Starting phenix.real_space_refine on Thu Aug 6 07:36:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ko9_62471/08_2026/9ko9_62471.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ko9_62471/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ko9_62471/08_2026/9ko9_62471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ko9_62471/08_2026/9ko9_62471.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ko9_62471/08_2026/9ko9_62471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ko9_62471/08_2026/9ko9_62471.map" } 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-2.2rc3-6140/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: 2.22, per 1000 atoms: 0.16 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: 0.99 Conformation dependent library (CDL) restraints added in 516.8 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: 1.41 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: 2.64 Time building geometry restraints manager: 1.36 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=" C3' U B 122 " pdb=" O3' U B 122 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.20e-02 6.94e+03 1.96e+00 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 ... (remaining 14338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 19739 2.81 - 5.62: 137 5.62 - 8.43: 17 8.43 - 11.24: 1 11.24 - 14.06: 2 Bond angle restraints: 19896 Sorted by residual: angle pdb=" C3' U B 122 " pdb=" O3' U B 122 " pdb=" P U B 123 " ideal model delta sigma weight residual 119.70 125.47 -5.77 1.20e+00 6.94e-01 2.31e+01 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 ... (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: 1691 0.041 - 0.082: 392 0.082 - 0.123: 119 0.123 - 0.164: 98 0.164 - 0.204: 3 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 0.20 2.00e-01 2.50e+01 1.04e+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=" C2' A B 60 " pdb=" C3' A B 60 " pdb=" O2' A B 60 " pdb=" C1' A B 60 " both_signs ideal model delta sigma weight residual False -2.62 -2.79 0.17 2.00e-01 2.50e+01 7.06e-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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.720 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.170 ------------------------------------------------------------------------------- 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= 0.160 Angle : 0.669 14.055 19896 Z= 0.440 Chirality : 0.046 0.204 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 0.00267 / 0.16 (14343) covalent geometry : angle 0.66862 / 0.44 (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 : 0.382 Fit side-chains REVERT: A 1 MET cc_start: 0.3125 (tpp) cc_final: 0.2035 (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: 0.6720 (t0) REVERT: A 491 MET cc_start: 0.7891 (mtm) cc_final: 0.7452 (mtt) REVERT: A 494 ASP cc_start: 0.5893 (t0) cc_final: 0.5625 (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: 0.4775 (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: 0.6355 (mm-30) REVERT: A 1012 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6840 (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: 0.5964 (mt-10) REVERT: A 1212 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7647 (mtp180) 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: 0.5631 time to fit residues: 71.8937 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 : 0.300 ------------------------------------------------------------------------------- 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: 8.9990 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 = 0.221998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.204876 restraints weight = 11231.681| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 0.46 r_work: 0.3812 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0760 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= 0.163 Angle : 0.615 11.044 19896 Z= 0.328 Chirality : 0.042 0.330 2303 Planarity : 0.005 0.048 2127 Dihedral : 19.104 179.373 3294 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.11 % Favored : 93.60 % 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: 0.34 (0.22), residues: 1407 helix: 0.88 (0.20), residues: 670 sheet: 0.43 (0.44), residues: 129 loop : -0.47 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 361 TYR 0.015 0.002 TYR A1399 PHE 0.020 0.002 PHE A 160 TRP 0.016 0.002 TRP A 727 HIS 0.006 0.002 HIS A 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (14343) covalent geometry : angle 0.61506 / 0.33 (19896) hydrogen bonds : bond 0.04665 / 3.17 ( 619) hydrogen bonds : angle 4.72445 / 3.26 ( 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 : 0.446 Fit side-chains REVERT: A 1 MET cc_start: 0.3410 (tpp) cc_final: 0.2183 (tmm) REVERT: A 40 MET cc_start: 0.8413 (tpt) cc_final: 0.8103 (mmp) REVERT: A 189 LYS cc_start: 0.1761 (OUTLIER) cc_final: 0.0649 (tmtt) REVERT: A 238 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8269 (mttt) REVERT: A 270 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7532 (mmtm) REVERT: A 381 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8293 (mtt-85) REVERT: A 464 ASP cc_start: 0.7348 (t70) cc_final: 0.6952 (t0) REVERT: A 491 MET cc_start: 0.8155 (mtm) cc_final: 0.7792 (mtt) REVERT: A 535 LYS cc_start: 0.5898 (ttpt) cc_final: 0.5144 (ttpp) REVERT: A 671 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7222 (mt-10) REVERT: A 693 GLN cc_start: 0.5959 (OUTLIER) cc_final: 0.5589 (tt0) REVERT: A 765 MET cc_start: 0.5394 (tpt) cc_final: 0.4341 (mmp) REVERT: A 768 MET cc_start: 0.2237 (ttt) cc_final: 0.1555 (tmm) REVERT: A 987 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6803 (mm-30) REVERT: A 1017 GLU cc_start: 0.7625 (pt0) cc_final: 0.7120 (pt0) REVERT: A 1129 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6541 (mt-10) REVERT: A 1133 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6693 (m-30) outliers start: 38 outliers final: 8 residues processed: 129 average time/residue: 0.5202 time to fit residues: 73.7469 Evaluate side-chains 108 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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: 1.9990 chunk 134 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1018 HIS A1359 ASN A1392 ASN A1406 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.219190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.204672 restraints weight = 11222.710| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 0.40 r_work: 0.3810 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14343 Z= 0.214 Angle : 0.649 11.919 19896 Z= 0.341 Chirality : 0.044 0.330 2303 Planarity : 0.005 0.050 2127 Dihedral : 19.210 179.019 3288 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.25 % Favored : 93.53 % Rotamer: Outliers : 3.50 % Allowed : 14.00 % Favored : 82.50 % 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: 0.12 (0.22), residues: 1407 helix: 0.67 (0.20), residues: 663 sheet: 0.20 (0.44), residues: 129 loop : -0.50 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 361 TYR 0.021 0.002 TYR A 184 PHE 0.021 0.002 PHE A 160 TRP 0.017 0.002 TRP A 727 HIS 0.010 0.002 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (14343) covalent geometry : angle 0.64910 / 0.34 (19896) hydrogen bonds : bond 0.04744 / 3.25 ( 619) hydrogen bonds : angle 4.65932 / 3.24 ( 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 146 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.451 Fit side-chains REVERT: A 1 MET cc_start: 0.3552 (tpp) cc_final: 0.2299 (tmm) REVERT: A 157 ILE cc_start: 0.4076 (OUTLIER) cc_final: 0.3817 (mm) REVERT: A 189 LYS cc_start: 0.1854 (OUTLIER) cc_final: 0.0792 (tmtt) REVERT: A 270 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7883 (mmtp) REVERT: A 334 ASP cc_start: 0.8344 (t0) cc_final: 0.7885 (t0) REVERT: A 381 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8291 (mtt-85) REVERT: A 464 ASP cc_start: 0.7242 (t70) cc_final: 0.6880 (t0) REVERT: A 491 MET cc_start: 0.8224 (mtm) cc_final: 0.7981 (mtt) REVERT: A 535 LYS cc_start: 0.5972 (ttpt) cc_final: 0.5289 (ttpp) REVERT: A 671 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7270 (mt-10) REVERT: A 693 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.5886 (tt0) REVERT: A 765 MET cc_start: 0.5619 (tpt) cc_final: 0.4539 (mmp) REVERT: A 768 MET cc_start: 0.2720 (ttt) cc_final: 0.2162 (tmm) REVERT: A 987 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6876 (mm-30) REVERT: A 1017 GLU cc_start: 0.7772 (pt0) cc_final: 0.7346 (pt0) REVERT: A 1129 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6496 (mt-10) outliers start: 44 outliers final: 11 residues processed: 134 average time/residue: 0.5902 time to fit residues: 86.4626 Evaluate side-chains 114 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 267 VAL 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 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 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: 3.9990 chunk 85 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.214264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.197805 restraints weight = 11239.109| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 0.51 r_work: 0.3868 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 14343 Z= 0.379 Angle : 0.827 11.743 19896 Z= 0.425 Chirality : 0.055 0.455 2303 Planarity : 0.007 0.063 2127 Dihedral : 19.548 179.088 3288 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.11 % Favored : 92.61 % Rotamer: Outliers : 4.69 % Allowed : 14.56 % Favored : 80.75 % 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: -0.64 (0.21), residues: 1407 helix: -0.05 (0.19), residues: 665 sheet: 0.04 (0.44), residues: 123 loop : -0.83 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 100 TYR 0.019 0.003 TYR A1399 PHE 0.023 0.003 PHE A 160 TRP 0.021 0.003 TRP A 727 HIS 0.011 0.003 HIS A1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00822 / 0.38 (14343) covalent geometry : angle 0.82663 / 0.42 (19896) hydrogen bonds : bond 0.05797 / 3.94 ( 619) hydrogen bonds : angle 5.10959 / 3.58 ( 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 163 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 104 time to evaluate : 0.286 Fit side-chains REVERT: A 1 MET cc_start: 0.3647 (tpp) cc_final: 0.2467 (tmm) REVERT: A 14 ARG cc_start: 0.7171 (ttm-80) cc_final: 0.6946 (ttp-110) REVERT: A 157 ILE cc_start: 0.3772 (OUTLIER) cc_final: 0.3557 (mm) REVERT: A 189 LYS cc_start: 0.2111 (OUTLIER) cc_final: 0.0974 (tmtt) REVERT: A 270 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8068 (mttm) REVERT: A 368 ILE cc_start: 0.6228 (OUTLIER) cc_final: 0.5746 (pp) REVERT: A 473 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8250 (mt) REVERT: A 491 MET cc_start: 0.8269 (mtm) cc_final: 0.8030 (mtt) REVERT: A 535 LYS cc_start: 0.6279 (ttpt) cc_final: 0.5573 (tptt) REVERT: A 671 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6855 (mt-10) REVERT: A 693 GLN cc_start: 0.6591 (OUTLIER) cc_final: 0.6118 (tt0) REVERT: A 765 MET cc_start: 0.5934 (tpt) cc_final: 0.4887 (mmp) REVERT: A 768 MET cc_start: 0.3582 (ttt) cc_final: 0.3229 (tmm) REVERT: A 907 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6899 (t70) REVERT: A 987 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6846 (mm-30) REVERT: A 1012 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7230 (mt-10) outliers start: 59 outliers final: 23 residues processed: 144 average time/residue: 0.5374 time to fit residues: 85.1889 Evaluate side-chains 128 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 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 23 THR Chi-restraints excluded: chain A residue 38 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 444 THR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 473 LEU 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 903 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 931 TRP 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 Chi-restraints excluded: chain A residue 1300 CYS Chi-restraints excluded: chain A residue 1393 SER 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: 10.0000 chunk 134 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 142 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4322 r_free = 0.4322 target = 0.219798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.200641 restraints weight = 11300.190| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 0.61 r_work: 0.3814 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14343 Z= 0.143 Angle : 0.591 10.522 19896 Z= 0.318 Chirality : 0.041 0.319 2303 Planarity : 0.004 0.060 2127 Dihedral : 19.338 177.340 3288 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.25 % Favored : 93.46 % Rotamer: Outliers : 3.42 % Allowed : 15.59 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.22), residues: 1407 helix: 0.43 (0.20), residues: 666 sheet: -0.12 (0.44), residues: 129 loop : -0.73 (0.25), residues: 612 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 952 TRP 0.018 0.002 TRP A 727 HIS 0.004 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (14343) covalent geometry : angle 0.59050 / 0.32 (19896) hydrogen bonds : bond 0.04279 / 2.91 ( 619) hydrogen bonds : angle 4.57034 / 3.18 ( 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 141 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.450 Fit side-chains REVERT: A 1 MET cc_start: 0.3518 (tpp) cc_final: 0.2369 (tmm) REVERT: A 14 ARG cc_start: 0.7157 (ttm-80) cc_final: 0.6917 (ttp-110) REVERT: A 157 ILE cc_start: 0.3875 (OUTLIER) cc_final: 0.3648 (mm) REVERT: A 189 LYS cc_start: 0.1808 (OUTLIER) cc_final: 0.0708 (tptp) REVERT: A 270 LYS cc_start: 0.8283 (mmtm) cc_final: 0.7940 (mmtm) REVERT: A 330 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6624 (mtm180) REVERT: A 381 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8374 (mtt-85) REVERT: A 384 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8014 (ttm170) REVERT: A 464 ASP cc_start: 0.6946 (t70) cc_final: 0.6655 (t0) REVERT: A 473 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8141 (mt) REVERT: A 535 LYS cc_start: 0.6173 (ttpt) cc_final: 0.5291 (tptt) REVERT: A 671 