Starting phenix.real_space_refine on Thu Aug 6 15:04:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9krl_62532/08_2026/9krl_62532_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9krl_62532/08_2026/9krl_62532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9krl_62532/08_2026/9krl_62532_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9krl_62532/08_2026/9krl_62532_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9krl_62532/08_2026/9krl_62532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9krl_62532/08_2026/9krl_62532.map" } resolution = 2.99 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= -0.001 sd= 0.090 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 37 5.16 5 C 4910 2.51 5 N 1257 2.21 5 O 1329 1.98 5 H 7718 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 15252 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 15230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 935, 15230 Classifications: {'peptide': 935} Link IDs: {'PTRANS': 28, 'TRANS': 906} Chain breaks: 4 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 2.25, per 1000 atoms: 0.15 Number of scatterers: 15252 At special positions: 0 Unit cell: (80.3, 103.4, 147.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 P 1 15.00 O 1329 8.00 N 1257 7.00 C 4910 6.00 H 7718 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 409.2 milliseconds 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1782 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 2 sheets defined 72.2% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 35 removed outlier: 4.145A pdb=" N PHE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 58 through 74 removed outlier: 3.944A pdb=" N ASP A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 86 removed outlier: 3.841A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 104 removed outlier: 4.111A pdb=" N TYR A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.865A pdb=" N LYS A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 150 removed outlier: 3.956A pdb=" N ASN A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N CYS A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 179 removed outlier: 4.176A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 190 through 200 removed outlier: 3.927A pdb=" N LEU A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.870A pdb=" N VAL A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 209' Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 213 through 231 Proline residue: A 219 - end of helix removed outlier: 3.728A pdb=" N MET A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 246 through 281 removed outlier: 3.734A pdb=" N CYS A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.970A pdb=" N MET A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 326 removed outlier: 4.481A pdb=" N PHE A 295 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 343 removed outlier: 4.090A pdb=" N GLY A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 390 removed outlier: 3.617A pdb=" N ALA A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Proline residue: A 370 - end of helix removed outlier: 3.721A pdb=" N ILE A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 removed outlier: 3.585A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 722 removed outlier: 3.560A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 744 removed outlier: 3.710A pdb=" N ALA A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 735 " --> pdb=" O GLN A 731 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET A 744 " --> pdb=" O ASN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 806 removed outlier: 4.163A pdb=" N TYR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 768 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 776 " --> pdb=" O THR A 772 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 783 " --> pdb=" O GLY A 779 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN A 799 " --> pdb=" O GLN A 795 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 800 " --> pdb=" O THR A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 835 removed outlier: 3.767A pdb=" N ILE A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 860 removed outlier: 3.720A pdb=" N VAL A 850 " --> pdb=" O THR A 846 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 853 " --> pdb=" O GLN A 849 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 860 " --> pdb=" O VAL A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 867 through 887 removed outlier: 4.109A pdb=" N LEU A 871 " --> pdb=" O PRO A 867 