Starting phenix.real_space_refine on Wed Aug 5 23:58:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfh_40441/08_2026/8sfh_40441.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfh_40441/08_2026/8sfh_40441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sfh_40441/08_2026/8sfh_40441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfh_40441/08_2026/8sfh_40441.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sfh_40441/08_2026/8sfh_40441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfh_40441/08_2026/8sfh_40441.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 26 5.16 5 C 7638 2.51 5 N 2120 2.21 5 O 2533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12407 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1286, 10527 Classifications: {'peptide': 1286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 1236} Chain breaks: 4 Chain: "B" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 568 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 11} Link IDs: {'rna2p': 6, 'rna3p': 20} Chain: "C" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 660 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Time building chain proxies: 2.81, per 1000 atoms: 0.23 Number of scatterers: 12407 At special positions: 0 Unit cell: (96.628, 109.123, 146.608, 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 26 16.00 P 90 15.00 O 2533 8.00 N 2120 7.00 C 7638 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: 0.79 Conformation dependent library (CDL) restraints added in 364.7 milliseconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 56.1% alpha, 11.4% beta 34 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 67 Proline residue: A 52 - end of helix removed outlier: 3.856A pdb=" N GLN A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.667A pdb=" N ASN A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 132 Processing helix chain 'A' and resid 134 through 140 removed outlier: 4.233A pdb=" N PHE A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 Processing helix chain 'A' and resid 152 through 162 removed outlier: 3.841A pdb=" N PHE A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 removed outlier: 3.512A pdb=" N TYR A 168 " --> pdb=" O PHE A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 169 through 181 removed outlier: 4.303A pdb=" N ASN A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 215 removed outlier: 4.163A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.802A pdb=" N HIS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 289 through 298 Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.647A pdb=" N THR A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'A' and resid 420 through 428 removed outlier: 3.545A pdb=" N GLY A 428 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 452 removed outlier: 3.592A pdb=" N GLU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 483 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 508 through 523 removed outlier: 3.943A pdb=" N SER A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 600 through 609 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.732A pdb=" N THR A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 647 Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.668A pdb=" N ALA A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 694 through 698 removed outlier: 4.243A pdb=" N SER A 697 " --> pdb=" O ASP A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.584A pdb=" N TYR A 704 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 727 through 737 removed outlier: 3.670A pdb=" N ILE A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 751 Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.595A pdb=" N PHE A 769 " --> pdb=" O TRP A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 819 through 831 removed outlier: 4.033A pdb=" N GLN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU A 825 " --> pdb=" O THR A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 846 through 849 removed outlier: 3.619A pdb=" N VAL A 849 " --> pdb=" O LEU A 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 846 through 849' Processing helix chain 'A' and resid 861 through 865 Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 940 through 954 Processing helix chain 'A' and resid 957 through 987 removed outlier: 3.656A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1025 removed outlier: 4.157A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1088 Processing helix chain 'A' and resid 1090 through 1101 removed outlier: 3.685A pdb=" N PHE A1101 " --> pdb=" O PHE A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1198 through 1205 removed outlier: 4.619A pdb=" N LYS A1202 " --> pdb=" O ASN A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1252 through 1254 No H-bonds generated for 'chain 'A' and resid 1252 through 1254' Processing helix chain 'A' and resid 1261 through 1284 removed outlier: 3.811A pdb=" N ASN A1265 " --> pdb=" O ASP A1261 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY A1266 " --> pdb=" O ALA A1262 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A1267 " --> pdb=" O ASP A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1307 removed outlier: 4.789A pdb=" N GLN A1303 " --> pdb=" O LEU A1299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.771A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 11.593A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.771A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.582A pdb=" N ILE A 418 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 807 Processing sheet with id=AA6, first strand: chain 'A' and resid 926 through 931 removed outlier: 6.599A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU A 993 " --> pdb=" O ILE A 907 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 934 through 935 Processing sheet with id=AA8, first strand: chain 'A' and resid 1103 through 1106 removed outlier: 4.009A pdb=" N PHE A1103 " --> pdb=" O HIS A1116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AB1, first strand: chain 'A' and resid 1159 through 1165 removed outlier: 5.181A pdb=" N ARG A1172 " --> pdb=" O VAL A1163 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLU A1165 " --> pdb=" O THR A1170 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N THR A1170 " --> pdb=" O GLU A1165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1226 through 1229 removed outlier: 4.509A pdb=" N PHE A1249 " --> pdb=" O SER A1239 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.01 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: 3000 1.33 - 1.46: 3398 1.46 - 1.58: 6247 1.58 - 1.70: 178 1.70 - 1.83: 44 Bond restraints: 12867 Sorted by residual: bond pdb=" C1' DT D 16 " pdb=" N1 DT D 16 " ideal model delta sigma weight residual 1.468 1.559 -0.091 1.40e-02 5.10e+03 4.27e+01 bond pdb=" N1 DT D 16 " pdb=" C2 DT D 16 " ideal model delta sigma weight residual 1.376 1.410 -0.034 8.00e-03 1.56e+04 1.78e+01 bond pdb=" C1' DT C 23 " pdb=" N1 DT C 23 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.06e+01 bond pdb=" C3' DT C 20 " pdb=" C2' DT C 20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.38e+00 bond pdb=" C3' DA D 23 " pdb=" C2' DA D 23 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.88e+00 ... (remaining 12862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 17476 3.35 - 6.70: 238 6.70 - 10.05: 43 10.05 - 13.40: 14 13.40 - 16.75: 5 Bond angle restraints: 17776 Sorted by residual: angle pdb=" C1' U B 4 " pdb=" N1 U B 4 " pdb=" C2 U B 4 " ideal model delta sigma weight residual 117.70 124.66 -6.96 1.20e+00 6.94e-01 3.36e+01 angle pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sigma weight residual 118.80 125.00 -6.20 1.10e+00 8.26e-01 3.17e+01 angle pdb=" CB MET A 732 " pdb=" CG MET A 732 " pdb=" SD MET A 732 " ideal model delta sigma weight residual 112.70 129.11 -16.41 3.00e+00 1.11e-01 2.99e+01 angle pdb=" C1' C B 9 " pdb=" N1 C B 9 " pdb=" C2 C B 9 " ideal model delta sigma weight residual 118.80 124.43 -5.63 1.10e+00 8.26e-01 2.62e+01 angle pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sigma weight residual 117.70 123.66 -5.96 1.20e+00 6.94e-01 2.47e+01 ... (remaining 17771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.39: 6984 29.39 - 58.78: 581 58.78 - 88.18: 63 88.18 - 117.57: 2 117.57 - 146.96: 2 Dihedral angle restraints: 7632 sinusoidal: 3835 harmonic: 3797 Sorted by residual: dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 200.00 53.04 146.96 1 1.50e+01 4.44e-03 7.84e+01 dihedral pdb=" O4' C B 11 " pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sinusoidal sigma weight residual 200.00 54.63 145.37 1 1.50e+01 4.44e-03 7.78e+01 dihedral pdb=" CA PRO A 599 " pdb=" C PRO A 599 " pdb=" N ASP A 600 " pdb=" CA ASP A 600 " ideal model delta harmonic sigma weight residual -180.00 -156.57 -23.43 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 7629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1746 0.094 - 0.189: 200 0.189 - 0.283: 11 0.283 - 0.377: 8 0.377 - 0.472: 7 Chirality restraints: 1972 Sorted by residual: chirality pdb=" P DC C 26 " pdb=" OP1 DC C 26 " pdb=" OP2 DC C 26 " pdb=" O5' DC C 26 " both_signs ideal model delta sigma weight residual True 2.34 -2.81 -0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" P DA D 14 " pdb=" OP1 DA D 14 " pdb=" OP2 DA D 14 " pdb=" O5' DA D 14 " both_signs ideal model delta sigma weight residual True 2.34 -2.80 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" P DC C 24 " pdb=" OP1 DC C 24 " pdb=" OP2 DC C 24 " pdb=" O5' DC C 24 " both_signs ideal model delta sigma weight residual True 2.34 -2.80 -0.47 2.00e-01 2.50e+01 5.44e+00 ... (remaining 1969 not shown) Planarity restraints: 1959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1255 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO A1256 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO A1256 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A1256 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1207 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ASP A1207 " 0.057 2.00e-02 2.50e+03 pdb=" O ASP A1207 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP A1208 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 