Starting phenix.real_space_refine on Sun Dec 29 19:55:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1v_27138/12_2024/8d1v_27138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1v_27138/12_2024/8d1v_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_27138/12_2024/8d1v_27138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1v_27138/12_2024/8d1v_27138.map" model { file = "/net/cci-nas-00/data/ceres_data/8d1v_27138/12_2024/8d1v_27138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1v_27138/12_2024/8d1v_27138.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.79, per 1000 atoms: 0.62 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: 2.75 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.05 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: 5.10 Time building geometry restraints manager: 3.19 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: 2.750 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: 0.290 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.250 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.360 ------------------------------------------------------------------------------- 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 11327 Z= 0.356 Angle : 0.743 24.374 15507 Z= 0.402 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (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 TRP 0.015 0.001 TRP A 597 HIS 0.010 0.001 HIS A 931 PHE 0.020 0.002 PHE A 757 TYR 0.015 0.002 TYR A 577 ARG 0.004 0.000 ARG A 53 *********************** 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 : 1.146 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: 0.7612 (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: 0.6168 (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: 1.7675 time to fit residues: 305.9964 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 : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.2980 chunk 95 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 0.1980 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 276 ASN A1376 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11327 Z= 0.285 Angle : 0.616 10.924 15507 Z= 0.329 Chirality : 0.042 0.168 1673 Planarity : 0.005 0.046 1829 Dihedral : 18.327 175.618 2133 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 26.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.98 % Allowed : 9.74 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1217 helix: 0.77 (0.30), residues: 319 sheet: 0.21 (0.35), residues: 209 loop : -0.56 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1512 HIS 0.007 0.002 HIS A 931 PHE 0.015 0.002 PHE A 757 TYR 0.019 0.002 TYR A 534 ARG 0.004 0.001 ARG A1504 *********************** 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 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 155 LEU cc_start: 0.7506 (mt) cc_final: 0.7276 (mp) REVERT: A 188 LYS cc_start: 0.7364 (ptpt) cc_final: 0.7106 (mtmt) REVERT: A 209 LYS cc_start: 0.5874 (pttm) cc_final: 0.5378 (pttp) REVERT: A 293 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.5787 (ptm-80) REVERT: A 294 ARG cc_start: 0.7585 (ptt-90) cc_final: 0.7285 (ttp-170) REVERT: A 409 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7124 (mm-30) REVERT: A 473 MET cc_start: 0.7450 (mmm) cc_final: 0.7235 (mmt) REVERT: A 507 PHE cc_start: 0.7658 (m-80) cc_final: 0.7453 (m-10) REVERT: A 576 LYS cc_start: 0.7587 (mttp) cc_final: 0.7282 (mtpt) REVERT: A 614 LEU cc_start: 0.7460 (tp) cc_final: 0.7054 (tt) REVERT: A 616 GLU cc_start: 0.6029 (tp30) cc_final: 0.5553 (tt0) REVERT: A 627 GLU cc_start: 0.8156 (tt0) cc_final: 0.7923 (tt0) REVERT: A 896 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6630 (ttp80) REVERT: A 970 ASP cc_start: 0.6896 (p0) cc_final: 0.6671 (p0) REVERT: A 1369 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: A 1375 LYS cc_start: 0.6342 (OUTLIER) cc_final: 0.5794 (ttpt) REVERT: A 1395 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6460 (mmp80) REVERT: A 1478 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: A 1487 MET cc_start: 0.8570 (ptt) cc_final: 0.8156 (ptt) outliers start: 21 outliers final: 4 residues processed: 119 average time/residue: 1.6496 time to fit residues: 210.3318 Evaluate side-chains 105 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 485 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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** A1405 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11327 Z= 0.254 Angle : 0.580 9.166 15507 Z= 0.307 Chirality : 0.042 0.162 1673 Planarity : 0.005 0.049 1829 Dihedral : 18.164 174.296 2133 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 29.