Starting phenix.real_space_refine on Wed Mar 4 05:42:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1v_27138/03_2026/8d1v_27138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1v_27138/03_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_27138/03_2026/8d1v_27138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1v_27138/03_2026/8d1v_27138.map" model { file = "/net/cci-nas-00/data/ceres_data/8d1v_27138/03_2026/8d1v_27138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1v_27138/03_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-5986/lib/python3.9/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: 2.78, per 1000 atoms: 0.25 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: 0.96 Conformation dependent library (CDL) restraints added in 488.6 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: 1.33 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: 2.33 Time building geometry restraints manager: 1.27 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: 6690 35.97 - 71.94: 215 71.94 - 107.90: 28 107.90 - 143.87: 0 143.87 - 179.84: 4 Dihedral angle restraints: 6937 sinusoidal: 3408 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 6934 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: 2.560 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: 0.100 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.200 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 17.310 179.839 4659 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 covalent geometry : bond 0.00601 (11327) covalent geometry : angle 0.74278 (15507) hydrogen bonds : bond 0.23799 ( 364) hydrogen bonds : angle 8.82194 ( 1097) metal coordination : bond 0.00820 ( 16) metal coordination : angle 3.36015 ( 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 : 0.428 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: 0.8213 time to fit residues: 141.8147 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 : 0.408 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4083 r_free = 0.4083 target = 0.179214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.153649 restraints weight = 11252.818| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.19 r_work: 0.3620 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 11343 Z= 0.345 Angle : 0.833 15.193 15528 Z= 0.429 Chirality : 0.050 0.181 1673 Planarity : 0.007 0.053 1829 Dihedral : 18.466 177.155 2133 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 30.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.84 % Allowed : 10.68 % Favored : 86.48 % 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: -0.63 (0.24), residues: 1217 helix: 0.24 (0.29), residues: 313 sheet: 0.09 (0.35), residues: 211 loop : -0.87 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1565 TYR 0.024 0.003 TYR A 534 PHE 0.021 0.003 PHE A 757 TRP 0.016 0.003 TRP A1512 HIS 0.012 0.002 HIS A 691 Details of bonding type rmsd covalent geometry : bond 0.00765 (11327) covalent geometry : angle 0.81729 (15507) hydrogen bonds : bond 0.06419 ( 364) hydrogen bonds : angle 6.18463 ( 1097) metal coordination : bond 0.01107 ( 16) metal coordination : angle 4.45133 ( 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 139 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 155 LEU cc_start: 0.7619 (mt) cc_final: 0.7333 (mp) REVERT: A 188 LYS cc_start: 0.7494 (ptpt) cc_final: 0.7231 (mtmt) REVERT: A 209 LYS cc_start: 0.5877 (pttm) cc_final: 0.5419 (pttp) REVERT: A 294 ARG cc_start: 0.7638 (ptt-90) cc_final: 0.7330 (ttp-170) REVERT: A 409 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7470 (mm-30) REVERT: A 473 MET cc_start: 0.7432 (mmm) cc_final: 0.7210 (mmt) REVERT: A 576 LYS cc_start: 0.7852 (mttp) cc_final: 0.7557 (mtpt) REVERT: A 616 GLU cc_start: 0.6081 (tp30) cc_final: 0.5570 (tt0) REVERT: A 896 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7229 (ttp80) REVERT: A 1310 ARG cc_start: 0.6690 (tpp80) cc_final: 0.6464 (mmm-85) REVERT: A 1369 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: A 1375 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.6099 (ttpt) REVERT: A 1395 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6979 (mmp80) REVERT: A 1478 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: A 1487 MET cc_start: 0.8551 (ptt) cc_final: 0.8086 (ptt) REVERT: A 1592 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7784 (mmtt) outliers start: 30 outliers final: 8 residues processed: 131 average time/residue: 0.7639 time to fit residues: 106.6176 Evaluate side-chains 109 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 350 GLU 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: 2.9990 chunk 11 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 106 optimal weight: 0.0270 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 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 = 0.4135 r_free = 0.4135 target = 0.183967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.158376 restraints weight = 11342.167| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.21 r_work: 0.3683 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11343 Z= 0.139 Angle : 0.546 9.622 15528 Z= 0.287 Chirality : 0.040 0.168 1673 Planarity : 0.004 0.050 1829 Dihedral : 18.187 173.704 2133 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 30.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.27 % Allowed : 14.08 % Favored : 83.65 % 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: -0.22 (0.24), residues: 1217 helix: 0.99 (0.30), residues: 319 sheet: 0.12 (0.34), residues: 214 loop : -0.78 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1346 TYR 0.013 0.002 TYR A 534 PHE 0.013 0.001 PHE A 757 TRP 0.007 0.001 TRP A1466 HIS 0.004 0.001 HIS A 691 Details of bonding type rmsd covalent geometry : bond 0.00292 (11327) covalent geometry : angle 0.53655 (15507) hydrogen bonds : bond 0.04660 ( 364) hydrogen bonds : angle 5.26872 ( 1097) metal coordination : bond 0.00533 ( 16) metal coordination : angle 2.74856 ( 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 129 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 17 MET cc_start: 0.8290 (ttp) cc_final: 0.8018 (ttp) REVERT: A 147 ARG cc_start: 0.6373 (ttp-170) cc_final: 0.6171 (ttp-170) REVERT: A 155 LEU cc_start: 0.7594 (mt) cc_final: 0.7351 (mp) REVERT: A 188 LYS cc_start: 0.7391 (ptpt) cc_final: 0.7142 (mtmt) REVERT: A 209 LYS cc_start: 0.5783 (pttm) cc_final: 0.5315 (pttp) REVERT: A 294 ARG cc_start: 0.7509 (ptt-90) cc_final: 0.7171 (ttp-170) REVERT: A 395 VAL cc_start: 0.6508 (OUTLIER) cc_final: 0.6063 (m) REVERT: A 473 MET cc_start: 0.7396 (mmm) cc_final: 0.7042 (mmt) REVERT: A 576 LYS cc_start: 0.7730 (mttp) cc_final: 0.7444 (mtpt) REVERT: A 614 LEU cc_start: 0.7581 (tp) cc_final: 0.7228 (tt) REVERT: A 616 GLU cc_start: 0.6085 (tp30) cc_final: 0.5556 (tt0) REVERT: A 627 GLU cc_start: 0.8126 (tt0) cc_final: 0.7871 (tt0) REVERT: A 664 GLU cc_start: 0.6149 (tp30) cc_final: 0.5858 (tp30) REVERT: A 735 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.5198 (pp20) REVERT: A 970 ASP cc_start: 0.7232 (p0) cc_final: 0.6845 (p0) REVERT: A 1363 SER cc_start: 0.8444 (m) cc_final: 0.8227 (m) REVERT: A 1369 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: A 1395 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6883 (mmp80) REVERT: A 1478 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: A 1487 MET cc_start: 0.8457 (ptt) cc_final: 0.8021 (ptt) outliers start: 24 outliers final: 5 residues processed: 123 average time/residue: 0.7907 time to fit residues: 103.1802 Evaluate side-chains 108 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 77 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 735 GLU Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1478 GLU 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: 10.0000 chunk 13 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 27 ASN ** 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 = 0.4083 r_free = 0.4083 target = 0.179144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.153556 restraints weight = 11403.120| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.20 r_work: 0.3627 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 11343 Z= 0.375 Angle : 0.847 13.993 15528 Z= 0.433 Chirality : 0.052 0.202 1673 Planarity : 0.007 0.052 1829 Dihedral : 18.263 176.025 2133 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 32.