Starting phenix.real_space_refine on Thu Jul 2 17:32:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9aso_43821/07_2026/9aso_43821.cif Found real_map, /net/cci-nas-00/data/ceres_data/9aso_43821/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9aso_43821/07_2026/9aso_43821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9aso_43821/07_2026/9aso_43821.map" model { file = "/net/cci-nas-00/data/ceres_data/9aso_43821/07_2026/9aso_43821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9aso_43821/07_2026/9aso_43821.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 2 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 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: 2.08, per 1000 atoms: 0.22 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: 0.85 Conformation dependent library (CDL) restraints added in 257.7 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: 0.72 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: 1.65 Time building geometry restraints manager: 1.04 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=" O5' C E 24 " pdb=" C5' C E 24 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.72e+00 bond pdb=" O5' C E 22 " pdb=" C5' C E 22 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.62e+00 bond pdb=" O5' A E 19 " pdb=" C5' A E 19 " ideal model delta sigma weight residual 1.420 1.448 -0.028 1.50e-02 4.44e+03 3.58e+00 bond pdb=" O5' U E 20 " pdb=" C5' U E 20 " ideal model delta sigma weight residual 1.420 1.448 -0.028 1.50e-02 4.44e+03 3.54e+00 bond pdb=" O5' C E 25 " pdb=" C5' C E 25 " ideal model delta sigma weight residual 1.420 1.447 -0.027 1.50e-02 4.44e+03 3.34e+00 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 13400 2.37 - 4.73: 123 4.73 - 7.10: 23 7.10 - 9.47: 6 9.47 - 11.83: 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 120.20 108.37 11.83 1.50e+00 4.44e-01 6.22e+01 angle pdb=" C3' G E 21 " pdb=" O3' G E 21 " pdb=" P C E 22 " ideal model delta sigma weight residual 120.20 108.49 11.71 1.50e+00 4.44e-01 6.10e+01 angle pdb=" C3' C E 24 " pdb=" O3' C E 24 " pdb=" P C E 25 " ideal model delta sigma weight residual 120.20 109.27 10.93 1.50e+00 4.44e-01 5.31e+01 angle pdb=" C3' U E 20 " pdb=" O3' U E 20 " pdb=" P G E 21 " ideal model delta sigma weight residual 120.20 109.49 10.71 1.50e+00 4.44e-01 5.10e+01 angle pdb=" C3' A E 19 " pdb=" O3' A E 19 " pdb=" P U E 20 " ideal model delta sigma weight residual 120.20 109.50 10.70 1.50e+00 4.44e-01 5.09e+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: 1438 0.081 - 0.161: 79 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 3.250 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: 6.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.450 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:5.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.930 ------------------------------------------------------------------------------- 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= 0.158 Angle : 0.603 11.832 13562 Z= 0.368 Chirality : 0.045 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 0.00288 / 0.16 ( 9784) covalent geometry : angle 0.60214 / 0.37 (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 : 0.209 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 63 average time/residue: 0.6477 time to fit residues: 43.1424 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 : 0.217 ------------------------------------------------------------------------------- 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: 10.0000 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: 8.9990 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 = 0.070769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.048645 restraints weight = 28374.063| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.90 r_work: 0.2819 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.0643 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= 0.155 Angle : 0.507 6.754 13562 Z= 0.274 Chirality : 0.037 0.164 1529 Planarity : 0.004 0.034 1497 Dihedral : 17.993 115.673 2191 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.50 % Allowed : 13.25 % Favored : 85.25 % 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: 1.40 (0.27), residues: 958 helix: 2.06 (0.24), residues: 493 sheet: 0.53 (0.47), residues: 102 loop : -0.52 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 961 TYR 0.009 0.001 TYR A1332 PHE 0.011 0.001 PHE A1148 TRP 0.012 0.001 TRP A1357 HIS 0.004 0.001 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 9784) covalent geometry : angle 0.50485 / 0.27 (13558) hydrogen bonds : bond 0.06260 / 4.24 ( 423) hydrogen bonds : angle 3.91932 / 2.84 ( 1208) metal coordination : bond 0.01228 / 0.60 ( 8) metal coordination : angle 2.97805 / 