Starting phenix.real_space_refine on Wed Aug 5 10:43:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9aso_43821/08_2026/9aso_43821.cif Found real_map, /net/cci-nas-00/data/ceres_data/9aso_43821/08_2026/9aso_43821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9aso_43821/08_2026/9aso_43821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9aso_43821/08_2026/9aso_43821.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9aso_43821/08_2026/9aso_43821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9aso_43821/08_2026/9aso_43821.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 Ca 2 9.91 5 Zn 2 6.06 5 P 71 5.49 5 S 52 5.16 5 C 5709 2.51 5 N 1652 2.21 5 O 1938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9426 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 7497 Classifications: {'peptide': 916} Link IDs: {'PTRANS': 52, 'TRANS': 863} Chain breaks: 1 Chain: "B" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 220 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "C" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 203 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "E" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1500 Classifications: {'RNA': 71} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 28, 'rna3p_pyr': 38} Link IDs: {'rna2p': 4, 'rna3p': 66} Chain breaks: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 961 SG CYS A 561 51.073 71.653 120.870 1.00172.12 S ATOM 1919 SG CYS A 676 53.071 68.480 120.056 1.00178.36 S ATOM 769 SG CYS A 536 62.414 49.991 102.297 1.00181.72 S ATOM 784 SG CYS A 538 63.025 49.510 98.508 1.00190.39 S Time building chain proxies: 1.31, per 1000 atoms: 0.14 Number of scatterers: 9426 At special positions: 0 Unit cell: (82.176, 98.44, 158.36, 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 2 29.99 Ca 2 19.99 S 52 16.00 P 71 15.00 O 1938 8.00 N 1652 7.00 C 5709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 245.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 609 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 680 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 676 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 561 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" NE2 HIS A1026 " pdb="ZN ZN A1402 " - pdb=" NE2 HIS A 549 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 536 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 538 " Number of angles added : 4 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 56.1% alpha, 11.6% beta 17 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 438 through 452 removed outlier: 3.538A pdb=" N ARG A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 463 removed outlier: 3.629A pdb=" N ALA A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 512 removed outlier: 3.559A pdb=" N GLU A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.698A pdb=" N THR A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 removed outlier: 3.527A pdb=" N ILE A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 709 removed outlier: 3.574A pdb=" N ILE A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 726 through 738 removed outlier: 3.524A pdb=" N GLU A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 786 Processing helix chain 'A' and resid 787 through 806 removed outlier: 3.644A pdb=" N ASN A 806 " --> pdb=" O HIS A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 830 removed outlier: 3.786A pdb=" N GLN A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 817 " --> pdb=" O THR A 813 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 861 Processing helix chain 'A' and resid 862 through 884 removed outlier: 3.734A pdb=" N LEU A 866 " --> pdb=" O MET A 862 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N MET A 877 " --> pdb=" O HIS A 873 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N HIS A 878 " --> pdb=" O GLN A 874 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 879 " --> pdb=" O CYS A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 897 removed outlier: 3.616A pdb=" N LEU A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 921 Processing helix chain 'A' and resid 929 through 934 removed outlier: 3.594A pdb=" N VAL A 932 " --> pdb=" O ASP A 929 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N HIS A 933 " --> pdb=" O ARG A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 950 removed outlier: 3.752A pdb=" N ILE A 946 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 947 " --> pdb=" O ASN A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 988 removed outlier: 3.670A pdb=" N PHE A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 971 " --> pdb=" O ARG A 967 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1004 Processing helix chain 'A' and resid 1005 through 1017 removed outlier: 3.768A pdb=" N LEU A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1021 Processing helix chain 'A' and resid 1027 through 1031 removed outlier: 4.024A pdb=" N LEU A1030 " --> pdb=" O GLY A1027 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A1031 " --> pdb=" O PRO A1028 