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.89 % Allowed : 13.14 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1217 helix: 1.09 (0.30), residues: 319 sheet: 0.15 (0.34), residues: 214 loop : -0.70 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1512 HIS 0.006 0.001 HIS A 931 PHE 0.013 0.002 PHE A 757 TYR 0.014 0.002 TYR A 534 ARG 0.005 0.001 ARG A1565 *********************** 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 127 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.7373 (ttp) cc_final: 0.7143 (ttm) REVERT: A 188 LYS cc_start: 0.7302 (ptpt) cc_final: 0.7042 (mtmt) REVERT: A 209 LYS cc_start: 0.5817 (pttm) cc_final: 0.5331 (pttp) REVERT: A 293 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.5814 (ptm-80) REVERT: A 294 ARG cc_start: 0.7525 (ptt-90) cc_final: 0.7261 (ttp-170) REVERT: A 409 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7124 (mm-30) REVERT: A 473 MET cc_start: 0.7383 (mmm) cc_final: 0.7070 (mmt) REVERT: A 576 LYS cc_start: 0.7632 (mttp) cc_final: 0.7345 (mtpt) REVERT: A 616 GLU cc_start: 0.5879 (tp30) cc_final: 0.5508 (tt0) REVERT: A 627 GLU cc_start: 0.8179 (tt0) cc_final: 0.7934 (tt0) REVERT: A 664 GLU cc_start: 0.5872 (tp30) cc_final: 0.5660 (pt0) REVERT: A 735 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.4915 (pp20) REVERT: A 970 ASP cc_start: 0.6964 (p0) cc_final: 0.6742 (p0) REVERT: A 1305 MET cc_start: 0.6250 (ptp) cc_final: 0.5982 (ptp) REVERT: A 1363 SER cc_start: 0.8575 (m) cc_final: 0.8343 (m) REVERT: A 1369 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: A 1375 LYS cc_start: 0.6395 (OUTLIER) cc_final: 0.5842 (ttpt) REVERT: A 1395 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6604 (mmp80) REVERT: A 1478 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7149 (mt-10) REVERT: A 1487 MET cc_start: 0.8549 (ptt) cc_final: 0.8144 (ptt) outliers start: 20 outliers final: 7 residues processed: 122 average time/residue: 1.5521 time to fit residues: 202.7002 Evaluate side-chains 113 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 409 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 818 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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** A1405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11327 Z= 0.490 Angle : 0.787 12.604 15507 Z= 0.409 Chirality : 0.050 0.190 1673 Planarity : 0.007 0.052 1829 Dihedral : 18.212 175.846 2133 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 32.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.40 % Favored : 92.52 % Rotamer: Outliers : 3.69 % Allowed : 13.99 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1217 helix: 0.35 (0.29), residues: 313 sheet: 0.03 (0.35), residues: 211 loop : -1.01 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1512 HIS 0.011 0.002 HIS A 691 PHE 0.021 0.003 PHE A 757 TYR 0.021 0.003 TYR A 534 ARG 0.009 0.001 ARG A1565 *********************** 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: 39 poor density : 104 time to evaluate : 1.225 Fit side-chains REVERT: A 46 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6930 (tptm) REVERT: A 155 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7525 (mp) REVERT: A 173 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8073 (mt) REVERT: A 188 LYS cc_start: 0.7457 (ptpt) cc_final: 0.7162 (mtmt) REVERT: A 209 LYS cc_start: 0.5744 (pttm) cc_final: 0.5178 (pttp) REVERT: A 293 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.6409 (ptm-80) REVERT: A 294 ARG cc_start: 0.7602 (ptt-90) cc_final: 0.7347 (ttp-170) REVERT: A 341 GLU cc_start: 0.6546 (pm20) cc_final: 0.6243 (pm20) REVERT: A 409 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: A 473 MET cc_start: 0.7585 (mmm) cc_final: 0.7140 (mmm) REVERT: A 576 LYS cc_start: 0.7726 (mttp) cc_final: 0.7412 (mtpt) REVERT: A 664 GLU cc_start: 0.6026 (tp30) cc_final: 0.5662 (pt0) REVERT: A 667 GLU cc_start: 0.5552 (OUTLIER) cc_final: 0.4892 (pt0) REVERT: A 735 GLU cc_start: 0.5846 (OUTLIER) cc_final: 0.5116 (pp20) REVERT: A 896 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6581 (ttp80) REVERT: A 970 ASP cc_start: 0.7237 (p0) cc_final: 0.6808 (p0) REVERT: A 1369 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: A 1375 LYS cc_start: 0.6426 (OUTLIER) cc_final: 0.5925 (ttpt) REVERT: A 1395 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6829 (mmp80) REVERT: A 1405 ASN cc_start: 0.6301 (m-40) cc_final: 0.5987 (m-40) REVERT: A 1478 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: A 1487 MET cc_start: 0.8543 (ptt) cc_final: 0.8226 (ptt) REVERT: A 1532 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: A 1592 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7711 (mmtt) outliers start: 39 outliers final: 14 residues processed: 136 average time/residue: 1.6527 time to fit residues: 239.8647 Evaluate side-chains 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 155 LEU 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 579 THR 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 818 LYS 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 Chi-restraints excluded: chain A residue 1532 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 101 optimal weight: 6.9990 chunk 69 optimal weight: 0.0060 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11327 Z= 0.132 Angle : 0.496 9.256 15507 Z= 0.264 Chirality : 0.039 0.158 1673 Planarity : 0.004 0.050 1829 Dihedral : 17.910 172.267 2133 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 31.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.08 % Allowed : 16.54 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1217 helix: 1.28 (0.30), residues: 321 sheet: 0.22 (0.35), residues: 214 loop : -0.72 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1466 HIS 0.003 0.001 HIS A 184 PHE 0.011 0.001 PHE A 757 TYR 0.009 0.001 TYR A 492 ARG 0.004 0.000 ARG A1310 *********************** 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 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 17 MET cc_start: 0.8191 (ttp) cc_final: 0.7901 (ttp) REVERT: A 90 PHE cc_start: 0.7258 (m-80) cc_final: 0.6662 (m-80) REVERT: A 209 LYS cc_start: 0.5757 (pttm) cc_final: 0.5270 (pttp) REVERT: A 294 ARG cc_start: 0.7566 (ptt-90) cc_final: 0.7266 (ttp-170) REVERT: A 341 GLU cc_start: 0.6434 (pm20) cc_final: 0.6230 (pm20) REVERT: A 473 MET cc_start: 0.7493 (mmm) cc_final: 0.6995 (mmt) REVERT: A 524 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: A 571 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7877 (ttp80) REVERT: A 576 LYS cc_start: 0.7687 (mttp) cc_final: 0.7420 (mtpt) REVERT: A 664 GLU cc_start: 0.5980 (tp30) cc_final: 0.5725 (pt0) REVERT: A 735 GLU cc_start: 0.5668 (OUTLIER) cc_final: 0.4920 (pp20) REVERT: A 1363 SER cc_start: 0.8503 (m) cc_final: 0.8255 (m) REVERT: A 1369 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: A 1395 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6690 (mmp80) REVERT: A 1405 ASN cc_start: 0.6247 (m-40) cc_final: 0.5946 (m-40) REVERT: A 1487 MET cc_start: 0.8407 (ptt) cc_final: 0.8021 (ptt) outliers start: 22 outliers final: 9 residues processed: 123 average time/residue: 1.6091 time to fit residues: 212.0991 Evaluate side-chains 112 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 421 ILE 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 511 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 671 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 117 optimal weight: 0.5980 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1555 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11327 Z= 0.318 Angle : 0.627 9.358 15507 Z= 0.329 Chirality : 0.043 0.154 1673 Planarity : 0.005 0.050 1829 Dihedral : 18.004 175.374 2133 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 31.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.15 % Favored : 92.77 % Rotamer: Outliers : 3.50 % Allowed : 16.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1217 helix: 0.98 (0.30), residues: 319 sheet: 0.11 (0.35), residues: 211 loop : -0.85 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1466 HIS 0.007 0.001 HIS A 691 PHE 0.017 0.002 PHE A 757 TYR 0.018 0.002 TYR A 534 ARG 0.008 0.001 ARG A1310 *********************** 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: 37 poor density : 104 time to evaluate : 1.209 Fit side-chains REVERT: A 17 MET cc_start: 0.8311 (ttp) cc_final: 0.8090 (ttp) REVERT: A 155 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7546 (mp) REVERT: A 209 LYS cc_start: 0.5699 (pttm) cc_final: 0.5200 (pttp) REVERT: A 294 ARG cc_start: 0.7551 (ptt-90) cc_final: 0.7287 (ttp-170) REVERT: A 298 LEU cc_start: 0.6204 (mt) cc_final: 0.5652 (mt) REVERT: A 341 GLU cc_start: 0.6535 (pm20) cc_final: 0.6270 (pm20) REVERT: A 395 