Starting phenix.real_space_refine on Tue Jul 29 10:42:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1v_27138/07_2025/8d1v_27138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1v_27138/07_2025/8d1v_27138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d1v_27138/07_2025/8d1v_27138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1v_27138/07_2025/8d1v_27138.map" model { file = "/net/cci-nas-00/data/ceres_data/8d1v_27138/07_2025/8d1v_27138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1v_27138/07_2025/8d1v_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-5711/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: 6.67, per 1000 atoms: 0.61 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: 2.74 Conformation dependent library (CDL) restraints added in 1.4 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: 3.58 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: 4.55 Time building geometry restraints manager: 3.21 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: 1.170 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: 0.070 Set scattering table: 0.100 Process input model: 32.670 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.740 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.23799 ( 364) hydrogen bonds : angle 8.82194 ( 1097) metal coordination : bond 0.00820 ( 16) metal coordination : angle 3.36015 ( 21) covalent geometry : bond 0.00601 (11327) covalent geometry : angle 0.74278 (15507) *********************** 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 : 1.121 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: 1.6906 time to fit residues: 292.9177 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 : 1.097 ------------------------------------------------------------------------------- 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: 6.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.181967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.154034 restraints weight = 11091.572| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.25 r_work: 0.3668 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 11343 Z= 0.204 Angle : 0.626 10.924 15528 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 Details of bonding type rmsd hydrogen bonds : bond 0.05814 ( 364) hydrogen bonds : angle 5.79170 ( 1097) metal coordination : bond 0.00849 ( 16) metal coordination : angle 3.17151 ( 21) covalent geometry : bond 0.00431 (11327) covalent geometry : angle 0.61591 (15507) *********************** 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 : 1.537 Fit side-chains revert: symmetry clash REVERT: A 155 LEU cc_start: 0.7569 (mt) cc_final: 0.7296 (mp) REVERT: A 188 LYS cc_start: 0.7431 (ptpt) cc_final: 0.7152 (mtmt) REVERT: A 209 LYS cc_start: 0.5811 (pttm) cc_final: 0.5339 (pttp) REVERT: A 293 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.5948 (ptm-80) REVERT: A 294 ARG cc_start: 0.7627 (ptt-90) cc_final: 0.7308 (ttp-170) REVERT: A 409 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7362 (mm-30) REVERT: A 473 MET cc_start: 0.7532 (mmm) cc_final: 0.7324 (mmt) REVERT: A 507 PHE cc_start: 0.7829 (m-80) cc_final: 0.7626 (m-10) REVERT: A 576 LYS cc_start: 0.7756 (mttp) cc_final: 0.7422 (mtpt) REVERT: A 614 LEU cc_start: 0.7513 (tp) cc_final: 0.7035 (tt) REVERT: A 616 GLU cc_start: 0.6141 (tp30) cc_final: 0.5591 (tt0) REVERT: A 627 GLU cc_start: 0.8124 (tt0) cc_final: 0.7881 (tt0) REVERT: A 896 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7055 (ttp80) REVERT: A 970 ASP cc_start: 0.6970 (p0) cc_final: 0.6590 (p0) REVERT: A 1369 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: A 1375 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6020 (ttpt) REVERT: A 1395 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6667 (mmp80) REVERT: A 1478 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7175 (mt-10) REVERT: A 1487 MET cc_start: 0.8531 (ptt) cc_final: 0.8086 (ptt) outliers start: 21 outliers final: 4 residues processed: 119 average time/residue: 1.5479 time to fit residues: 197.5100 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 : 1.180 ------------------------------------------------------------------------------- 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 56 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 83 optimal weight: 0.4980 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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** A1405 ASN 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 = 0.183997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158078 restraints weight = 11340.004| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.28 r_work: 0.3688 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11343 Z= 0.160 Angle : 0.560 9.370 15528 Z= 0.292 Chirality : 0.041 0.158 1673 Planarity : 0.004 0.050 1829 Dihedral : 18.139 173.860 2133 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 29.