Starting phenix.real_space_refine on Wed Aug 5 23:17:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jwn_61854/08_2026/9jwn_61854.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jwn_61854/08_2026/9jwn_61854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jwn_61854/08_2026/9jwn_61854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jwn_61854/08_2026/9jwn_61854.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jwn_61854/08_2026/9jwn_61854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jwn_61854/08_2026/9jwn_61854.map" } resolution = 2.89 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 107 atoms to isotropic. 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 152 5.49 5 S 31 5.16 5 C 6992 2.51 5 N 2053 2.21 5 O 2667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s 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: 11895 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "B" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2380 Classifications: {'RNA': 112} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 13, 'rna3p_pur': 52, 'rna3p_pyr': 41} Link IDs: {'rna2p': 19, 'rna3p': 92} Chain breaks: 1 Chain: "C" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 552 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 8691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8691 Classifications: {'peptide': 1063} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 1030} Chain breaks: 7 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.53, per 1000 atoms: 0.21 Number of scatterers: 11895 At special positions: 0 Unit cell: (114.688, 122.88, 117.965, 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 31 16.00 P 152 15.00 O 2667 8.00 N 2053 7.00 C 6992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 460.1 milliseconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 49.9% alpha, 7.0% beta 42 base pairs and 102 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 56 through 84 removed outlier: 4.559A pdb=" N ARG A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 90 removed outlier: 3.705A pdb=" N LYS A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 101 removed outlier: 3.695A pdb=" N GLU A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 190 removed outlier: 3.753A pdb=" N GLN A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.560A pdb=" N ILE A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 287 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 300 through 312 removed outlier: 3.578A pdb=" N LEU A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 352 removed outlier: 3.573A pdb=" N ALA A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.584A pdb=" N PHE A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 389 through 402 removed outlier: 3.560A pdb=" N GLU A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 435 through 452 removed outlier: 3.922A pdb=" N GLU A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 452 " --> pdb=" O GLN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.927A pdb=" N GLU A 459 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 477 Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.515A pdb=" N ILE A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 562 removed outlier: 3.589A pdb=" N GLU A 554 " --> pdb=" O TYR A 550 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 555 " --> pdb=" O GLN A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 636 removed outlier: 4.788A pdb=" N GLU A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 658 removed outlier: 3.800A pdb=" N ILE A 651 " --> pdb=" O MET A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 673 removed outlier: 3.945A pdb=" N LEU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 667 " --> pdb=" O LYS A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 687 Processing helix chain 'A' and resid 696 through 701 Processing helix chain 'A' and resid 715 through 722 removed outlier: 3.607A pdb=" N LEU A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG A 720 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 removed outlier: 4.326A pdb=" N LYS A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 784 removed outlier: 3.710A pdb=" N GLU A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 976 removed outlier: 3.559A pdb=" N SER A 971 " --> pdb=" O LYS A 967 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 972 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS A 976 " --> pdb=" O LEU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 997 Processing helix chain 'A' and resid 1007 through 1021 removed outlier: 4.210A pdb=" N ALA A1011 " --> pdb=" O ASN A1007 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A1019 " --> pdb=" O TYR A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1082 Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.538A pdb=" N ASN A1127 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1133 Processing helix chain 'A' and resid 1164 through 1166 No H-bonds generated for 'chain 'A' and resid 1164 through 1166' Processing helix chain 'A' and resid 1171 through 1182 Processing helix chain 'A' and resid 1229 through 1244 removed outlier: 4.065A pdb=" N ALA A1234 " --> pdb=" O ALA A1230 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS A1235 " --> pdb=" O LYS A1231 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A1241 " --> pdb=" O ARG A1237 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A1242 " --> pdb=" O MET A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1274 