Starting phenix.real_space_refine on Mon Jun 9 08:20:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dou_47091/06_2025/9dou_47091.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dou_47091/06_2025/9dou_47091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dou_47091/06_2025/9dou_47091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dou_47091/06_2025/9dou_47091.map" model { file = "/net/cci-nas-00/data/ceres_data/9dou_47091/06_2025/9dou_47091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dou_47091/06_2025/9dou_47091.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 147 5.49 5 Mg 1 5.21 5 S 45 5.16 5 C 6130 2.51 5 N 1891 2.21 5 O 2276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10494 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7429 Classifications: {'peptide': 924} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 882} Chain breaks: 4 Chain: "B" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "P" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1599 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 35, 'rna3p_pyr': 26} Link IDs: {'rna2p': 14, 'rna3p': 60} Chain: "T" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 635 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 34 Unusual residues: {' MG': 1, ' ZN': 4, 'TTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 533 SG CYS A 297 54.277 84.020 34.739 1.00 72.44 S ATOM 555 SG CYS A 300 54.733 84.197 38.602 1.00 65.33 S ATOM 5995 SG CYS A1212 85.350 71.211 92.026 1.00 58.26 S ATOM 6022 SG CYS A1215 88.370 70.593 94.281 1.00 70.33 S ATOM 6121 SG CYS A1229 85.570 67.836 94.055 1.00 57.38 S ATOM 326 SG CYS A 262 68.772 90.617 59.398 1.00131.51 S ATOM 346 SG CYS A 265 67.249 91.177 55.945 1.00145.26 S ATOM 481 SG CYS A 282 70.741 91.818 56.209 1.00129.38 S ATOM 97 SG CYS A 232 57.282 87.036 77.028 1.00155.87 S Time building chain proxies: 7.21, per 1000 atoms: 0.69 Number of scatterers: 10494 At special positions: 0 Unit cell: (117.862, 102.209, 123.387, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 45 16.00 P 147 15.00 Mg 1 11.99 O 2276 8.00 N 1891 7.00 C 6130 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: 2.57 Conformation dependent library (CDL) restraints added in 991.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1403 " pdb="ZN ZN A1403 " - pdb=" NE2 HIS A 318 " pdb="ZN ZN A1403 " - pdb=" NE2 HIS A 313 " pdb="ZN ZN A1403 " - pdb=" SG CYS A 297 " pdb="ZN ZN A1403 " - pdb=" SG CYS A 300 " pdb=" ZN A1404 " pdb="ZN ZN A1404 " - pdb=" NE2 HIS A1224 " pdb="ZN ZN A1404 " - pdb=" SG CYS A1215 " pdb="ZN ZN A1404 " - pdb=" SG CYS A1212 " pdb="ZN ZN A1404 " - pdb=" SG CYS A1229 " pdb=" ZN A1405 " pdb="ZN ZN A1405 " - pdb=" ND1 HIS A 278 " pdb="ZN ZN A1405 " - pdb=" SG CYS A 265 " pdb="ZN ZN A1405 " - pdb=" SG CYS A 282 " pdb="ZN ZN A1405 " - pdb=" SG CYS A 262 " pdb=" ZN A1406 " pdb="ZN ZN A1406 " - pdb=" SG CYS A 232 " pdb="ZN ZN A1406 " - pdb=" NE2 HIS A 253 " pdb="ZN ZN A1406 " - pdb=" NE2 HIS A 248 " Number of angles added : 8 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 55.7% alpha, 12.3% beta 52 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 241 through 254 removed outlier: 3.581A pdb=" N HIS A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.521A pdb=" N VAL A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'A' and resid 551 through 573 removed outlier: 4.152A pdb=" N ASP A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A 571 " --> pdb=" O GLN A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.992A pdb=" N ASP A 584 " --> pdb=" O ILE A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 606 Processing helix chain 'A' and resid 624 through 629 removed outlier: 3.654A pdb=" N ALA A 627 " --> pdb=" O ASP A 624 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 628 " --> pdb=" O ASN A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 644 Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 667 through 681 Processing helix chain 'A' and resid 684 through 687 removed outlier: 3.702A pdb=" N VAL A 687 " --> pdb=" O PRO A 684 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 684 through 687' Processing helix chain 'A' and resid 706 through 708 No H-bonds generated for 'chain 'A' and resid 706 through 708' Processing helix chain 'A' and resid 717 through 735 removed outlier: 3.773A pdb=" N