 restraints weight = 11406.122| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.20 r_work: 0.3651 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11343 Z= 0.265 Angle : 0.709 11.360 15528 Z= 0.366 Chirality : 0.046 0.172 1673 Planarity : 0.006 0.051 1829 Dihedral : 14.591 175.720 1963 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 33.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.56 % Favored : 92.28 % Rotamer: Outliers : 3.88 % Allowed : 16.73 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.65 (0.24), residues: 1217 helix: 0.58 (0.30), residues: 313 sheet: -0.02 (0.35), residues: 211 loop : -1.05 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1565 TYR 0.020 0.003 TYR A 534 PHE 0.019 0.002 PHE A 757 TRP 0.012 0.002 TRP A1466 HIS 0.009 0.002 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.26 (11327) covalent geometry : angle 0.69778 / 0.36 (15507) hydrogen bonds : bond 0.05518 / 3.61 ( 364) hydrogen bonds : angle 5.58355 / 3.90 ( 1097) metal coordination : bond 0.00619 / 0.33 ( 16) metal coordination : angle 3.48871 / 1.69 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.415 Fit side-chains REVERT: A 155 LEU cc_start: 0.7654 (mt) cc_final: 0.7403 (mp) REVERT: A 173 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8088 (mt) REVERT: A 209 LYS cc_start: 0.5720 (pttm) cc_final: 0.5250 (pttp) REVERT: A 293 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7352 (ptm-80) REVERT: A 294 ARG cc_start: 0.7545 (ptt-90) cc_final: 0.7256 (ttp-170) REVERT: A 298 LEU cc_start: 0.5993 (mt) cc_final: 0.5727 (OUTLIER) REVERT: A 409 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7401 (mm-30) REVERT: A 473 MET cc_start: 0.7627 (mmm) cc_final: 0.7158 (mmt) REVERT: A 524 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: A 576 LYS cc_start: 0.7785 (mttp) cc_final: 0.7520 (mtpt) REVERT: A 664 GLU cc_start: 0.6198 (tp30) cc_final: 0.5786 (pt0) REVERT: A 667 GLU cc_start: 0.5591 (OUTLIER) cc_final: 0.5133 (pt0) REVERT: A 707 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5714 (tt0) REVERT: A 735 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5503 (pp20) REVERT: A 896 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7039 (ttp80) REVERT: A 929 GLU cc_start: 0.6664 (tt0) cc_final: 0.6289 (tt0) REVERT: A 1305 MET cc_start: 0.6510 (ptp) cc_final: 0.6136 (ptp) REVERT: A 1369 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: A 1375 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.5967 (ttpt) REVERT: A 1395 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7117 (mmp80) REVERT: A 1478 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: A 1487 MET cc_start: 0.8465 (ptt) cc_final: 0.8172 (ptt) REVERT: A 1532 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: A 1579 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6503 (mp) REVERT: A 1592 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7786 (mmtt) outliers start: 41 outliers final: 18 residues processed: 132 average time/residue: 0.6995 time to fit residues: 98.8820 Evaluate side-chains 127 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 718 TYR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 930 TYR Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1478 GLU Chi-restraints excluded: chain A residue 1532 GLU Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1592 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 114 optimal weight: 0.0040 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 712 GLN A1405 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.186087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.160837 restraints weight = 11283.038| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.26 r_work: 0.3727 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11343 Z= 0.098 Angle : 0.496 9.582 15528 Z= 0.261 Chirality : 0.039 0.144 1673 Planarity : 0.004 0.052 1829 Dihedral : 14.192 172.540 1963 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 32.