removed outlier: 3.605A pdb=" N GLU A1272 " --> pdb=" O ASP A1268 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS A1274 " --> pdb=" O LEU A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1281 Processing helix chain 'A' and resid 1286 through 1293 Processing helix chain 'A' and resid 1293 through 1299 removed outlier: 3.619A pdb=" N VAL A1298 " --> pdb=" O ARG A1294 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A1299 " --> pdb=" O GLU A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1307 Processing helix chain 'A' and resid 1308 through 1314 Processing helix chain 'A' and resid 1315 through 1317 No H-bonds generated for 'chain 'A' and resid 1315 through 1317' Processing sheet with id=AA1, first strand: chain 'A' and resid 981 through 984 removed outlier: 5.912A pdb=" N ILE A 793 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 17 " --> pdb=" O PHE A 794 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 1116 through 1117 Processing sheet with id=AA4, first strand: chain 'A' and resid 1189 through 1195 removed outlier: 9.843A pdb=" N ASP A1189 " --> pdb=" O GLN A1149 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N GLN A1149 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG A1191 " --> pdb=" O GLU A1147 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N GLU A1147 " --> pdb=" O ARG A1191 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N THR A1193 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU A1145 " --> pdb=" O THR A1193 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL A1161 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE A1143 " --> pdb=" O GLU A1159 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU A1159 " --> pdb=" O PHE A1143 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU A1145 " --> pdb=" O SER A1157 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER A1157 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU A1147 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE A1155 " --> pdb=" O GLU A1147 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN A1149 " --> pdb=" O LYS A1153 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LYS A1153 " --> pdb=" O GLN A1149 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A1156 " --> pdb=" O LEU A1344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1199 through 1203 removed outlier: 3.812A pdb=" N SER A1199 " --> pdb=" O LEU A1210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A1340 " --> pdb=" O LEU A1218 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N MET A1338 " --> pdb=" O LEU A1220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1355 through 1357 320 hydrogen bonds defined for protein. 933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 96 hydrogen bonds 180 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 102 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 1.43 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: 2744 1.33 - 1.45: 3289 1.45 - 1.57: 6047 1.57 - 1.69: 300 1.69 - 1.81: 51 Bond restraints: 12431 Sorted by residual: bond pdb=" C3' DC C 1 " pdb=" C2' DC C 1 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.08e+00 bond pdb=" C3' DA C -6 " pdb=" C2' DA C -6 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.80e+00 bond pdb=" C3' DT D 1 " pdb=" C2' DT D 1 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.52e+00 bond pdb=" C3' DG C 15 " pdb=" C2' DG C 15 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.70e+00 bond pdb=" C3' DA D 4 " pdb=" C2' DA D 4 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.04e+00 ... (remaining 12426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 16864 1.95 - 3.91: 565 3.91 - 5.86: 29 5.86 - 7.81: 4 7.81 - 9.76: 2 Bond angle restraints: 17464 Sorted by residual: angle pdb=" C3' U B 101 " pdb=" O3' U B 101 " pdb=" P G B 102 " ideal model delta sigma weight residual 119.70 125.63 -5.93 1.20e+00 6.94e-01 2.44e+01 angle pdb=" N3 DT D 6 " pdb=" C4 DT D 6 " pdb=" O4 DT D 6 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT D 1 " pdb=" C4 DT D 1 " pdb=" O4 DT D 1 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT C 10 " pdb=" C4 DT C 10 " pdb=" O4 DT C 10 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT C 6 " pdb=" C4 DT C 6 " pdb=" O4 DT C 6 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 ... (remaining 17459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6913 35.97 - 71.94: 574 71.94 - 107.92: 47 107.92 - 143.89: 3 143.89 - 179.86: 7 Dihedral angle restraints: 7544 sinusoidal: 4416 harmonic: 3128 Sorted by residual: dihedral pdb=" O4' C B 69 " pdb=" C1' C B 69 " pdb=" N1 C B 69 " pdb=" C2 C B 69 " ideal model delta sinusoidal sigma weight residual 200.00 45.24 154.76 1 1.50e+01 4.44e-03 8.13e+01 dihedral pdb=" O4' U B 85 " pdb=" C1' U B 85 " pdb=" N1 U B 85 " pdb=" C2 U B 85 " ideal model delta sinusoidal sigma weight residual 232.00 52.14 179.86 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 93 " pdb=" C1' U B 93 " pdb=" N1 U B 93 " pdb=" C2 U B 93 " ideal model delta sinusoidal sigma weight residual 232.00 55.34 176.66 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 7541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1602 0.049 - 0.098: 277 0.098 - 0.147: 138 0.147 - 0.197: 4 0.197 - 0.246: 1 Chirality restraints: 2022 Sorted by residual: chirality pdb=" C3' U B 101 " pdb=" C4' U B 101 " pdb=" O3' U B 101 " pdb=" C2' U B 101 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB ILE A 298 " pdb=" CA ILE A 298 " pdb=" CG1 ILE A 298 " pdb=" CG2 ILE A 298 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" C3' DA C -6 " pdb=" C4' DA C -6 " pdb=" O3' DA C -6 " pdb=" C2' DA C -6 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 2019 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A1287 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A1288 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A1288 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1288 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 977 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A 978 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 978 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 978 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 766 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO A 767 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 767 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 767 " 0.025 5.00e-02 4.00e+02 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1119 2.74 - 3.28: 11598 3.28 - 3.82: 21688 3.82 - 4.36: 27519 4.36 - 4.90: 41182 Nonbonded interactions: 103106 Sorted by model distance: nonbonded pdb=" OH TYR A 394 " pdb=" O PHE A 422 " model vdw 2.198 3.040 nonbonded pdb=" O THR A1076 " pdb=" OG1 THR A1080 " model vdw 2.203 3.040 nonbonded pdb=" O SER A 520 " pdb=" OH TYR A 658 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR A 535 " pdb=" O ASN A 694 " model vdw 2.206 3.040 nonbonded pdb=" O2' U B 62 " pdb=" OE1 GLN A 426 " model vdw 2.231 3.040 ... (remaining 103101 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.190 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 0.033 12431 Z= 0.260 Angle : 0.660 9.763 17464 Z= 0.476 Chirality : 0.047 0.246 2022 Planarity : 0.004 0.064 1674 Dihedral : 22.601 179.862 5526 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.40 % Allowed : 32.60 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.25), residues: 1047 helix: -0.30 (0.24), residues: 455 sheet: -0.50 (0.85), residues: 50 loop : -1.09 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1003 TYR 0.011 0.001 TYR A 322 PHE 0.030 0.001 PHE A 553 TRP 0.005 0.001 TRP A 496 HIS 0.008 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.26 (12431) covalent geometry : angle 0.66006 / 0.48 (17464) hydrogen bonds : bond 0.26673 / 28.37 ( 416) hydrogen bonds : angle 8.43096 / 11.32 ( 1113) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.382 Fit side-chains REVERT: A 12 ASN cc_start: 0.5425 (m-40) cc_final: 0.4954 (m110) REVERT: A 32 ASP cc_start: 0.7119 (p0) cc_final: 0.6763 (p0) REVERT: A 34 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7444 (mp0) REVERT: A 78 ARG cc_start: 0.7696 (ttp80) cc_final: 0.7350 (ttp80) REVERT: A 85 GLN cc_start: 0.7023 (tt0) cc_final: 0.6674 (tt0) REVERT: A 105 VAL cc_start: 0.8124 (t) cc_final: 0.7750 (m) REVERT: A 147 GLU cc_start: 0.6727 (pt0) cc_final: 0.6507 (mm-30) REVERT: A 192 MET cc_start: 0.3834 (mpt) cc_final: 0.3438 (mpt) REVERT: A 310 LEU cc_start: 0.7700 (mp) cc_final: 0.7214 (mm) REVERT: A 313 TYR cc_start: 0.5715 (m-80) cc_final: 0.5497 (m-80) REVERT: A 315 LYS cc_start: 0.7909 (tptp) cc_final: 0.7576 (tptt) REVERT: A 362 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7295 (ttmm) REVERT: A 365 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7129 (tptm) REVERT: A 453 HIS cc_start: 0.7313 (m-70) cc_final: 0.6845 (m90) REVERT: A 514 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6764 (mm-30) REVERT: A 545 LYS cc_start: 0.5451 (tttt) cc_final: 0.5216 (mtpp) REVERT: A 647 MET cc_start: 0.4179 (tpt) cc_final: 0.2749 (tpt) REVERT: A 741 GLN cc_start: 0.5861 (OUTLIER) cc_final: 0.5585 (mt0) REVERT: A 762 MET cc_start: 0.7404 (mtp) cc_final: 0.7134 (mtp) REVERT: A 789 SER cc_start: 0.8165 (m) cc_final: 0.7841 (p) REVERT: A 795 MET cc_start: 0.7706 (ptm) cc_final: 0.7228 (ptp) REVERT: A 797 MET cc_start: 0.5945 (mpt) cc_final: 0.5723 (mmt) REVERT: A 986 LYS cc_start: 0.6521 (mtpp) cc_final: 0.6160 (mtpt) REVERT: A 1003 ARG cc_start: 0.7306 (ttm110) cc_final: 0.6297 (ttt90) REVERT: A 1075 LYS cc_start: 0.7615 (mmtp) cc_final: 0.7040 (mtmp) REVERT: A 1151 LYS cc_start: 0.7919 (mmtp) cc_final: 0.7705 (mmtp) REVERT: A 1153 LYS cc_start: 0.7688 (mtmt) cc_final: 0.7462 (mttp) REVERT: A 1275 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7262 (ttp80) REVERT: A 1299 LYS cc_start: 0.7639 (mtmt) cc_final: 0.7306 (mtpm) outliers start: 23 outliers final: 15 residues processed: 114 average time/residue: 0.6671 time to fit residues: 81.7340 Evaluate side-chains 88 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1224 VAL Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1357 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.0060 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 40.