ARG A 730 " --> pdb=" O ILE A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 767 removed outlier: 3.514A pdb=" N GLU A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 785 removed outlier: 3.936A pdb=" N VAL A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 797 removed outlier: 3.565A pdb=" N ARG A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 811 removed outlier: 3.634A pdb=" N TYR A 811 " --> pdb=" O VAL A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 861 Proline residue: A 852 - end of helix Processing helix chain 'A' and resid 886 through 905 removed outlier: 3.678A pdb=" N MET A 890 " --> pdb=" O SER A 886 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN A 891 " --> pdb=" O TRP A 887 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR A 892 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 912 Processing helix chain 'A' and resid 966 through 980 removed outlier: 3.704A pdb=" N LYS A 970 " --> pdb=" O GLY A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 995 Processing helix chain 'A' and resid 996 through 999 Processing helix chain 'A' and resid 1000 through 1007 Processing helix chain 'A' and resid 1010 through 1029 removed outlier: 3.652A pdb=" N LEU A1014 " --> pdb=" O LYS A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1042 Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1053 through 1071 Proline residue: A1059 - end of helix Processing helix chain 'A' and resid 1082 through 1097 Processing helix chain 'A' and resid 1100 through 1104 removed outlier: 3.628A pdb=" N ASN A1103 " --> pdb=" O ASP A1100 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE A1104 " --> pdb=" O ARG A1101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1100 through 1104' Processing helix chain 'A' and resid 1140 through 1151 Processing helix chain 'A' and resid 1158 through 1163 removed outlier: 3.515A pdb=" N ASN A1161 " --> pdb=" O GLY A1158 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A1163 " --> pdb=" O VAL A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1174 removed outlier: 4.332A pdb=" N GLN A1173 " --> pdb=" O ASN A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1192 Processing helix chain 'A' and resid 1196 through 1202 Processing helix chain 'A' and resid 1221 through 1228 Processing helix chain 'A' and resid 1229 through 1231 No H-bonds generated for 'chain 'A' and resid 1229 through 1231' Processing helix chain 'A' and resid 1232 through 1254 removed outlier: 3.647A pdb=" N GLU A1250 " --> pdb=" O LEU A1246 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A1254 " --> pdb=" O GLU A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1310 Processing helix chain 'A' and resid 1311 through 1313 No H-bonds generated for 'chain 'A' and resid 1311 through 1313' Processing helix chain 'A' and resid 1314 through 1323 Processing helix chain 'A' and resid 1343 through 1351 removed outlier: 4.125A pdb=" N LEU A1347 " --> pdb=" O ASP A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1386 removed outlier: 3.792A pdb=" N VAL A1359 " --> pdb=" O LYS A1355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 221 through 224 removed outlier: 6.133A pdb=" N VAL A 221 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ARG A 261 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A 223 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AA3, first strand: chain 'A' and resid 710 through 715 removed outlier: 7.032A pdb=" N CYS A 690 " --> pdb=" O TYR A 817 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR A 819 " --> pdb=" O CYS A 690 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR A 692 " --> pdb=" O THR A 819 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE A 818 " --> pdb=" O ASP A 827 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ASP A 827 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR A 820 " --> pdb=" O HIS A 825 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N HIS A 825 " --> pdb=" O THR A 820 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 873 through 876 Processing sheet with id=AA5, first strand: chain 'A' and resid 873 through 876 Processing sheet with id=AA6, first strand: chain 'A' and resid 864 through 866 Processing sheet with id=AA7, first strand: chain 'A' and resid 934 through 935 removed outlier: 3.651A pdb=" N THR A 938 " --> pdb=" O ILE A 935 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 949 through 951 Processing sheet with id=AA9, first strand: chain 'A' and resid 1257 through 1260 removed outlier: 6.445A pdb=" N ALA A1284 " --> pdb=" O THR A1328 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A1330 " --> pdb=" O ALA A1284 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL A1286 " --> pdb=" O VAL A1330 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE A1332 " --> pdb=" O VAL A1286 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASP A1288 " --> pdb=" O PHE A1332 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A1334 " --> pdb=" O ASP A1288 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR A1290 " --> pdb=" O LEU A1334 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1264 through 1265 383 hydrogen bonds defined for protein. 1083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 130 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2314 1.34 - 1.46: 3218 1.46 - 1.58: 5125 1.58 - 1.70: 290 1.70 - 1.83: 64 Bond restraints: 11011 Sorted by residual: bond pdb=" C ILE A 997 " pdb=" N PRO A 998 " ideal model delta sigma weight residual 1.336 1.405 -0.070 1.08e-02 8.57e+03 4.16e+01 bond pdb=" C ILE A 943 " pdb=" N ASP A 944 " ideal model delta sigma weight residual 1.329 1.266 0.062 1.86e-02 2.89e+03 1.13e+01 bond pdb=" C ILE A1058 " pdb=" N PRO A1059 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.28e-02 6.10e+03 7.25e+00 bond pdb=" C3' DT P 16 " pdb=" O3' DT P 16 " ideal model delta sigma weight residual 1.422 1.500 -0.078 3.00e-02 1.11e+03 6.78e+00 bond pdb=" C3' DA P 15 " pdb=" O3' DA P 15 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.56e+00 ... (remaining 11006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 14898 2.44 - 4.89: 528 4.89 - 7.33: 84 7.33 - 9.78: 11 9.78 - 12.22: 12 Bond angle restraints: 15533 Sorted by residual: angle pdb=" C LYS A 821 " pdb=" N ARG A 822 " pdb=" CA ARG A 822 " ideal model delta sigma weight residual 121.54 133.16 -11.62 1.91e+00 2.74e-01 3.70e+01 angle pdb=" C THR A 826 " pdb=" N ASP A 827 " pdb=" CA ASP A 827 " ideal model delta sigma weight residual 121.54 131.94 -10.40 1.91e+00 2.74e-01 2.97e+01 angle pdb=" CA ARG A1204 " pdb=" CB ARG A1204 " pdb=" CG ARG A1204 " ideal model delta sigma weight residual 114.10 124.47 -10.37 2.00e+00 2.50e-01 2.69e+01 angle pdb=" CG ARG A1204 " pdb=" CD ARG A1204 " pdb=" NE ARG A1204 " ideal model delta sigma weight residual 112.00 122.61 -10.61 2.20e+00 2.07e-01 2.32e+01 angle pdb=" CD ARG A1204 " pdb=" NE ARG A1204 " pdb=" CZ ARG A1204 " ideal model delta sigma weight residual 124.40 130.99 -6.59 1.40e+00 5.10e-01 2.22e+01 ... (remaining 15528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 6045 35.81 - 71.61: 442 71.61 - 107.42: 33 107.42 - 143.22: 2 143.22 - 179.03: 7 Dihedral angle restraints: 6529 sinusoidal: 3840 harmonic: 2689 Sorted by residual: dihedral pdb=" CA VAL A 225 " pdb=" C VAL A 225 " pdb=" N PRO A 226 " pdb=" CA PRO A 226 " ideal model delta harmonic sigma weight residual 180.00 143.79 36.21 0 5.00e+00 4.00e-02 5.25e+01 dihedral pdb=" C2 TTP A1402 " pdb=" C1' TTP A1402 " pdb=" N1 TTP A1402 " pdb=" O4' TTP A1402 " ideal model delta sinusoidal sigma weight residual 301.68 153.79 147.89 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O2G TTP A1402 " pdb=" O3B TTP A1402 " pdb=" PG TTP A1402 " pdb=" PB TTP A1402 " ideal model delta sinusoidal sigma weight residual 180.00 55.59 124.41 1 2.00e+01 2.50e-03 3.76e+01 ... (remaining 6526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1590 0.093 - 0.185: 187 0.185 - 0.278: 8 0.278 - 0.371: 0 0.371 - 0.463: 2 Chirality restraints: 1787 Sorted by residual: chirality pdb=" P DG B 49 " pdb=" OP1 DG B 49 " pdb=" OP2 DG B 49 " pdb=" O5' DG B 49 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" P DT P 24 " pdb=" OP1 DT P 24 " pdb=" OP2 DT P 24 " pdb=" O5' DT P 24 " both_signs ideal model delta sigma weight residual True 2.35 -2.75 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C3' U R 282 " pdb=" C4' U R 282 " pdb=" O3' U R 282 " pdb=" C2' U R 282 " both_signs ideal model delta sigma weight residual False -2.48 -2.21 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1784 not shown) Planarity restraints: 1443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 