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 : 0.330 Fit side-chains revert: symmetry clash REVERT: C 734 LYS cc_start: 0.8862 (mtpp) cc_final: 0.8658 (mtmt) outliers start: 13 outliers final: 4 residues processed: 64 average time/residue: 0.6344 time to fit residues: 43.0362 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 : 0.247 ------------------------------------------------------------------------------- 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: 0.9990 chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 84 optimal weight: 0.0050 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.070718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.048516 restraints weight = 28325.426| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.99 r_work: 0.2792 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9792 Z= 0.115 Angle : 0.466 6.680 13562 Z= 0.251 Chirality : 0.036 0.158 1529 Planarity : 0.003 0.034 1497 Dihedral : 17.913 107.181 2179 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.15 % Allowed : 14.06 % Favored : 84.79 % 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 (0.27), residues: 958 helix: 2.07 (0.24), residues: 495 sheet: 0.43 (0.47), residues: 103 loop : -0.51 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 961 TYR 0.006 0.001 TYR A 705 PHE 0.011 0.001 PHE A1148 TRP 0.016 0.001 TRP A1357 HIS 0.006 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 9784) covalent geometry : angle 0.46399 / 0.25 (13558) hydrogen bonds : bond 0.05200 / 3.58 ( 423) hydrogen bonds : angle 3.66947 / 2.66 ( 1208) metal coordination : bond 0.01204 / 0.57 ( 8) metal coordination : angle 2.61412 / 1.53 ( 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: 10 poor density : 54 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 1355 MET cc_start: 0.7868 (ttm) cc_final: 0.7569 (ttp) outliers start: 10 outliers final: 5 residues processed: 62 average time/residue: 0.6407 time to fit residues: 41.9232 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 : 0.340 ------------------------------------------------------------------------------- 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: 0.5980 chunk 84 optimal weight: 0.0470 chunk 99 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 93 optimal weight: 0.0370 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.070820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.048605 restraints weight = 28438.586| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.01 r_work: 0.2795 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9792 Z= 0.109 Angle : 0.462 7.717 13562 Z= 0.246 Chirality : 0.036 0.147 1529 Planarity : 0.004 0.037 1497 Dihedral : 17.862 103.046 2178 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.15 % Allowed : 14.40 % Favored : 84.45 % 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: 1.46 (0.27), residues: 958 helix: 2.12 (0.24), residues: 495 sheet: 0.44 (0.48), residues: 103 loop : -0.50 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 835 TYR 0.006 0.001 TYR A 705 PHE 0.011 0.001 PHE A1148 TRP 0.017 0.001 TRP A1357 HIS 0.007 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9784) covalent geometry : angle 0.46026 / 0.25 (13558) hydrogen bonds : bond 0.04788 / 3.29 ( 423) hydrogen bonds : angle 3.56720 / 2.58 ( 1208) metal coordination : bond 0.01203 / 0.57 ( 8) metal coordination : angle 2.59878 / 1.51 ( 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 64 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 1355 MET cc_start: 0.7880 (ttm) cc_final: 0.7584 (ttp) REVERT: C 734 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8612 (mtmt) outliers start: 10 outliers final: 5 residues processed: 62 average time/residue: 0.6349 time to fit residues: 41.7843 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 : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.069475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.047124 restraints weight = 28380.460| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.99 r_work: 0.2753 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9792 Z= 0.174 Angle : 0.513 6.971 13562 Z= 0.272 Chirality : 0.038 0.165 1529 Planarity : 0.004 0.036 1497 Dihedral : 17.832 99.153 2176 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.04 % Allowed : 14.98 % Favored : 83.99 % 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: 1.32 (0.27), residues: 958 helix: 2.02 (0.24), residues: 495 sheet: 0.35 (0.48), residues: 103 loop : -0.57 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 746 TYR 0.011 0.001 TYR A1332 PHE 0.013 0.001 PHE A1148 TRP 0.019 0.001 TRP A1357 HIS 0.006 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 9784) covalent geometry : angle 0.50884 / 0.27 (13558) hydrogen