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.80 % Allowed : 13.14 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.03 (0.24), residues: 1217 helix: 1.23 (0.30), residues: 319 sheet: 0.16 (0.34), residues: 214 loop : -0.67 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1512 HIS 0.006 0.001 HIS A 931 PHE 0.014 0.002 PHE A 757 TYR 0.015 0.002 TYR A 534 ARG 0.005 0.001 ARG A1565 Details of bonding type rmsd hydrogen bonds : bond 0.04822 ( 364) hydrogen bonds : angle 5.14415 ( 1097) metal coordination : bond 0.00604 ( 16) metal coordination : angle 2.70985 ( 21) covalent geometry : bond 0.00344 (11327) covalent geometry : angle 0.55112 (15507) *********************** 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 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.7667 (ttp) cc_final: 0.7440 (ttm) REVERT: A 155 LEU cc_start: 0.7562 (mt) cc_final: 0.7320 (mp) REVERT: A 188 LYS cc_start: 0.7281 (ptpt) cc_final: 0.7044 (mtmt) REVERT: A 209 LYS cc_start: 0.5793 (pttm) cc_final: 0.5329 (pttp) REVERT: A 293 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6006 (ptm-80) REVERT: A 294 ARG cc_start: 0.7596 (ptt-90) cc_final: 0.7259 (ttp-170) REVERT: A 409 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: A 473 MET cc_start: 0.7458 (mmm) cc_final: 0.7163 (mmt) REVERT: A 576 LYS cc_start: 0.7717 (mttp) cc_final: 0.7439 (mtpt) REVERT: A 579 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7813 (t) REVERT: A 600 GLU cc_start: 0.6136 (tp30) cc_final: 0.5876 (tp30) REVERT: A 614 LEU cc_start: 0.7625 (tp) cc_final: 0.7246 (tt) REVERT: A 616 GLU cc_start: 0.6017 (tp30) cc_final: 0.5537 (tt0) REVERT: A 627 GLU cc_start: 0.8146 (tt0) cc_final: 0.7899 (tt0) REVERT: A 664 GLU cc_start: 0.6113 (tp30) cc_final: 0.5706 (pt0) REVERT: A 735 GLU cc_start: 0.5821 (OUTLIER) cc_final: 0.5028 (pp20) REVERT: A 970 ASP cc_start: 0.7059 (p0) cc_final: 0.6846 (p0) REVERT: A 1305 MET cc_start: 0.6335 (ptp) cc_final: 0.6107 (ptp) REVERT: A 1363 SER cc_start: 0.8411 (m) cc_final: 0.8174 (m) REVERT: A 1369 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: A 1375 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5889 (ttpt) REVERT: A 1395 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6831 (mmp80) REVERT: A 1487 MET cc_start: 0.8481 (ptt) cc_final: 0.8036 (ptt) outliers start: 19 outliers final: 7 residues processed: 122 average time/residue: 1.5306 time to fit residues: 199.8149 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 : 1.231 ------------------------------------------------------------------------------- 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 579 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 10.0000 chunk 100 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.181031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155860 restraints weight = 11241.679| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.24 r_work: 0.3653 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 11343 Z= 0.262 Angle : 0.699 12.389 15528 Z= 0.359 Chirality : 0.046 0.165 1673 Planarity : 0.006 0.052 1829 Dihedral : 18.145 175.739 2133 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 32.