549 " 0.017 2.00e-02 2.50e+03 2.03e-02 7.18e+00 pdb=" CG PHE A 549 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 549 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 549 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 549 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 549 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 549 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1320 " 0.020 2.00e-02 2.50e+03 2.14e-02 6.85e+00 pdb=" CG HIS A1320 " -0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS A1320 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS A1320 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS A1320 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A1320 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 40 " -0.035 2.00e-02 2.50e+03 1.63e-02 6.67e+00 pdb=" N1 DT T 40 " 0.027 2.00e-02 2.50e+03 pdb=" C2 DT T 40 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DT T 40 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT T 40 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DT T 40 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT T 40 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DT T 40 " -0.005 2.00e-02 2.50e+03 pdb=" C7 DT T 40 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DT T 40 " 0.022 2.00e-02 2.50e+03 ... (remaining 1440 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 426 2.72 - 3.26: 8839 3.26 - 3.81: 17697 3.81 - 4.35: 23035 4.35 - 4.90: 34510 Nonbonded interactions: 84507 Sorted by model distance: nonbonded pdb="MG MG A1401 " pdb=" O1B TTP A1402 " model vdw 2.173 2.170 nonbonded pdb=" OD2 ASP A 878 " pdb="MG MG A1401 " model vdw 2.180 2.170 nonbonded pdb=" OD2 ASP A 777 " pdb="MG MG A1401 " model vdw 2.215 2.170 nonbonded pdb="MG MG A1401 " pdb=" O1A TTP A1402 " model vdw 2.271 2.170 nonbonded pdb=" O ILE A 778 " pdb="MG MG A1401 " model vdw 2.333 2.170 ... (remaining 84502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.550 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 11026 Z= 0.300 Angle : 1.117 12.223 15541 Z= 0.611 Chirality : 0.059 0.463 1787 Planarity : 0.009 0.066 1443 Dihedral : 21.228 179.031 4781 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.24 % Allowed : 4.16 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.25), residues: 914 helix: -0.56 (0.22), residues: 435 sheet: 0.32 (0.51), residues: 107 loop : -0.59 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 552 HIS 0.024 0.003 HIS A1320 PHE 0.047 0.004 PHE A 549 TYR 0.021 0.003 TYR A 864 ARG 0.017 0.002 ARG A1383 Details of bonding type rmsd hydrogen bonds : bond 0.14473 ( 497) hydrogen bonds : angle 6.08457 ( 1331) metal coordination : bond 0.02382 ( 15) metal coordination : angle 4.88649 ( 8) covalent geometry : bond 0.00593 (11011) covalent geometry : angle 1.11142 (15533) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.916 Fit side-chains REVERT: A 644 MET cc_start: 0.8785 (mmm) cc_final: 0.8438 (mtp) REVERT: A 686 MET cc_start: 0.7159 (ptt) cc_final: 0.6952 (ptm) REVERT: A 777 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8503 (p0) REVERT: A 1085 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8236 (mtpt) REVERT: A 1294 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: A 1350 GLU cc_start: 0.8233 (tp30) cc_final: 0.7983 (tp30) outliers start: 2 outliers final: 0 residues processed: 110 average time/residue: 0.3331 time to fit residues: 49.5923 Evaluate side-chains 86 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 1294 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.158543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117727 restraints weight = 12392.859| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.30 r_work: 0.2956 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11026 Z= 0.157 Angle : 0.630 9.401 15541 Z= 0.346 Chirality : 0.041 0.164 1787 Planarity : 0.005 0.045 1443 Dihedral : 23.498 176.449 2905 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.61 % Allowed : 5.75 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 914 helix: 0.89 (0.24), residues: 436 sheet: 0.54 (0.51), residues: 99 loop : -0.65 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 552 HIS 0.012 0.001 HIS A1320 PHE 0.021 0.002 PHE A1371 TYR 0.013 0.002 TYR A1174 ARG 0.005 0.000 ARG A1204 Details of bonding type rmsd hydrogen