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 876 " --> pdb=" O GLY A 872 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 908 Proline residue: A 899 - end of helix Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.511A pdb=" N TYR A 917 " --> pdb=" O THR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 970 removed outlier: 3.788A pdb=" N GLN A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE A 948 " --> pdb=" O THR A 944 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA A 949 " --> pdb=" O SER A 945 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 950 " --> pdb=" O ARG A 946 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 955 " --> pdb=" O ARG A 951 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 960 " --> pdb=" O CYS A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 987 removed outlier: 3.584A pdb=" N VAL A 979 " --> pdb=" O ASP A 975 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1014 removed outlier: 4.203A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A1000 " --> pdb=" O CYS A 996 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA A1001 " --> pdb=" O VAL A 997 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1089 Processing helix chain 'A' and resid 1110 through 1115 Processing helix chain 'A' and resid 1142 through 1150 Processing helix chain 'A' and resid 1156 through 1161 removed outlier: 3.962A pdb=" N GLU A1160 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A1161 " --> pdb=" O GLU A1157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1156 through 1161' Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1212 through 1223 removed outlier: 3.650A pdb=" N PHE A1223 " --> pdb=" O ILE A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1238 Processing helix chain 'A' and resid 1257 through 1261 removed outlier: 3.622A pdb=" N VAL A1260 " --> pdb=" O GLU A1257 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1064 through 1065 Processing sheet with id=AA2, first strand: chain 'A' and resid 1117 through 1120 removed outlier: 3.564A pdb=" N SER A1118 " --> pdb=" O ILE A1197 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A1201 " --> pdb=" O ILE A1120 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7705 1.03 - 1.23: 13 1.23 - 1.42: 3186 1.42 - 1.62: 4452 1.62 - 1.81: 62 Bond restraints: 15418 Sorted by residual: bond pdb=" C4' CMP A1401 " pdb=" C5' CMP A1401 " ideal model delta sigma weight residual 1.524 1.498 0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" C3' CMP A1401 " pdb=" C4' CMP A1401 " ideal model delta sigma weight residual 1.524 1.500 0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" C4 CMP A1401 " pdb=" C5 CMP A1401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" C1' CMP A1401 " pdb=" C2' CMP A1401 " ideal model delta sigma weight residual 1.524 1.542 -0.018 2.00e-02 2.50e+03 7.87e-01 bond pdb=" CB THR A 335 " pdb=" CG2 THR A 335 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.70e-01 ... (remaining 15413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 27764 2.02 - 4.05: 148 4.05 - 6.07: 5 6.07 - 8.09: 5 8.09 - 10.11: 3 Bond angle restraints: 27925 Sorted by residual: angle pdb=" N ILE A 245 " pdb=" CA ILE A 245 " pdb=" C ILE A 245 " ideal model delta sigma weight residual 112.96 109.47 3.49 1.00e+00 1.00e+00 1.22e+01 angle pdb=" C1' CMP A1401 " pdb=" C2' CMP A1401 " pdb=" C3' CMP A1401 " ideal model delta sigma weight residual 111.00 100.89 10.11 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C2' CMP A1401 " pdb=" C3' CMP A1401 " pdb=" C4' CMP A1401 " ideal model delta sigma weight residual 111.00 101.86 9.14 3.00e+00 1.11e-01 9.28e+00 angle pdb=" O1P CMP A1401 " pdb=" P CMP A1401 " pdb=" O2P CMP A1401 " ideal model delta sigma weight residual 109.50 118.57 -9.07 3.00e+00 1.11e-01 9.14e+00 angle pdb=" C2' CMP A1401 " pdb=" C3' CMP A1401 " pdb=" O3' CMP A1401 " ideal model delta sigma weight residual 109.47 117.25 -7.78 3.00e+00 1.11e-01 6.73e+00 ... (remaining 27920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.48: 6943 28.48 - 56.97: 213 56.97 - 85.45: 16 85.45 - 113.94: 2 113.94 - 142.42: 1 Dihedral angle restraints: 7175 sinusoidal: 3879 harmonic: 3296 Sorted by residual: dihedral pdb=" C8 CMP A1401 " pdb=" C1' CMP A1401 " pdb=" N9 CMP A1401 " pdb=" O4' CMP A1401 " ideal model delta sinusoidal sigma weight residual -28.22 -170.65 142.42 1 2.00e+01 2.50e-03 4.30e+01 dihedral pdb=" CA ASP A 834 " pdb=" C ASP A 834 " pdb=" N LEU A 835 " pdb=" CA LEU A 835 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA CYS A1226 " pdb=" C CYS A1226 " pdb=" N THR A1227 " pdb=" CA THR A1227 " ideal model delta harmonic sigma weight residual 180.00 162.75 17.25 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 7172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 985 0.048 - 0.096: 205 0.096 - 0.143: 28 0.143 - 0.191: 1 0.191 - 0.239: 1 Chirality restraints: 1220 Sorted by residual: chirality pdb=" C2' CMP A1401 " pdb=" C1' CMP A1401 " pdb=" C3' CMP A1401 " pdb=" O2' CMP A1401 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA VAL A 860 " pdb=" N VAL A 860 " pdb=" C VAL A 860 " pdb=" CB VAL A 860 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE A 861 " pdb=" N ILE A 861 " pdb=" C ILE A 861 " pdb=" CB ILE A 861 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1217 not shown) Planarity restraints: 2185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 11 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 12 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 12 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 12 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 218 " -0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO A 219 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 219 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 219 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 799 " 0.005 2.00e-02 2.50e+03 9.69e-03 9.40e-01 pdb=" C ASN A 799 " -0.017 2.00e-02 2.50e+03 pdb=" O ASN A 799 " 0.006 2.00e-02 2.50e+03 pdb=" N LYS A 800 " 0.006 2.00e-02 2.50e+03 ... (remaining 2182 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1533 2.25 - 2.84: 34305 2.84 - 3.42: 35826 3.42 - 4.01: 47527 4.01 - 4.60: 75353 Nonbonded interactions: 194544 Sorted by model distance: nonbonded pdb=" O LEU A 181 " pdb="HH22 ARG A 915 " model vdw 1.659 2.450 nonbonded pdb=" O GLU A 803 " pdb=" HZ3 LYS A 807 " model vdw 1.686 2.450 nonbonded pdb=" O TYR A1016 " pdb=" HG1 THR A1017 " model vdw 1.702 2.450 nonbonded pdb=" O TYR A 768 " pdb=" HG1 THR A 772 " model vdw 1.705 2.450 nonbonded pdb=" O LEU A 940 " pdb=" HG1 THR A 944 " model vdw 1.710 2.450 ... (remaining 194539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.050 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.540 Find NCS groups from input model: 0.040 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:8.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.004 0.029 7700 Z= 0.162 Angle : 0.598 10.114 10443 Z= 0.332 Chirality : 0.039 0.239 1220 Planarity : 0.003 0.029 1283 Dihedral : 12.743 142.422 2799 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.24), residues: 925 helix: -1.53 (0.19), residues: 636 sheet: -3.27 (0.80), residues: 34 loop : -4.04 (0.27), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 887 TYR 0.016 0.001 TYR A 768 PHE 0.012 0.001 PHE A 948 TRP 0.015 0.001 TRP A 763 HIS 0.004 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 7700) covalent geometry : angle 0.59790 / 0.33 (10443) hydrogen bonds : bond 0.14452 / 9.26 ( 406) hydrogen bonds : angle 4.83218 / 3.23 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7620 (tm-30) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 1.0826 time to fit residues: 138.3950 Evaluate side-chains 70 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 746 ASN A1141 HIS A1195 ASN A1236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.182132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122324 restraints weight = 25958.395| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.53 r_work: 0.3444 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7700 Z= 0.150 Angle : 0.569 8.732 10443 Z= 0.293 Chirality : 0.039 0.176 1220 Planarity : 0.004 0.037 1283 Dihedral : 5.932 141.121 1018 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.58 % Allowed : 9.59 % Favored : 88.83 % 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: -2.17 (0.27), residues: 925 helix: -0.47 (0.21), residues: 641 sheet: -2.82 (0.87), residues: 34 loop : -3.65 (0.30), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 820 TYR 0.011 0.001 TYR A 92 PHE 0.015 0.001 PHE A 336 TRP 0.009 0.001 TRP A 947 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 7700) covalent geometry : angle 0.56942 / 0.29 (10443) hydrogen bonds : bond 0.06393 / 4.10 ( 406) hydrogen bonds : angle 4.06052 / 2.78 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 MET cc_start: 0.6973 (tpp) cc_final: 0.6519 (tpp) REVERT: A 706 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.5888 (ttm170) REVERT: A 721 ASN cc_start: 0.7575 (m-40) cc_final: 0.7300 (m110) REVERT: A 803 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7321 (pm20) REVERT: A 952 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6373 (tt) REVERT: A 1020 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7140 (mp0) REVERT: A 1049 MET cc_start: 0.5911 (ptm) cc_final: 0.5340 (ptp) REVERT: A 1086 SER cc_start: 0.8080 (m) cc_final: 0.7826 (p) outliers start: 13 outliers final: 1 residues processed: 81 average time/residue: 0.9341 time to fit residues: 80.8385 Evaluate side-chains 69 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 706 ARG Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 952 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 994 GLN A1236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.181057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120769 restraints weight = 26090.225| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.52 r_work: 0.3428 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7700 Z= 0.127 Angle : 0.538 8.469 10443 Z= 0.275 Chirality : 0.037 0.160 1220 Planarity : 0.003 0.040 1283 Dihedral : 5.820 139.506 1018 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.70 % Allowed : 11.53 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.28), residues: 925 helix: 0.06 (0.21), residues: 646 sheet: -2.50 (0.90), residues: 34 loop : -3.21 (0.34), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 998 TYR 0.014 0.001 TYR A 92 PHE 0.012 0.001 PHE A 352 TRP 0.008 0.001 TRP A 947 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 7700) covalent geometry : angle 0.53829 / 0.27 (10443) hydrogen bonds : bond 0.05921 / 3.77 ( 406) hydrogen bonds : angle 3.83420 / 2.62 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6959 (tm-30) REVERT: A 278 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: A 803 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7264 (pm20) REVERT: A 952 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6446 (tt) REVERT: A 1049 MET cc_start: 0.6183 (ptm) cc_final: 0.5671 (ptp) REVERT: A 1086 SER cc_start: 0.8249 (m) cc_final: 0.8010 (p) outliers start: 14 outliers final: 1 residues processed: 79 average time/residue: 0.8730 time to fit residues: 74.2124 Evaluate side-chains 66 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 387 GLN A1236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.177285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118395 restraints weight = 26147.173| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.01 r_work: 0.3337 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7700 Z= 0.151 Angle : 0.561 8.459 10443 Z= 0.288 Chirality : 0.038 0.155 1220 Planarity : 0.003 0.042 1283 Dihedral : 5.879 140.335 1018 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.46 % Allowed : 13.11 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.28), residues: 925 helix: 0.18 (0.21), residues: 646 sheet: -2.26 (0.92), residues: 34 loop : -3.07 (0.34), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 998 TYR 0.013 0.001 TYR A 339 PHE 0.014 0.001 PHE A 336 TRP 0.009 0.001 TRP A 947 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 7700) covalent geometry : angle 0.56136 / 0.29 (10443) hydrogen bonds : bond 0.06418 / 4.07 ( 406) hydrogen bonds : angle 3.92405 / 2.69 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7372 (t0) cc_final: 0.7142 (p0) REVERT: A 67 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7336 (tm-30) REVERT: A 803 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7314 (pm20) REVERT: A 952 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6557 (tt) outliers start: 12 outliers final: 2 residues processed: 76 average time/residue: 0.9020 time to fit residues: 73.8179 Evaluate side-chains 70 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A1236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.178902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.126455 restraints weight = 25449.847| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.39 r_work: 0.3370 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7700 Z= 0.121 Angle : 0.525 8.246 10443 Z= 0.268 Chirality : 0.037 0.145 1220 Planarity : 0.003 0.039 1283 Dihedral : 5.774 138.568 1018 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.58 % Allowed : 12.99 % Favored : 85.44 % 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: -0.80 (0.29), residues: 925 helix: 0.48 (0.22), residues: 642 sheet: -2.03 (0.93), residues: 34 loop : -2.94 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 998 TYR 0.009 0.001 TYR A 339 PHE 0.013 0.001 PHE A 324 TRP 0.007 0.001 TRP A 733 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 