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.50 % Allowed : 13.61 % Favored : 82.89 % 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: -0.40 (0.24), residues: 1217 helix: 0.75 (0.30), residues: 313 sheet: 0.13 (0.35), residues: 211 loop : -0.86 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1466 HIS 0.009 0.002 HIS A 691 PHE 0.019 0.002 PHE A 757 TYR 0.019 0.003 TYR A 534 ARG 0.008 0.001 ARG A1565 Details of bonding type rmsd hydrogen bonds : bond 0.05511 ( 364) hydrogen bonds : angle 5.52552 ( 1097) metal coordination : bond 0.00709 ( 16) metal coordination : angle 3.62308 ( 21) covalent geometry : bond 0.00574 (11327) covalent geometry : angle 0.68624 (15507) *********************** 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 144 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 1.300 Fit side-chains REVERT: A 5 MET cc_start: 0.7691 (ttp) cc_final: 0.7473 (ttm) REVERT: A 46 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.7096 (tptm) REVERT: A 90 PHE cc_start: 0.7293 (m-80) cc_final: 0.6931 (m-80) REVERT: A 155 LEU cc_start: 0.7660 (mt) cc_final: 0.7394 (mp) REVERT: A 188 LYS cc_start: 0.7353 (ptpt) cc_final: 0.7136 (mtmt) REVERT: A 209 LYS cc_start: 0.5696 (pttm) cc_final: 0.5238 (pttp) REVERT: A 294 ARG cc_start: 0.7649 (ptt-90) cc_final: 0.7301 (ttp-170) REVERT: A 341 GLU cc_start: 0.6619 (pm20) cc_final: 0.6363 (pm20) REVERT: A 409 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7479 (mm-30) REVERT: A 473 MET cc_start: 0.7575 (mmm) cc_final: 0.7128 (mmt) REVERT: A 576 LYS cc_start: 0.7838 (mttp) cc_final: 0.7556 (mtpt) REVERT: A 627 GLU cc_start: 0.8178 (tt0) cc_final: 0.7943 (tt0) REVERT: A 664 GLU cc_start: 0.6134 (tp30) cc_final: 0.5695 (pt0) REVERT: A 667 GLU cc_start: 0.5458 (OUTLIER) cc_final: 0.5001 (pt0) REVERT: A 707 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5638 (tt0) REVERT: A 735 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.5378 (pp20) REVERT: A 855 ARG cc_start: 0.7081 (mmp-170) cc_final: 0.6862 (mpp-170) REVERT: A 896 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7055 (ttp80) REVERT: A 930 TYR cc_start: 0.7470 (p90) cc_final: 0.7249 (p90) REVERT: A 970 ASP cc_start: 0.7285 (p0) cc_final: 0.6824 (p0) REVERT: A 1305 MET cc_start: 0.6375 (ptp) cc_final: 0.6106 (ptp) REVERT: A 1369 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: A 1375 LYS cc_start: 0.6547 (OUTLIER) cc_final: 0.6012 (ttpt) REVERT: A 1395 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7083 (mmp80) REVERT: A 1405 ASN cc_start: 0.6426 (m-40) cc_final: 0.6123 (m-40) REVERT: A 1478 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: A 1487 MET cc_start: 0.8518 (ptt) cc_final: 0.8152 (ptt) REVERT: A 1532 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7065 (tm-30) REVERT: A 1592 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7782 (mmtt) outliers start: 37 outliers final: 14 residues processed: 137 average time/residue: 1.5477 time to fit residues: 226.3172 Evaluate side-chains 130 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 169 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 307 ASP 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 667 GLU 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 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 31 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 55 optimal weight: 0.0980 chunk 114 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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** A1555 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.184084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157366 restraints weight = 11200.510| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.46 r_work: 0.3688 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2496 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= 0.142 Angle : 0.537 9.588 15528 Z= 0.281 Chirality : 0.040 0.156 1673 Planarity : 0.004 0.052 1829 Dihedral : 17.939 173.504 2133 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 31.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.27 % Allowed : 15.88 % Favored : 81.85 % 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: -0.09 (0.24), residues: 1217 helix: 1.21 (0.30), residues: 319 sheet: 0.23 (0.35), residues: 214 loop : -0.76 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1466 HIS 0.005 0.001 HIS A 691 PHE 0.013 0.001 PHE A 757 TYR 0.012 0.002 TYR A 534 ARG 0.003 0.000 ARG A1310 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 364) hydrogen bonds : angle 4.97998 ( 1097) metal coordination : bond 0.00434 ( 16) metal coordination : angle 2.51992 ( 21) covalent geometry : bond 0.00302 (11327) covalent geometry : angle 0.52904 (15507) *********************** 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 131 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.146 