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1027 through 1031' Processing helix chain 'A' and resid 1032 through 1055 Processing helix chain 'A' and resid 1056 through 1069 removed outlier: 3.573A pdb=" N ALA A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1079 Processing helix chain 'A' and resid 1084 through 1090 removed outlier: 3.919A pdb=" N GLU A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1100 removed outlier: 4.220A pdb=" N GLU A1099 " --> pdb=" O GLN A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1115 removed outlier: 3.672A pdb=" N THR A1108 " --> pdb=" O LEU A1104 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU A1109 " --> pdb=" O GLN A1105 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE A1110 " --> pdb=" O LYS A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 removed outlier: 4.057A pdb=" N LEU A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1166 removed outlier: 3.714A pdb=" N GLU A1147 " --> pdb=" O ASN A1143 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE A1148 " --> pdb=" O GLN A1144 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A1149 " --> pdb=" O ARG A1145 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1182 Processing helix chain 'A' and resid 1183 through 1195 removed outlier: 3.571A pdb=" N ALA A1188 " --> pdb=" O ASN A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1208 removed outlier: 4.232A pdb=" N LYS A1207 " --> pdb=" O ASN A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1232 Processing helix chain 'A' and resid 1234 through 1245 Processing helix chain 'A' and resid 1248 through 1256 Processing helix chain 'A' and resid 1260 through 1271 removed outlier: 3.584A pdb=" N THR A1271 " --> pdb=" O GLN A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1332 Processing helix chain 'A' and resid 1334 through 1348 removed outlier: 3.573A pdb=" N ALA A1338 " --> pdb=" O PHE A1334 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A1347 " --> pdb=" O PHE A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1358 Processing helix chain 'B' and resid 728 through 749 removed outlier: 3.808A pdb=" N LEU B 732 " --> pdb=" O ASN B 728 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 749 Processing sheet with id=AA1, first strand: chain 'A' and resid 413 through 415 removed outlier: 6.484A pdb=" N ARG A 414 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N PHE A 688 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N TYR A 599 " --> pdb=" O PHE A 688 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 415 removed outlier: 6.484A pdb=" N ARG A 414 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N PHE A 688 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N TYR A 599 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 11.962A pdb=" N GLU A 602 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL A 578 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE A 604 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N CYS A 618 " --> pdb=" O ILE A 629 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA4, first strand: chain 'A' and resid 711 through 712 removed outlier: 3.815A pdb=" N LYS A 711 " --> pdb=" O LYS A 849 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 850 " --> pdb=" O ILE A 741 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE A 741 " --> pdb=" O THR A 850 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 756 through 758 removed outlier: 3.558A pdb=" N GLN A 756 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1283 through 1290 removed outlier: 6.901A pdb=" N THR A1299 " --> pdb=" O LEU A1287 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR A1289 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR A1297 " --> pdb=" O THR A1289 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A1310 " --> pdb=" O VAL A1302 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2811 1.34 - 1.46: 1975 1.46 - 1.58: 4774 1.58 - 1.70: 140 1.70 - 1.82: 84 Bond restraints: 9784 Sorted by residual: bond pdb=" P C E 24 " pdb=" O5' C E 24 " ideal model delta sigma weight residual 1.593 1.613 -0.020 1.00e-02 1.00e+04 4.02e+00 bond pdb=" P A E 19 " pdb=" O5' A E 19 " ideal model delta sigma weight residual 1.593 1.613 -0.020 1.00e-02 1.00e+04 3.89e+00 bond pdb=" P C E 25 " pdb=" O5' C E 25 " ideal model delta sigma weight residual 1.593 1.611 -0.018 1.00e-02 1.00e+04 3.39e+00 bond pdb=" C1' G E 21 " pdb=" N9 G E 21 " ideal model delta sigma weight residual 1.483 1.457 0.026 1.50e-02 4.44e+03 2.91e+00 bond pdb=" C1' A E 19 " pdb=" N9 A E 19 " ideal model delta sigma weight residual 1.483 1.458 0.025 1.50e-02 4.44e+03 2.86e+00 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 13289 2.27 - 4.53: 233 4.53 - 6.80: 24 6.80 - 9.07: 6 9.07 - 11.33: 6 Bond angle restraints: 13558 Sorted by residual: angle pdb=" C3' C E 22 " pdb=" O3' C E 22 " pdb=" P U E 23 " ideal model delta sigma weight residual 119.70 108.37 11.33 1.20e+00 6.94e-01 8.92e+01 angle pdb=" C3' G E 21 " pdb=" O3' G E 21 " pdb=" P C E 22 " ideal model delta sigma weight residual 119.70 108.49 