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.97 % Favored : 91.87 % Rotamer: Outliers : 3.88 % Allowed : 16.16 % Favored : 79.96 % 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: -0.90 (0.23), residues: 1217 helix: 0.14 (0.29), residues: 313 sheet: -0.03 (0.35), residues: 211 loop : -1.13 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1565 TYR 0.023 0.004 TYR A 534 PHE 0.021 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 covalent geometry : bond 0.00835 (11327) covalent geometry : angle 0.83300 (15507) hydrogen bonds : bond 0.06378 ( 364) hydrogen bonds : angle 6.02342 ( 1097) metal coordination : bond 0.00889 ( 16) metal coordination : angle 4.23983 ( 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 143 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 102 time to evaluate : 0.467 Fit side-chains REVERT: A 46 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.7034 (tptm) REVERT: A 155 LEU cc_start: 0.7689 (mt) cc_final: 0.7438 (mp) REVERT: A 173 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8159 (mt) REVERT: A 188 LYS cc_start: 0.7507 (ptpt) cc_final: 0.7214 (mtmt) REVERT: A 209 LYS cc_start: 0.5710 (pttm) cc_final: 0.5178 (pttp) REVERT: A 409 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: A 473 MET cc_start: 0.7639 (mmm) cc_final: 0.7287 (mmt) REVERT: A 524 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: A 576 LYS cc_start: 0.7850 (mttp) cc_final: 0.7544 (mtpt) REVERT: A 664 GLU cc_start: 0.6169 (tp30) cc_final: 0.5591 (pt0) REVERT: A 735 GLU cc_start: 0.6104 (OUTLIER) cc_final: 0.5511 (pp20) REVERT: A 896 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7123 (ttp80) REVERT: A 970 ASP cc_start: 0.7401 (p0) cc_final: 0.6975 (p0) REVERT: A 1369 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: A 1375 LYS cc_start: 0.6521 (OUTLIER) cc_final: 0.6024 (ttpt) REVERT: A 1395 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7170 (mmp80) REVERT: A 1478 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7441 (mt-10) REVERT: A 1592 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7773 (mmtt) outliers start: 41 outliers final: 18 residues processed: 136 average time/residue: 0.7904 time to fit residues: 114.0480 Evaluate side-chains 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 173 LEU Chi-restraints excluded: chain A residue 228 LEU 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 671 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 930 TYR Chi-restraints excluded: chain A residue 943 ILE 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 1592 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 712 GLN A1555 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.184495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156633 restraints weight = 11254.256| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.50 r_work: 0.3700 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2624 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= 0.112 Angle : 0.515 9.159 15528 Z= 0.271 Chirality : 0.039 0.165 1673 Planarity : 0.004 0.051 1829 Dihedral : 17.972 172.891 2133 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 31.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 1.80 % Allowed : 18.24 % Favored : 79.96 % 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: -0.18 (0.24), residues: 1217 helix: 1.12 (0.30), residues: 321 sheet: 0.11 (0.34), residues: 214 loop : -0.80 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1310 TYR 0.009 0.001 TYR A 492 PHE 0.012 0.001 PHE A 757 TRP 0.009 0.001 TRP A1466 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00237 (11327) covalent geometry : angle 0.50742 (15507) hydrogen bonds : bond 0.04169 ( 364) hydrogen bonds : angle 4.97834 ( 1097) metal coordination : bond 0.00385 ( 16) metal coordination : angle 2.45945 ( 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 123 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.343 Fit side-chains REVERT: A 188 LYS cc_start: 0.7438 (ptpt) cc_final: 0.7201 (mtmt) REVERT: A 209 LYS cc_start: 0.5647 (pttm) cc_final: 0.5180 (pttp) REVERT: A 293 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.6997 (ptm-80) REVERT: A 294 ARG cc_start: 0.7315 (ptt-90) cc_final: 0.7048 (ttp-170) REVERT: A 401 LEU cc_start: 0.6537 (tp) cc_final: 0.6301 (tp) REVERT: A 473 MET cc_start: 0.7575 (mmm) cc_final: 0.7034 (mmt) REVERT: A 576 LYS cc_start: 0.7818 (mttp) cc_final: 0.7490 (mtpt) REVERT: A 664 GLU cc_start: 0.6117 (tp30) cc_final: 