Fit side-chains REVERT: A 5 MET cc_start: 0.7662 (ttp) cc_final: 0.7445 (ttm) REVERT: A 17 MET cc_start: 0.8298 (ttp) cc_final: 0.8048 (ttp) REVERT: A 155 LEU cc_start: 0.7615 (mt) cc_final: 0.7396 (mp) REVERT: A 173 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8104 (mt) REVERT: A 209 LYS cc_start: 0.5732 (pttm) cc_final: 0.5275 (pttp) REVERT: A 294 ARG cc_start: 0.7594 (ptt-90) cc_final: 0.7288 (ttp-170) REVERT: A 341 GLU cc_start: 0.6611 (pm20) cc_final: 0.6305 (pm20) REVERT: A 401 LEU cc_start: 0.6644 (tp) cc_final: 0.6420 (tp) REVERT: A 473 MET cc_start: 0.7553 (mmm) cc_final: 0.7057 (mmt) REVERT: A 576 LYS cc_start: 0.7777 (mttp) cc_final: 0.7503 (mtpt) REVERT: A 664 GLU cc_start: 0.6075 (tp30) cc_final: 0.5266 (pt0) REVERT: A 735 GLU cc_start: 0.5907 (OUTLIER) cc_final: 0.5189 (pp20) REVERT: A 1363 SER cc_start: 0.8402 (m) cc_final: 0.8165 (m) REVERT: A 1369 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: A 1375 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.5983 (ttpt) REVERT: A 1395 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7020 (mmp80) REVERT: A 1487 MET cc_start: 0.8456 (ptt) cc_final: 0.8063 (ptt) outliers start: 24 outliers final: 9 residues processed: 127 average time/residue: 1.4719 time to fit residues: 199.9788 Evaluate side-chains 116 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 334 THR 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 579 THR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.178638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.153250 restraints weight = 11371.194| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.19 r_work: 0.3622 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 11343 Z= 0.401 Angle : 0.875 13.774 15528 Z= 0.447 Chirality : 0.053 0.210 1673 Planarity : 0.007 0.056 1829 Dihedral : 18.166 176.207 2133 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 32.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.30 % Favored : 91.54 % Rotamer: Outliers : 3.97 % Allowed : 15.50 % Favored : 80.53 % 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: -0.97 (0.23), residues: 1217 helix: 0.13 (0.29), residues: 313 sheet: -0.03 (0.35), residues: 213 loop : -1.22 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A1512 HIS 0.013 0.002 HIS A 691 PHE 0.023 0.003 PHE A 757 TYR 0.022 0.004 TYR A 534 ARG 0.008 0.001 ARG A1565 Details of bonding type rmsd hydrogen bonds : bond 0.06416 ( 364) hydrogen bonds : angle 5.96057 ( 1097) metal coordination : bond 0.00942 ( 16) metal coordination : angle 4.23107 ( 21) covalent geometry : bond 0.00894 (11327) covalent geometry : angle 0.86203 (15507) *********************** 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 144 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 1.231 Fit side-chains REVERT: A 155 LEU cc_start: 0.7764 (mt) cc_final: 0.7491 (mp) REVERT: A 173 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8104 (mt) REVERT: A 209 LYS cc_start: 0.5734 (pttm) cc_final: 0.5205 (pttp) REVERT: A 298 LEU cc_start: 0.6098 (mt) cc_final: 0.5575 (mt) REVERT: A 341 GLU cc_start: 0.6781 (pm20) cc_final: 0.6407 (pm20) REVERT: A 409 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7558 (mm-30) REVERT: A 473 MET cc_start: 0.7639 (mmm) cc_final: 0.7258 (mmm) REVERT: A 524 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7455 (mt-10) REVERT: A 576 LYS cc_start: 0.7827 (mttp) cc_final: 0.7568 (mtpt) REVERT: A 664 GLU cc_start: 0.5933 (tp30) cc_final: 0.5460 (pt0) REVERT: A 707 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.5791 (tt0) REVERT: A 735 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5492 (pp20) REVERT: A 896 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7044 (ttp80) REVERT: A 970 ASP cc_start: 0.7368 (p0) cc_final: 0.7002 (p0) REVERT: A 1369 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 1375 LYS cc_start: 0.6505 (OUTLIER) cc_final: 0.6075 (ttpt) REVERT: A 1395 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7073 (mmp80) REVERT: A 1405 ASN cc_start: 0.6486 (m-40) cc_final: 0.6215 (m-40) REVERT: A 1478 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: A 1487 MET cc_start: 0.8506 (ptt) cc_final: 0.8271 (ptt) REVERT: A 1579 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6583 (mp) REVERT: A 1592 