VAL cc_start: 0.6454 (OUTLIER) cc_final: 0.6014 (m) REVERT: A 409 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7151 (mm-30) REVERT: A 473 MET cc_start: 0.7566 (mmm) cc_final: 0.7200 (mmt) REVERT: A 524 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: A 576 LYS cc_start: 0.7747 (mttp) cc_final: 0.7453 (mtpt) REVERT: A 664 GLU cc_start: 0.5952 (tp30) cc_final: 0.5710 (pt0) REVERT: A 667 GLU cc_start: 0.5390 (OUTLIER) cc_final: 0.5067 (pt0) REVERT: A 707 GLU cc_start: 0.6025 (OUTLIER) cc_final: 0.5348 (tt0) REVERT: A 735 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.5085 (pp20) REVERT: A 970 ASP cc_start: 0.7122 (p0) cc_final: 0.6795 (p0) REVERT: A 1369 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: A 1375 LYS cc_start: 0.6433 (OUTLIER) cc_final: 0.5885 (ttpt) REVERT: A 1395 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6617 (mmp80) REVERT: A 1405 ASN cc_start: 0.6310 (m-40) cc_final: 0.5999 (m-40) REVERT: A 1487 MET cc_start: 0.8525 (ptt) cc_final: 0.8235 (ptt) REVERT: A 1592 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7691 (mmtt) outliers start: 37 outliers final: 15 residues processed: 134 average time/residue: 1.5610 time to fit residues: 224.2056 Evaluate side-chains 127 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 162 ASP 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 579 THR 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 818 LYS 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 1592 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11327 Z= 0.238 Angle : 0.559 9.496 15507 Z= 0.296 Chirality : 0.041 0.148 1673 Planarity : 0.004 0.050 1829 Dihedral : 17.917 174.037 2133 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 31.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.41 % Favored : 93.51 % Rotamer: Outliers : 3.21 % Allowed : 16.92 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1217 helix: 1.06 (0.30), residues: 321 sheet: 0.13 (0.35), residues: 214 loop : -0.82 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1466 HIS 0.006 0.001 HIS A 691 PHE 0.015 0.002 PHE A 757 TYR 0.014 0.002 TYR A 534 ARG 0.007 0.000 ARG A1310 *********************** 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 138 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 1.085 Fit side-chains REVERT: A 17 MET cc_start: 0.8315 (ttp) cc_final: 0.8077 (ttp) REVERT: A 155 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7509 (mp) REVERT: A 173 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8077 (mt) REVERT: A 209 LYS cc_start: 0.5753 (pttm) cc_final: 0.5258 (pttp) REVERT: A 294 ARG cc_start: 0.7514 (ptt-90) cc_final: 0.7212 (ttp-170) REVERT: A 298 LEU cc_start: 0.6067 (mt) cc_final: 0.5814 (mp) REVERT: A 341 GLU cc_start: 0.6503 (pm20) cc_final: 0.6209 (pm20) REVERT: A 473 MET cc_start: 0.7512 (mmm) cc_final: 0.6955 (mmt) REVERT: A 524 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: A 576 LYS cc_start: 0.7745 (mttp) cc_final: 0.7468 (mtpt) REVERT: A 664 GLU cc_start: 0.6006 (tp30) cc_final: 0.5357 (pt0) REVERT: A 707 GLU cc_start: 0.5985 (OUTLIER) cc_final: 0.5269 (tt0) REVERT: A 735 GLU cc_start: 0.5723 (OUTLIER) cc_final: 0.4988 (pp20) REVERT: A 1363 SER cc_start: 0.8565 (m) cc_final: 0.8346 (m) REVERT: A 1369 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: A 1375 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.5903 (ttpt) REVERT: A 1395 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6716 (mmp80) REVERT: A 1478 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: A 1487 MET cc_start: 0.8488 (ptt) cc_final: 0.8186 (ptt) REVERT: A 1579 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6435 (mp) outliers start: 34 outliers final: 13 residues processed: 129 average time/residue: 1.6191 time to fit residues: 223.9323 Evaluate side-chains 125 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 155 LEU 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 334 THR 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 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 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 72 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 95 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11327 Z= 0.317 Angle : 0.628 9.637 15507 Z= 0.331 Chirality : 0.044 0.151 1673 Planarity : 0.005 0.050 1829 Dihedral : 17.956 175.254 2133 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 31.