0.5603 (pt0) REVERT: A 735 GLU cc_start: 0.5906 (OUTLIER) cc_final: 0.5238 (pp20) REVERT: A 970 ASP cc_start: 0.7145 (p0) cc_final: 0.6745 (p0) REVERT: A 1363 SER cc_start: 0.8453 (m) cc_final: 0.8245 (m) REVERT: A 1369 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: A 1375 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.6046 (ttpt) REVERT: A 1395 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6948 (mmp80) outliers start: 19 outliers final: 6 residues processed: 118 average time/residue: 0.8235 time to fit residues: 103.0832 Evaluate side-chains 110 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP 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 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 0.0670 chunk 96 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 109 optimal weight: 0.0170 chunk 24 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN A 640 ASN A 834 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.185780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.161124 restraints weight = 11346.529| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.34 r_work: 0.3716 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11343 Z= 0.107 Angle : 0.493 8.695 15528 Z= 0.259 Chirality : 0.038 0.141 1673 Planarity : 0.004 0.049 1829 Dihedral : 17.832 172.009 2133 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 32.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.65 % Allowed : 17.86 % Favored : 79.49 % 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: 0.10 (0.24), residues: 1217 helix: 1.53 (0.30), residues: 321 sheet: 0.21 (0.34), residues: 212 loop : -0.68 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1310 TYR 0.011 0.001 TYR A 534 PHE 0.012 0.001 PHE A 418 TRP 0.008 0.001 TRP A1466 HIS 0.003 0.001 HIS A 691 Details of bonding type rmsd covalent geometry : bond 0.00226 (11327) covalent geometry : angle 0.48767 (15507) hydrogen bonds : bond 0.03927 ( 364) hydrogen bonds : angle 4.66119 ( 1097) metal coordination : bond 0.00298 ( 16) metal coordination : angle 2.03187 ( 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 133 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.416 Fit side-chains REVERT: A 17 MET cc_start: 0.8129 (ttp) cc_final: 0.7875 (ttp) REVERT: A 46 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6894 (tptm) REVERT: A 90 PHE cc_start: 0.7405 (m-80) cc_final: 0.6870 (m-80) REVERT: A 155 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7394 (mp) REVERT: A 209 LYS cc_start: 0.5690 (pttm) cc_final: 0.5232 (pttp) REVERT: A 293 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7120 (ptm-80) REVERT: A 294 ARG cc_start: 0.7194 (ptt-90) cc_final: 0.6921 (ttp-170) REVERT: A 473 MET cc_start: 0.7544 (mmm) cc_final: 0.7156 (mmt) REVERT: A 576 LYS cc_start: 0.7758 (mttp) cc_final: 0.7480 (mtpt) REVERT: A 664 GLU cc_start: 0.6125 (tp30) cc_final: 0.5796 (pt0) REVERT: A 666 GLU cc_start: 0.6472 (tt0) cc_final: 0.6115 (mt-10) REVERT: A 735 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.5137 (pp20) REVERT: A 833 MET cc_start: 0.7274 (mpp) cc_final: 0.6899 (mtp) REVERT: A 970 ASP cc_start: 0.7182 (p0) cc_final: 0.6837 (p0) REVERT: A 1363 SER cc_start: 0.8348 (m) cc_final: 0.8139 (m) REVERT: A 1369 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: A 1375 LYS cc_start: 0.6534 (OUTLIER) cc_final: 0.6025 (ttpt) REVERT: A 1395 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7056 (mmp80) outliers start: 28 outliers final: 11 residues processed: 126 average time/residue: 0.7943 time to fit residues: 106.4464 Evaluate side-chains 120 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 293 ARG 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 541 LEU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.181541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.155883 restraints weight = 11316.902| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.31 r_work: 0.3666 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11343 Z= 0.243 Angle : 0.664 9.977 15528 Z= 0.343 Chirality : 0.045 0.155 1673 Planarity : 0.005 0.048 1829 Dihedral : 17.991 175.946 2133 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 31.