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6906 (mt-10) REVERT: A 765 MET cc_start: 0.5706 (tpt) cc_final: 0.4547 (mmt) REVERT: A 768 MET cc_start: 0.3132 (ttt) cc_final: 0.2742 (tmm) REVERT: A 907 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6771 (t70) REVERT: A 987 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6736 (mm-30) REVERT: A 1012 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7033 (mt-10) REVERT: A 1071 TYR cc_start: 0.8378 (m-80) cc_final: 0.8174 (m-80) REVERT: A 1133 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6437 (m-30) REVERT: A 1369 ARG cc_start: 0.8035 (ttt180) cc_final: 0.7813 (ttp80) outliers start: 43 outliers final: 15 residues processed: 127 average time/residue: 0.5330 time to fit residues: 74.7284 Evaluate side-chains 119 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL 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 330 ARG 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 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 999 LEU 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 1153 ILE 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 1382 LEU 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: 0.1980 chunk 73 optimal weight: 5.9990 chunk 69 optimal weight: 0.0470 chunk 61 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.217184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.198934 restraints weight = 11258.365| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 0.44 r_work: 0.3762 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work: 0.3465 rms_B_bonded: 4.64 restraints_weight: 0.1250 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1829 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 : 0.643 14.307 19896 Z= 0.336 Chirality : 0.044 0.325 2303 Planarity : 0.005 0.061 2127 Dihedral : 19.293 177.632 3288 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.54 % Favored : 93.18 % Rotamer: Outliers : 3.50 % Allowed : 15.83 % Favored : 80.67 % 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: -0.21 (0.22), residues: 1407 helix: 0.44 (0.20), residues: 665 sheet: -0.11 (0.44), residues: 129 loop : -0.69 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 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 0.00435 / 0.20 (14343) covalent geometry : angle 0.64273 / 0.34 (19896) hydrogen bonds : bond 0.04523 / 3.09 ( 619) hydrogen bonds : angle 4.59473 / 3.20 ( 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 143 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 0.425 Fit side-chains REVERT: A 1 MET cc_start: 0.3559 (tpp) cc_final: 0.2338 (tmm) REVERT: A 14 ARG cc_start: 0.7358 (ttm-80) cc_final: 0.7097 (ttp-170) REVERT: A 189 LYS cc_start: 0.1745 (OUTLIER) cc_final: 0.0637 (tptp) REVERT: A 270 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8019 (mttm) REVERT: A 330 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6869 (mtm180) REVERT: A 381 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8450 (mtt-85) REVERT: A 384 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8050 (ttm170) REVERT: A 473 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8229 (mt) REVERT: A 535 LYS cc_start: 0.6076 (ttpt) cc_final: 0.5190 (ttpp) REVERT: A 671 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: A 765 MET cc_start: 0.5890 (OUTLIER) cc_final: 0.4532 (mmp) REVERT: A 768 MET cc_start: 0.3736 (ttt) cc_final: 0.3150 (tmm) REVERT: A 903 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.8011 (m) REVERT: A 907 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7034 (t70) REVERT: A 978 LYS cc_start: 0.7503 (tppt) cc_final: 0.7161 (ttpt) REVERT: A 987 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7096 (mm-30) REVERT: A 1012 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: A 1133 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6663 (m-30) REVERT: A 1288 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7024 (tt0) REVERT: A 1335 ILE cc_start: 0.6643 (OUTLIER) cc_final: 0.6383 (pp) REVERT: A 1369 ARG cc_start: 0.8108 (ttt180) cc_final: 0.7858 (ttp80) outliers start: 44 outliers final: 14 residues processed: 126 average time/residue: 0.5553 time to fit residues: 76.7242 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 : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL 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 330 ARG Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 384 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 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 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 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: 1.9990 chunk 112 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN A1406 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.219786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.206521 restraints weight = 11213.826| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 0.40 r_work: 0.3837 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work: 0.3545 rms_B_bonded: 4.80 restraints_weight: 0.1250 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14343 Z= 0.159 Angle : 0.594 12.615 19896 Z= 0.315 Chirality : 0.041 0.312 2303 Planarity : 0.004 0.063 2127 Dihedral : 19.230 177.163 3288 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.40 % Favored : 93.32 % Rotamer: Outliers : 3.26 % Allowed : 16.55 % 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: -0.07 (0.22), residues: 1407 helix: 0.59 (0.20), residues: 665 sheet: -0.09 (0.44), residues: 129 loop : -0.66 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 222 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 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (14343) covalent geometry : angle 0.59368 / 0.32 (19896) hydrogen bonds : bond 0.04161 / 2.83 ( 619) hydrogen bonds : angle 4.45565 / 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 137 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 0.476 Fit side-chains REVERT: A 1 MET cc_start: 0.3722 (tpp) cc_final: 0.2351 (tmm) REVERT: A 14 ARG cc_start: 0.7299 (ttm-80) cc_final: 0.7062 (ttp-170) REVERT: A 32 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7075 (mt-10) REVERT: A 157 ILE cc_start: 0.4121 (OUTLIER) cc_final: 0.3879 (mm) REVERT: A 189 LYS cc_start: 0.1622 (OUTLIER) cc_final: 0.0626 (tptp) REVERT: A 270 LYS cc_start: 0.8393 (mmtm) cc_final: 0.7997 (mttm) REVERT: A 330 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6863 (mtm180) REVERT: A 334 ASP cc_start: 0.8366 (t0) cc_final: 0.8098 (t0) REVERT: A 381 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8456 (mtt-85) REVERT: A 384 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8068 (ttm170) REVERT: A 535 LYS cc_start: 0.6139 (ttpt) cc_final: 0.5326 (ttpp) REVERT: A 671 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7042 (mt-10) REVERT: A 765 MET cc_start: 0.5688 (OUTLIER) cc_final: 0.4445 (mmp) REVERT: A 768 MET cc_start: 0.3671 (ttt) cc_final: 0.3169 (tmm) REVERT: A 907 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.6982 (t70) REVERT: A 987 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7086 (mm-30) REVERT: A 1012 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: A 1133 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6642 (m-30) REVERT: A 1154 THR cc_start: 0.8032 (t) cc_final: 0.7729 (m) REVERT: A 1288 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: A 1369 ARG cc_start: 0.8112 (ttt180) cc_final: 0.7895 (ttp80) outliers start: 41 outliers final: 13 residues processed: 121 average time/residue: 0.5847 time to fit residues: 77.5884 Evaluate side-chains 113 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 32 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 330 ARG 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 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 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 1288 GLN Chi-restraints excluded: chain A residue 1300 CYS Chi-restraints excluded: chain A residue 1364 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 146 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 86 optimal weight: 0.0980 chunk 99 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1359 ASN A1406 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.219673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.202686 restraints weight = 11169.121| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 0.44 r_work: 0.3786 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14343 Z= 0.162 Angle : 0.603 12.804 19896 Z= 0.316 Chirality : 0.042 0.309 2303 Planarity : 0.004 0.062 2127 Dihedral : 19.178 177.137 3288 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.54 % Favored : 93.18 % Rotamer: Outliers : 2.70 % Allowed : 17.42 % 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: -0.05 (0.22), residues: 1407 helix: 0.61 (0.20), residues: 671 sheet: -0.06 (0.44), residues: 128 loop : -0.67 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1088 TYR 0.015 0.002 TYR A 257 PHE 0.017 0.002 PHE A 160 TRP 0.018 0.002 TRP A 727 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (14343) covalent geometry : angle 0.60316 / 0.32 (19896) hydrogen bonds : bond 0.04154 / 2.83 ( 619) hydrogen bonds : angle 4.42200 / 3.07 ( 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 130 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.467 Fit side-chains REVERT: A 1 MET cc_start: 0.3794 (tpp) cc_final: 