Starting phenix.real_space_refine on Fri Jul 3 05:08:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jwn_61854/07_2026/9jwn_61854.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jwn_61854/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jwn_61854/07_2026/9jwn_61854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jwn_61854/07_2026/9jwn_61854.map" model { file = "/net/cci-nas-00/data/ceres_data/9jwn_61854/07_2026/9jwn_61854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jwn_61854/07_2026/9jwn_61854.cif" } 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-dev-6108/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: 2.38, per 1000 atoms: 0.20 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: 0.95 Conformation dependent library (CDL) restraints added in 392.8 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: 1.33 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: 3.00 Time building geometry restraints manager: 1.29 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: 17128 1.95 - 3.91: 302 3.91 - 5.86: 29 5.86 - 7.81: 3 7.81 - 9.76: 2 Bond angle restraints: 17464 Sorted by residual: 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 angle pdb=" N3 DT D 5 " pdb=" C4 DT D 5 " pdb=" O4 DT D 5 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+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: 1715 0.049 - 0.098: 260 0.098 - 0.147: 42 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:7.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.350 ------------------------------------------------------------------------------- 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 : 0.003 0.033 12431 Z= 0.252 Angle : 0.578 9.763 17464 Z= 0.407 Chirality : 0.036 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 0.00348 / 0.25 (12431) covalent geometry : angle 0.57819 / 0.41 (17464) hydrogen bonds : bond 0.26673 / 27.70 ( 416) hydrogen bonds : angle 8.43096 / 11.04 ( 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 : 0.232 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: 0.6236 time to fit residues: 76.4418 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 : 0.403 ------------------------------------------------------------------------------- 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: 30.0000 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 = 0.168910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136908 restraints weight = 14328.817| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.82 r_work: 0.3265 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12431 Z= 0.150 Angle : 0.599 7.880 17464 Z= 0.337 Chirality : 0.040 0.262 2022 Planarity : 0.005 0.059 1674 Dihedral : 22.295 179.858 3341 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.96 % Allowed : 27.38 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.25), residues: 1047 helix: 0.03 (0.23), residues: 475 sheet: -0.07 (0.99), residues: 40 loop : -1.15 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1003 TYR 0.019 0.001 TYR A 550 PHE 0.025 0.002 PHE A 63 TRP 0.007 0.001 TRP A 307 HIS 0.008 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (12431) covalent geometry : angle 0.59926 / 0.34 (17464) hydrogen bonds : bond 0.07307 / 7.56 ( 416) hydrogen bonds : angle 5.31032 / 6.68 ( 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 137 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 80 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6134 (m-40) cc_final: 0.5814 (m110) REVERT: A 78 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7743 (ttp80) REVERT: A 85 GLN cc_start: 0.7631 (tt0) cc_final: 0.7313 (tp-100) REVERT: A 105 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8370 (m) REVERT: A 192 MET cc_start: 0.4441 (mpt) cc_final: 0.3928 (mpt) REVERT: A 453 HIS cc_start: 0.7710 (m-70) cc_final: 0.7441 (m90) REVERT: A 465 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7588 (mtm) REVERT: A 505 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7407 (mp-120) REVERT: A 647 MET cc_start: 0.4809 (OUTLIER) cc_final: 0.3046 (tmt) REVERT: A 675 GLU cc_start: 0.6025 (OUTLIER) cc_final: 0.5537 (pp20) REVERT: A 689 PHE cc_start: 0.5980 (OUTLIER) cc_final: 0.5239 (p90) REVERT: A 741 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.5997 (mt0) REVERT: A 795 MET cc_start: 0.7845 (ptm) cc_final: 0.7605 (ptp) REVERT: A 797 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.6162 (mmt) REVERT: A 972 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6726 (pt) REVERT: A 986 LYS cc_start: 0.6879 (mtpp) cc_final: 0.6632 (mtpt) REVERT: A 996 ARG cc_start: 0.6954 (ptm-80) cc_final: 0.6567 (ptm-80) REVERT: A 1003 ARG cc_start: 0.7369 (ttm110) cc_final: 0.7085 (ttt90) REVERT: A 1071 ASP cc_start: 0.4697 (OUTLIER) cc_final: 0.4445 (m-30) REVERT: A 1075 LYS cc_start: 0.7396 (mmtp) cc_final: 0.7025 (mtmp) REVERT: A 1151 LYS cc_start: 0.7761 (mmtp) cc_final: 0.7463 (mmtp) REVERT: A 1166 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7963 (ttpt) REVERT: A 1237 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.5786 (ttt90) REVERT: A 1275 ARG cc_start: 0.7856 (ttp80) cc_final: 0.7535 (ttp80) REVERT: A 1372 ILE cc_start: 0.6905 (OUTLIER) cc_final: 0.6214 (tp) outliers start: 57 outliers final: 11 residues processed: 121 average time/residue: 0.6033 time to fit residues: 78.7725 Evaluate side-chains 93 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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: 0.0870 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 84 optimal weight: 0.0470 chunk 38 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 12 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN A1177 HIS ** A1305 GLN ** 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 = 0.4065 r_free = 0.4065 target = 0.169491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.135407 restraints weight = 14396.584| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.99 r_work: 0.3257 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12431 Z= 0.122 Angle : 0.551 12.038 17464 Z= 0.308 Chirality : 0.038 0.279 2022 Planarity : 0.004 0.056 1674 Dihedral : 22.242 179.504 3323 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.81 % Allowed : 27.06 % 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 (0.26), residues: 1047 helix: 0.36 (0.24), residues: 480 sheet: -0.78 (0.81), residues: 50 loop : -1.09 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 994 TYR 0.014 0.001 TYR A 356 PHE 0.016 0.001 PHE A 63 TRP 0.009 0.001 TRP A 307 HIS 0.007 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (12431) covalent geometry : angle 0.55104 / 0.31 (17464) hydrogen bonds : bond 0.06234 / 6.38 ( 416) hydrogen bonds : angle 4.92111 / 6.17 ( 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 124 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 78 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6161 (m-40) cc_final: 0.5657 (m110) REVERT: A 32 ASP cc_start: 0.7286 (p0) cc_final: 0.7068 (p0) REVERT: A 78 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7595 (ttp80) REVERT: A 85 GLN cc_start: 0.7541 (tt0) cc_final: 0.7270 (tp-100) REVERT: A 105 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8326 (m) REVERT: A 192 MET cc_start: 0.4207 (mpt) cc_final: 0.3722 (mpt) REVERT: A 675 GLU cc_start: 0.6009 (OUTLIER) cc_final: 0.5521 (pp20) REVERT: A 741 GLN cc_start: 0.6393 (OUTLIER) cc_final: 0.5810 (mt0) REVERT: A 797 MET cc_start: 0.6555 (OUTLIER) cc_final: 0.6137 (mmt) REVERT: A 973 ILE cc_start: 0.5658 (OUTLIER) cc_final: 0.5456 (tt) REVERT: A 986 LYS cc_start: 0.6886 (mtpp) cc_final: 0.6625 (mtpt) REVERT: A 996 ARG cc_start: 0.7031 (ptm-80) cc_final: 0.6742 (ptm-80) REVERT: A 1003 ARG cc_start: 0.7332 (ttm110) cc_final: 0.7013 (ttt90) REVERT: A 1071 ASP cc_start: 0.4727 (OUTLIER) cc_final: 0.4437 (m-30) REVERT: A 1151 LYS cc_start: 0.7692 (mmtp) cc_final: 0.7448 (mmtp) REVERT: A 1166 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.8005 (ttpt) REVERT: A 1237 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.5754 (ttt90) REVERT: A 1275 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7510 (ttp80) REVERT: A 1372 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6201 (tp) outliers start: 46 outliers final: 12 residues processed: 115 average time/residue: 0.6001 time to fit residues: 74.5632 Evaluate side-chains 89 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 283 LEU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 301 ILE 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 675 GLU Chi-restraints excluded: chain A residue 741 GLN 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 1071 ASP Chi-restraints excluded: chain A residue 1166 LYS 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 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: 0.7980 chunk 29 optimal weight: 0.1980 chunk 92 optimal weight: 5.9990 chunk 1 optimal weight: 30.0000 chunk 70 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.169435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.139318 restraints weight = 14383.493| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.65 r_work: 0.3271 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12431 Z= 0.124 Angle : 0.546 12.255 17464 Z= 0.306 Chirality : 0.039 0.290 2022 Planarity : 0.004 0.055 1674 Dihedral : 22.207 179.645 3321 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.39 % Allowed : 27.48 % 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: -0.45 (0.26), residues: 1047 helix: 0.59 (0.24), residues: 480 sheet: -0.94 (0.77), residues: 54 loop : -1.06 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 361 TYR 0.013 0.001 TYR A 356 PHE 0.018 0.001 PHE A 687 TRP 0.009 0.001 TRP A 307 HIS 0.006 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (12431) covalent geometry : angle 0.54613 / 0.31 (17464) hydrogen bonds : bond 0.05469 / 5.63 ( 416) hydrogen bonds : angle 4.67582 / 5.86 ( 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 115 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 73 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6229 (m-40) cc_final: 0.5639 (m110) REVERT: A 32 ASP cc_start: 0.7203 (p0) cc_final: 0.6977 (p0) REVERT: A 78 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7659 (ttp80) REVERT: A 85 GLN cc_start: 0.7502 (tt0) cc_final: 0.7297 (tp-100) REVERT: A 105 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8312 (m) REVERT: A 192 MET cc_start: 0.4345 (mpt) cc_final: 0.3846 (mpt) REVERT: A 647 MET cc_start: 0.5108 (tpt) cc_final: 0.3830 (tpt) REVERT: A 675 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.5514 (pp20) REVERT: A 689 PHE cc_start: 0.6018 (OUTLIER) cc_final: 0.5271 (p90) REVERT: A 741 GLN cc_start: 0.6373 (OUTLIER) cc_final: 0.5809 (mt0) REVERT: A 797 MET cc_start: 0.6541 (OUTLIER) cc_final: 0.6074 (mmt) REVERT: A 986 LYS cc_start: 0.6946 (mtpp) cc_final: 0.6670 (mtpt) REVERT: A 996 ARG cc_start: 0.7047 (ptm-80) cc_final: 0.6809 (ptm-80) REVERT: A 1003 ARG cc_start: 0.7296 (ttm110) cc_final: 0.6981 (ttt90) REVERT: A 1151 LYS cc_start: 0.7709 (mmtp) cc_final: 0.7460 (mmtp) REVERT: A 1166 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7952 (ttpt) REVERT: A 1237 ARG cc_start: 0.6369 (OUTLIER) cc_final: 0.5695 (ttt90) REVERT: A 1275 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7524 (ttp80) REVERT: A 1372 ILE cc_start: 0.6866 (OUTLIER) cc_final: 0.6193 (tp) outliers start: 42 outliers final: 17 residues processed: 108 average time/residue: 0.6072 time to fit residues: 70.9031 Evaluate side-chains 91 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 689 PHE 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 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 1224 VAL 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 1343 LEU 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: 0.8980 chunk 47 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 68 optimal weight: 0.0980 chunk 66 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN A 453 HIS ** A1305 GLN ** 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 = 0.169870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.137652 restraints weight = 14403.630| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.68 r_work: 0.3289 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12431 Z= 0.128 Angle : 0.552 13.036 17464 Z= 0.306 Chirality : 0.038 0.297 2022 Planarity : 0.004 0.054 1674 Dihedral : 22.212 179.705 3320 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.87 % Allowed : 27.80 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.26), residues: 1047 helix: 0.72 (0.24), residues: 479 sheet: -0.94 (0.75), residues: 54 loop : -1.05 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 994 TYR 0.013 0.001 TYR A 351 PHE 0.015 0.001 PHE A 687 TRP 0.012 0.001 TRP A 307 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 (12431) covalent geometry : angle 0.55158 / 0.31 (17464) hydrogen bonds : bond 0.05296 / 5.47 ( 416) hydrogen bonds : angle 4.56542 / 5.77 ( 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 106 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 69 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6248 (m-40) cc_final: 0.5687 (m110) REVERT: A 32 ASP cc_start: 0.7205 (p0) cc_final: 0.6992 (p0) REVERT: A 78 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7641 (ttp80) REVERT: A 85 GLN cc_start: 0.7556 (tt0) cc_final: 0.7312 (tp-100) REVERT: A 105 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8332 (m) REVERT: A 192 MET cc_start: 0.4290 (mpt) cc_final: 0.3824 (mpt) REVERT: A 647 MET cc_start: 0.5024 (tpt) cc_final: 0.4695 (tpt) REVERT: A 675 GLU cc_start: 0.5845 (OUTLIER) cc_final: 0.5440 (pp20) REVERT: A 689 PHE cc_start: 0.6094 (OUTLIER) cc_final: 0.5364 (p90) REVERT: A 741 GLN cc_start: 0.6453 (OUTLIER) cc_final: 0.5905 (mt0) REVERT: A 795 MET cc_start: 0.7617 (mtm) cc_final: 0.7260 (ptp) REVERT: A 797 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6048 (mmt) REVERT: A 986 LYS cc_start: 0.6982 (mtpp) cc_final: 0.6709 (mtpt) REVERT: A 992 