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.90 % Favored : 93.02 % Rotamer: Outliers : 3.21 % Allowed : 17.96 % 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: -0.34 (0.24), residues: 1217 helix: 0.94 (0.30), residues: 313 sheet: 0.09 (0.35), residues: 211 loop : -0.87 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1310 TYR 0.019 0.002 TYR A 534 PHE 0.018 0.002 PHE A 757 TRP 0.010 0.002 TRP A1466 HIS 0.008 0.002 HIS A 691 Details of bonding type rmsd covalent geometry : bond 0.00534 (11327) covalent geometry : angle 0.65401 (15507) hydrogen bonds : bond 0.05134 ( 364) hydrogen bonds : angle 5.30419 ( 1097) metal coordination : bond 0.00566 ( 16) metal coordination : angle 3.18958 ( 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 134 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.409 Fit side-chains REVERT: A 209 LYS cc_start: 0.5704 (pttm) cc_final: 0.5231 (pttp) REVERT: A 293 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7357 (ptm-80) REVERT: A 294 ARG cc_start: 0.7312 (ptt-90) cc_final: 0.7092 (ttp-170) REVERT: A 298 LEU cc_start: 0.6199 (mt) cc_final: 0.5639 (mt) REVERT: A 473 MET cc_start: 0.7664 (mmm) cc_final: 0.7336 (mmt) REVERT: A 524 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: A 576 LYS cc_start: 0.7824 (mttp) cc_final: 0.7544 (mtpt) REVERT: A 664 GLU cc_start: 0.6109 (tp30) cc_final: 0.5766 (pt0) REVERT: A 707 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.5684 (tt0) REVERT: A 735 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5386 (pp20) REVERT: A 929 GLU cc_start: 0.6693 (tt0) cc_final: 0.6345 (tt0) REVERT: A 970 ASP cc_start: 0.7309 (p0) cc_final: 0.6947 (p0) REVERT: A 1369 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: A 1375 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.5966 (ttpt) REVERT: A 1395 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6925 (mmp80) REVERT: A 1478 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: A 1579 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6350 (mp) outliers start: 34 outliers final: 12 residues processed: 128 average time/residue: 0.7901 time to fit residues: 107.6503 Evaluate side-chains 121 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 ARG 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 541 LEU 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 735 GLU Chi-restraints excluded: chain A residue 792 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 0.1980 chunk 27 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 0.0050 chunk 118 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 overall best weight: 2.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.182196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156432 restraints weight = 11259.763| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.32 r_work: 0.3672 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11343 Z= 0.207 Angle : 0.620 9.726 15528 Z= 0.323 Chirality : 0.043 0.149 1673 Planarity : 0.005 0.049 1829 Dihedral : 17.977 174.650 2133 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 31.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.07 % Favored : 92.85 % Rotamer: Outliers : 2.93 % Allowed : 19.00 % Favored : 78.07 % 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: -0.40 (0.24), residues: 1217 helix: 0.92 (0.30), residues: 319 sheet: 0.02 (0.35), residues: 211 loop : -0.93 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1310 TYR 0.017 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 covalent geometry : bond 0.00453 (11327) covalent geometry : angle 0.61126 (15507) hydrogen bonds : bond 0.04875 ( 364) hydrogen bonds : angle 5.20322 ( 1097) metal coordination : bond 0.00518 ( 16) metal coordination : angle 2.93255 ( 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 134 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.438 Fit side-chains REVERT: A 173 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8050 (mt) REVERT: A 209 LYS cc_start: 0.5742 (pttm) cc_final: 0.5270 (pttp) REVERT: A 293 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7357 (ptm-80) REVERT: A 294 ARG cc_start: 0.7261 (ptt-90) cc_final: 0.7058 (ttp-170) REVERT: A 298 LEU cc_start: 0.6167 (mt) cc_final: 0.5644 (mt) REVERT: A 473 MET cc_start: 0.7625 (mmm) cc_final: 0.7294 (mmt) REVERT: A 524 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: A 576 LYS cc_start: 