440 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C SER A 440 " -0.050 2.00e-02 2.50e+03 pdb=" O SER A 440 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A 441 " 0.017 2.00e-02 2.50e+03 ... (remaining 1956 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2746 2.79 - 3.32: 11640 3.32 - 3.84: 21454 3.84 - 4.37: 25161 4.37 - 4.90: 40855 Nonbonded interactions: 101856 Sorted by model distance: nonbonded pdb=" OD2 ASP A 326 " pdb=" OG1 THR A 457 " model vdw 2.261 3.040 nonbonded pdb=" O ARG A 862 " pdb=" OG1 THR A 865 " model vdw 2.275 3.040 nonbonded pdb=" NH2 ARG A 863 " pdb=" OP2 C B 6 " model vdw 2.297 3.120 nonbonded pdb=" OG1 THR A 151 " pdb=" OD1 ASN A 156 " model vdw 2.314 3.040 nonbonded pdb=" O SER A 922 " pdb=" NE2 GLN A1275 " model vdw 2.317 3.120 ... (remaining 101851 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.990 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.006 0.091 12867 Z= 0.362 Angle : 1.109 16.745 17776 Z= 0.658 Chirality : 0.067 0.472 1972 Planarity : 0.007 0.116 1959 Dihedral : 19.219 146.960 5172 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.52 % Allowed : 13.19 % Favored : 86.28 % 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: 0.43 (0.23), residues: 1276 helix: 0.43 (0.20), residues: 629 sheet: 0.24 (0.41), residues: 144 loop : 0.36 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A1194 TYR 0.037 0.003 TYR A 83 PHE 0.027 0.003 PHE A1253 TRP 0.027 0.003 TRP A 382 HIS 0.008 0.002 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.36 (12867) covalent geometry : angle 1.10922 / 0.66 (17776) hydrogen bonds : bond 0.13173 / 9.01 ( 624) hydrogen bonds : angle 5.76391 / 4.16 ( 1710) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.337 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 56 average time/residue: 0.0984 time to fit residues: 8.3383 Evaluate side-chains 39 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 913 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.0010 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 HIS A 206 HIS A 552 ASN A 800 HIS A1167 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.045767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.032595 restraints weight = 73267.475| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 4.14 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12867 Z= 0.139 Angle : 0.640 10.952 17776 Z= 0.348 Chirality : 0.043 0.275 1972 Planarity : 0.004 0.074 1959 Dihedral : 20.033 149.037 2511 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.30 % Allowed : 11.63 % Favored : 87.07 % 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: 0.91 (0.24), residues: 1276 helix: 0.98 (0.20), residues: 645 sheet: -0.28 (0.41), residues: 126 loop : 0.58 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1194 TYR 0.016 0.001 TYR A 827 PHE 0.013 0.001 PHE A 138 TRP 0.014 0.001 TRP A 382 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (12867) covalent geometry : angle 0.63999 / 0.35 (17776) hydrogen bonds : bond 0.04548 / 3.05 ( 624) hydrogen bonds : angle 4.49293 / 3.24 ( 1710) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.273 Fit side-chains REVERT: A 132 LEU cc_start: 0.9784 (tp) cc_final: 0.9479 (tp) REVERT: A 328 GLU cc_start: 0.9754 (OUTLIER) cc_final: 0.9436 (tt0) REVERT: A 458 LEU cc_start: 0.9331 (mt) cc_final: 0.9130 (mm) REVERT: A 911 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8402 (mt-10) REVERT: A 1014 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8516 (tm-30) REVERT: A 1260 MET cc_start: 0.9233 (mmm) cc_final: 0.9008 (mmm) outliers start: 15 outliers final: 2 residues processed: 51 average time/residue: 0.0894 time to fit residues: 7.0279 Evaluate side-chains 40 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 911 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 5 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.044955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.031818 restraints weight = 74662.491| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 4.15 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12867 Z= 0.154 Angle : 0.571 9.716 17776 Z= 0.313 Chirality : 0.041 0.199 1972 Planarity : 0.004 0.056 1959 Dihedral : 20.027 149.652 2509 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.39 % Allowed : 11.20 % Favored : 87.41 % 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: 1.42 (0.24), residues: 1276 helix: 1.50 (0.21), residues: 645 sheet: -0.33 (0.40), residues: 134 loop : 0.79 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 160 TYR 0.015 0.001 TYR A 173 PHE 0.016 0.001 PHE A 138 TRP 0.012 0.001 TRP A 382 HIS 0.006 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (12867) covalent geometry : angle 0.57124 / 0.31 (17776) hydrogen bonds : bond 0.04063 / 2.73 ( 624) hydrogen bonds : angle 4.19077 / 3.02 ( 1710) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9758 (OUTLIER) cc_final: 0.9442 (tt0) REVERT: A 356 LEU cc_start: 0.9699 (OUTLIER) cc_final: 0.9343 (mt) REVERT: A 387 ASN cc_start: 0.9585 (m-40) cc_final: 0.9175 (p0) REVERT: A 539 