7700) covalent geometry : angle 0.52530 / 0.27 (10443) hydrogen bonds : bond 0.05802 / 3.69 ( 406) hydrogen bonds : angle 3.76362 / 2.58 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 803 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: A 1049 MET cc_start: 0.6440 (ptm) cc_final: 0.5841 (ptp) outliers start: 13 outliers final: 1 residues processed: 82 average time/residue: 0.7968 time to fit residues: 70.5616 Evaluate side-chains 69 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 803 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 33 optimal weight: 0.3980 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A1236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.177393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.116685 restraints weight = 26217.309| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.51 r_work: 0.3357 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7700 Z= 0.133 Angle : 0.540 8.338 10443 Z= 0.275 Chirality : 0.037 0.149 1220 Planarity : 0.003 0.039 1283 Dihedral : 5.742 137.482 1018 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.33 % Allowed : 14.32 % Favored : 84.34 % 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: -0.70 (0.29), residues: 925 helix: 0.52 (0.22), residues: 646 sheet: -1.99 (0.95), residues: 34 loop : -2.85 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 998 TYR 0.010 0.001 TYR A 339 PHE 0.013 0.001 PHE A 336 TRP 0.008 0.001 TRP A 733 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7700) covalent geometry : angle 0.53978 / 0.28 (10443) hydrogen bonds : bond 0.05941 / 3.77 ( 406) hydrogen bonds : angle 3.76601 / 2.58 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6202 (pp) REVERT: A 67 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 803 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7268 (pm20) REVERT: A 1049 MET cc_start: 0.6438 (ptm) cc_final: 0.5830 (ptp) outliers start: 11 outliers final: 2 residues processed: 79 average time/residue: 0.8816 time to fit residues: 74.8361 Evaluate side-chains 73 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 5 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A1236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.177879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.125123 restraints weight = 25844.890| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.42 r_work: 0.3336 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7700 Z= 0.138 Angle : 0.547 8.296 10443 Z= 0.280 Chirality : 0.038 0.149 1220 Planarity : 0.003 0.039 1283 Dihedral : 5.732 137.198 1018 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.82 % Allowed : 14.20 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.29), residues: 925 helix: 0.56 (0.22), residues: 646 sheet: -1.91 (0.97), residues: 34 loop : -2.81 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 998 TYR 0.010 0.001 TYR A 339 PHE 0.018 0.001 PHE A 324 TRP 0.008 0.001 TRP A 733 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 7700) covalent geometry : angle 0.54700 / 0.28 (10443) hydrogen bonds : bond 0.06097 / 3.86 ( 406) hydrogen bonds : angle 3.77876 / 2.59 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6405 (pp) REVERT: A 67 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7370 (tm-30) REVERT: A 278 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: A 803 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7450 (pm20) REVERT: A 1049 MET cc_start: 0.6567 (ptm) cc_final: 0.5972 (ptp) outliers start: 15 outliers final: 4 residues processed: 79 average time/residue: 0.8260 time to fit residues: 70.1685 Evaluate side-chains 75 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 33 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A1236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.178172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125345 restraints weight = 26105.647| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.48 r_work: 0.3338 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7700 Z= 0.130 Angle : 0.543 8.362 10443 Z= 0.278 Chirality : 0.037 0.151 1220 Planarity : 0.003 0.039 1283 Dihedral : 5.654 134.816 1018 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.82 % Allowed : 14.32 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.29), residues: 925 helix: 0.63 (0.22), residues: 648 sheet: -1.78 (1.00), residues: 34 loop : -2.73 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 998 TYR 0.010 0.001 TYR A 339 PHE 0.013 0.001 PHE A 336 TRP 0.008 0.001 TRP A 733 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7700) covalent