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 GLN A 532 ASN A1137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.168886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136466 restraints weight = 14348.250| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.80 r_work: 0.3262 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12431 Z= 0.146 Angle : 0.602 7.859 17464 Z= 0.336 Chirality : 0.042 0.461 2022 Planarity : 0.005 0.059 1674 Dihedral : 22.196 179.849 3341 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.85 % Allowed : 27.59 % Favored : 66.56 % 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: -0.86 (0.25), residues: 1047 helix: 0.04 (0.23), residues: 475 sheet: -0.06 (1.00), residues: 40 loop : -1.15 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1003 TYR 0.018 0.001 TYR A 550 PHE 0.026 0.002 PHE A 63 TRP 0.005 0.001 TRP A 496 HIS 0.008 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (12431) covalent geometry : angle 0.60233 / 0.34 (17464) hydrogen bonds : bond 0.07396 / 7.78 ( 416) hydrogen bonds : angle 5.30441 / 6.80 ( 1113) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 78 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6125 (m-40) cc_final: 0.5800 (m110) REVERT: A 78 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7766 (ttp80) REVERT: A 85 GLN cc_start: 0.7606 (tt0) cc_final: 0.7315 (tp-100) REVERT: A 105 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8366 (m) REVERT: A 192 MET cc_start: 0.4336 (mpt) cc_final: 0.3805 (mpt) REVERT: A 453 HIS cc_start: 0.7669 (m-70) cc_final: 0.7402 (m90) REVERT: A 465 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7587 (mtm) REVERT: A 505 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7392 (mp-120) REVERT: A 647 MET cc_start: 0.4728 (OUTLIER) cc_final: 0.2924 (tmt) REVERT: A 675 GLU cc_start: 0.6045 (OUTLIER) cc_final: 0.5539 (pp20) REVERT: A 689 PHE cc_start: 0.5911 (OUTLIER) cc_final: 0.5165 (p90) REVERT: A 741 GLN cc_start: 0.6388 (OUTLIER) cc_final: 0.5863 (mt0) REVERT: A 795 MET cc_start: 0.7846 (ptm) cc_final: 0.7606 (ptp) REVERT: A 797 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.6167 (mmt) REVERT: A 972 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6763 (pt) REVERT: A 986 LYS cc_start: 0.6899 (mtpp) cc_final: 0.6640 (mtpt) REVERT: A 996 ARG cc_start: 0.6990 (ptm-80) cc_final: 0.6720 (ptm-80) REVERT: A 1003 ARG cc_start: 0.7356 (ttm110) cc_final: 0.7073 (ttt90) REVERT: A 1071 ASP cc_start: 0.4737 (OUTLIER) cc_final: 0.4473 (m-30) REVERT: A 1151 LYS cc_start: 0.7749 (mmtp) cc_final: 0.7448 (mmtp) REVERT: A 1166 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7980 (ttpt) REVERT: A 1237 ARG cc_start: 0.6456 (OUTLIER) cc_final: 0.5775 (ttt90) REVERT: A 1275 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7534 (ttp80) REVERT: A 1372 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6204 (tp) outliers start: 56 outliers final: 11 residues processed: 118 average time/residue: 0.6379 time to fit residues: 80.8897 Evaluate side-chains 94 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1166 LYS Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1372 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN A 73 GLN A 974 ASN A1164 HIS A1177 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.166396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135308 restraints weight = 14199.303| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.67 r_work: 0.3195 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12431 Z= 0.216 Angle : 0.660 11.664 17464 Z= 0.357 Chirality : 0.045 0.474 2022 Planarity : 0.005 0.056 1674 Dihedral : 22.256 179.565 3323 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.43 % Allowed : 26.54 % Favored : 68.03 % 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: -0.95 (0.25), residues: 1047 helix: -0.03 (0.23), residues: 477 sheet: -0.58 (1.00), residues: 39 loop : -1.16 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 994 TYR 0.018 0.002 TYR A 550 PHE 0.016 0.002 PHE A 393 TRP 0.010 0.002 TRP A 307 HIS 0.008 0.002 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.22 (12431) covalent geometry : angle 0.65957 / 0.36 (17464) hydrogen bonds : bond 0.06910 / 7.31 ( 416) hydrogen bonds : angle 5.11764 / 6.59 ( 1113) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 77 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6204 (m-40) cc_final: 0.5695 (m110) REVERT: A 32 ASP cc_start: 0.7342 (p0) cc_final: 0.7114 (p0) REVERT: A 78 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7806 (ttp80) REVERT: A 85 GLN cc_start: 0.7787 (tt0) cc_final: 0.7454 (tp-100) REVERT: A 105 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8522 (m) REVERT: A 192 MET cc_start: 0.4561 (mpt) cc_final: 0.4045 (mpt) REVERT: A 453 HIS cc_start: 0.7807 (m-70) cc_final: 0.7538 (m90) REVERT: A 465 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7658 (mtm) REVERT: A 647 MET cc_start: 0.4761 (OUTLIER) cc_final: 0.3021 (tmt) REVERT: A 653 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6690 (tp30) REVERT: A 675 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5435 (pp20) REVERT: A 689 PHE cc_start: 0.6128 (OUTLIER) cc_final: 0.5203 (p90) REVERT: A 741 GLN cc_start: 0.6518 (OUTLIER) cc_final: 0.5918 (mt0) REVERT: A 797 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.6126 (mmt) REVERT: A 973 ILE cc_start: 0.5784 (OUTLIER) cc_final: 0.5482 (tt) REVERT: A 986 LYS cc_start: 0.7080 (mtpp) cc_final: 0.6854 (mtpt) REVERT: A 996 ARG cc_start: 0.7124 (ptm-80) cc_final: 0.6650 (ptm-80) REVERT: A 1003 ARG cc_start: 0.7474 (ttm110) cc_final: 0.7143 (ttt90) REVERT: A 1151 LYS cc_start: 0.7808 (mmtp) cc_final: 0.7577 (mmtp) REVERT: A 1166 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8030 (ttpt) REVERT: A 1185 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8209 (mtt) REVERT: A 1237 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.5941 (ttt90) REVERT: A 1275 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7742 (ttp80) REVERT: A 1372 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6313 (tp) outliers start: 52 outliers final: 17 residues processed: 114 average time/residue: 0.5632 time to fit residues: 69.1397 Evaluate side-chains 