bonds : bond 0.05801 / 3.95 ( 423) hydrogen bonds : angle 3.67769 / 2.64 ( 1208) metal coordination : bond 0.01488 / 0.72 ( 8) metal coordination : angle 3.68013 / 2.11 ( 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 61 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 1355 MET cc_start: 0.7934 (ttm) cc_final: 0.7604 (ttp) REVERT: C 738 GLU cc_start: 0.8729 (tp30) cc_final: 0.8499 (tp30) outliers start: 9 outliers final: 3 residues processed: 59 average time/residue: 0.6480 time to fit residues: 40.4445 Evaluate side-chains 55 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 84 optimal weight: 0.0270 chunk 8 optimal weight: 0.0770 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.071076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049020 restraints weight = 28227.742| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.99 r_work: 0.2806 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9792 Z= 0.094 Angle : 0.465 7.942 13562 Z= 0.247 Chirality : 0.035 0.153 1529 Planarity : 0.003 0.033 1497 Dihedral : 17.815 95.234 2176 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.81 % Allowed : 15.44 % Favored : 83.76 % 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: 1.48 (0.28), residues: 958 helix: 2.13 (0.24), residues: 495 sheet: 0.42 (0.49), residues: 103 loop : -0.47 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 741 TYR 0.006 0.001 TYR A 705 PHE 0.010 0.001 PHE A1148 TRP 0.018 0.001 TRP A1357 HIS 0.004 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 9784) covalent geometry : angle 0.46355 / 0.25 (13558) hydrogen bonds : bond 0.04190 / 2.89 ( 423) hydrogen bonds : angle 3.48215 / 2.52 ( 1208) metal coordination : bond 0.01110 / 0.52 ( 8) metal coordination : angle 2.34616 / 1.38 ( 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 61 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 1355 MET cc_start: 0.7868 (ttm) cc_final: 0.7533 (ttp) REVERT: C 734 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8577 (mtmt) outliers start: 7 outliers final: 3 residues processed: 60 average time/residue: 0.7337 time to fit residues: 46.7611 Evaluate side-chains 55 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 0.2980 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.070657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.048467 restraints weight = 28232.167| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.00 r_work: 0.2790 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9792 Z= 0.112 Angle : 0.479 7.647 13562 Z= 0.253 Chirality : 0.036 0.179 1529 Planarity : 0.003 0.034 1497 Dihedral : 17.625 92.056 2174 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.81 % Allowed : 15.44 % Favored : 83.76 % 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: 1.53 (0.28), residues: 958 helix: 2.15 (0.24), residues: 495 sheet: 0.44 (0.46), residues: 108 loop : -0.42 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 0.005 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 9784) covalent geometry : angle 0.47662 / 0.25 (13558) hydrogen bonds : bond 0.04499 / 3.10 ( 423) hydrogen bonds : angle 3.47193 / 2.50 ( 1208) metal coordination : bond 0.01223 / 0.57 ( 8) metal coordination : angle 2.63203 / 1.53 ( 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 59 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 1355 MET cc_start: 0.7871 (ttm) cc_final: 0.7533 (ttp) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.7029 time to fit residues: 43.1498 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 : 0.246 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0970 chunk 36 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.070582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.048379 restraints weight = 28185.145| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.00 r_work: 0.2790 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1217 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= 0.115 Angle : 0.492 8.095 13562 Z= 0.259 Chirality : 0.036 0.180 1529 Planarity : 0.003 0.034 1497 Dihedral : 17.547 88.396 2174 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.04 % Allowed : 15.55 % 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: 1.54 (0.27), residues: 958 helix: 2.17 (0.24), residues: 495 sheet: 0.46 (0.46), residues: 108 loop : -0.43 (0.32), residues: 355 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 0.025 0.001 TRP A1357 HIS 0.006 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 9784) covalent geometry : angle 0.48971 / 0.26 (13558) hydrogen bonds : bond 0.04490 / 3.08 ( 423) hydrogen bonds : angle 3.46178 / 2.49 ( 1208) metal coordination : bond 0.01229 / 0.59 ( 8) metal coordination : angle 2.75068 / 1.60 ( 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 