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 1.61 % Allowed : 19.57 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.03 (0.24), residues: 1217 helix: 1.36 (0.31), residues: 321 sheet: 0.35 (0.35), residues: 204 loop : -0.81 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1310 TYR 0.007 0.001 TYR A 591 PHE 0.010 0.001 PHE A 776 TRP 0.010 0.001 TRP A1466 HIS 0.003 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (11327) covalent geometry : angle 0.48945 / 0.26 (15507) hydrogen bonds : bond 0.03942 / 2.63 ( 364) hydrogen bonds : angle 4.74231 / 3.32 ( 1097) metal coordination : bond 0.00271 / 0.14 ( 16) metal coordination : angle 2.16578 / 1.01 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.434 Fit side-chains REVERT: A 17 MET cc_start: 0.8145 (ttp) cc_final: 0.7883 (ttp) REVERT: A 155 LEU cc_start: 0.7590 (mt) cc_final: 0.7388 (mp) REVERT: A 173 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8039 (mt) REVERT: A 209 LYS cc_start: 0.5762 (pttm) cc_final: 0.5295 (pttp) REVERT: A 293 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7082 (ptm160) REVERT: A 294 ARG cc_start: 0.7408 (ptt-90) cc_final: 0.7056 (ttp-170) REVERT: A 401 LEU cc_start: 0.6462 (tp) cc_final: 0.6247 (tp) REVERT: A 473 MET cc_start: 0.7510 (mmm) cc_final: 0.7117 (mmt) REVERT: A 576 LYS cc_start: 0.7766 (mttp) cc_final: 0.7476 (mtpt) REVERT: A 614 LEU cc_start: 0.7578 (tp) cc_final: 0.7363 (tt) REVERT: A 664 GLU cc_start: 0.6105 (tp30) cc_final: 0.5772 (pt0) REVERT: A 735 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.5210 (pp20) REVERT: A 833 MET cc_start: 0.7166 (mpp) cc_final: 0.6752 (mtp) REVERT: A 970 ASP cc_start: 0.7156 (p0) cc_final: 0.6774 (p0) REVERT: A 1305 MET cc_start: 0.6302 (ptp) cc_final: 0.6002 (ptp) REVERT: A 1363 SER cc_start: 0.8342 (m) cc_final: 0.8118 (m) REVERT: A 1369 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: A 1395 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7015 (mmp80) REVERT: A 1487 MET cc_start: 0.8382 (ptt) cc_final: 0.8053 (ptt) outliers start: 17 outliers final: 8 residues processed: 120 average time/residue: 0.6994 time to fit residues: 89.8232 Evaluate side-chains 114 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 718 TYR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1395 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 887 HIS A1405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.180200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154749 restraints weight = 11263.749| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.19 r_work: 0.3641 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 11343 Z= 0.323 Angle : 0.769 11.167 15528 Z= 0.395 Chirality : 0.049 0.181 1673 Planarity : 0.006 0.049 1829 Dihedral : 14.418 176.425 1963 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 32.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.81 % Favored : 92.03 % Rotamer: Outliers : 3.21 % Allowed : 18.24 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.70 (0.23), residues: 1217 helix: 0.55 (0.29), residues: 313 sheet: -0.01 (0.35), residues: 211 loop : -1.09 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1310 TYR 0.021 0.003 TYR A 534 PHE 0.019 0.003 PHE A 757 TRP 0.013 0.002 TRP A1512 HIS 0.011 0.002 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.32 (11327) covalent geometry : angle 0.75732 / 0.39 (15507) hydrogen bonds : bond 0.05804 / 3.79 ( 364) hydrogen bonds : angle 5.64324 / 3.96 ( 1097) metal coordination : bond 0.00727 / 0.40 ( 16) metal coordination : angle 3.75280 / 1.94 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.450 Fit side-chains REVERT: A 5 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7400 (ttm) REVERT: A 155 LEU cc_start: 0.7649 (mt) cc_final: 0.7386 (mp) REVERT: A 173 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8055 (mt) REVERT: A 209 LYS cc_start: 0.5705 (pttm) cc_final: 0.5223 (pttp) REVERT: A 293 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7392 (ptm-80) REVERT: A 294 ARG cc_start: 0.7497 (ptt-90) cc_final: 0.7236 (ttp-170) REVERT: A 298 LEU cc_start: 0.5868 (mt) cc_final: 0.5623 (OUTLIER) REVERT: A 409 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: A 473 MET cc_start: 0.7654 (mmm) cc_final: 0.7274 (mmm) REVERT: A 524 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: A 664 GLU cc_start: 0.6183 (tp30) cc_final: 0.5795 (pt0) REVERT: A 667 GLU cc_start: 0.5572 (OUTLIER) cc_final: 0.5225 (pt0) REVERT: A 735 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5540 (pp20) REVERT: A 929 GLU cc_start: 0.6642 (tt0) cc_final: 0.6279 (tt0) REVERT: A 970 ASP cc_start: 0.7287 (p0) cc_final: 0.6978 (p0) REVERT: A 1305 MET cc_start: 0.6547 (ptp) cc_final: 0.6141 (ptp) REVERT: A 1369 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: A 1375 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.5944 (ttpt) REVERT: A 1395 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7023 (mmp80) REVERT: A 1487 MET cc_start: 0.8476 (ptt) cc_final: 0.8242 (ptt) outliers start: 34 outliers final: 16 residues processed: 127 average time/residue: 0.6203 time to fit residues: 84.5552 Evaluate side-chains 121 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 0.0040 chunk 31 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 834 ASN A 887 HIS A1405 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.183313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157718 restraints weight = 11288.768| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.34 r_work: 0.3686 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11343 Z= 0.157 Angle : 0.573 9.804 15528 Z= 0.301 Chirality : 0.041 0.153 1673 Planarity : 0.004 0.051 1829 Dihedral : 14.235 174.733 1963 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 32.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 2.84 % Allowed : 18.71 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.35 (0.24), residues: 1217 helix: 1.03 (0.30), residues: 319 sheet: 0.07 (0.35), residues: 214 loop : -0.95 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1310 TYR 0.013 0.002 TYR A 534 PHE 0.015 0.002 PHE A 757 TRP 0.011 0.001 TRP A1466 HIS 0.005 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (11327) covalent geometry : angle 0.56532 / 0.30 (15507) hydrogen bonds : bond 0.04585 / 3.02 ( 364) hydrogen bonds : angle 5.08333 / 3.56 ( 1097) metal coordination : bond 0.00455 / 0.28 ( 16) metal coordination : angle 2.64379 / 1.32 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.429 Fit side-chains REVERT: A 5 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7314 (ttm) REVERT: A 155 LEU cc_start: 0.7626 (mt) cc_final: 0.7383 (mp) REVERT: A 173 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8079 (mt) REVERT: A 209 LYS cc_start: 0.5735 (pttm) cc_final: 0.5259 (pttp) REVERT: A 293 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7237 (ptm160) REVERT: A 294 ARG cc_start: 0.7421 (ptt-90) cc_final: 0.7110 (ttp-170) REVERT: A 473 MET cc_start: 0.7619 (mmm) cc_final: 0.7291 (mmt) REVERT: A 524 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: A 664 GLU cc_start: 0.6155 (tp30) cc_final: 0.5365 (pt0) REVERT: A 735 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.5431 (pp20) REVERT: A 876 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7014 (mpt180) REVERT: A 970 ASP cc_start: 0.7198 (p0) cc_final: 0.6824 (p0) REVERT: A 1305 MET cc_start: 0.6447 (ptp) cc_final: 0.6075 (ptp) REVERT: A 1369 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: A 1375 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.5936 (ttpt) REVERT: A 1395 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6960 (mmp80) REVERT: A 1487 MET cc_start: 0.8431 (ptt) cc_final: 0.8157 (ptt) REVERT: A 1592 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7856 (mmtt) outliers start: 30 outliers final: 11 residues processed: 119 average time/residue: 0.6458 time to fit residues: 82.2478 Evaluate side-chains 120 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 718 TYR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 876 ARG Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1592 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 26 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 887 HIS A1405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.181943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156222 restraints weight = 11406.164| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.32 r_work: 0.3667 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11343 Z= 0.215 Angle : 0.640 9.711 15528 Z= 0.332 Chirality : 0.044 0.153 1673 Planarity : 0.005 0.051 1829 Dihedral : 14.262 175.405 1963 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 32.