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7764 (mmtt) outliers start: 42 outliers final: 18 residues processed: 137 average time/residue: 1.4816 time to fit residues: 217.7971 Evaluate side-chains 125 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.184664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.157869 restraints weight = 11332.543| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.39 r_work: 0.3697 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11343 Z= 0.106 Angle : 0.517 9.464 15528 Z= 0.272 Chirality : 0.039 0.157 1673 Planarity : 0.004 0.050 1829 Dihedral : 17.906 172.816 2133 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 31.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 2.08 % Allowed : 17.86 % Favored : 80.06 % 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: -0.18 (0.24), residues: 1217 helix: 1.19 (0.30), residues: 321 sheet: 0.22 (0.35), residues: 204 loop : -0.87 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1466 HIS 0.003 0.001 HIS A 691 PHE 0.012 0.001 PHE A 776 TYR 0.008 0.001 TYR A 492 ARG 0.004 0.000 ARG A1310 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 364) hydrogen bonds : angle 4.84624 ( 1097) metal coordination : bond 0.00299 ( 16) metal coordination : angle 2.42464 ( 21) covalent geometry : bond 0.00215 (11327) covalent geometry : angle 0.51006 (15507) *********************** 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 127 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.154 Fit side-chains REVERT: A 5 MET cc_start: 0.7674 (ttp) cc_final: 0.7472 (ttm) REVERT: A 173 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8062 (mt) REVERT: A 209 LYS cc_start: 0.5691 (pttm) cc_final: 0.5229 (pttp) REVERT: A 293 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7218 (ptm-80) REVERT: A 341 GLU cc_start: 0.6494 (pm20) cc_final: 0.6155 (pm20) REVERT: A 401 LEU cc_start: 0.6547 (tp) cc_final: 0.6344 (tp) REVERT: A 473 MET cc_start: 0.7534 (mmm) cc_final: 0.7065 (mmt) REVERT: A 524 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7183 (mt-10) REVERT: A 576 LYS cc_start: 0.7841 (mttp) cc_final: 0.7595 (mtpt) REVERT: A 664 GLU cc_start: 0.5928 (tp30) cc_final: 0.5505 (pt0) REVERT: A 735 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.5249 (pp20) REVERT: A 833 MET cc_start: 0.7153 (mpp) cc_final: 0.6744 (mtp) REVERT: A 970 ASP cc_start: 0.7186 (p0) cc_final: 0.6789 (p0) REVERT: A 1363 SER cc_start: 0.8415 (m) cc_final: 0.8189 (m) REVERT: A 1369 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: A 1395 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6884 (mmp80) REVERT: A 1487 MET cc_start: 0.8390 (ptt) cc_final: 0.8036 (ptt) REVERT: A 1592 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7769 (mmtt) outliers start: 22 outliers final: 7 residues processed: 120 average time/residue: 1.8886 time to fit residues: 243.1544 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 : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 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 718 TYR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1592 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 A1405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.185510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.157516 restraints weight = 11276.423| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.52 r_work: 0.3719 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2843 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= 0.102 Angle : 0.486 8.785 15528 Z= 0.254 Chirality : 0.038 0.135 1673 Planarity : 0.004 0.050 1829 Dihedral : 17.753 171.362 2133 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 31.