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6689 (m-30) REVERT: A 996 ARG cc_start: 0.7085 (ptm-80) cc_final: 0.6723 (ptm-80) REVERT: A 1003 ARG cc_start: 0.7298 (ttm110) cc_final: 0.6996 (ttt90) REVERT: A 1151 LYS cc_start: 0.7732 (mmtp) cc_final: 0.7493 (mmtp) REVERT: A 1166 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7953 (ttpt) REVERT: A 1237 ARG cc_start: 0.6389 (OUTLIER) cc_final: 0.5682 (ttt90) REVERT: A 1260 ARG cc_start: 0.7728 (tpp-160) cc_final: 0.7450 (mmt90) REVERT: A 1275 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7540 (ttp80) REVERT: A 1372 ILE cc_start: 0.6901 (OUTLIER) cc_final: 0.6253 (tp) outliers start: 37 outliers final: 15 residues processed: 100 average time/residue: 0.6712 time to fit residues: 72.3751 Evaluate side-chains 91 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 287 GLU Chi-restraints excluded: chain A residue 301 ILE 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 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 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 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 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: 8.9990 chunk 84 optimal weight: 0.8980 chunk 94 optimal weight: 0.0050 chunk 82 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 974 ASN A1164 HIS ** A1305 GLN ** 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 = 0.4058 r_free = 0.4058 target = 0.168347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.137743 restraints weight = 14344.953| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.64 r_work: 0.3241 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2104 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= 0.157 Angle : 0.576 13.665 17464 Z= 0.318 Chirality : 0.040 0.314 2022 Planarity : 0.004 0.054 1674 Dihedral : 22.249 179.614 3319 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.87 % Allowed : 27.48 % Favored : 68.65 % 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: -0.37 (0.26), residues: 1047 helix: 0.67 (0.24), residues: 480 sheet: -0.71 (0.85), residues: 44 loop : -1.06 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 994 TYR 0.011 0.002 TYR A 334 PHE 0.019 0.002 PHE A 687 TRP 0.015 0.001 TRP A 307 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (12431) covalent geometry : angle 0.57579 / 0.32 (17464) hydrogen bonds : bond 0.05347 / 5.57 ( 416) hydrogen bonds : angle 4.57720 / 5.77 ( 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 109 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6311 (m-40) cc_final: 0.5723 (m110) REVERT: A 78 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7684 (ttp80) REVERT: A 85 GLN cc_start: 0.7685 (tt0) cc_final: 0.7408 (tp-100) REVERT: A 105 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8461 (m) REVERT: A 192 MET cc_start: 0.4361 (mpt) cc_final: 0.3902 (mpt) REVERT: A 310 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7803 (mm) REVERT: A 465 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7506 (mtm) REVERT: A 647 MET cc_start: 0.5098 (tpt) cc_final: 0.4836 (tpt) REVERT: A 653 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6577 (tp30) REVERT: A 675 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.5405 (pp20) REVERT: A 689 PHE cc_start: 0.6103 (OUTLIER) cc_final: 0.5170 (p90) REVERT: A 741 GLN cc_start: 0.6512 (OUTLIER) cc_final: 0.6018 (mt0) REVERT: A 797 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.6074 (mmt) REVERT: A 986 LYS cc_start: 0.6996 (mtpp) cc_final: 0.6755 (mtpt) REVERT: A 996 ARG cc_start: 0.7182 (ptm-80) cc_final: 0.6790 (ptm-80) REVERT: A 1003 ARG cc_start: 0.7454 (ttm110) cc_final: 0.7098 (ttt90) REVERT: A 1151 LYS cc_start: 0.7829 (mmtp) cc_final: 0.7608 (mmtp) REVERT: A 1166 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.8017 (ttpt) REVERT: A 1185 MET cc_start: 0.8693 (mtt) cc_final: 0.8489 (mtt) REVERT: A 1237 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.5700 (ttt90) REVERT: A 1260 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7484 (mmt90) REVERT: A 1275 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7601 (ttp80) REVERT: A 1372 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6350 (tp) outliers start: 37 outliers final: 17 residues processed: 96 average time/residue: 0.6906 time to fit residues: 71.3238 Evaluate side-chains 95 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 462 GLU 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 753 SER Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 972 LEU 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 1260 ARG Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1298 VAL Chi-restraints excluded: chain A residue 1343 LEU 