bonds : bond 0.05358 ( 497) hydrogen bonds : angle 4.26094 ( 1331) metal coordination : bond 0.01505 ( 15) metal coordination : angle 3.08172 ( 8) covalent geometry : bond 0.00337 (11011) covalent geometry : angle 0.62594 (15533) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 1.707 Fit side-chains REVERT: A 644 MET cc_start: 0.8743 (mmm) cc_final: 0.8420 (mtp) REVERT: A 1177 ARG cc_start: 0.7413 (mtm180) cc_final: 0.7130 (mmt-90) REVERT: A 1294 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7805 (pm20) REVERT: A 1350 GLU cc_start: 0.8360 (tp30) cc_final: 0.8015 (tp30) outliers start: 5 outliers final: 4 residues processed: 90 average time/residue: 0.3183 time to fit residues: 40.8721 Evaluate side-chains 84 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1294 GLU Chi-restraints excluded: chain A residue 1299 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 0 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 301 ASN A 625 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 HIS ** A1320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.150863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.109000 restraints weight = 12511.972| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.49 r_work: 0.2840 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.861 11026 Z= 0.460 Angle : 0.811 9.797 15541 Z= 0.432 Chirality : 0.052 0.195 1787 Planarity : 0.007 0.091 1443 Dihedral : 23.852 172.644 2903 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.84 % Allowed : 7.59 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.27), residues: 914 helix: 0.55 (0.24), residues: 437 sheet: -0.02 (0.50), residues: 107 loop : -0.81 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 552 HIS 0.013 0.002 HIS A1320 PHE 0.031 0.003 PHE A1371 TYR 0.022 0.003 TYR A1311 ARG 0.008 0.001 ARG A 574 Details of bonding type rmsd hydrogen bonds : bond 0.07553 ( 497) hydrogen bonds : angle 4.49500 ( 1331) metal coordination : bond 0.22329 ( 15) metal coordination : angle 4.12338 ( 8) covalent geometry : bond 0.00866 (11011) covalent geometry : angle 0.80609 (15533) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 1.009 Fit side-chains REVERT: A 644 MET cc_start: 0.8677 (mmm) cc_final: 0.8459 (mtp) REVERT: A 1294 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: A 1350 GLU cc_start: 0.8426 (tp30) cc_final: 0.7966 (tp30) outliers start: 15 outliers final: 11 residues processed: 92 average time/residue: 0.2662 time to fit residues: 33.4743 Evaluate side-chains 85 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 976 GLN Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1222 CYS Chi-restraints excluded: chain A residue 1294 GLU Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1330 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 75 optimal weight: 3.9990 chunk 73 optimal weight: 0.0270 chunk 17 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.156569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115809 restraints weight = 12408.760| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.43 r_work: 0.2947 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11026 Z= 0.134 Angle : 0.580 7.764 15541 Z= 0.316 Chirality : 0.039 0.164 1787 Planarity : 0.004 0.044 1443 Dihedral : 23.495 174.135 2903 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.61 % Allowed : 9.67 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 914 helix: 1.32 (0.25), residues: 439 sheet: 0.40 (0.50), residues: 99 loop : -0.77 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 552 HIS 0.003 0.001 HIS A1180 PHE 0.020 0.002 PHE A 549 TYR 0.010 0.001 TYR A1174 ARG 0.004 0.000 ARG A1309 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 497) hydrogen bonds : angle 3.96030 ( 1331) metal coordination : bond 0.01788 ( 15) metal coordination : angle 3.01213 ( 8) covalent geometry : bond 0.00280 (11011) covalent geometry : angle 0.57614 (15533) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.889 Fit side-chains REVERT: A 644 MET cc_start: 0.8621 (mmm) cc_final: 0.8126 (mmm) REVERT: A 823 ASN cc_start: 0.6248 (OUTLIER) cc_final: 0.5922 (t0) REVERT: A 1132 LYS cc_start: 0.6359 (mmtt) cc_final: 0.6119 (ptmt) REVERT: A 1177 ARG cc_start: 0.7499 (mtm180) cc_final: 0.7201 (mmt-90) REVERT: A 1350 GLU cc_start: 0.8425 (tp30) cc_final: 0.8024 (tp30) outliers