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.33 % Favored : 93.59 % Rotamer: Outliers : 1.98 % Allowed : 18.81 % Favored : 79.21 % 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: 0.15 (0.25), residues: 1217 helix: 1.61 (0.30), residues: 323 sheet: 0.15 (0.34), residues: 212 loop : -0.65 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1466 HIS 0.003 0.001 HIS A 691 PHE 0.012 0.001 PHE A 776 TYR 0.011 0.001 TYR A 534 ARG 0.008 0.000 ARG A1310 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 364) hydrogen bonds : angle 4.52722 ( 1097) metal coordination : bond 0.00306 ( 16) metal coordination : angle 1.89357 ( 21) covalent geometry : bond 0.00214 (11327) covalent geometry : angle 0.48088 (15507) *********************** 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 127 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.153 Fit side-chains REVERT: A 17 MET cc_start: 0.8103 (ttp) cc_final: 0.7854 (ttp) REVERT: A 46 LYS cc_start: 0.6811 (tmtt) cc_final: 0.6498 (tptm) REVERT: A 209 LYS cc_start: 0.5658 (pttm) cc_final: 0.5198 (pttp) REVERT: A 341 GLU cc_start: 0.6511 (pm20) cc_final: 0.6197 (pm20) REVERT: A 473 MET cc_start: 0.7547 (mmm) cc_final: 0.7194 (mmt) REVERT: A 524 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: A 576 LYS cc_start: 0.7784 (mttp) cc_final: 0.7501 (mtpt) REVERT: A 664 GLU cc_start: 0.5751 (tp30) cc_final: 0.5415 (pt0) REVERT: A 666 GLU cc_start: 0.6539 (tt0) cc_final: 0.6159 (mt-10) REVERT: A 735 GLU cc_start: 0.5857 (OUTLIER) cc_final: 0.5169 (pp20) REVERT: A 970 ASP cc_start: 0.7134 (p0) cc_final: 0.6509 (p0) REVERT: A 1363 SER cc_start: 0.8371 (m) cc_final: 0.8148 (m) REVERT: A 1369 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: A 1395 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7019 (mmp80) REVERT: A 1487 MET cc_start: 0.8419 (ptt) cc_final: 0.8101 (ptt) outliers start: 21 outliers final: 10 residues processed: 123 average time/residue: 1.4181 time to fit residues: 187.2719 Evaluate side-chains 116 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 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 511 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 735 GLU 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 1395 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 60 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 94 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 103 optimal weight: 0.0370 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 0.0370 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 HIS A 640 ASN ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.189294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.163203 restraints weight = 11321.776| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.39 r_work: 0.3766 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11343 Z= 0.076 Angle : 0.441 8.630 15528 Z= 0.231 Chirality : 0.036 0.136 1673 Planarity : 0.003 0.049 1829 Dihedral : 17.531 167.659 2133 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 32.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.51 % Allowed : 19.47 % 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: 0.45 (0.25), residues: 1217 helix: 1.92 (0.31), residues: 325 sheet: 0.33 (0.35), residues: 208 loop : -0.50 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1466 HIS 0.003 0.000 HIS A 883 PHE 0.011 0.001 PHE A 776 TYR 0.008 0.001 TYR A 591 ARG 0.007 0.000 ARG A1310 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 364) hydrogen bonds : angle 4.16182 ( 1097) metal coordination : bond 0.00202 ( 16) metal coordination : angle 1.46573 ( 21) covalent geometry : bond 0.00162 (11327) covalent geometry : angle 0.43760 (15507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.136 Fit side-chains REVERT: A 17 MET cc_start: 0.7887 (ttp) cc_final: 0.7661 (ttp) REVERT: A 46 LYS cc_start: 0.6734 (tmtt) cc_final: 0.6420 (tptm) REVERT: A 209 LYS cc_start: 0.5719 (pttm) cc_final: 0.5242 (pttp) REVERT: A 293 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7175 (ptm-80) REVERT: A 311 ASP cc_start: 0.6046 (t0) cc_final: 0.5375 (p0) REVERT: A 350 GLU cc_start: 0.7554 (tp30) cc_final: 0.7248 (tm-30) REVERT: A 473 MET cc_start: 0.7556 (mmm) cc_final: 0.7327 (mmt) REVERT: A 524 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6804 (mt-10) REVERT: A 590 ASP cc_start: 0.6951 (p0) cc_final: 0.6156 (m-30) REVERT: A 664 GLU cc_start: 0.5667 (tp30) cc_final: 0.5429 (pt0) REVERT: A 666 GLU cc_start: 0.6490 (tt0) cc_final: 0.6146 (mt-10) REVERT: A 896 ARG cc_start: 0.7378 (ttp80) cc_final: 0.7034 (ttm-80) REVERT: A 970 ASP cc_start: 0.7019 (p0) cc_final: 0.6649 (p0) REVERT: A 1369 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: A 1395 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7063 (mmp80) REVERT: A 1487 MET cc_start: 0.8360 (ptt) cc_final: 0.8034 (ptt) outliers start: 16 outliers final: 6 residues processed: 123 average time/residue: 1.4155 time to fit residues: 187.1240 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 : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 511 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 1369 GLU 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 99 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 81 optimal weight: 0.