Starting phenix.real_space_refine on Fri Jul 3 12:46:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ko9_62471/07_2026/9ko9_62471.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ko9_62471/07_2026/9ko9_62471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ko9_62471/07_2026/9ko9_62471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ko9_62471/07_2026/9ko9_62471.map" model { file = "/net/cci-nas-00/data/ceres_data/9ko9_62471/07_2026/9ko9_62471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ko9_62471/07_2026/9ko9_62471.cif" } resolution = 2.7 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= 0.050 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: 5 Type Number sf(0) Gaussians P 114 5.49 5 S 38 5.16 5 C 8314 2.51 5 N 2456 2.21 5 O 2929 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 13851 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11424 Classifications: {'peptide': 1409} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 1370} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2427 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 12, 'rna3p_pur': 54, 'rna3p_pyr': 41} Link IDs: {'rna2p': 19, 'rna3p': 94} Time building chain proxies: 3.12, per 1000 atoms: 0.23 Number of scatterers: 13851 At special positions: 0 Unit cell: (92.07, 105.09, 146.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 114 15.00 O 2929 8.00 N 2456 7.00 C 8314 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: 1.22 Conformation dependent library (CDL) restraints added in 594.4 milliseconds 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 9 sheets defined 54.5% alpha, 13.1% beta 30 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 50 through 82 Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 113 through 117 removed outlier: 4.059A pdb=" N GLY A 116 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 124 removed outlier: 3.599A pdb=" N PHE A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 123 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS A 124 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 148 Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.676A pdb=" N GLN A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.952A pdb=" N PHE A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 190 through 202 removed outlier: 4.026A pdb=" N SER A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 207 through 218 removed outlier: 4.033A pdb=" N LEU A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 235 through 248 Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.502A pdb=" N LEU A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 266 removed outlier: 3.506A pdb=" N LYS A 264 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A 265 " --> pdb=" O SER A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 350 through 361 removed outlier: 3.562A pdb=" N ILE A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.540A pdb=" N LYS A 366 " --> pdb=" O PRO A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.748A pdb=" N LEU A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 397 through 412 Processing helix chain 'A' and resid 433 through 443 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 451 through 472 Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.536A pdb=" N ILE A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A 478 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 525 through 541 Processing helix chain 'A' and resid 543 through 557 removed outlier: 3.512A pdb=" N LEU A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 587 removed outlier: 4.046A pdb=" N ASP A 567 " --> pdb=" O ALA A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 597 removed outlier: 4.175A pdb=" N PHE A 596 " --> pdb=" O GLN A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 652 through 676 removed outlier: 3.626A pdb=" N THR A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 704 removed outlier: 4.180A pdb=" N SER A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 728 removed outlier: 3.656A pdb=" N LYS A 718 " --> pdb=" O GLN A 714 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 719 " --> pdb=" O LYS A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 790 removed outlier: 3.894A pdb=" N LEU A 790 " --> pdb=" O ASN A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 800 through 808 Processing helix chain 'A' and resid 812 through 826 Processing helix chain 'A' and resid 828 through 834 Processing helix chain 'A' and resid 835 through 838 Processing helix chain 'A' and resid 839 through 849 Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 875 through 893 Processing helix chain 'A' and resid 893 through 899 Processing helix chain 'A' and resid 912 through 929 removed outlier: 3.945A pdb=" N ARG A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS A 922 " --> pdb=" O GLN A 918 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 923 " --> pdb=" O ASP A 919 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 954 removed outlier: 4.033A pdb=" N ALA A 945 " --> pdb=" O ILE A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 957 No H-bonds generated for 'chain 'A' and resid 955 through 957' Processing helix chain 'A' and resid 972 through 984 removed outlier: 3.826A pdb=" N GLN A 982 " --> pdb=" O LYS A 978 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1007 Processing helix chain 'A' and resid 1045 through 1053 removed outlier: 3.957A pdb=" N LEU A1049 " --> pdb=" O ASP