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.40 % Favored : 92.52 % Rotamer: Outliers : 3.69 % Allowed : 17.01 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1217 helix: 0.86 (0.30), residues: 313 sheet: 0.01 (0.35), residues: 211 loop : -0.89 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1466 HIS 0.008 0.001 HIS A 691 PHE 0.017 0.002 PHE A 757 TYR 0.017 0.002 TYR A 534 ARG 0.006 0.001 ARG A1310 *********************** 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 142 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 1.134 Fit side-chains REVERT: A 155 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7511 (mp) REVERT: A 173 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8062 (mt) REVERT: A 209 LYS cc_start: 0.5788 (pttm) cc_final: 0.5290 (pttp) REVERT: A 294 ARG cc_start: 0.7438 (ptt-90) cc_final: 0.7169 (ttp-170) REVERT: A 298 LEU cc_start: 0.5984 (mt) cc_final: 0.5505 (mt) REVERT: A 341 GLU cc_start: 0.6599 (pm20) cc_final: 0.6226 (pm20) REVERT: A 409 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7091 (mm-30) REVERT: A 473 MET cc_start: 0.7553 (mmm) cc_final: 0.7139 (mmt) REVERT: A 524 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: A 664 GLU cc_start: 0.5855 (tp30) cc_final: 0.5618 (pt0) REVERT: A 707 GLU cc_start: 0.6076 (OUTLIER) cc_final: 0.5377 (tt0) REVERT: A 735 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.5108 (pp20) REVERT: A 1369 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: A 1375 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.5870 (ttpt) REVERT: A 1395 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6726 (mmp80) REVERT: A 1478 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: A 1487 MET cc_start: 0.8527 (ptt) cc_final: 0.8256 (ptt) REVERT: A 1579 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6486 (mp) REVERT: A 1592 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7705 (mmtt) outliers start: 39 outliers final: 18 residues processed: 136 average time/residue: 1.4748 time to fit residues: 215.0640 Evaluate side-chains 130 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 155 LEU 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 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 579 THR Chi-restraints excluded: chain A residue 656 VAL 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 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 1579 LEU Chi-restraints excluded: chain A residue 1592 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 107 optimal weight: 0.3980 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11327 Z= 0.333 Angle : 0.642 9.893 15507 Z= 0.338 Chirality : 0.044 0.159 1673 Planarity : 0.005 0.049 1829 Dihedral : 17.968 174.968 2133 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 31.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.98 % Favored : 92.85 % Rotamer: Outliers : 3.12 % Allowed : 17.86 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.24), residues: 1217 helix: 0.77 (0.30), residues: 313 sheet: -0.05 (0.35), residues: 211 loop : -0.95 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1466 HIS 0.008 0.001 HIS A 691 PHE 0.020 0.002 PHE A 757 TYR 0.018 0.002 TYR A 534 ARG 0.007 0.001 ARG A1310 *********************** 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 134 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 1.208 Fit side-chains REVERT: A 5 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7075 (ttm) REVERT: A 155 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7537 (mp) REVERT: A 173 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8025 (mt) REVERT: A 209 LYS cc_start: 0.5785 (pttm) cc_final: 0.5282 (pttp) REVERT: A 294 ARG cc_start: 0.7446 (ptt-90) cc_final: 0.7168 (ttp-170) REVERT: A 298 LEU cc_start: 0.6001 (mt) cc_final: 0.5771 (OUTLIER) REVERT: A 341 GLU cc_start: 0.6589 (pm20) cc_final: 0.6190 (pm20) REVERT: A 473 MET cc_start: 0.7556 (mmm) cc_final: 0.7071 (mmt) REVERT: A 524 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7315 (mt-10) REVERT: A 664 GLU cc_start: 0.5775 (tp30) cc_final: 0.5498 (pt0) REVERT: A 666 GLU cc_start: 0.6333 (tt0) cc_final: 0.6006 (mt-10) REVERT: A 735 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.5209 (pp20) REVERT: A 1305 MET cc_start: 0.6273 (ptp) cc_final: 0.6045 (ptp) REVERT: A 1369 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: A 1375 LYS cc_start: 0.6398 (OUTLIER) cc_final: 0.5841 (ttpt) REVERT: A 1395 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6726 (mmp80) REVERT: A 1478 