start: 5 outliers final: 2 residues processed: 87 average time/residue: 0.3117 time to fit residues: 35.8357 Evaluate side-chains 76 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 1308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 11 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.154714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112952 restraints weight = 12332.144| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.45 r_work: 0.2899 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11026 Z= 0.184 Angle : 0.611 8.195 15541 Z= 0.329 Chirality : 0.041 0.171 1787 Planarity : 0.005 0.046 1443 Dihedral : 23.452 174.463 2900 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.98 % Allowed : 9.91 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.28), residues: 914 helix: 1.38 (0.25), residues: 439 sheet: 0.37 (0.50), residues: 99 loop : -0.78 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 552 HIS 0.004 0.001 HIS A1006 PHE 0.022 0.002 PHE A1371 TYR 0.014 0.002 TYR A1174 ARG 0.007 0.000 ARG A1309 Details of bonding type rmsd hydrogen bonds : bond 0.05131 ( 497) hydrogen bonds : angle 3.93738 ( 1331) metal coordination : bond 0.01418 ( 15) metal coordination : angle 3.06758 ( 8) covalent geometry : bond 0.00417 (11011) covalent geometry : angle 0.60690 (15533) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.900 Fit side-chains REVERT: A 644 MET cc_start: 0.8660 (mmm) cc_final: 0.8384 (mtp) REVERT: A 1132 LYS cc_start: 0.6339 (mmtt) cc_final: 0.6093 (ptmm) REVERT: A 1180 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8239 (m90) REVERT: A 1320 HIS cc_start: 0.8003 (p-80) cc_final: 0.7756 (p-80) REVERT: A 1321 LEU cc_start: 0.8032 (tp) cc_final: 0.7338 (mp) REVERT: A 1350 GLU cc_start: 0.8471 (tp30) cc_final: 0.8059 (tp30) outliers start: 8 outliers final: 6 residues processed: 81 average time/residue: 0.2851 time to fit residues: 31.4622 Evaluate side-chains 84 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 976 GLN Chi-restraints excluded: chain A residue 1180 HIS Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1330 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 47 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.157270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115841 restraints weight = 12424.122| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.51 r_work: 0.2943 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11026 Z= 0.132 Angle : 0.551 7.546 15541 Z= 0.297 Chirality : 0.038 0.160 1787 Planarity : 0.004 0.041 1443 Dihedral : 23.293 175.071 2900 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.61 % Allowed : 10.40 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.28), residues: 914 helix: 1.72 (0.26), residues: 438 sheet: 0.32 (0.48), residues: 113 loop : -0.77 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 552 HIS 0.003 0.001 HIS A1170 PHE 0.017 0.002 PHE A1371 TYR 0.009 0.001 TYR A1174 ARG 0.004 0.000 ARG A1309 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 497) hydrogen bonds : angle 3.72143 ( 1331) metal coordination : bond 0.01058 ( 15) metal coordination : angle 2.54351 ( 8) covalent geometry : bond 0.00287 (11011) covalent geometry : angle 0.54766 (15533) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.884 Fit side-chains REVERT: A 644 MET cc_start: 0.8608 (mmm) cc_final: 0.8316 (mtp) REVERT: A 980 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7450 (mt0) REVERT: A 1132 LYS cc_start: 0.6429 (mmtt) cc_final: 0.6118 (ptmm) REVERT: A 1320 HIS cc_start: 0.7893 (p-80) cc_final: 0.7670 (p-80) REVERT: A 1321 LEU cc_start: 0.8072 (tp) cc_final: 0.7331 (mp) REVERT: A 1350 GLU cc_start: 0.8474 (tp30) cc_final: 0.8051 (tp30) outliers start: 5 outliers final: 3 residues processed: 84 average time/residue: 0.2624 time to fit residues: 30.6202 Evaluate side-chains 80 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 1330 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 22 optimal weight: 6.9990 chunk 48 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 0.0870 chunk 72 optimal weight: 0.8980 chunk 100 optimal weight: 30.0000 chunk 8 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 overall best weight: 2.