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.187370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.159138 restraints weight = 11307.453| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.55 r_work: 0.3734 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2966 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= 0.100 Angle : 0.465 8.477 15528 Z= 0.243 Chirality : 0.037 0.136 1673 Planarity : 0.003 0.046 1829 Dihedral : 17.513 170.015 2133 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 31.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.32 % Allowed : 19.66 % 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: 0.45 (0.25), residues: 1217 helix: 1.92 (0.30), residues: 325 sheet: 0.33 (0.35), residues: 208 loop : -0.49 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 20 HIS 0.003 0.001 HIS A 691 PHE 0.011 0.001 PHE A 776 TYR 0.010 0.001 TYR A 534 ARG 0.008 0.000 ARG A1310 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 364) hydrogen bonds : angle 4.25527 ( 1097) metal coordination : bond 0.00240 ( 16) metal coordination : angle 1.63442 ( 21) covalent geometry : bond 0.00214 (11327) covalent geometry : angle 0.46106 (15507) ********************** 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 113 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.209 Fit side-chains REVERT: A 17 MET cc_start: 0.7998 (ttp) cc_final: 0.7775 (ttp) REVERT: A 46 LYS cc_start: 0.6751 (tmtt) cc_final: 0.6428 (tptm) REVERT: A 209 LYS cc_start: 0.5682 (pttm) cc_final: 0.5221 (pttp) REVERT: A 293 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7178 (ptm-80) REVERT: A 311 ASP cc_start: 0.6112 (t0) cc_final: 0.5406 (p0) REVERT: A 350 GLU cc_start: 0.7512 (tp30) cc_final: 0.7158 (tm-30) REVERT: A 473 MET cc_start: 0.7580 (mmm) cc_final: 0.7342 (mmt) REVERT: A 524 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6909 (mt-10) REVERT: A 590 ASP cc_start: 0.6974 (p0) cc_final: 0.6166 (m-30) REVERT: A 664 GLU cc_start: 0.5630 (tp30) cc_final: 0.5401 (pt0) REVERT: A 666 GLU cc_start: 0.6504 (tt0) cc_final: 0.6105 (mt-10) REVERT: A 970 ASP cc_start: 0.7110 (p0) cc_final: 0.6441 (p0) REVERT: A 1369 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: A 1487 MET cc_start: 0.8413 (ptt) cc_final: 0.8102 (ptt) outliers start: 14 outliers final: 6 residues processed: 111 average time/residue: 1.4660 time to fit residues: 174.6570 Evaluate side-chains 107 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 511 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 1369 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 16 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 A1405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.181833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153894 restraints weight = 11242.970| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.42 r_work: 0.3670 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11343 Z= 0.230 Angle : 0.643 9.706 15528 Z= 0.332 Chirality : 0.043 0.146 1673 Planarity : 0.005 0.046 1829 Dihedral : 17.832 176.286 2133 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 31.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.90 % Favored : 93.02 % Rotamer: Outliers : 1.80 % Allowed : 19.38 % 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: -0.12 (0.24), residues: 1217 helix: 1.16 (0.29), residues: 323 sheet: 0.13 (0.35), residues: 209 loop : -0.74 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 20 HIS 0.009 0.002 HIS A 691 PHE 0.016 0.002 PHE A 757 TYR 0.018 0.002 TYR A 534 ARG 0.008 0.001 ARG A1310 Details of bonding type rmsd hydrogen bonds : bond 0.04860 ( 364) hydrogen bonds : angle 5.05248 ( 1097) metal coordination : bond 0.00531 ( 16) metal coordination : angle 3.15441 ( 21) covalent geometry : bond 0.00505 (11327) covalent geometry : angle 0.63309 (15507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8509.63 seconds wall clock time: 149 minutes 21.32 seconds (8961.32 seconds total)