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: A 1487 MET cc_start: 0.8530 (ptt) cc_final: 0.8272 (ptt) REVERT: A 1579 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6486 (mp) REVERT: A 1592 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7692 (mmtt) outliers start: 33 outliers final: 18 residues processed: 129 average time/residue: 1.4677 time to fit residues: 203.5398 Evaluate side-chains 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 155 LEU 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 334 THR 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 656 VAL 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 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 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 73 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 HIS A1405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11327 Z= 0.214 Angle : 0.550 9.410 15507 Z= 0.293 Chirality : 0.041 0.152 1673 Planarity : 0.004 0.050 1829 Dihedral : 17.905 173.650 2133 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 32.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.57 % Favored : 93.34 % Rotamer: Outliers : 2.84 % Allowed : 18.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.24), residues: 1217 helix: 1.07 (0.30), residues: 321 sheet: 0.05 (0.35), residues: 214 loop : -0.85 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1466 HIS 0.005 0.001 HIS A 691 PHE 0.014 0.001 PHE A 757 TYR 0.013 0.002 TYR A 534 ARG 0.006 0.000 ARG A1310 ********************** 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 130 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 1.318 Fit side-chains REVERT: A 17 MET cc_start: 0.8322 (ttp) cc_final: 0.8035 (ttp) REVERT: A 173 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8055 (mt) REVERT: A 209 LYS cc_start: 0.5758 (pttm) cc_final: 0.5260 (pttp) REVERT: A 294 ARG cc_start: 0.7434 (ptt-90) cc_final: 0.7099 (ttp-170) REVERT: A 341 GLU cc_start: 0.6458 (pm20) cc_final: 0.6077 (pm20) REVERT: A 473 MET cc_start: 0.7536 (mmm) cc_final: 0.7124 (mmt) REVERT: A 524 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7214 (mt-10) REVERT: A 664 GLU cc_start: 0.5774 (tp30) cc_final: 0.5557 (pt0) REVERT: A 666 GLU cc_start: 0.6274 (tt0) cc_final: 0.5950 (mt-10) REVERT: A 735 GLU cc_start: 0.5827 (OUTLIER) cc_final: 0.5217 (pp20) REVERT: A 1369 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6604 (mp0) REVERT: A 1375 LYS cc_start: 0.6397 (OUTLIER) cc_final: 0.5850 (ttpt) REVERT: A 1395 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6693 (mmp80) REVERT: A 1478 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: A 1487 MET cc_start: 0.8471 (ptt) cc_final: 0.8187 (ptt) REVERT: A 1579 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6518 (mp) REVERT: A 1592 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7674 (mmtt) outliers start: 30 outliers final: 18 residues processed: 125 average time/residue: 1.5114 time to fit residues: 204.1219 Evaluate side-chains 124 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 334 THR 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 656 VAL Chi-restraints excluded: chain A residue 671 VAL 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 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 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 30 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 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 = 0.4142 r_free = 0.4142 target = 0.184343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.157955 restraints weight = 11167.259| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.44 r_work: 0.3709 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.003 0.030 11327 Z= 0.178 Angle : 0.506 9.205 15507 Z= 0.269 Chirality : 0.039 0.143 1673 Planarity : 0.004 0.050 1829 Dihedral : 17.834 172.588 2133 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 32.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.24 % Favored : 93.67 % Rotamer: Outliers : 2.46 % Allowed : 18.62 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1217 helix: 1.35 (0.30), residues: 323 sheet: 0.14 (0.35), residues: 214 loop : -0.72 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1466 HIS 0.004 0.001 HIS A 691 PHE 0.015 0.001 PHE A1584 TYR 0.011 0.001 TYR A 534 ARG 0.005 0.000 ARG A1310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3945.85 seconds wall clock time: 72 minutes 28.26 seconds (4348.26 seconds total)