0.2362 (tmm) REVERT: A 14 ARG cc_start: 0.7235 (ttm-80) cc_final: 0.6997 (ttp-170) REVERT: A 157 ILE cc_start: 0.4187 (OUTLIER) cc_final: 0.3940 (mm) REVERT: A 189 LYS cc_start: 0.1379 (OUTLIER) cc_final: 0.0480 (tptp) REVERT: A 191 MET cc_start: 0.5731 (ppp) cc_final: 0.5515 (ppp) REVERT: A 270 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7968 (mttm) REVERT: A 330 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6788 (mtm180) REVERT: A 334 ASP cc_start: 0.8249 (t0) cc_final: 0.8002 (t0) REVERT: A 381 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8415 (mtt-85) REVERT: A 384 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8022 (ttm170) REVERT: A 535 LYS cc_start: 0.5994 (ttpt) cc_final: 0.5134 (ttpp) REVERT: A 671 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7006 (mt-10) REVERT: A 765 MET cc_start: 0.5768 (OUTLIER) cc_final: 0.4457 (mmp) REVERT: A 768 MET cc_start: 0.3836 (ttt) cc_final: 0.3352 (tmm) REVERT: A 907 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6892 (t70) REVERT: A 987 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6986 (mm-30) REVERT: A 1012 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: A 1154 THR cc_start: 0.7958 (t) cc_final: 0.7642 (m) REVERT: A 1369 ARG cc_start: 0.8052 (ttt180) cc_final: 0.7819 (ttp80) outliers start: 34 outliers final: 14 residues processed: 117 average time/residue: 0.6365 time to fit residues: 81.5970 Evaluate side-chains 117 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 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 157 ILE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 384 ARG Chi-restraints excluded: chain A residue 392 ARG 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 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 1153 ILE 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 1382 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 75 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 0.0060 chunk 119 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 126 optimal weight: 0.0570 chunk 41 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.5314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN A1406 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.222604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.205788 restraints weight = 11323.128| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 0.45 r_work: 0.3824 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work: 0.3485 rms_B_bonded: 4.76 restraints_weight: 0.1250 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14343 Z= 0.117 Angle : 0.557 12.297 19896 Z= 0.298 Chirality : 0.039 0.290 2303 Planarity : 0.004 0.059 2127 Dihedral : 19.087 176.725 3288 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.18 % Favored : 93.53 % Rotamer: Outliers : 2.39 % Allowed : 17.98 % 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: 0.09 (0.22), residues: 1407 helix: 0.74 (0.20), residues: 674 sheet: -0.02 (0.44), residues: 128 loop : -0.61 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 222 TYR 0.014 0.001 TYR A 348 PHE 0.013 0.001 PHE A 952 TRP 0.017 0.001 TRP A 727 HIS 0.004 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (14343) covalent geometry : angle 0.55715 / 0.30 (19896) hydrogen bonds : bond 0.03814 / 2.58 ( 619) hydrogen bonds : angle 4.26331 / 2.94 ( 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 127 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.454 Fit side-chains REVERT: A 1 MET cc_start: 0.3736 (tpp) cc_final: 0.2318 (tmm) REVERT: A 157 ILE cc_start: 0.4119 (OUTLIER) cc_final: 0.3877 (mm) REVERT: A 189 LYS cc_start: 0.1354 (OUTLIER) cc_final: 0.0503 (tptp) REVERT: A 270 LYS cc_start: 0.8380 (mmtm) cc_final: 0.7932 (mttm) REVERT: A 330 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.7007 (mtm180) REVERT: A 381 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8449 (mtt-85) REVERT: A 384 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8090 (ttm170) REVERT: A 464 ASP cc_start: 0.7259 (t70) cc_final: 0.6924 (t0) REVERT: A 470 LYS cc_start: 0.7830 (mmtt) cc_final: 0.7443 (mmpt) REVERT: A 535 LYS cc_start: 0.5933 (ttpt) cc_final: 0.4811 (tptt) REVERT: A 765 MET cc_start: 0.5376 (OUTLIER) cc_final: 0.4228 (mmt) REVERT: A 768 MET cc_start: 0.3653 (ttt) cc_final: 0.3159 (tmm) REVERT: A 907 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6979 (t70) REVERT: A 987 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6921 (mm-30) REVERT: A 1012 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: A 1017 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7686 (pt0) REVERT: A 1154 THR cc_start: 0.7979 (t) cc_final: 0.7703 (m) REVERT: A 1369 ARG cc_start: 0.8119 (ttt180) cc_final: 0.7882 (ttp80) outliers start: 30 outliers final: 12 residues processed: 120 average time/residue: 0.5796 time to fit residues: 76.5695 Evaluate side-chains 114 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL 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 330 ARG Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 384 ARG Chi-restraints excluded: chain A residue 392 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 149 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN A1406 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.219585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.202680 restraints weight = 11241.948| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 0.43 r_work: 0.3783 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14343 Z= 0.181 Angle : 0.610 12.058 19896 Z= 0.318 Chirality : 0.042 0.300 2303 Planarity : 0.005 0.061 2127 Dihedral : 19.093 177.140 3288 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.54 % Favored : 93.18 % Rotamer: Outliers : 2.31 % Allowed : 18.30 % Favored : 79.40 % 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: 0.03 (0.22), residues: 1407 helix: 0.69 (0.20), residues: 673 sheet: 0.03 (0.45), residues: 128 loop : -0.66 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 222 TYR 0.018 0.002 TYR A 348 PHE 0.015 0.002 PHE A 66 TRP 0.018 0.002 TRP A 727 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (14343) covalent geometry : angle 0.60952 / 0.32 (19896) hydrogen bonds : bond 0.04127 / 2.81 ( 619) hydrogen bonds : angle 4.36569 / 3.02 ( 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 124 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.348 Fit side-chains REVERT: A 1 MET cc_start: 0.3746 (tpp) cc_final: 0.2356 (tmm) REVERT: A 157 ILE cc_start: 0.3972 (OUTLIER) cc_final: 0.3723 (mm) REVERT: A 189 LYS cc_start: 0.1353 (OUTLIER) cc_final: 0.0522 (tptp) REVERT: A 191 MET cc_start: 0.5151 (ppp) cc_final: 0.4933 (ppp) REVERT: A 270 LYS cc_start: 0.8239 (mmtm) cc_final: 0.7895 (mttm) REVERT: A 381 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8290 (mtt-85) REVERT: A 470 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7468 (mmtt) REVERT: A 535 LYS cc_start: 0.6096 (ttpt) cc_final: 0.5142 (tptt) REVERT: A 693 GLN cc_start: 0.6475 (OUTLIER) cc_final: 0.6046 (tt0) REVERT: A 765 MET cc_start: 0.5800 (OUTLIER) cc_final: 0.4514 (mmp) REVERT: A 768 MET cc_start: 0.3639 (ttt) cc_final: 0.3245 (tmm) REVERT: A 907 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6767 (t70) REVERT: A 968 PHE cc_start: 0.3191 (OUTLIER) cc_final: 0.2058 (m-80) REVERT: A 987 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6810 (mm-30) REVERT: A 1012 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6923 (mt-10) REVERT: A 1154 THR cc_start: 0.7891 (t) cc_final: 0.7596 (m) REVERT: A 1292 MET cc_start: 0.8185 (mmt) cc_final: 0.7818 (mmt) outliers start: 29 outliers final: 12 residues processed: 113 average time/residue: 0.5953 time to fit residues: 73.9034 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 : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL 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 381 ARG Chi-restraints excluded: chain A residue 392 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 904 LEU Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 968 PHE 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 Chi-restraints excluded: chain A residue 1364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.221196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.203976 restraints weight = 11327.687| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 0.45 r_work: 0.3811 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1929 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= 0.133 Angle : 0.565 11.638 19896 Z= 0.301 Chirality : 0.040 0.288 2303 Planarity : 0.004 0.061 2127 Dihedral : 19.050 176.849 3288 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.61 % Favored : 93.11 % Rotamer: Outliers : 1.59 % Allowed : 19.09 % Favored : 79.32 % 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: 0.09 (0.22), residues: 1407 helix: 0.76 (0.20), residues: 673 sheet: -0.00 (0.44), residues: 128 loop : -0.63 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 222 TYR 0.016 0.001 TYR A 348 PHE 0.014 0.001 PHE A 66 TRP 0.017 0.001 TRP A 727 HIS 0.004 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (14343) covalent geometry : angle 0.56483 / 0.30 (19896) hydrogen bonds : bond 0.03859 / 2.62 ( 619) hydrogen bonds : angle 4.27512 / 2.95 ( 1746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4022.27 seconds wall clock time: 69 minutes 31.89 seconds (4171.89 seconds total)