11.21 1.20e+00 6.94e-01 8.73e+01 angle pdb=" C3' C E 24 " pdb=" O3' C E 24 " pdb=" P C E 25 " ideal model delta sigma weight residual 119.70 109.27 10.43 1.20e+00 6.94e-01 7.56e+01 angle pdb=" C3' U E 20 " pdb=" O3' U E 20 " pdb=" P G E 21 " ideal model delta sigma weight residual 119.70 109.49 10.21 1.20e+00 6.94e-01 7.24e+01 angle pdb=" C3' A E 19 " pdb=" O3' A E 19 " pdb=" P U E 20 " ideal model delta sigma weight residual 119.70 109.50 10.20 1.20e+00 6.94e-01 7.23e+01 ... (remaining 13553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.42: 5548 25.42 - 50.84: 368 50.84 - 76.25: 139 76.25 - 101.67: 1 101.67 - 127.09: 1 Dihedral angle restraints: 6057 sinusoidal: 3220 harmonic: 2837 Sorted by residual: dihedral pdb=" O4' C E 22 " pdb=" C1' C E 22 " pdb=" N1 C E 22 " pdb=" C2 C E 22 " ideal model delta sinusoidal sigma weight residual -160.00 -32.91 -127.09 1 1.50e+01 4.44e-03 6.84e+01 dihedral pdb=" O4' A E 90 " pdb=" C1' A E 90 " pdb=" N9 A E 90 " pdb=" C4 A E 90 " ideal model delta sinusoidal sigma weight residual -90.00 -22.97 -67.03 1 2.00e+01 2.50e-03 1.46e+01 dihedral pdb=" CA MET A 935 " pdb=" C MET A 935 " pdb=" N HIS A 936 " pdb=" CA HIS A 936 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 6054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1377 0.081 - 0.161: 140 0.161 - 0.242: 5 0.242 - 0.322: 0 0.322 - 0.403: 7 Chirality restraints: 1529 Sorted by residual: chirality pdb=" P A E 19 " pdb=" OP1 A E 19 " pdb=" OP2 A E 19 " pdb=" O5' A E 19 " both_signs ideal model delta sigma weight residual True 2.41 -2.81 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" P U E 20 " pdb=" OP1 U E 20 " pdb=" OP2 U E 20 " pdb=" O5' U E 20 " both_signs ideal model delta sigma weight residual True 2.41 -2.79 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" P U E 23 " pdb=" OP1 U E 23 " pdb=" OP2 U E 23 " pdb=" O5' U E 23 " both_signs ideal model delta sigma weight residual True 2.41 -2.79 -0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 1526 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 745 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" CD GLU C 745 " 0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU C 745 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 745 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 744 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" CD GLU C 744 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU C 744 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU C 744 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 737 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" CD GLU B 737 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU B 737 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 737 " -0.012 2.00e-02 2.50e+03 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2334 2.80 - 3.33: 8160 3.33 - 3.85: 15244 3.85 - 4.38: 17752 4.38 - 4.90: 29543 Nonbonded interactions: 73033 Sorted by model distance: nonbonded pdb=" N ASP A 955 " pdb=" OD1 ASP A 955 " model vdw 2.281 3.120 nonbonded pdb=" OP1 U E 31 " pdb=" O HOH E 201 " model vdw 2.319 3.040 nonbonded pdb=" OE2 GLU A1147 " pdb="CA CA A1403 " model vdw 2.356 2.510 nonbonded pdb=" NH2 ARG A1213 " pdb=" OP2 U E 89 " model vdw 2.380 3.120 nonbonded pdb=" NH1 ARG A1095 " pdb=" O PHE A1118 " model vdw 2.395 3.120 ... (remaining 73028 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 726 through 749) selection = chain 'C' } 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: 4.720 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.350 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 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 : 0.003 0.039 9792 Z= 0.170 Angle : 0.655 11.332 13562 Z= 0.432 Chirality : 0.052 0.403 1529 Planarity : 0.003 0.031 1497 Dihedral : 17.619 127.090 4215 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.04 % Allowed : 14.06 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.27), residues: 958 helix: 2.01 (0.24), residues: 480 sheet: 0.63 (0.50), residues: 92 loop : -0.57 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 746 TYR 0.006 0.001 TYR A1229 PHE 0.011 0.001 PHE A 970 TRP 0.032 0.001 TRP A1357 HIS 0.004 0.001 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.17 ( 9784) covalent geometry : angle 0.65458 / 0.43 (13558) hydrogen bonds : bond 0.18157 / 11.87 ( 423) hydrogen bonds : angle 5.28085 / 3.78 ( 1208) metal coordination : bond 0.01014 / 0.47 ( 8) metal coordination : angle 2.11452 / 1.24 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.329 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 63 average time/residue: 0.6440 time to fit residues: 42.9048 Evaluate side-chains 64 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1274 THR Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain C residue 731 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.0050 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 730 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.070790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.048698 restraints