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: 0.9990 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.169124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.137254 restraints weight = 14316.940| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.67 r_work: 0.3269 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12431 Z= 0.136 Angle : 0.556 14.377 17464 Z= 0.308 Chirality : 0.039 0.312 2022 Planarity : 0.004 0.054 1674 Dihedral : 22.261 179.175 3319 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.97 % Allowed : 27.59 % 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: -0.27 (0.26), residues: 1047 helix: 0.76 (0.24), residues: 481 sheet: -0.30 (0.87), residues: 42 loop : -1.06 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 994 TYR 0.013 0.001 TYR A 550 PHE 0.019 0.001 PHE A 687 TRP 0.021 0.001 TRP A 307 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (12431) covalent geometry : angle 0.55613 / 0.31 (17464) hydrogen bonds : bond 0.05149 / 5.35 ( 416) hydrogen bonds : angle 4.48132 / 5.65 ( 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 110 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 72 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6318 (m-40) cc_final: 0.5804 (m110) REVERT: A 32 ASP cc_start: 0.7248 (p0) cc_final: 0.6969 (t0) REVERT: A 78 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7707 (ttp80) REVERT: A 85 GLN cc_start: 0.7642 (tt0) cc_final: 0.7433 (tp-100) REVERT: A 105 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8427 (m) REVERT: A 192 MET cc_start: 0.4347 (mpt) cc_final: 0.3950 (mpt) REVERT: A 310 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7839 (mm) REVERT: A 465 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7533 (mtm) REVERT: A 553 PHE cc_start: 0.7495 (t80) cc_final: 0.7133 (t80) REVERT: A 647 MET cc_start: 0.5108 (tpt) cc_final: 0.4887 (tpt) REVERT: A 653 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6621 (tp30) REVERT: A 675 GLU cc_start: 0.5763 (OUTLIER) cc_final: 0.5422 (pp20) REVERT: A 689 PHE cc_start: 0.6157 (OUTLIER) cc_final: 0.5256 (p90) REVERT: A 741 GLN cc_start: 0.6559 (OUTLIER) cc_final: 0.6080 (mt0) REVERT: A 797 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6191 (mmt) REVERT: A 986 LYS cc_start: 0.7088 (mtpp) cc_final: 0.6788 (mtpt) REVERT: A 992 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6737 (m-30) REVERT: A 996 ARG cc_start: 0.7159 (ptm-80) cc_final: 0.6787 (ptm-80) REVERT: A 1003 ARG cc_start: 0.7394 (ttm110) cc_final: 0.7075 (ttt90) REVERT: A 1166 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7982 (ttpt) REVERT: A 1237 ARG cc_start: 0.6423 (OUTLIER) cc_final: 0.5731 (ttt90) REVERT: A 1275 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7639 (ttp80) REVERT: A 1372 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6262 (tp) outliers start: 38 outliers final: 16 residues processed: 99 average time/residue: 0.7106 time to fit residues: 75.7030 Evaluate side-chains 97 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 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 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 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 753 SER Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 797 MET 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 1103 VAL 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 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: 0.0570 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.168623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.136134 restraints weight = 14304.303| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.77 r_work: 0.3238 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12431 Z= 0.145 Angle : 0.565 13.174 17464 Z= 0.313 Chirality : 0.039 0.317 2022 Planarity : 0.004 0.054 1674 Dihedral : 22.258 179.349 3319 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.66 % Allowed : 28.32 % 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: -0.22 (0.26), residues: 1047 helix: 0.81 (0.24), residues: 475 sheet: -0.56 (0.85), residues: 44 loop : -0.99 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 749 TYR 0.013 0.001 TYR A 550 PHE 0.020 0.001 PHE A 687 TRP 0.026 0.001 TRP A 307 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (12431) covalent geometry : angle 0.56486 / 0.31 (17464) hydrogen bonds : bond 0.05120 / 5.34 ( 416) hydrogen bonds : angle 4.45650 / 5.59 ( 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 102 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6374 (m-40) cc_final: 0.5848 (m110) REVERT: A 78 ARG cc_start: 0.7973 (ttp80) cc_final: 0.7725 (ttp80) REVERT: A 85 GLN cc_start: 0.7730 (tt0) cc_final: 