62 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 1355 MET cc_start: 0.7891 (ttm) cc_final: 0.7578 (ttp) REVERT: C 734 LYS cc_start: 0.8865 (mtpp) cc_final: 0.8588 (mtmt) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 0.7480 time to fit residues: 47.6421 Evaluate side-chains 56 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 59 optimal weight: 0.7980 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: 0.6980 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.070774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.048688 restraints weight = 28148.956| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.98 r_work: 0.2800 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9792 Z= 0.108 Angle : 0.487 9.223 13562 Z= 0.258 Chirality : 0.035 0.173 1529 Planarity : 0.003 0.034 1497 Dihedral : 17.535 88.250 2174 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.04 % Allowed : 15.55 % 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: 1.59 (0.27), residues: 958 helix: 2.23 (0.24), residues: 494 sheet: 0.47 (0.46), residues: 108 loop : -0.43 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 741 TYR 0.007 0.001 TYR A 705 PHE 0.010 0.001 PHE A1148 TRP 0.026 0.001 TRP A1357 HIS 0.005 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9784) covalent geometry : angle 0.48535 / 0.26 (13558) hydrogen bonds : bond 0.04293 / 2.96 ( 423) hydrogen bonds : angle 3.42566 / 2.46 ( 1208) metal coordination : bond 0.01167 / 0.55 ( 8) metal coordination : angle 2.51961 / 1.47 ( 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 61 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 1355 MET cc_start: 0.7846 (ttm) cc_final: 0.7526 (ttp) outliers start: 9 outliers final: 4 residues processed: 59 average time/residue: 0.7552 time to fit residues: 47.0150 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 : 0.247 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 18 optimal weight: 0.0170 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.069192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.046883 restraints weight = 28133.024| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.98 r_work: 0.2746 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9792 Z= 0.189 Angle : 0.566 14.581 13562 Z= 0.292 Chirality : 0.038 0.167 1529 Planarity : 0.004 0.033 1497 Dihedral : 17.519 88.023 2174 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.81 % Allowed : 15.90 % 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 (0.27), residues: 958 helix: 2.09 (0.24), residues: 494 sheet: 0.35 (0.46), residues: 108 loop : -0.47 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 741 TYR 0.011 0.001 TYR A1332 PHE 0.012 0.001 PHE A 970 TRP 0.027 0.002 TRP A1357 HIS 0.006 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 ( 9784) covalent geometry : angle 0.56166 / 0.29 (13558) hydrogen bonds : bond 0.05809 / 3.95 ( 423) hydrogen bonds : angle 3.62052 / 2.59 ( 1208) metal coordination : bond 0.01509 / 0.74 ( 8) metal coordination : angle 3.89344 / 2.23 ( 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 60 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 1355 MET cc_start: 0.7845 (ttm) cc_final: 0.7519 (ttp) REVERT: C 734 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8692 (mtmt) outliers start: 7 outliers final: 6 residues processed: 59 average time/residue: 0.7617 time to fit residues: 47.3847 Evaluate side-chains 59 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 1198 GLU Chi-restraints excluded: chain A residue 1283 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.070374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048272 restraints weight = 27943.164| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.98 r_work: 0.2786 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9792 Z= 0.108 Angle : 0.510 11.286 13562 Z= 0.266 Chirality : 0.035 0.156 1529 Planarity : 0.003 0.034 1497 Dihedral : 17.558 88.161 2174 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.81 % Allowed : 16.01 % 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: 1.56 (0.28), residues: 958 helix: 2.21 (0.24), residues: 494 sheet: 0.43 (0.47), residues: 108 loop : -0.44 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 746 TYR 0.007 0.001 TYR A 705 PHE 0.010 0.001 PHE A1148 TRP 0.028 0.001 TRP A1357 HIS 0.007 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 9784) covalent geometry : angle 0.50756 / 0.27 (13558) hydrogen bonds : bond 0.04446 / 3.06 ( 423) hydrogen bonds : angle 3.46191 / 2.49 ( 1208) metal coordination : bond 0.01348 / 0.67 ( 8) metal coordination : angle 2.65233 / 1.56 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2405.93 seconds wall clock time: 41 minutes 48.00 seconds (2508.00 seconds total)