weight = 28383.737| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.89 r_work: 0.2820 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9792 Z= 0.156 Angle : 0.515 6.511 13562 Z= 0.276 Chirality : 0.038 0.162 1529 Planarity : 0.004 0.034 1497 Dihedral : 17.905 116.205 2191 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.50 % Allowed : 13.36 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.27), residues: 958 helix: 2.05 (0.24), residues: 493 sheet: 0.52 (0.47), residues: 102 loop : -0.53 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 961 TYR 0.009 0.001 TYR A1332 PHE 0.012 0.001 PHE A1148 TRP 0.010 0.001 TRP A 730 HIS 0.004 0.001 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 9784) covalent geometry : angle 0.51215 / 0.28 (13558) hydrogen bonds : bond 0.06309 / 4.29 ( 423) hydrogen bonds : angle 3.92350 / 2.84 ( 1208) metal coordination : bond 0.01202 / 0.59 ( 8) metal coordination : angle 2.99075 / 1.73 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: C 734 LYS cc_start: 0.8861 (mtpp) cc_final: 0.8657 (mtmt) outliers start: 13 outliers final: 4 residues processed: 64 average time/residue: 0.6267 time to fit residues: 42.4310 Evaluate side-chains 58 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1274 THR Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain B residue 729 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 730 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.069733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.047405 restraints weight = 28378.178| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.99 r_work: 0.2761 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9792 Z= 0.163 Angle : 0.504 6.617 13562 Z= 0.269 Chirality : 0.038 0.162 1529 Planarity : 0.004 0.035 1497 Dihedral : 17.843 107.403 2179 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.27 % Allowed : 13.59 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.27), residues: 958 helix: 1.97 (0.24), residues: 495 sheet: 0.35 (0.47), residues: 103 loop : -0.57 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 961 TYR 0.010 0.001 TYR A1332 PHE 0.012 0.001 PHE A 970 TRP 0.017 0.001 TRP A1357 HIS 0.006 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 9784) covalent geometry : angle 0.50048 / 0.27 (13558) hydrogen bonds : bond 0.06067 / 4.15 ( 423) hydrogen bonds : angle 3.78245 / 2.73 ( 1208) metal coordination : bond 0.01431 / 0.69 ( 8) metal coordination : angle 3.46126 / 2.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: C 737 GLU cc_start: 0.8576 (pm20) cc_final: 0.8373 (pm20) outliers start: 11 outliers final: 5 residues processed: 62 average time/residue: 0.6890 time to fit residues: 45.2697 Evaluate side-chains 58 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1154 MET Chi-restraints excluded: chain A residue 1283 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 0.0060 chunk 99 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 GLN C 730 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.069114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.046776 restraints weight = 28499.449| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.00 r_work: 0.2741 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9792 Z= 0.183 Angle : 0.518 6.607 13562 Z= 0.274 Chirality : 0.039 0.167 1529 Planarity : 0.004 0.048 1497 Dihedral : 17.733 102.494 2178 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.15 % Allowed : 14.75 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.27), residues: 958 helix: 1.92 (0.24), residues: 494 sheet: 0.28 (0.48), residues: 103 loop : -0.57 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 835 TYR 0.010 0.001 TYR A1332 PHE 0.013 0.001 PHE A 970 TRP 0.018 0.001 TRP A1357 HIS 0.007 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 9784) covalent geometry : angle 0.51328 / 0.27 (13558) hydrogen bonds : bond 0.06085 / 4.13 ( 423) hydrogen bonds : angle 3.75990 / 2.70 ( 1208) metal coordination : bond 0.01538 / 0.77 ( 8) metal coordination : angle 3.88891 / 2.25 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 1355 MET cc_start: 0.7826 (ttm) cc_final: 0.7512 (ttp) REVERT: C 734 LYS cc_start: 0.8846 (mtpp) cc_final: 0.8613 (mtmt) outliers start: 10 outliers final: 5 residues processed: 61 average time/residue: 0.6283 time to fit residues: 40.5599 Evaluate side-chains 57 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1154 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.0000 chunk 42 optimal weight: 0.5980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 GLN C 730 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.070352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048154 restraints weight = 28381.167| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.00 r_work: 0.2782 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9792 Z= 0.105 Angle : 0.466 6.666 13562 Z= 0.248 Chirality : 0.035 0.143 1529 Planarity : 0.003 0.035 1497 Dihedral : 17.599 98.273 2176 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.27 % Allowed : 14.52 