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.48 % Favored : 92.36 % Rotamer: Outliers : 2.84 % Allowed : 18.53 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.50 (0.24), residues: 1217 helix: 0.83 (0.30), residues: 319 sheet: -0.03 (0.35), residues: 211 loop : -1.00 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1310 TYR 0.018 0.002 TYR A 534 PHE 0.017 0.002 PHE A 757 TRP 0.010 0.002 TRP A1466 HIS 0.007 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (11327) covalent geometry : angle 0.63063 / 0.33 (15507) hydrogen bonds : bond 0.04999 / 3.28 ( 364) hydrogen bonds : angle 5.27039 / 3.70 ( 1097) metal coordination : bond 0.00495 / 0.27 ( 16) metal coordination : angle 3.03827 / 1.56 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.503 Fit side-chains REVERT: A 5 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7376 (ttm) REVERT: A 155 LEU cc_start: 0.7613 (mt) cc_final: 0.7374 (mp) REVERT: A 173 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8056 (mt) REVERT: A 209 LYS cc_start: 0.5740 (pttm) cc_final: 0.5270 (pttp) REVERT: A 293 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7301 (ptm-80) REVERT: A 294 ARG cc_start: 0.7448 (ptt-90) cc_final: 0.7152 (ttp-170) REVERT: A 338 ASP cc_start: 0.6799 (OUTLIER) cc_final: 0.6577 (p0) REVERT: A 473 MET cc_start: 0.7647 (mmm) cc_final: 0.7256 (mmt) REVERT: A 524 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: A 664 GLU cc_start: 0.5959 (tp30) cc_final: 0.5523 (pt0) REVERT: A 707 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5668 (tt0) REVERT: A 735 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5525 (pp20) REVERT: A 876 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7082 (mpt180) REVERT: A 929 GLU cc_start: 0.6613 (tt0) cc_final: 0.6214 (tt0) REVERT: A 1305 MET cc_start: 0.6462 (ptp) cc_final: 0.6094 (ptp) REVERT: A 1369 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: A 1375 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.5941 (ttpt) REVERT: A 1395 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7021 (mmp80) REVERT: A 1478 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: A 1579 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6462 (mp) REVERT: A 1592 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7825 (mmtt) outliers start: 30 outliers final: 12 residues processed: 125 average time/residue: 0.6402 time to fit residues: 86.0078 Evaluate side-chains 125 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 718 TYR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 876 ARG Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1478 GLU Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1592 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 887 HIS A1405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.184097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157885 restraints weight = 11315.683| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.53 r_work: 0.3689 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11343 Z= 0.137 Angle : 0.544 9.566 15528 Z= 0.286 Chirality : 0.040 0.150 1673 Planarity : 0.004 0.051 1829 Dihedral : 14.132 174.229 1963 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 32.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 2.46 % Allowed : 19.09 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.21 (0.24), residues: 1217 helix: 1.18 (0.30), residues: 321 sheet: 0.08 (0.35), residues: 214 loop : -0.86 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1310 TYR 0.012 0.001 TYR A 534 PHE 0.013 0.001 PHE A 757 TRP 0.011 0.001 TRP A1466 HIS 0.004 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (11327) covalent geometry : angle 0.53785 / 0.29 (15507) hydrogen bonds : bond 0.04331 / 2.85 ( 364) hydrogen bonds : angle 4.92478 / 3.46 ( 1097) metal coordination : bond 0.00382 / 0.23 ( 16) metal coordination : angle 2.36068 / 1.18 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3772.62 seconds wall clock time: 65 minutes 20.84 seconds (3920.84 seconds total)