A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1088 removed outlier: 3.527A pdb=" N PHE A1086 " --> pdb=" O LEU A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1104 Processing helix chain 'A' and resid 1126 through 1131 Processing helix chain 'A' and resid 1132 through 1135 Processing helix chain 'A' and resid 1143 through 1147 removed outlier: 3.606A pdb=" N GLY A1147 " --> pdb=" O ASN A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1166 removed outlier: 4.009A pdb=" N GLU A1160 " --> pdb=" O PRO A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1172 removed outlier: 4.716A pdb=" N ASN A1172 " --> pdb=" O SER A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1181 Processing helix chain 'A' and resid 1188 through 1198 removed outlier: 3.821A pdb=" N LEU A1192 " --> pdb=" O ASP A1188 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A1197 " --> pdb=" O ILE A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1272 Processing helix chain 'A' and resid 1325 through 1332 Processing helix chain 'A' and resid 1338 through 1342 Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.771A pdb=" N GLN A1361 " --> pdb=" O VAL A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1366 Processing helix chain 'A' and resid 1368 through 1370 No H-bonds generated for 'chain 'A' and resid 1368 through 1370' Processing helix chain 'A' and resid 1392 through 1409 removed outlier: 3.987A pdb=" N GLN A1409 " --> pdb=" O VAL A1405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 904 through 910 removed outlier: 6.785A pdb=" N ALA A 35 " --> pdb=" O ASN A 989 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE A 991 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL A 37 " --> pdb=" O ILE A 991 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE A1376 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN A1372 " --> pdb=" O CYS A1387 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N CYS A1387 " --> pdb=" O GLN A1372 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS A1383 " --> pdb=" O ILE A1376 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU A1378 " --> pdb=" O THR A1381 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N THR A1381 " --> pdb=" O LEU A1378 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 904 through 910 removed outlier: 6.785A pdb=" N ALA A 35 " --> pdb=" O ASN A 989 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE A 991 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL A 37 " --> pdb=" O ILE A 991 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE A1376 " --> pdb=" O LEU A 990 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA4, first strand: chain 'A' and resid 754 through 757 removed outlier: 3.527A pdb=" N ASP A 756 " --> pdb=" O ILE A 779 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1215 through 1218 removed outlier: 6.201A pdb=" N ASN A1110 " --> pdb=" O ILE A1014 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ILE A1014 " --> pdb=" O ASN A1110 " (cutoff:3.500A) removed outlier: 13.287A pdb=" N SER A1112 " --> pdb=" O GLU A1012 " (cutoff:3.500A) removed outlier: 18.457A pdb=" N GLU A1012 " --> pdb=" O SER A1112 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET A1243 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY A1013 " --> pdb=" O LEU A1241 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU A1241 " --> pdb=" O GLY A1013 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N PHE A1015 " --> pdb=" O TYR A1239 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N TYR A1239 " --> pdb=" O PHE A1015 " (cutoff:3.500A) removed outlier: 13.185A pdb=" N GLU A1017 " --> pdb=" O ASP A1237 " (cutoff:3.500A) removed outlier: 15.055A pdb=" N ASP A1237 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1040 through 1043 removed outlier: 4.631A pdb=" N CYS A1029 " --> pdb=" O VAL A1043 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1117 through 1118 Processing sheet with id=AA8, first strand: chain 'A' and resid 1137 through 1142 Processing sheet with id=AA9, first strand: chain 'A' and resid 1260 through 1267 removed outlier: 4.053A pdb=" N VAL A1253 " --> pdb=" O ASP A1261 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N SER A1263 " --> pdb=" O GLY A1251 " (cutoff:3.500A) removed outlier: 10.982A pdb=" N GLY A1251 " --> pdb=" O SER A1263 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N ASP A1265 " --> pdb=" O CYS A1249 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N CYS A1249 " --> pdb=" O ASP A1265 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3546 1.33 - 1.46: 3460 1.46 - 1.58: 7051 1.58 - 1.70: 227 1.70 - 1.82: 59 Bond restraints: 14343 Sorted by residual: bond pdb=" C2 U B 121 " pdb=" N3 U B 121 " ideal model delta sigma weight residual 1.373 1.364 0.009 7.00e-03 2.04e+04 1.63e+00 bond pdb=" N ALA A 972 " pdb=" CA ALA A 972 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.57e+00 bond pdb=" N1 U B 58 " pdb=" C2 U B 58 " ideal model delta sigma weight residual 1.381 1.392 -0.011 9.00e-03 1.23e+04 1.53e+00 bond pdb=" C8 A B 94 " pdb=" N7 A B 94 " ideal model delta sigma weight residual 1.311 1.303 0.008 7.00e-03 2.04e+04 1.43e+00 bond pdb=" CB GLU A 677 " pdb=" CG GLU A 677 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.39e+00 ... (remaining 14338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 19751 2.81 - 5.62: 126 5.62 - 8.43: 16 8.43 - 11.24: 1 11.24 - 14.06: 2 Bond angle restraints: 19896 Sorted by residual: angle pdb=" C1' U B 112 " pdb=" N1 U B 112 " pdb=" C2 U B 112 " ideal model delta sigma weight residual 117.70 123.43 -5.73 1.20e+00 6.94e-01 2.28e+01 angle pdb=" O2 U B 112 " pdb=" C2 U B 112 " pdb=" N3 U B 112 " ideal model delta sigma weight residual 122.20 118.86 3.34 7.00e-01 2.04e+00 2.27e+01 angle pdb=" CB MET A 984 " pdb=" CG MET A 984 " pdb=" SD MET A 984 " ideal model delta sigma weight residual 112.70 126.76 -14.06 3.00e+00 1.11e-01 2.19e+01 angle pdb=" C1' U B 34 " pdb=" N1 U B 34 " pdb=" C2 U B 34 " ideal model delta sigma weight residual 117.70 123.17 -5.47 1.20e+00 6.94e-01 2.07e+01 angle pdb=" C1' U B 58 " pdb=" N1 U B 58 " pdb=" C2 U B 58 " ideal model delta sigma weight residual 117.70 123.01 -5.31 1.20e+00 6.94e-01 1.96e+01 ... (remaining 19891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 8414 35.91 - 71.81: 409 71.81 - 107.72: 38 107.72 - 143.63: 4 143.63 - 179.53: 5 Dihedral angle restraints: 8870 sinusoidal: 4721 harmonic: 4149 Sorted by residual: dihedral pdb=" O4' U B 34 " pdb=" C1' U B 34 " pdb=" N1 U B 34 " pdb=" C2 U B 34 " ideal model delta sinusoidal sigma weight residual 200.00 20.47 179.53 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U B 58 " pdb=" C1' U B 58 " pdb=" N1 U B 58 " pdb=" C2 U B 58 " ideal model delta sinusoidal sigma weight residual -160.00 13.17 -173.17 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U B 112 " pdb=" C1' U B 112 " pdb=" N1 U B 112 " pdb=" C2 U B 112 " ideal model delta sinusoidal sigma weight residual -160.00 4.87 -164.87 1 1.50e+01 4.44e-03 8.39e+01 ... (remaining 8867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1821 0.041 - 0.082: 376 0.082 - 0.124: 93 0.124 - 0.165: 11 0.165 - 0.206: 2 Chirality restraints: 2303 Sorted by residual: chirality pdb=" C1' A B 42 " pdb=" O4' A B 42 " pdb=" C2' A B 42 " pdb=" N9 A B 42 " both_signs ideal model delta sigma weight residual False 2.44 2.23 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C3' C B 43 " pdb=" C4' C B 43 " pdb=" O3' C B 43 " pdb=" C2' C B 43 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" C3' U B 122 " pdb=" C4' U B 122 " pdb=" O3' U B 122 " pdb=" C2' U B 122 " both_signs ideal model delta sigma weight residual False -2.74 -2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 2300 not shown) Planarity restraints: 2127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 99 " 0.032 2.00e-02 2.50e+03 1.38e-02 5.74e+00 pdb=" N9 G B 99 " -0.032 2.00e-02 2.50e+03 pdb=" C8 G B 99 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G B 99 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G B 99 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 99 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 99 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G B 99 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B 99 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G B 99 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 99 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B 99 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 939 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 940 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 940 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 940 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 494 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.47e+00 pdb=" C ASP A 494 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP A 494 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 495 " 0.012 2.00e-02 2.50e+03 ... (remaining 2124 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 489 2.69 - 3.25: 13708 3.25 - 3.80: 24332 3.80 - 4.35: 32428 4.35 - 4.90: 49260 Nonbonded interactions: 120217 Sorted by model distance: nonbonded pdb=" OE1 GLN A 939 " pdb=" OG SER A 943 " model vdw 2.144 3.040 nonbonded pdb=" O ASN A 777 " pdb=" ND2 ASN A 777 " model vdw 2.185 3.120 nonbonded pdb=" OG SER A1215 " pdb=" OP1 U B 24 " model vdw 2.197 3.040 nonbonded pdb=" O2 C B 57 " pdb=" N6 A B 61 " model vdw 2.200 3.120 nonbonded pdb=" OD1 ASN A 875 " pdb=" N GLY A 876 " model vdw 2.205 3.120 ... (remaining 120212 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: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.790 Find NCS groups from input model: 0.060 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 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 0.035 14343 Z= 0.149 Angle : 0.600 14.055 19896 Z= 0.371 Chirality : 0.037 0.206 2303 Planarity : 0.004 0.055 2127 Dihedral : 18.875 179.535 6180 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.54 % Favored : 94.17 % Rotamer: Outliers : 0.56 % Allowed : 16.15 % 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: 0.36 (0.23), residues: 1407 helix: 0.93 (0.20), residues: 662 sheet: 0.47 (0.46), residues: 132 loop : -0.51 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 361 TYR 0.014 0.001 TYR A 744 PHE 0.029 0.002 PHE A1068 TRP 0.017 0.001 TRP A 139 HIS 0.005 0.001 HIS A 944 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (14343) covalent geometry : angle 0.59953 / 0.37 (19896) hydrogen bonds : bond 0.14675 / 9.87 ( 619) hydrogen bonds : angle 5.81333 / 4.00 ( 1746) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.430 Fit side-chains REVERT: A 1 MET cc_start: 0.3125 (tpp) cc_final: 0.2034 (tmm) REVERT: A 40 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8106 (tpp) REVERT: A 50 MET cc_start: 0.8574 (mmm) cc_final: 0.7954 (mmt) REVERT: A 464 ASP cc_start: 0.7013 (t70) cc_final: 0.6717 (t0) REVERT: A 491 