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.154404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.114015 restraints weight = 12561.483| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.50 r_work: 0.2895 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11026 Z= 0.183 Angle : 0.595 7.915 15541 Z= 0.320 Chirality : 0.041 0.168 1787 Planarity : 0.005 0.046 1443 Dihedral : 23.355 174.476 2900 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.22 % Allowed : 11.02 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.28), residues: 914 helix: 1.58 (0.25), residues: 438 sheet: 0.27 (0.48), residues: 113 loop : -0.83 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 552 HIS 0.004 0.001 HIS A1006 PHE 0.023 0.002 PHE A1371 TYR 0.013 0.002 TYR A1174 ARG 0.006 0.000 ARG A1309 Details of bonding type rmsd hydrogen bonds : bond 0.05041 ( 497) hydrogen bonds : angle 3.83787 ( 1331) metal coordination : bond 0.01272 ( 15) metal coordination : angle 2.75750 ( 8) covalent geometry : bond 0.00414 (11011) covalent geometry : angle 0.59205 (15533) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.881 Fit side-chains REVERT: A 644 MET cc_start: 0.8666 (mmm) cc_final: 0.8422 (mtp) REVERT: A 980 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7509 (mt0) REVERT: A 1132 LYS cc_start: 0.6426 (mmtt) cc_final: 0.6111 (ptmm) REVERT: A 1180 HIS cc_start: 0.9000 (OUTLIER) cc_final: 0.8285 (m90) REVERT: A 1320 HIS cc_start: 0.7865 (p-80) cc_final: 0.7646 (p-80) REVERT: A 1321 LEU cc_start: 0.8092 (tp) cc_final: 0.7343 (mp) REVERT: A 1350 GLU cc_start: 0.8520 (tp30) cc_final: 0.8093 (tp30) outliers start: 10 outliers final: 7 residues processed: 83 average time/residue: 0.2716 time to fit residues: 31.0477 Evaluate side-chains 82 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 1180 HIS Chi-restraints excluded: chain A residue 1330 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 5 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 100 optimal weight: 30.0000 chunk 84 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.152295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110448 restraints weight = 12344.620| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.44 r_work: 0.2919 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11026 Z= 0.232 Angle : 0.649 8.479 15541 Z= 0.346 Chirality : 0.044 0.172 1787 Planarity : 0.005 0.064 1443 Dihedral : 23.479 173.799 2900 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.08 % Allowed : 10.65 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.28), residues: 914 helix: 1.32 (0.25), residues: 438 sheet: 0.23 (0.50), residues: 101 loop : -0.96 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 933 HIS 0.004 0.001 HIS A1214 PHE 0.029 0.002 PHE A 549 TYR 0.015 0.002 TYR A1174 ARG 0.006 0.001 ARG A1022 Details of bonding type rmsd hydrogen bonds : bond 0.05723 ( 497) hydrogen bonds : angle 4.01326 ( 1331) metal coordination : bond 0.01635 ( 15) metal coordination : angle 3.24708 ( 8) covalent geometry : bond 0.00534 (11011) covalent geometry : angle 0.64507 (15533) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 1.002 Fit side-chains REVERT: A 980 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: A 1132 LYS cc_start: 0.6555 (mmtt) cc_final: 0.6075 (ptmm) REVERT: A 1180 HIS cc_start: 0.9088 (OUTLIER) cc_final: 0.8271 (m90) REVERT: A 1350 GLU cc_start: 0.8703 (tp30) cc_final: 0.8232 (tp30) outliers start: 17 outliers final: 11 residues processed: 90 average time/residue: 0.2837 time to fit residues: 34.7611 Evaluate side-chains 87 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 976 GLN Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 1180 HIS Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1330 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 38 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.153936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.113311 restraints weight = 12476.835| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.52 r_work: 0.2913 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11026 Z= 0.173 Angle : 0.589 8.110 15541 Z= 0.316 Chirality : 0.040 0.162 1787 Planarity : 0.005 0.046 1443 Dihedral : 23.421 174.231 2900 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.47 % Allowed : 11.02 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 914 helix: 1.51 (0.25), residues: 438 sheet: 0.15 (0.49), residues: 113 loop : -0.98 