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.28), residues: 958 helix: 2.04 (0.24), residues: 494 sheet: 0.33 (0.48), residues: 103 loop : -0.53 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 746 TYR 0.006 0.001 TYR A 705 PHE 0.011 0.001 PHE A1148 TRP 0.016 0.001 TRP A1357 HIS 0.005 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 9784) covalent geometry : angle 0.46327 / 0.25 (13558) hydrogen bonds : bond 0.04738 / 3.25 ( 423) hydrogen bonds : angle 3.57864 / 2.59 ( 1208) metal coordination : bond 0.01316 / 0.63 ( 8) metal coordination : angle 2.72645 / 1.60 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 1355 MET cc_start: 0.7827 (ttm) cc_final: 0.7500 (ttp) REVERT: C 737 GLU cc_start: 0.8580 (pm20) cc_final: 0.8375 (pm20) outliers start: 11 outliers final: 5 residues processed: 60 average time/residue: 0.6778 time to fit residues: 43.1346 Evaluate side-chains 56 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1283 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 84 optimal weight: 0.0020 chunk 8 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 730 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.070791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.048716 restraints weight = 28193.637| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.99 r_work: 0.2799 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9792 Z= 0.099 Angle : 0.461 7.458 13562 Z= 0.243 Chirality : 0.035 0.141 1529 Planarity : 0.003 0.034 1497 Dihedral : 17.520 93.598 2176 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.50 % Allowed : 15.21 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.28), residues: 958 helix: 2.13 (0.24), residues: 493 sheet: 0.39 (0.49), residues: 103 loop : -0.53 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 746 TYR 0.006 0.001 TYR A 705 PHE 0.014 0.001 PHE A 906 TRP 0.021 0.001 TRP A1357 HIS 0.007 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 9784) covalent geometry : angle 0.45861 / 0.24 (13558) hydrogen bonds : bond 0.04332 / 2.97 ( 423) hydrogen bonds : angle 3.46010 / 2.51 ( 1208) metal coordination : bond 0.01208 / 0.55 ( 8) metal coordination : angle 2.50769 / 1.47 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 1092 ASN cc_start: 0.8640 (m-40) cc_final: 0.8370 (OUTLIER) REVERT: A 1355 MET cc_start: 0.7831 (ttm) cc_final: 0.7504 (ttp) REVERT: C 734 LYS cc_start: 0.8826 (mtpp) cc_final: 0.8615 (mtmt) outliers start: 13 outliers final: 5 residues processed: 62 average time/residue: 0.6197 time to fit residues: 40.8430 Evaluate side-chains 54 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1048 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1340 GLN C 730 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.070363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.048244 restraints weight = 28172.823| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.98 r_work: 0.2785 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9792 Z= 0.122 Angle : 0.484 8.204 13562 Z= 0.254 Chirality : 0.036 0.142 1529 Planarity : 0.003 0.034 1497 Dihedral : 17.511 91.076 2176 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.15 % Allowed : 15.44 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.28), residues: 958 helix: 2.11 (0.24), residues: 494 sheet: 0.34 (0.48), residues: 103 loop : -0.52 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 741 TYR 0.007 0.001 TYR A 705 PHE 0.011 0.001 PHE A1148 TRP 0.020 0.001 TRP A1357 HIS 0.004 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 9784) covalent geometry : angle 0.48143 / 0.25 (13558) hydrogen bonds : bond 0.04660 / 3.18 ( 423) hydrogen bonds : angle 3.47984 / 2.51 ( 1208) metal coordination : bond 0.01285 / 0.61 ( 8) metal coordination : angle 2.87124 / 1.67 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 1355 MET cc_start: 0.7840 (ttm) cc_final: 0.7532 (ttp) outliers start: 10 outliers final: 6 residues processed: 59 average time/residue: 0.6620 time to fit residues: 41.2817 Evaluate side-chains 56 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1198 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0170 chunk 36 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 0.0770 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 936 HIS A1340 GLN C 730 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.070488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.048329 restraints weight = 28217.074| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.00 r_work: 0.2790 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9792 Z= 0.111 Angle : 0.478 8.534 13562 Z= 0.251 Chirality : 0.035 0.139 1529 Planarity : 0.003 0.034 1497 Dihedral : 17.512 88.390 2176 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.50 % Allowed : 15.44 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.28), residues: 958 helix: 2.14 (0.24), residues: 494 sheet: 0.35 (0.48), residues: 103 loop : -0.52 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 741 TYR 0.007 0.001 TYR A 705 PHE 0.010 0.001 PHE A 970 TRP 0.023 0.001 TRP A1357 HIS 0.006 