101 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1166 LYS Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1298 VAL Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1372 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 50 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 1 optimal weight: 40.0000 chunk 70 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 117 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.169876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.141025 restraints weight = 14225.448| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.52 r_work: 0.3277 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12431 Z= 0.126 Angle : 0.567 12.263 17464 Z= 0.314 Chirality : 0.040 0.479 2022 Planarity : 0.004 0.056 1674 Dihedral : 22.248 179.366 3321 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.43 % Allowed : 26.44 % Favored : 68.13 % 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: -0.63 (0.25), residues: 1047 helix: 0.37 (0.24), residues: 480 sheet: -0.56 (0.89), residues: 44 loop : -1.14 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.013 0.001 TYR A 550 PHE 0.014 0.001 PHE A 63 TRP 0.010 0.001 TRP A 307 HIS 0.006 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (12431) covalent geometry : angle 0.56654 / 0.31 (17464) hydrogen bonds : bond 0.05717 / 6.01 ( 416) hydrogen bonds : angle 4.80618 / 6.14 ( 1113) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 78 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6136 (m-40) cc_final: 0.5623 (m110) REVERT: A 78 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7590 (ttp80) REVERT: A 85 GLN cc_start: 0.7713 (tt0) cc_final: 0.7411 (tp-100) REVERT: A 105 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8414 (m) REVERT: A 192 MET cc_start: 0.4438 (mpt) cc_final: 0.3967 (mpt) REVERT: A 207 VAL cc_start: 0.4831 (OUTLIER) cc_final: 0.4619 (t) REVERT: A 387 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7790 (mtpt) REVERT: A 675 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.5408 (pp20) REVERT: A 741 GLN cc_start: 0.6493 (OUTLIER) cc_final: 0.5926 (mt0) REVERT: A 797 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.6116 (mmt) REVERT: A 986 LYS cc_start: 0.7014 (mtpp) cc_final: 0.6717 (mtpt) REVERT: A 992 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6776 (m-30) REVERT: A 996 ARG cc_start: 0.7049 (ptm-80) cc_final: 0.6843 (ptm-80) REVERT: A 1003 ARG cc_start: 0.7367 (ttm110) cc_final: 0.7126 (ttt90) REVERT: A 1071 ASP cc_start: 0.4635 (OUTLIER) cc_final: 0.4423 (m-30) REVERT: A 1166 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7953 (ttpt) REVERT: A 1237 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.5742 (ttt90) REVERT: A 1275 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7654 (ttp80) REVERT: A 1372 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6234 (tp) outliers start: 52 outliers final: 16 residues processed: 118 average time/residue: 0.5912 time to fit residues: 75.7140 Evaluate side-chains 96 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1166 LYS Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1372 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN A 73 GLN A 159 HIS A 163 GLN A 436 ASN A1263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.162200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.132523 restraints weight = 14343.194| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.54 r_work: 0.3130 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 12431 Z= 0.398 Angle : 0.852 12.851 17464 Z= 0.443 Chirality : 0.055 0.495 2022 Planarity : 0.006 0.060 1674 Dihedral : 22.503 178.963 3321 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 6.27 % Allowed : 24.76 % Favored : 68.97 % 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: -1.29 (0.24), residues: 1047 helix: -0.37 (0.22), residues: 472 sheet: -0.56 (0.82), residues: 47 loop : -1.30 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 770 TYR 0.020 0.003 TYR A 628 PHE 0.021 0.003 PHE A 687 TRP 0.015 0.003 TRP A 307 HIS 0.012 0.003 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00866 / 0.40 (12431) covalent geometry : angle 0.85214 / 0.44 (17464) hydrogen bonds : bond 0.07300 / 7.94 ( 416) hydrogen bonds : angle 5.23137 / 6.75 ( 1113) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 74 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6222 (m-40) cc_final: 0.5720 (m110) REVERT: A 78 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7800 (ttp80) REVERT: A 85 GLN cc_start: 0.7880 (tt0) cc_final: 0.7473 (tp-100) REVERT: A 105 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8656 (m) REVERT: A 192 MET cc_start: 0.4601 (mpt) cc_final: 0.4116 (mpt) REVERT: A 199 ILE cc_start: 0.4233 (OUTLIER) cc_final: 0.3966 (tt) REVERT: A 647 MET cc_start: 0.5155 (tpt) cc_final: 0.3529 (tpt) REVERT: A 653 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6862 (tp30) REVERT: A 671 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.6458 (t70) REVERT: A 675 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.5299 (pp20) REVERT: A 689 PHE cc_start: 0.6256 (OUTLIER) cc_final: 0.5246 (p90) REVERT: A 741 GLN cc_start: 0.6222 (OUTLIER) cc_final: 0.5730 (mt0) REVERT: A 986 LYS cc_start: 0.7077 (mtpp) cc_final: 0.6741 (mtpt) REVERT: A 992 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6751 (m-30) REVERT: A 1003 ARG cc_start: 0.7633 (ttm110) cc_final: 0.7243 (ttt90) REVERT: A 1071 ASP cc_start: 0.4758 (OUTLIER) cc_final: 0.4334 (m-30) REVERT: A 1166 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8055 (ttpt) REVERT: A 1232 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: A 1237 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6104 (ttt180) REVERT: A 1275 ARG cc_start: 0.8291 (ttp80) cc_final: 0.7965 (ttp80) REVERT: A 1290 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7327 (mt) REVERT: A 1372 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.6570 (tp) outliers start: 60 outliers final: 29 residues processed: 123 average time/residue: 0.5508 time to fit residues: 73.5322 Evaluate side-chains 110 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 67 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 788 TYR Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1166 LYS Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1232 GLU Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1290 LEU Chi-restraints excluded: chain A residue 1298 VAL Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1372 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 97 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 0.0670 chunk 91 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN A 453 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.167505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.138076 restraints weight = 14367.415| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.57 r_work: 0.3256 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12431 Z= 0.135 Angle : 0.599 11.036 17464 Z= 0.330 Chirality : 0.041 0.484 2022 Planarity : 0.004 0.055 1674 Dihedral : 22.438 179.248 3321 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.97 % Allowed : 27.48 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.25), residues: 1047 helix: 0.32 (0.24), residues: 475 sheet: -0.34 (0.84), residues: 44 loop : -1.18 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 60 TYR 0.015 0.001 TYR A1208 PHE 0.019 0.002 PHE A 687 TRP 0.013 0.001 TRP A 307 HIS 0.006 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (12431) covalent geometry : angle 0.59884 / 0.33 (17464) hydrogen bonds : bond 0.05553 / 5.87 ( 416) hydrogen bonds : angle 4.78830 / 6.17 ( 1113) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 68 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6381 (m-40) cc_final: 0.5899 (m110) REVERT: A 32 ASP cc_start: 0.7126 (p0) cc_final: 0.6909 (t0) REVERT: A 85 GLN cc_start: 0.7653 (tt0) cc_final: 0.7379 (tp-100) REVERT: A 105 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8542 (m) REVERT: A 192 MET cc_start: 0.4389 (mpt) cc_final: 0.3937 (mpt) REVERT: A 465 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7514 (mtm) REVERT: A 647 MET cc_start: 0.4844 (tpt) cc_final: 0.3213 (tpt) REVERT: A 675 GLU cc_start: 0.5888 (OUTLIER) cc_final: 0.5375 (pp20) REVERT: A 689 PHE cc_start: 0.6042 (OUTLIER) cc_final: 0.5136 (p90) REVERT: A 741 GLN cc_start: 0.6086 (OUTLIER) cc_final: 0.5639 (mt0) REVERT: A 797 MET cc_start: 0.6577 (OUTLIER) cc_final: 0.6213 (mmt) REVERT: A 986 LYS cc_start: 0.6995 (mtpp) cc_final: 0.6676 (mtpt) REVERT: A 992 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6652 (m-30) REVERT: A 1003 ARG cc_start: 0.7444 (ttm110) cc_final: 0.7151 (ttt90) REVERT: A 1166 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7955 (ttpt) REVERT: A 1237 ARG cc_start: 0.6423 (OUTLIER) cc_final: 0.5747 (ttt90) REVERT: A 1275 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7786 (ttp80) REVERT: A 1372 ILE cc_start: 0.7032 (OUTLIER) cc_final: 0.6218 (tp) outliers start: 38 outliers final: 15 residues processed: 94 average time/residue: 0.6139 time to fit residues: 62.3790 Evaluate side-chains 86 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1166 LYS Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1372 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 80 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.165684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.135215 restraints weight = 14306.681| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.67 r_work: 0.3222 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12431 Z= 0.193 Angle : 0.634 13.583 17464 Z= 0.344 Chirality : 0.043 0.490 2022 Planarity : 0.005 0.055 1674 Dihedral : 22.395 178.991 3320 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.18 % Allowed : 27.38 % Favored : 68.44 % 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: -0.71 (0.25), residues: 1047 helix: 0.29 (0.23), residues: 475 sheet: -0.12 (0.87), residues: 42 loop : -1.19 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 994 TYR 0.015 0.002 TYR A 788 PHE 0.021 0.002 PHE A 687 TRP 0.019 0.002 TRP A 307 HIS 0.006 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (12431) covalent geometry : angle 0.63405 / 0.34 (17464) hydrogen bonds : bond 0.05729 / 6.08 ( 416) hydrogen bonds : angle 4.79547 / 6.17 ( 1113) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 69 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6368 (m-40) cc_final: 0.5855 (m110) REVERT: A 32 ASP cc_start: 0.7199 (p0) cc_final: 0.6979 (t0) REVERT: A 85 GLN cc_start: 0.7681 (tt0) cc_final: 0.7419 (tp-100) REVERT: A 105 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8548 (m) REVERT: A 192 MET cc_start: 0.4328 (mpt) cc_final: 0.3880 (mpt) REVERT: A 465 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7667 (mtm) REVERT: A 553 PHE cc_start: 0.7347 (t80) cc_final: 0.6976 (t80) REVERT: A 625 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5523 (pp) REVERT: A 647 MET