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 552 HIS 0.003 0.001 HIS A1170 PHE 0.026 0.002 PHE A 549 TYR 0.012 0.002 TYR A1174 ARG 0.005 0.000 ARG A1204 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 497) hydrogen bonds : angle 3.83794 ( 1331) metal coordination : bond 0.01278 ( 15) metal coordination : angle 2.92827 ( 8) covalent geometry : bond 0.00392 (11011) covalent geometry : angle 0.58508 (15533) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 1.019 Fit side-chains REVERT: A 980 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7492 (mt0) REVERT: A 1132 LYS cc_start: 0.6617 (mmtt) cc_final: 0.6129 (ptmm) REVERT: A 1180 HIS cc_start: 0.8986 (OUTLIER) cc_final: 0.8240 (m90) REVERT: A 1288 ASP cc_start: 0.7772 (t0) cc_final: 0.7353 (t0) REVERT: A 1311 TYR cc_start: 0.8295 (m-10) cc_final: 0.7679 (m-80) REVERT: A 1350 GLU cc_start: 0.8566 (tp30) cc_final: 0.8128 (tp30) outliers start: 12 outliers final: 9 residues processed: 77 average time/residue: 0.2458 time to fit residues: 26.9203 Evaluate side-chains 82 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 976 GLN Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 1180 HIS Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1330 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 95 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.151219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.110118 restraints weight = 12398.039| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.54 r_work: 0.2854 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 11026 Z= 0.280 Angle : 0.685 8.552 15541 Z= 0.364 Chirality : 0.046 0.181 1787 Planarity : 0.006 0.074 1443 Dihedral : 23.593 173.547 2900 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.84 % Allowed : 10.65 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.28), residues: 914 helix: 1.18 (0.25), residues: 436 sheet: -0.01 (0.49), residues: 113 loop : -1.12 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1171 HIS 0.005 0.001 HIS A1006 PHE 0.028 0.003 PHE A1371 TYR 0.014 0.002 TYR A1174 ARG 0.008 0.001 ARG A1022 Details of bonding type rmsd hydrogen bonds : bond 0.06164 ( 497) hydrogen bonds : angle 4.07617 ( 1331) metal coordination : bond 0.01759 ( 15) metal coordination : angle 3.44479 ( 8) covalent geometry : bond 0.00651 (11011) covalent geometry : angle 0.68106 (15533) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 1.033 Fit side-chains REVERT: A 980 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7405 (mt0) REVERT: A 1180 HIS cc_start: 0.9070 (OUTLIER) cc_final: 0.8255 (m90) REVERT: A 1350 GLU cc_start: 0.8649 (tp30) cc_final: 0.8190 (tp30) outliers start: 15 outliers final: 12 residues processed: 86 average time/residue: 0.2678 time to fit residues: 32.3311 Evaluate side-chains 88 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 976 GLN Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 1180 HIS Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1330 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.4980 chunk 92 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 1 optimal weight: 0.0570 chunk 65 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.158076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.116858 restraints weight = 12390.306| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.50 r_work: 0.2962 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11026 Z= 0.121 Angle : 0.545 8.017 15541 Z= 0.293 Chirality : 0.037 0.157 1787 Planarity : 0.004 0.042 1443 Dihedral : 23.325 174.922 2900 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.86 % Allowed : 11.51 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.29), residues: 914 helix: 1.74 (0.26), residues: 437 sheet: 0.25 (0.50), residues: 110 loop : -0.86 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 552 HIS 0.003 0.001 HIS A1180 PHE 0.021 0.002 PHE A 549 TYR 0.011 0.001 TYR A1174 ARG 0.005 0.000 ARG A1204 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 497) hydrogen bonds : angle 3.69568 ( 1331) metal coordination : bond 0.00935 ( 15) metal coordination : angle 2.67779 ( 8) covalent geometry : bond 0.00253 (11011) covalent geometry : angle 0.54211 (15533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5413.34 seconds wall clock time: 95 minutes 9.85 seconds (5709.85 seconds total)