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 9784) covalent geometry : angle 0.47579 / 0.25 (13558) hydrogen bonds : bond 0.04466 / 3.06 ( 423) hydrogen bonds : angle 3.45737 / 2.50 ( 1208) metal coordination : bond 0.01239 / 0.59 ( 8) metal coordination : angle 2.71712 / 1.59 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 1355 MET cc_start: 0.7866 (ttm) cc_final: 0.7561 (ttp) REVERT: C 734 LYS cc_start: 0.8859 (mtpp) cc_final: 0.8562 (mtmt) outliers start: 13 outliers final: 4 residues processed: 63 average time/residue: 0.6109 time to fit residues: 40.7870 Evaluate side-chains 54 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1198 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1340 GLN C 730 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.070290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.048161 restraints weight = 28077.881| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.98 r_work: 0.2784 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9792 Z= 0.124 Angle : 0.512 12.992 13562 Z= 0.264 Chirality : 0.036 0.144 1529 Planarity : 0.003 0.033 1497 Dihedral : 17.477 87.903 2174 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.92 % Allowed : 15.90 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.28), residues: 958 helix: 2.13 (0.24), residues: 494 sheet: 0.32 (0.48), residues: 103 loop : -0.53 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 741 TYR 0.007 0.001 TYR A1332 PHE 0.011 0.001 PHE A 970 TRP 0.025 0.001 TRP A1357 HIS 0.005 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 9784) covalent geometry : angle 0.50926 / 0.26 (13558) hydrogen bonds : bond 0.04689 / 3.21 ( 423) hydrogen bonds : angle 3.46587 / 2.49 ( 1208) metal coordination : bond 0.01259 / 0.60 ( 8) metal coordination : angle 2.89222 / 1.68 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 1355 MET cc_start: 0.7872 (ttm) cc_final: 0.7568 (ttp) outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 0.6684 time to fit residues: 41.1218 Evaluate side-chains 55 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1198 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 GLN A1340 GLN C 730 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.069192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.046912 restraints weight = 28095.891| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.98 r_work: 0.2749 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9792 Z= 0.176 Angle : 0.554 9.867 13562 Z= 0.288 Chirality : 0.038 0.165 1529 Planarity : 0.004 0.035 1497 Dihedral : 17.505 87.331 2174 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.04 % Allowed : 15.90 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.28), residues: 958 helix: 2.04 (0.24), residues: 494 sheet: 0.22 (0.48), residues: 103 loop : -0.58 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 741 TYR 0.010 0.001 TYR A1332 PHE 0.015 0.001 PHE A 906 TRP 0.028 0.002 TRP A1357 HIS 0.006 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 9784) covalent geometry : angle 0.55055 / 0.29 (13558) hydrogen bonds : bond 0.05728 / 3.89 ( 423) hydrogen bonds : angle 3.62994 / 2.60 ( 1208) metal coordination : bond 0.01513 / 0.75 ( 8) metal coordination : angle 3.80143 / 2.19 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 1355 MET cc_start: 0.7846 (ttm) cc_final: 0.7513 (ttp) REVERT: C 734 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8632 (mtmt) outliers start: 9 outliers final: 5 residues processed: 59 average time/residue: 0.6515 time to fit residues: 40.6591 Evaluate side-chains 57 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1198 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.0050 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 81 optimal weight: 0.0170 chunk 1 optimal weight: 0.6980 overall best weight: 0.3832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 GLN C 730 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.070799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.048821 restraints weight = 27921.932| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.98 r_work: 0.2803 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9792 Z= 0.101 Angle : 0.502 9.948 13562 Z= 0.264 Chirality : 0.035 0.135 1529 Planarity : 0.003 0.034 1497 Dihedral : 17.519 87.491 2174 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.81 % Allowed : 16.13 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.28), residues: 958 helix: 2.17 (0.24), residues: 494 sheet: 0.34 (0.48), residues: 103 loop : -0.52 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 741 TYR 0.007 0.001 TYR A 705 PHE 0.013 0.001 PHE A 906 TRP 0.030 0.001 TRP A1357 HIS 0.007 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 9784) covalent geometry : angle 0.50057 / 0.26 (13558) hydrogen bonds : bond 0.04112 / 2.82 ( 423) hydrogen bonds : angle 3.42179 / 2.47 ( 1208) metal coordination : bond 0.01205 / 0.57 ( 8) metal coordination : angle 2.43060 / 1.43 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2172.55 seconds wall clock time: 37 minutes 44.30 seconds (2264.30 seconds total)