0.7433 (tp-100) REVERT: A 105 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8452 (m) REVERT: A 192 MET cc_start: 0.4321 (mpt) cc_final: 0.3883 (mpt) REVERT: A 465 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7539 (mtm) REVERT: A 553 PHE cc_start: 0.7468 (t80) cc_final: 0.7115 (t80) REVERT: A 647 MET cc_start: 0.4930 (tpt) cc_final: 0.4703 (tpt) REVERT: A 653 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6616 (tp30) REVERT: A 675 GLU cc_start: 0.5829 (OUTLIER) cc_final: 0.5451 (pp20) REVERT: A 689 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5120 (p90) REVERT: A 741 GLN cc_start: 0.6487 (OUTLIER) cc_final: 0.6018 (mt0) REVERT: A 970 ILE cc_start: 0.6804 (mt) cc_final: 0.6149 (mp) REVERT: A 986 LYS cc_start: 0.7101 (mtpp) cc_final: 0.6757 (mtpt) REVERT: A 992 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6750 (m-30) REVERT: A 996 ARG cc_start: 0.7165 (ptm-80) cc_final: 0.6802 (ptm-80) REVERT: A 1003 ARG cc_start: 0.7399 (ttm110) cc_final: 0.7061 (ttt90) REVERT: A 1166 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.8012 (ttpt) REVERT: A 1237 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.5708 (ttt90) REVERT: A 1275 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7685 (ttp80) REVERT: A 1372 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6302 (tp) outliers start: 35 outliers final: 19 residues processed: 93 average time/residue: 0.6932 time to fit residues: 69.6621 Evaluate side-chains 94 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 306 SER 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 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 1004 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 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 1343 LEU 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: 5.9990 chunk 73 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 GLN A1305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.165553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133041 restraints weight = 14167.864| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.74 r_work: 0.3204 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12431 Z= 0.234 Angle : 0.654 12.956 17464 Z= 0.357 Chirality : 0.044 0.353 2022 Planarity : 0.005 0.054 1674 Dihedral : 22.372 179.883 3319 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % 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: -0.54 (0.25), residues: 1047 helix: 0.45 (0.24), residues: 475 sheet: -0.24 (0.85), residues: 42 loop : -1.11 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 49 TYR 0.016 0.002 TYR A 550 PHE 0.022 0.002 PHE A 687 TRP 0.030 0.002 TRP A 307 HIS 0.006 0.002 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 (12431) covalent geometry : angle 0.65364 / 0.36 (17464) hydrogen bonds : bond 0.05781 / 6.15 ( 416) hydrogen bonds : angle 4.69141 / 5.89 ( 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 102 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6250 (m-40) cc_final: 0.5757 (m110) REVERT: A 32 ASP cc_start: 0.7177 (p0) cc_final: 0.6933 (t0) REVERT: A 78 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7743 (ttp80) REVERT: A 85 GLN cc_start: 0.7727 (tt0) cc_final: 0.7414 (tp-100) REVERT: A 105 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8565 (m) REVERT: A 192 MET cc_start: 0.4229 (mpt) cc_final: 0.3794 (mpt) REVERT: A 465 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7625 (mtm) REVERT: A 553 PHE cc_start: 0.7337 (t80) cc_final: 0.7038 (t80) REVERT: A 653 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6598 (tp30) REVERT: A 675 GLU cc_start: 0.5829 (OUTLIER) cc_final: 0.5472 (pp20) REVERT: A 689 PHE cc_start: 0.6264 (OUTLIER) cc_final: 0.5166 (p90) REVERT: A 741 GLN cc_start: 0.6118 (OUTLIER) cc_final: 0.5706 (mt0) REVERT: A 986 LYS cc_start: 0.7093 (mtpp) cc_final: 0.6696 (mtpt) REVERT: A 992 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6676 (m-30) REVERT: A 996 ARG cc_start: 0.7128 (ptm-80) cc_final: 0.6773 (ptm-80) REVERT: A 1003 ARG cc_start: 0.7476 (ttm110) cc_final: 0.7138 (ttt90) REVERT: A 1166 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8047 (ttpt) REVERT: A 1237 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.5871 (ttt180) REVERT: A 1275 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7813 (ttp80) REVERT: A 1372 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6370 (tp) outliers start: 35 outliers final: 17 residues processed: 93 average time/residue: 0.6651 time to fit residues: 66.7877 Evaluate side-chains 93 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 462 GLU 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 753 