MET cc_start: 0.7891 (mtm) cc_final: 0.7450 (mtt) REVERT: A 494 ASP cc_start: 0.5893 (t0) cc_final: 0.5624 (t0) REVERT: A 535 LYS cc_start: 0.6103 (ttpt) cc_final: 0.5596 (tptt) REVERT: A 765 MET cc_start: 0.5524 (tpt) cc_final: 0.4774 (mmp) REVERT: A 768 MET cc_start: 0.2295 (ttt) cc_final: 0.1823 (tmm) REVERT: A 987 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6356 (mm-30) REVERT: A 1012 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6838 (mt-10) REVERT: A 1017 GLU cc_start: 0.7559 (pt0) cc_final: 0.7062 (pt0) REVERT: A 1129 GLU cc_start: 0.6370 (mt-10) cc_final: 0.5965 (mt-10) REVERT: A 1394 MET cc_start: 0.6252 (pmm) cc_final: 0.6021 (ptt) outliers start: 7 outliers final: 3 residues processed: 117 average time/residue: 0.6732 time to fit residues: 85.7789 Evaluate side-chains 101 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1270 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0040 chunk 149 optimal weight: 6.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 HIS A1351 GLN A1359 ASN A1406 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.222021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.205047 restraints weight = 11224.283| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 0.47 r_work: 0.3815 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14343 Z= 0.167 Angle : 0.601 10.795 19896 Z= 0.326 Chirality : 0.041 0.212 2303 Planarity : 0.005 0.049 2127 Dihedral : 19.165 178.178 3294 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.04 % Favored : 93.67 % Rotamer: Outliers : 3.02 % Allowed : 14.24 % Favored : 82.74 % 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: 0.35 (0.22), residues: 1407 helix: 0.88 (0.20), residues: 670 sheet: 0.45 (0.44), residues: 129 loop : -0.45 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 361 TYR 0.015 0.002 TYR A 744 PHE 0.020 0.002 PHE A 160 TRP 0.016 0.002 TRP A 727 HIS 0.005 0.001 HIS A 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (14343) covalent geometry : angle 0.60114 / 0.33 (19896) hydrogen bonds : bond 0.04773 / 3.24 ( 619) hydrogen bonds : angle 4.73309 / 3.27 ( 1746) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.490 Fit side-chains REVERT: A 1 MET cc_start: 0.3462 (tpp) cc_final: 0.2221 (tmm) REVERT: A 40 MET cc_start: 0.8426 (tpt) cc_final: 0.8111 (mmp) REVERT: A 189 LYS cc_start: 0.1814 (OUTLIER) cc_final: 0.0710 (tmtt) REVERT: A 219 ASP cc_start: 0.7049 (m-30) cc_final: 0.6784 (m-30) REVERT: A 238 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8305 (mttt) REVERT: A 270 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7575 (mmtm) REVERT: A 381 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8209 (mtt-85) REVERT: A 464 ASP cc_start: 0.7396 (t70) cc_final: 0.7006 (t0) REVERT: A 491 MET cc_start: 0.8136 (mtm) cc_final: 0.7789 (mtt) REVERT: A 535 LYS cc_start: 0.5938 (ttpt) cc_final: 0.5199 (ttpp) REVERT: A 671 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7305 (mt-10) REVERT: A 693 GLN cc_start: 0.6022 (OUTLIER) cc_final: 0.5653 (tt0) REVERT: A 765 MET cc_start: 0.5405 (tpt) cc_final: 0.4400 (mmp) REVERT: A 768 MET cc_start: 0.2336 (ttt) cc_final: 0.1629 (tmm) REVERT: A 984 MET cc_start: 0.6174 (tpp) cc_final: 0.5887 (tpt) REVERT: A 987 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6956 (mm-30) REVERT: A 1017 GLU cc_start: 0.7653 (pt0) cc_final: 0.7137 (pt0) REVERT: A 1129 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6625 (mt-10) REVERT: A 1133 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6678 (m-30) outliers start: 38 outliers final: 8 residues processed: 129 average time/residue: 0.6262 time to fit residues: 88.7949 Evaluate side-chains 110 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 1133 ASP Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1270 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1359 ASN A1392 ASN A1406 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.219858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.207023 restraints weight = 11231.893| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 0.47 r_work: 0.3834 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14343 Z= 0.203 Angle : 0.614 11.436 19896 Z= 0.329 Chirality : 0.042 0.218 2303 Planarity : 0.005 0.048 2127 Dihedral : 19.211 178.495 3288 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.18 % Favored : 93.60 % Rotamer: Outliers : 2.86 % Allowed : 14.32 % Favored : 82.82 % 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: 0.19 (0.22), residues: 1407 helix: 0.74 (0.20), residues: 666 sheet: 0.23 (0.44), residues: 129 loop : -0.48 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 61 TYR 0.018 0.002 TYR A 184 PHE 0.020 0.002 PHE A 160 TRP 0.017 0.002 TRP A 727 HIS 0.008 0.002 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (14343) covalent geometry : angle 0.61422 / 0.33 (19896) hydrogen bonds : bond 0.04549 / 3.11 ( 619) hydrogen bonds : angle 4.61393 / 3.20 ( 1746) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.469 Fit side-chains REVERT: A 1 MET cc_start: 0.3465 (tpp) cc_final: 0.2321 (tmm) REVERT: A 157 ILE cc_start: 0.3828 (OUTLIER) cc_final: 0.3598 (mm) REVERT: A 189 LYS cc_start: 0.1867 (OUTLIER) cc_final: 0.0834 (tmtt) REVERT: A 238 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8162 (mttt) REVERT: A 270 LYS cc_start: 0.8200 (mmtm) cc_final: 0.7839 (mmtp) REVERT: A 334 ASP cc_start: 0.8332 (t0) cc_final: 0.7829 (t0) REVERT: A 381 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8248 (mtt-85) REVERT: A 464 ASP cc_start: 0.7058 (t70) cc_final: 0.6713 (t0) REVERT: A 491 MET cc_start: 0.8086 (mtm) cc_final: 0.7843 (mtt) REVERT: A 535 LYS cc_start: 0.6033 (ttpt) cc_final: 0.5483 (ttpp) REVERT: A 671 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6943 (mt-10) REVERT: A 693 GLN cc_start: 0.6191 (OUTLIER) cc_final: 0.5758 (tt0) REVERT: A 765 MET cc_start: 0.5651 (tpt) cc_final: 0.4690 (mmp) REVERT: A 768 MET cc_start: 0.2571 (ttt) cc_final: 0.2194 (tmm) REVERT: A 907 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6680 (t70) REVERT: A 987 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6569 (mm-30) REVERT: A 1017 GLU cc_start: 0.7688 (pt0) cc_final: 0.7257 (pt0) REVERT: A 1129 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6396 (mt-10) outliers start: 36 outliers final: 11 residues processed: 127 average time/residue: 0.6557 time to fit residues: 90.9424 Evaluate side-chains 111 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1145 ARG Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1270 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 HIS A1359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.213723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.195777 restraints weight = 11234.532| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 0.53 r_work: 0.3861 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 14343 Z= 0.427 Angle : 0.809 11.679 19896 Z= 0.427 Chirality : 0.056 0.289 2303 Planarity : 0.007 0.062 2127 Dihedral : 19.496 178.976 3288 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.89 % Favored : 92.82 % Rotamer: Outliers : 4.38 % Allowed : 14.48 % Favored : 81.15 % 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: -0.56 (0.21), residues: 1407 helix: -0.02 (0.19), residues: 663 sheet: 0.11 (0.44), residues: 123 loop : -0.74 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 100 TYR 0.019 0.003 TYR A1399 PHE 0.022 0.003 PHE A 160 TRP 0.021 0.004 TRP A 727 HIS 0.008 0.003 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00922 / 0.43 (14343) covalent geometry : angle 0.80879 / 0.43 (19896) hydrogen bonds : bond 0.05770 / 3.91 ( 619) hydrogen bonds : angle 5.09876 / 3.57 ( 1746) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 103 time to evaluate : 0.475 Fit side-chains REVERT: A 1 MET cc_start: 0.3670 (tpp) cc_final: 0.2491 (tmm) REVERT: A 157 ILE cc_start: 0.3757 (OUTLIER) cc_final: 0.3538 (mm) REVERT: A 189 LYS cc_start: 0.2064 (OUTLIER) cc_final: 0.0946 (tmtt) REVERT: A 270 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8047 (mttm) REVERT: A 334 ASP cc_start: 0.8360 (t0) cc_final: 0.7943 (t0) REVERT: A 368 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.5770 (pp) REVERT: A 491 MET cc_start: 0.8257 (mtm) cc_final: 0.7990 (mtt) REVERT: A 535 LYS cc_start: 0.6247 (ttpt) cc_final: 0.5544 (tptt) REVERT: A 671 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6899 (mt-10) REVERT: A 693 GLN cc_start: 0.6572 (OUTLIER) cc_final: 0.6106 (tt0) REVERT: A 700 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6991 (mp) REVERT: A 765 MET cc_start: 0.5995 (tpt) cc_final: 0.4885 (mmp) REVERT: A 768 MET cc_start: 0.3500 (ttt) cc_final: 0.3131 (tmm) REVERT: A 907 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6870 (t70) REVERT: A 987 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6859 (mm-30) REVERT: A 1012 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: A 1299 ASP cc_start: 0.6895 (t0) cc_final: 0.6510 (t70) outliers start: 55 outliers final: 20 residues processed: 142 average time/residue: 0.6318 time to fit residues: 98.3997 Evaluate side-chains 126 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1088 ARG Chi-restraints excluded: chain A residue 1145 ARG Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1270 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 107 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 142 optimal weight: 30.0000 chunk 93 optimal weight: 4.9990 chunk 139 optimal weight: 0.0570 chunk 24 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1406 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.221020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.208129 restraints weight = 11298.377| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 0.39 r_work: 0.3854 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14343 Z= 0.135 Angle : 0.569 10.399 19896 Z= 0.312 Chirality : 0.040 0.223 2303 Planarity : 0.004 0.058 2127 Dihedral : 19.338 177.672 3288 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.04 % Favored : 93.67 % Rotamer: Outliers : 3.10 % Allowed : 15.43 % Favored : 81.46 % 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: -0.14 (0.22), residues: 1407 helix: 0.50 (0.20), residues: 668 sheet: -0.07 (0.44), residues: 129 loop : -0.66 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1030 TYR 0.018 0.002 TYR A 257 PHE 0.015 0.002 PHE A 160 TRP 0.018 0.001 TRP A 727 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (14343) covalent geometry : angle 0.56852 / 0.31 (19896) hydrogen bonds : bond 0.04130 / 2.82 ( 619) hydrogen bonds : angle 4.52043 / 3.14 ( 1746) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.362 Fit side-chains REVERT: A 1 MET cc_start: 0.3527 (tpp) cc_final: 0.2391 (tmm) REVERT: A 157 ILE cc_start: 0.3878 (OUTLIER) cc_final: 0.3660 (mm) REVERT: A 189 LYS cc_start: 0.1828 (OUTLIER) cc_final: 0.0757 (tptp) REVERT: A 270 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7895 (mttm) REVERT: A 384 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7953 (ttm170) REVERT: A 464 ASP cc_start: 0.6934 (t70) cc_final: 0.6642 (t0) REVERT: A 535 LYS cc_start: 0.6130 (ttpt) cc_final: 0.5299 (tptt) REVERT: A 765 MET cc_start: 0.5695 (tpt) cc_final: 0.4600 (mmp) REVERT: A 768 MET cc_start: 0.2825 (ttt) cc_final: 0.2466 (tmm) REVERT: A 907 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6659 (t70) REVERT: A 987 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6646 (mm-30) REVERT: A 1012 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6939 (mt-10) REVERT: A 1071 TYR cc_start: 0.8354 (m-80) cc_final: 0.8151 (m-80) REVERT: A 1133 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.6394 (m-30) REVERT: A 1154 THR cc_start: 0.7922 (t) cc_final: 0.7594 (m) outliers start: 39 outliers final: 9 residues processed: 126 average time/residue: 0.5629 time to fit residues: 77.8651 Evaluate side-chains 106 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 ARG Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1133 ASP Chi-restraints excluded: chain A residue 1145 ARG Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1300 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN A1359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.214405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.196187 restraints weight = 11223.894| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 0.50 r_work: 0.3848 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 14343 Z= 0.361 Angle : 0.748 13.933 19896 Z= 0.394 Chirality : 0.052 0.257 2303 Planarity : 0.006 0.064 2127 Dihedral : 19.419 178.422 3288 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.68 % Favored : 93.11 % Rotamer: Outliers : 3.50 % Allowed : 16.07 % Favored : 80.43 % 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: -0.51 (0.22), residues: 1407 helix: 0.10 (0.19), residues: 664 sheet: 0.04 (0.45), residues: 123 loop : -0.80 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 61 TYR 0.018 0.003 TYR A1399 PHE 0.020 0.003 PHE A 160 TRP 0.021 0.003 TRP A 727 HIS 0.008 0.002 HIS A1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00782 / 0.36 (14343) covalent geometry : angle 0.74838 / 0.39 (19896) hydrogen bonds : bond 0.05293 / 3.60 ( 619) hydrogen bonds : angle 4.88968 / 3.42 ( 1746) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 95 time to evaluate : 0.449 Fit side-chains REVERT: A 1 MET cc_start: 0.3677 (tpp) cc_final: 0.2504 (tmm) REVERT: A 189 LYS cc_start: 0.1998 (OUTLIER) cc_final: 0.0896 (tmtt) REVERT: A 270 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8085 (mttm) REVERT: A 334 ASP cc_start: 0.8399 (t0) cc_final: 0.8129 (t0) REVERT: A 381 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8349 (mtt-85) REVERT: A 473 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8170 (mt) REVERT: A 535 LYS cc_start: 0.6260 (ttpt) cc_final: 0.5508 (tptt) REVERT: A 671 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6871 (mt-10) REVERT: A 693 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.5975 (tt0) REVERT: A 765 MET cc_start: 0.6071 (tpt) cc_final: 0.4939 (mmp) REVERT: A 768 MET cc_start: 0.3684 (ttt) cc_final: 0.3324 (tmm) REVERT: A 907 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6848 (t70) REVERT: A 987 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6876 (mm-30) REVERT: A 1012 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: A 1160 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: A 1288 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6690 (tt0) REVERT: A 1335 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6796 (pp) outliers start: 44 outliers final: 19 residues processed: 124 average time/residue: 0.6058 time to fit residues: 82.0847 Evaluate side-chains 126 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1145 ARG Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1160 GLU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1288 GLN Chi-restraints excluded: chain A residue 1300 CYS Chi-restraints excluded: chain A residue 1335 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 130 optimal weight: 0.1980 chunk 41 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN A1406 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.221079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.204135 restraints weight = 11232.422| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 0.44 r_work: 0.3805 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14343 Z= 0.127 Angle : 0.570 12.808 19896 Z= 0.310 Chirality : 0.039 0.223 2303 Planarity : 0.004 0.062 2127 Dihedral : 19.297 177.390 3288 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.11 % Favored : 93.60 % Rotamer: Outliers : 2.23 % Allowed : 17.58 % Favored : 80.19 % 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: -0.14 (0.22), residues: 1407 helix: 0.54 (0.20), residues: 668 sheet: -0.15 (0.44), residues: 129 loop : -0.69 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1030 TYR 0.017 0.001 TYR A 257 PHE 0.014 0.001 PHE A 952 TRP 0.017 0.001 TRP A 727 HIS 0.003 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (14343) covalent geometry : angle 0.56971 / 0.31 (19896) hydrogen bonds : bond 0.04034 / 2.75 ( 619) hydrogen bonds : angle 4.44910 / 3.09 ( 1746) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.512 Fit side-chains REVERT: A 1 MET cc_start: 0.3590 (tpp) cc_final: 0.2344 (tmm) REVERT: A 189 LYS cc_start: 0.1600 (OUTLIER) cc_final: 0.0564 (tptp) REVERT: A 270 