geometry : angle 0.54339 / 0.28 (10443) hydrogen bonds : bond 0.05907 / 3.74 ( 406) hydrogen bonds : angle 3.72761 / 2.56 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6421 (pp) REVERT: A 67 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7392 (tm-30) REVERT: A 278 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: A 803 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7482 (pm20) REVERT: A 1049 MET cc_start: 0.6606 (ptm) cc_final: 0.5988 (ptp) outliers start: 15 outliers final: 4 residues processed: 81 average time/residue: 0.8130 time to fit residues: 70.7456 Evaluate side-chains 77 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.175087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113965 restraints weight = 26258.194| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.46 r_work: 0.3326 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7700 Z= 0.159 Angle : 0.571 8.416 10443 Z= 0.293 Chirality : 0.038 0.156 1220 Planarity : 0.003 0.039 1283 Dihedral : 5.705 134.966 1018 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.33 % Allowed : 14.93 % Favored : 83.74 % 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: -0.56 (0.29), residues: 925 helix: 0.58 (0.22), residues: 647 sheet: -1.72 (1.02), residues: 34 loop : -2.70 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 165 TYR 0.011 0.001 TYR A 339 PHE 0.016 0.001 PHE A 324 TRP 0.008 0.001 TRP A 947 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 7700) covalent geometry : angle 0.57092 / 0.29 (10443) hydrogen bonds : bond 0.06458 / 4.08 ( 406) hydrogen bonds : angle 3.84346 / 2.63 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: A 803 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: A 1049 MET cc_start: 0.6697 (ptm) cc_final: 0.6100 (ptp) outliers start: 11 outliers final: 5 residues processed: 76 average time/residue: 0.9164 time to fit residues: 74.6045 Evaluate side-chains 74 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 50 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.177773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125155 restraints weight = 26229.379| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.43 r_work: 0.3340 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7700 Z= 0.129 Angle : 0.547 8.329 10443 Z= 0.280 Chirality : 0.037 0.150 1220 Planarity : 0.003 0.039 1283 Dihedral : 5.599 132.066 1018 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.97 % Allowed : 15.53 % Favored : 83.50 % 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: -0.40 (0.29), residues: 925 helix: 0.69 (0.22), residues: 648 sheet: -1.77 (1.00), residues: 34 loop : -2.62 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 998 TYR 0.010 0.001 TYR A 339 PHE 0.012 0.001 PHE A 352 TRP 0.008 0.001 TRP A 733 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7700) covalent geometry : angle 0.54690 / 0.28 (10443) hydrogen bonds : bond 0.05952 / 3.76 ( 406) hydrogen bonds : angle 3.74642 / 2.57 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 278 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: A 803 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: A 1049 MET cc_start: 0.6820 (ptm) cc_final: 0.6244 (ptp) outliers start: 8 outliers final: 4 residues processed: 73 average time/residue: 0.8820 time to fit residues: 69.5440 Evaluate side-chains 74 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 36 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.177297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.124497 restraints weight = 26091.192| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.48 r_work: 0.3323 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7700 Z= 0.133 Angle : 0.551 8.329 10443 Z= 0.282 Chirality : 0.038 0.150 1220 Planarity : 0.003 0.038 1283 Dihedral : 5.557 130.817 1018 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.09 % Allowed : 15.41 % Favored : 83.50 % 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: -0.34 (0.29), residues: 925 helix: 0.74 (0.22), residues: 648 sheet: -1.70 (1.02), residues: 34 loop : -2.59 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 165 TYR 0.010 0.001 TYR A 339 PHE 0.019 0.001 PHE A 324 TRP 0.008 0.001 TRP A 733 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7700) covalent geometry : angle 0.55130 / 0.28 (10443) hydrogen bonds : bond 0.06021 / 3.80 ( 406) hydrogen bonds : angle 3.75347 / 2.57 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4622.04 seconds wall clock time: 78 minutes 38.11 seconds (4718.11 seconds total)