SER Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 975 GLN Chi-restraints excluded: chain A residue 992 ASP 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 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 1343 LEU 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: 0.9980 chunk 90 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 116 optimal weight: 0.0570 chunk 18 optimal weight: 0.0670 chunk 54 optimal weight: 0.6980 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.169330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.136950 restraints weight = 14392.067| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.82 r_work: 0.3263 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12431 Z= 0.122 Angle : 0.566 14.593 17464 Z= 0.314 Chirality : 0.039 0.314 2022 Planarity : 0.004 0.055 1674 Dihedral : 22.368 179.100 3319 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.82 % Allowed : 29.36 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.26), residues: 1047 helix: 0.79 (0.24), residues: 476 sheet: -0.32 (0.83), residues: 44 loop : -1.03 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 994 TYR 0.014 0.001 TYR A1208 PHE 0.029 0.002 PHE A 977 TRP 0.037 0.002 TRP A 307 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (12431) covalent geometry : angle 0.56586 / 0.31 (17464) hydrogen bonds : bond 0.05054 / 5.29 ( 416) hydrogen bonds : angle 4.48177 / 5.64 ( 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 96 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6281 (m-40) cc_final: 0.5785 (m110) REVERT: A 32 ASP cc_start: 0.7187 (p0) cc_final: 0.6927 (t0) REVERT: A 78 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7699 (ttp80) REVERT: A 85 GLN cc_start: 0.7671 (tt0) cc_final: 0.7373 (tp-100) REVERT: A 105 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8434 (m) REVERT: A 192 MET cc_start: 0.4222 (mpt) cc_final: 0.3776 (mpt) REVERT: A 465 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7624 (mtm) REVERT: A 553 PHE cc_start: 0.7336 (t80) cc_final: 0.7020 (t80) REVERT: A 653 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6470 (tp30) REVERT: A 675 GLU cc_start: 0.5847 (OUTLIER) cc_final: 0.5505 (pp20) REVERT: A 689 PHE cc_start: 0.6084 (OUTLIER) cc_final: 0.5006 (p90) REVERT: A 741 GLN cc_start: 0.6100 (OUTLIER) cc_final: 0.5720 (mt0) REVERT: A 796 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7067 (tm-30) REVERT: A 986 LYS cc_start: 0.7083 (mtpp) cc_final: 0.6701 (mtpt) REVERT: A 992 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6694 (m-30) REVERT: A 996 ARG cc_start: 0.7099 (ptm-80) cc_final: 0.6737 (ptm-80) REVERT: A 1003 ARG cc_start: 0.7335 (ttm110) cc_final: 0.7053 (ttt90) REVERT: A 1166 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.8030 (ttpt) REVERT: A 1237 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.5705 (ttt90) REVERT: A 1275 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7736 (ttp80) REVERT: A 1372 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6267 (tp) outliers start: 27 outliers final: 13 residues processed: 87 average time/residue: 0.7540 time to fit residues: 70.4880 Evaluate side-chains 89 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 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 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 462 GLU 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 753 SER Chi-restraints excluded: chain A residue 992 ASP 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: 2.9990 chunk 3 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 42 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.168278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138374 restraints weight = 14300.890| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.54 r_work: 0.3269 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 0.032 12431 Z= 0.146 Angle : 0.573 13.956 17464 Z= 0.316 Chirality : 0.040 0.329 2022 Planarity : 0.004 0.055 1674 Dihedral : 22.311 179.302 3319 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.51 % Allowed : 29.89 % 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: -0.25 (0.26), residues: 1047 helix: 0.76 (0.24), residues: 476 sheet: -0.06 (0.85), residues: 42 loop : -1.02 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1282 TYR 0.013 0.001 TYR A 550 PHE 0.020 0.001 PHE A 687 TRP 0.034 0.002 TRP A 307 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (12431) covalent geometry : angle 0.57283 / 0.32 (17464) hydrogen bonds : bond 0.05066 / 5.29 ( 416) hydrogen bonds : angle 4.44947 / 5.59 ( 1113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3281.42 seconds wall clock time: 57 minutes 2.79 seconds (3422.79 seconds total)