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7951 (mttm) REVERT: A 384 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7963 (ttm170) REVERT: A 464 ASP cc_start: 0.7148 (t70) cc_final: 0.6839 (t0) REVERT: A 535 LYS cc_start: 0.5988 (ttpt) cc_final: 0.5110 (ttpp) REVERT: A 765 MET cc_start: 0.5501 (OUTLIER) cc_final: 0.4333 (mmp) REVERT: A 768 MET cc_start: 0.3225 (ttt) cc_final: 0.2677 (tmm) REVERT: A 903 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8045 (m) REVERT: A 907 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6817 (t70) REVERT: A 987 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6948 (mm-30) REVERT: A 1012 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: A 1017 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7524 (pt0) REVERT: A 1154 THR cc_start: 0.7967 (t) cc_final: 0.7657 (m) REVERT: A 1335 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.6182 (pp) outliers start: 28 outliers final: 7 residues processed: 114 average time/residue: 0.5555 time to fit residues: 69.6573 Evaluate side-chains 105 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 384 ARG Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1300 CYS Chi-restraints excluded: chain A residue 1335 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 146 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 692 ASN A1406 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.217687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.201408 restraints weight = 11136.449| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 0.56 r_work: 0.3818 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work: 0.3569 rms_B_bonded: 4.81 restraints_weight: 0.1250 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14343 Z= 0.234 Angle : 0.643 12.873 19896 Z= 0.341 Chirality : 0.044 0.222 2303 Planarity : 0.005 0.063 2127 Dihedral : 19.267 177.770 3288 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.75 % Favored : 92.96 % Rotamer: Outliers : 2.31 % Allowed : 17.82 % Favored : 79.87 % 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: -0.22 (0.22), residues: 1407 helix: 0.45 (0.20), residues: 665 sheet: -0.14 (0.44), residues: 129 loop : -0.70 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1075 TYR 0.016 0.002 TYR A 257 PHE 0.018 0.002 PHE A 160 TRP 0.019 0.002 TRP A 727 HIS 0.006 0.002 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 (14343) covalent geometry : angle 0.64292 / 0.34 (19896) hydrogen bonds : bond 0.04548 / 3.11 ( 619) hydrogen bonds : angle 4.58729 / 3.19 ( 1746) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.436 Fit side-chains REVERT: A 1 MET cc_start: 0.3874 (tpp) cc_final: 0.2438 (tmm) REVERT: A 189 LYS cc_start: 0.1578 (OUTLIER) cc_final: 0.0668 (tmtt) REVERT: A 270 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8073 (mttm) REVERT: A 334 ASP cc_start: 0.8435 (t0) cc_final: 0.8134 (t0) REVERT: A 381 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8437 (mtt-85) REVERT: A 384 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8008 (ttm170) REVERT: A 535 LYS cc_start: 0.6227 (ttpt) cc_final: 0.5474 (ttpp) REVERT: A 765 MET cc_start: 0.6016 (OUTLIER) cc_final: 0.4783 (mmp) REVERT: A 768 MET cc_start: 0.3748 (ttt) cc_final: 0.3318 (tmm) REVERT: A 903 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.8049 (m) REVERT: A 907 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7064 (t70) REVERT: A 987 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7090 (mm-30) REVERT: A 1012 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: A 1154 THR cc_start: 0.8140 (t) cc_final: 0.7855 (m) REVERT: A 1288 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6989 (tt0) REVERT: A 1335 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6526 (pp) outliers start: 29 outliers final: 12 residues processed: 113 average time/residue: 0.5729 time to fit residues: 71.0931 Evaluate side-chains 118 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 384 ARG Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1288 GLN Chi-restraints excluded: chain A residue 1300 CYS Chi-restraints excluded: chain A residue 1335 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 75 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 119 optimal weight: 0.3980 chunk 16 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1406 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.220365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.200009 restraints weight = 11279.343| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 0.54 r_work: 0.3772 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14343 Z= 0.143 Angle : 0.572 12.400 19896 Z= 0.309 Chirality : 0.040 0.222 2303 Planarity : 0.004 0.063 2127 Dihedral : 19.200 177.348 3288 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.47 % Favored : 93.25 % Rotamer: Outliers : 2.47 % Allowed : 18.06 % Favored : 79.47 % 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: -0.08 (0.22), residues: 1407 helix: 0.58 (0.20), residues: 673 sheet: -0.16 (0.44), residues: 129 loop : -0.66 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1088 TYR 0.015 0.002 TYR A 257 PHE 0.014 0.002 PHE A 66 TRP 0.017 0.002 TRP A 727 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (14343) covalent geometry : angle 0.57206 / 0.31 (19896) hydrogen bonds : bond 0.04007 / 2.73 ( 619) hydrogen bonds : angle 4.40414 / 3.06 ( 1746) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.473 Fit side-chains REVERT: A 1 MET cc_start: 