0.7835 (mttp) cc_final: 0.7557 (mtpt) REVERT: A 580 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7127 (mt) REVERT: A 664 GLU cc_start: 0.6123 (tp30) cc_final: 0.5751 (pt0) REVERT: A 735 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5397 (pp20) REVERT: A 929 GLU cc_start: 0.6600 (tt0) cc_final: 0.6225 (tt0) REVERT: A 970 ASP cc_start: 0.7301 (p0) cc_final: 0.7022 (p0) REVERT: A 1369 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: A 1375 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.6001 (ttpt) REVERT: A 1395 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.6997 (mmp80) REVERT: A 1478 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: A 1579 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6419 (mp) outliers start: 31 outliers final: 13 residues processed: 127 average time/residue: 0.7886 time to fit residues: 106.6950 Evaluate side-chains 120 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR 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 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 541 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 580 LEU 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 792 LEU Chi-restraints excluded: chain A residue 818 LYS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 31 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.180990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.154737 restraints weight = 11275.648| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.46 r_work: 0.3650 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2931 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 : 0.700 10.568 15528 Z= 0.363 Chirality : 0.046 0.169 1673 Planarity : 0.006 0.049 1829 Dihedral : 18.034 175.467 2133 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 32.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.13 % Favored : 91.70 % Rotamer: Outliers : 3.12 % Allowed : 18.81 % Favored : 78.07 % 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: 0.64 (0.30), residues: 313 sheet: -0.08 (0.35), residues: 211 loop : -1.06 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1310 TYR 0.020 0.003 TYR A 534 PHE 0.019 0.002 PHE A 757 TRP 0.011 0.002 TRP A 144 HIS 0.009 0.002 HIS A 691 Details of bonding type rmsd covalent geometry : bond 0.00583 (11327) covalent geometry : angle 0.68886 (15507) hydrogen bonds : bond 0.05394 ( 364) hydrogen bonds : angle 5.49422 ( 1097) metal coordination : bond 0.00618 ( 16) metal coordination : angle 3.45365 ( 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 132 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.442 Fit side-chains REVERT: A 173 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8091 (mt) REVERT: A 209 LYS cc_start: 0.5698 (pttm) cc_final: 0.5222 (pttp) REVERT: A 293 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7371 (ptm-80) REVERT: A 294 ARG cc_start: 0.7350 (ptt-90) cc_final: 0.7092 (ttp-170) REVERT: A 298 LEU cc_start: 0.6225 (mt) cc_final: 0.5681 (mt) REVERT: A 473 MET cc_start: 0.7653 (mmm) cc_final: 0.7284 (mmm) REVERT: A 524 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: A 664 GLU cc_start: 0.6179 (tp30) cc_final: 0.5802 (pt0) REVERT: A 735 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5604 (pp20) REVERT: A 929 GLU cc_start: 0.6673 (tt0) cc_final: 0.6277 (tt0) REVERT: A 970 ASP cc_start: 0.7323 (p0) cc_final: 0.7007 (p0) REVERT: A 1305 MET cc_start: 0.6421 (ptp) cc_final: 0.6067 (ptp) REVERT: A 1369 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: A 1375 LYS cc_start: 0.6470 (OUTLIER) cc_final: 0.5973 (ttpt) REVERT: A 1395 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7043 (mmp80) REVERT: A 1478 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: A 1579 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6430 (mp) outliers start: 33 outliers final: 17 residues processed: 127 average time/residue: 0.7364 time to fit residues: 99.7257 Evaluate side-chains 123 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR 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 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 541 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 580 LEU 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 792 LEU Chi-restraints excluded: chain A residue 818 