cc_start: 0.4993 (tpt) cc_final: 0.3279 (tpt) REVERT: A 653 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6578 (tp30) REVERT: A 675 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.5347 (pp20) REVERT: A 689 PHE cc_start: 0.6186 (OUTLIER) cc_final: 0.5150 (p90) REVERT: A 741 GLN cc_start: 0.6074 (OUTLIER) cc_final: 0.5637 (mt0) REVERT: A 986 LYS cc_start: 0.7041 (mtpp) cc_final: 0.6728 (mtpt) REVERT: A 992 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6657 (m-30) REVERT: A 1003 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7159 (ttt90) REVERT: A 1166 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7985 (ttpt) REVERT: A 1237 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.5845 (ttt90) REVERT: A 1275 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7876 (ttp80) REVERT: A 1290 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7270 (mt) REVERT: A 1372 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6291 (tp) outliers start: 40 outliers final: 18 residues processed: 99 average time/residue: 0.5821 time to fit residues: 62.3360 Evaluate side-chains 95 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1166 LYS Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1290 LEU Chi-restraints excluded: chain A residue 1298 VAL Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1372 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 99 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 96 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 75 optimal weight: 0.1980 chunk 76 optimal weight: 7.9990 chunk 79 optimal weight: 0.3980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN A 163 GLN ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.169977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.139358 restraints weight = 14345.462| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.60 r_work: 0.3303 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12431 Z= 0.114 Angle : 0.566 14.659 17464 Z= 0.311 Chirality : 0.040 0.482 2022 Planarity : 0.004 0.057 1674 Dihedral : 22.287 179.080 3320 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.66 % Allowed : 28.21 % Favored : 68.13 % 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: -0.30 (0.26), residues: 1047 helix: 0.75 (0.24), residues: 474 sheet: -0.19 (0.84), residues: 44 loop : -1.08 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 60 TYR 0.014 0.001 TYR A1208 PHE 0.018 0.001 PHE A 687 TRP 0.021 0.001 TRP A 307 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.11 (12431) covalent geometry : angle 0.56589 / 0.31 (17464) hydrogen bonds : bond 0.05131 / 5.40 ( 416) hydrogen bonds : angle 4.53721 / 5.82 ( 1113) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6309 (m-40) cc_final: 0.5802 (m110) REVERT: A 85 GLN cc_start: 0.7601 (tt0) cc_final: 0.7367 (tp-100) REVERT: A 105 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8365 (m) REVERT: A 192 MET cc_start: 0.4234 (mpt) cc_final: 0.3803 (mpt) REVERT: A 553 PHE cc_start: 0.7324 (t80) cc_final: 0.6967 (t80) REVERT: A 647 MET cc_start: 0.4897 (tpt) cc_final: 0.4432 (tpt) REVERT: A 653 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6515 (tp30) REVERT: A 675 GLU cc_start: 0.5885 (OUTLIER) cc_final: 0.5398 (pp20) REVERT: A 689 PHE cc_start: 0.6015 (OUTLIER) cc_final: 0.5063 (p90) REVERT: A 741 GLN cc_start: 0.6189 (OUTLIER) cc_final: 0.5783 (mt0) REVERT: A 986 LYS cc_start: 0.7083 (mtpp) cc_final: 0.6768 (mtpt) REVERT: A 992 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6674 (m-30) REVERT: A 1003 ARG cc_start: 0.7355 (ttm110) cc_final: 0.7106 (ttt90) REVERT: A 1166 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7911 (ttpt) REVERT: A 1237 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.5730 (ttt90) REVERT: A 1275 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7739 (ttp80) REVERT: A 1372 ILE cc_start: 0.6861 (OUTLIER) cc_final: 0.6178 (tp) outliers start: 35 outliers final: 13 residues processed: 97 average time/residue: 0.5661 time to fit residues: 59.5080 Evaluate side-chains 87 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1166 LYS Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1298 VAL Chi-restraints excluded: chain A residue 1372 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 17 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 0.0770 chunk 119 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.169008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.138391 restraints weight = 14230.488| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.58 r_work: 0.3275 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12431 Z= 0.128 Angle : 0.577 13.514 17464 Z= 0.314 Chirality : 0.040 0.483 2022 Planarity : 0.004 0.056 1674 Dihedral : 22.220 179.280 3319 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.03 % Allowed : 29.26 % Favored : 67.71 % 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: -0.23 (0.26), residues: 1047 helix: 0.78 (0.24), residues: 474 sheet: -0.01 (0.86), residues: 42 loop : -1.02 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 994 TYR 0.013 0.001 TYR A 788 PHE 0.020 0.001 PHE A 687 TRP 0.029 0.002 TRP A 307 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (12431) covalent geometry : angle 0.57666 / 0.31 (17464) hydrogen bonds : bond 0.05071 / 5.34 ( 416) hydrogen bonds : angle 4.51256 / 5.76 ( 1113) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6211 (m-40) cc_final: 0.5689 (m110) REVERT: A 85 GLN cc_start: 0.7599 (tt0) cc_final: 0.7354 (tp-100) REVERT: A 105 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8375 (m) REVERT: A 192 MET cc_start: 0.4198 (mpt) cc_final: 0.3776 (mpt) REVERT: A 465 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7515 (mtm) REVERT: A 553 PHE cc_start: 0.7283 (t80) cc_final: 0.6922 (t80) REVERT: A 647 MET cc_start: 0.4939 (tpt) cc_final: 0.4456 (tpt) REVERT: A 653 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6513 (tp30) REVERT: A 675 GLU cc_start: 0.5875 (OUTLIER) cc_final: 0.5382 (pp20) REVERT: A 689 PHE cc_start: 0.5965 (OUTLIER) cc_final: 0.4873 (p90) REVERT: A 741 GLN cc_start: 0.6101 (OUTLIER) cc_final: 0.5727 (mt0) REVERT: A 973 ILE cc_start: 0.5513 (OUTLIER) cc_final: 0.5158 (tp) REVERT: A 986 LYS cc_start: 0.7120 (mtpp) cc_final: 0.6771 (mtpt) REVERT: A 1003 ARG cc_start: 0.7383 (ttm110) cc_final: 0.7075 (ttt90) REVERT: A 1166 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7948 (ttpt) REVERT: A 1237 ARG cc_start: 0.6380 (OUTLIER) cc_final: 0.5676 (ttt90) REVERT: A 1275 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7768 (ttp80) REVERT: A 1372 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6220 (tp) outliers start: 29 outliers final: 14 residues processed: 86 average time/residue: 0.5862 time to fit residues: 54.2990 Evaluate side-chains 90 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1166 LYS Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1298 VAL Chi-restraints excluded: chain A residue 1372 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 118 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 66 optimal weight: 0.3980 chunk 96 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.167183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.136820 restraints weight = 14341.328| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.56 r_work: 0.3235 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12431 Z= 0.170 Angle : 0.611 13.021 17464 Z= 0.330 Chirality : 0.042 0.485 2022 Planarity : 0.004 0.055 1674 Dihedral : 22.257 179.433 3319 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.13 % Allowed : 29.15 % Favored : 67.71 % 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: -0.39 (0.25), residues: 1047 helix: 0.60 (0.24), residues: 475 sheet: -0.09 (0.85), residues: 42 loop : -1.06 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1294 TYR 0.017 0.002 TYR A 788 PHE 0.022 0.002 PHE A 687 TRP 0.029 0.002 TRP A 307 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (12431) covalent geometry : angle 0.61122 / 0.33 (17464) hydrogen bonds : bond 0.05373 / 5.71 ( 416) hydrogen bonds : angle 4.60168 / 5.89 ( 1113) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6244 (m-40) cc_final: 0.5728 (m110) REVERT: A 85 GLN cc_start: 0.7718 (tt0) cc_final: 0.7444 (tp-100) REVERT: A 105 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8481 (m) REVERT: A 192 MET cc_start: 0.4315 (mpt) cc_final: 0.3873 (mpt) REVERT: A 465 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7616 (mtm) REVERT: A 553 PHE cc_start: 0.7391 (t80) cc_final: 0.7011 (t80) REVERT: A 647 MET cc_start: 0.5161 (tpt) cc_final: 0.4694 (tpt) REVERT: A 653 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6700 (tp30) REVERT: A 675 GLU cc_start: 0.5827 (OUTLIER) cc_final: 0.5371 (pp20) REVERT: A 689 PHE cc_start: 0.6204 (OUTLIER) cc_final: 0.5033 (p90) REVERT: A 741 GLN cc_start: 0.6327 (OUTLIER) cc_final: 0.5893 (mt0) REVERT: A 973 ILE cc_start: 0.5599 (OUTLIER) cc_final: 0.5221 (tp) REVERT: A 986 LYS cc_start: 0.7038 (mtpp) cc_final: 0.6677 (mtpt) REVERT: A 992 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6707 (m-30) REVERT: A 1003 ARG cc_start: 0.7428 (ttm110) cc_final: 0.7149 (ttt90) REVERT: A 1166 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8002 (ttpt) REVERT: A 1237 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.5800 (ttt90) REVERT: A 1275 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7864 (ttp80) REVERT: A 1372 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6374 (tp) outliers start: 30 outliers final: 15 residues processed: 86 average time/residue: 0.5745 time to fit residues: 53.4307 Evaluate side-chains 91 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1166 LYS Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1298 VAL Chi-restraints excluded: chain A residue 1372 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 104 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.169170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137063 restraints weight = 14377.675| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.74 r_work: 0.3268 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12431 Z= 0.126 Angle : 0.580 13.079 17464 Z= 0.317 Chirality : 0.040 0.480 2022 Planarity : 0.004 0.056 1674 Dihedral : 22.237 179.346 3319 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.61 % Allowed : 29.78 % Favored : 67.61 % 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: -0.27 (0.26), residues: 1047 helix: 0.75 (0.24), residues: 476 sheet: -0.03 (0.86), residues: 42 loop : -1.04 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 749 TYR 0.014 0.001 TYR A 788 PHE 0.020 0.001 PHE A 687 TRP 0.035 0.002 TRP A 307 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (12431) covalent geometry : angle 0.58026 / 0.32 (17464) hydrogen bonds : bond 0.05110 / 5.41 ( 416) hydrogen bonds : angle 4.47166 / 5.69 ( 1113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2996.74 seconds wall clock time: 52 minutes 0.61 seconds (3120.61 seconds total)