0.3801 (tpp) cc_final: 0.2381 (tmm) REVERT: A 189 LYS cc_start: 0.1294 (OUTLIER) cc_final: 0.0518 (tptp) REVERT: A 270 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7967 (mttm) REVERT: A 381 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8331 (mtt-85) REVERT: A 384 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7948 (ttm170) REVERT: A 464 ASP cc_start: 0.7156 (t70) cc_final: 0.6834 (t0) REVERT: A 470 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7449 (mmtt) REVERT: A 535 LYS cc_start: 0.6066 (ttpt) cc_final: 0.5250 (ttpp) REVERT: A 671 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7023 (mt-10) REVERT: A 700 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.6868 (mp) REVERT: A 765 MET cc_start: 0.5603 (OUTLIER) cc_final: 0.4347 (mmp) REVERT: A 768 MET cc_start: 0.3490 (ttt) cc_final: 0.3075 (tmm) REVERT: A 907 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6846 (t70) REVERT: A 987 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6980 (mm-30) REVERT: A 1012 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7320 (mt-10) REVERT: A 1154 THR cc_start: 0.8012 (t) cc_final: 0.7699 (m) outliers start: 31 outliers final: 9 residues processed: 114 average time/residue: 0.5994 time to fit residues: 75.2198 Evaluate side-chains 109 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 384 ARG Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1300 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 149 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 102 optimal weight: 0.0980 chunk 125 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1406 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.218601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.202208 restraints weight = 11219.926| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 0.46 r_work: 0.3782 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14343 Z= 0.205 Angle : 0.621 12.235 19896 Z= 0.330 Chirality : 0.043 0.221 2303 Planarity : 0.005 0.062 2127 Dihedral : 19.190 177.567 3288 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.82 % Favored : 92.89 % Rotamer: Outliers : 1.75 % Allowed : 18.62 % Favored : 79.63 % 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: -0.14 (0.22), residues: 1407 helix: 0.51 (0.20), residues: 671 sheet: -0.06 (0.44), residues: 128 loop : -0.70 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1088 TYR 0.016 0.002 TYR A 257 PHE 0.015 0.002 PHE A 66 TRP 0.018 0.002 TRP A 727 HIS 0.005 0.002 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (14343) covalent geometry : angle 0.62065 / 0.33 (19896) hydrogen bonds : bond 0.04319 / 2.95 ( 619) hydrogen bonds : angle 4.49164 / 3.12 ( 1746) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.367 Fit side-chains REVERT: A 1 MET cc_start: 0.3771 (tpp) cc_final: 0.2341 (tmm) REVERT: A 189 LYS cc_start: 0.1301 (OUTLIER) cc_final: 0.0528 (tptp) REVERT: A 191 MET cc_start: 0.5274 (ppp) cc_final: 0.5040 (ppp) REVERT: A 270 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7959 (mttm) REVERT: A 334 ASP cc_start: 0.8160 (t0) cc_final: 0.7850 (t0) REVERT: A 381 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8347 (mtt-85) REVERT: A 384 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7886 (ttm170) REVERT: A 470 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7540 (mmtt) REVERT: A 535 LYS cc_start: 0.6104 (ttpt) cc_final: 0.5258 (ttpp) REVERT: A 671 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: A 693 GLN cc_start: 0.6581 (OUTLIER) cc_final: 0.6154 (tt0) REVERT: A 765 MET cc_start: 0.5851 (OUTLIER) cc_final: 0.4564 (mmp) REVERT: A 768 MET cc_start: 0.3763 (ttt) cc_final: 0.3270 (tmm) REVERT: A 907 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6853 (t70) REVERT: A 987 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7035 (mm-30) REVERT: A 1012 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: A 1154 THR cc_start: 0.7984 (t) cc_final: 0.7720 (m) outliers start: 22 outliers final: 11 residues processed: 112 average time/residue: 0.6651 time to fit residues: 81.5326 Evaluate side-chains 113 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 384 ARG Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1300 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1406 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.215215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.195623 restraints weight = 11251.162| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 0.56 r_work: 0.3857 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 14343 Z= 0.306 Angle : 0.707 11.939 19896 Z= 0.375 Chirality : 0.049 0.244 2303 Planarity : 0.006 0.064 2127 Dihedral : 19.341 178.195 3288 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.46 % Favored : 92.25 % Rotamer: Outliers : 1.99 % Allowed : 18.46 % Favored : 79.55 % 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: -0.44 (0.22), residues: 1407 helix: 0.21 (0.19), residues: 670 sheet: 0.02 (0.44), residues: 122 loop : -0.82 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 61 TYR 0.019 0.003 TYR A1399 PHE 0.019 0.003 PHE A 66 TRP 0.020 0.003 TRP A 727 HIS 0.009 0.002 HIS A1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.31 (14343) covalent geometry : angle 0.70697 / 0.37 (19896) hydrogen bonds : bond 0.04972 / 3.37 ( 619) hydrogen bonds : angle 4.75548 / 3.32 ( 1746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4138.44 seconds wall clock time: 71 minutes 46.93 seconds (4306.93 seconds total)