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 26 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 102 optimal weight: 0.2980 chunk 103 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 887 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.184468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.156097 restraints weight = 11301.259| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.55 r_work: 0.3696 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11343 Z= 0.120 Angle : 0.524 9.453 15528 Z= 0.276 Chirality : 0.039 0.151 1673 Planarity : 0.004 0.051 1829 Dihedral : 17.889 172.761 2133 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 32.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 2.17 % Allowed : 20.04 % Favored : 77.79 % 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: -0.15 (0.24), residues: 1217 helix: 1.24 (0.30), residues: 321 sheet: 0.22 (0.36), residues: 204 loop : -0.85 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1310 TYR 0.010 0.001 TYR A 534 PHE 0.011 0.001 PHE A 15 TRP 0.012 0.001 TRP A1466 HIS 0.004 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00253 (11327) covalent geometry : angle 0.51691 (15507) hydrogen bonds : bond 0.04147 ( 364) hydrogen bonds : angle 4.86151 ( 1097) metal coordination : bond 0.00405 ( 16) metal coordination : angle 2.33051 ( 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 122 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.382 Fit side-chains REVERT: A 17 MET cc_start: 0.8229 (ttp) cc_final: 0.7970 (ttp) REVERT: A 209 LYS cc_start: 0.5638 (pttm) cc_final: 0.5166 (pttp) REVERT: A 293 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7263 (ptm-80) REVERT: A 294 ARG cc_start: 0.7180 (ptt-90) cc_final: 0.6974 (ttp-170) REVERT: A 473 MET cc_start: 0.7611 (mmm) cc_final: 0.7115 (mmt) REVERT: A 580 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.7018 (mt) REVERT: A 664 GLU cc_start: 0.6098 (tp30) cc_final: 0.5728 (pt0) REVERT: A 735 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5399 (pp20) REVERT: A 832 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7796 (mp) REVERT: A 929 GLU cc_start: 0.6555 (tt0) cc_final: 0.6158 (tt0) REVERT: A 970 ASP cc_start: 0.7163 (p0) cc_final: 0.6763 (p0) REVERT: A 1305 MET cc_start: 0.6375 (ptp) cc_final: 0.6059 (ptp) REVERT: A 1369 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: A 1375 LYS cc_start: 0.6559 (OUTLIER) cc_final: 0.6046 (ttpt) REVERT: A 1395 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6967 (mmp80) outliers start: 23 outliers final: 12 residues processed: 120 average time/residue: 0.6894 time to fit residues: 88.4308 Evaluate side-chains 113 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 ARG 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 579 THR Chi-restraints excluded: chain A residue 580 LEU 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 832 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 887 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.182734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.156971 restraints weight = 11325.732| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.39 r_work: 0.3671 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11343 Z= 0.187 Angle : 0.598 9.573 15528 Z= 0.312 Chirality : 0.042 0.148 1673 Planarity : 0.005 0.050 1829 Dihedral : 17.936 174.736 2133 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 32.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.23 % Favored : 92.69 % Rotamer: Outliers : 2.27 % Allowed : 20.42 % Favored : 77.32 % 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: -0.28 (0.24), residues: 1217 helix: 1.09 (0.30), residues: 319 sheet: 0.08 (0.36), residues: 209 loop : -0.89 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1310 TYR 0.017 0.002 TYR A 534 PHE 0.016 0.002 PHE A 757 TRP 0.010 0.001 TRP A 20 HIS 0.006 0.001 HIS A 691 Details of bonding type rmsd covalent geometry : bond 0.00407 (11327) covalent geometry : angle 0.58933 (15507) hydrogen bonds : bond 0.04670 ( 364) hydrogen bonds : angle 5.11225 ( 1097) metal coordination : bond 0.00462 ( 16) metal coordination : angle 2.79136 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4054.44 seconds wall clock time: 70 minutes 1.51 seconds (4201.51 seconds total)