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9069 (p) REVERT: A 786 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8256 (mm-30) REVERT: A 911 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: A 1014 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8654 (tm-30) REVERT: A 1260 MET cc_start: 0.9212 (mmm) cc_final: 0.8869 (mmt) outliers start: 16 outliers final: 5 residues processed: 53 average time/residue: 0.0916 time to fit residues: 7.8524 Evaluate side-chains 46 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 911 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 23 optimal weight: 0.0670 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 130 optimal weight: 40.0000 chunk 74 optimal weight: 0.6980 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 HIS A1290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.044621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.031484 restraints weight = 74867.194| |-----------------------------------------------------------------------------| r_work (start): 0.2588 rms_B_bonded: 4.12 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12867 Z= 0.152 Angle : 0.561 9.134 17776 Z= 0.303 Chirality : 0.041 0.385 1972 Planarity : 0.003 0.052 1959 Dihedral : 20.055 150.949 2509 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.95 % Allowed : 11.98 % Favored : 87.07 % 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: 1.73 (0.25), residues: 1276 helix: 1.76 (0.21), residues: 645 sheet: -0.14 (0.40), residues: 143 loop : 0.92 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 386 TYR 0.013 0.001 TYR A 595 PHE 0.013 0.001 PHE A 198 TRP 0.012 0.001 TRP A 382 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (12867) covalent geometry : angle 0.56147 / 0.30 (17776) hydrogen bonds : bond 0.03842 / 2.57 ( 624) hydrogen bonds : angle 4.05713 / 2.93 ( 1710) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9758 (OUTLIER) cc_final: 0.9440 (tt0) REVERT: A 356 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9295 (mt) REVERT: A 387 ASN cc_start: 0.9569 (m-40) cc_final: 0.9132 (p0) REVERT: A 786 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8283 (mm-30) REVERT: A 911 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8383 (mt-10) REVERT: A 1014 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8723 (tm-30) REVERT: A 1260 MET cc_start: 0.9280 (mmm) cc_final: 0.8914 (mmt) outliers start: 11 outliers final: 5 residues processed: 47 average time/residue: 0.0878 time to fit residues: 6.9003 Evaluate side-chains 47 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 911 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 125 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3137 r_free = 0.3137 target = 0.044294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.031166 restraints weight = 75138.963| |-----------------------------------------------------------------------------| r_work (start): 0.2583 rms_B_bonded: 4.12 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12867 Z= 0.152 Angle : 0.545 11.420 17776 Z= 0.295 Chirality : 0.040 0.179 1972 Planarity : 0.003 0.047 1959 Dihedral : 20.041 151.674 2509 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.48 % Allowed : 12.15 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.25), residues: 1276 helix: 2.06 (0.21), residues: 643 sheet: -0.09 (0.39), residues: 143 loop : 0.97 (0.32), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1194 TYR 0.014 0.001 TYR A 595 PHE 0.014 0.001 PHE A 138 TRP 0.011 0.001 TRP A 382 HIS 0.004 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (12867) covalent geometry : angle 0.54528 / 0.29 (17776) hydrogen bonds : bond 0.03735 / 2.51 ( 624) hydrogen bonds : angle 3.91507 / 2.82 ( 1710) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.402 Fit side-chains REVERT: A 328 GLU cc_start: 0.9777 (OUTLIER) cc_final: 0.9442 (tt0) REVERT: A 356 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9295 (mt) REVERT: A 387 ASN cc_start: 0.9586 (m-40) cc_final: 0.9159 (p0) REVERT: A 721 ILE cc_start: 0.9547 (OUTLIER) cc_final: 0.9337 (mm) REVERT: A 786 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8319 (mm-30) REVERT: A 911 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8395 (mt-10) REVERT: A 1260 MET cc_start: 0.9267 (mmm) cc_final: 0.8850 (mmt) outliers start: 17 outliers final: 5 residues processed: 54 average time/residue: 0.1030 time to fit residues: 8.8412 Evaluate side-chains 43 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 1051 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 72 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 18 optimal weight: 0.0370 chunk 83 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- 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 = 0.3144 r_free = 0.3144 target = 0.044437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.031388 restraints weight = 74974.239| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 4.13 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12867 Z= 0.127 Angle : 0.550 10.888 17776 Z= 0.292 Chirality : 0.039 0.331 1972 Planarity : 0.003 0.045 1959 Dihedral : 20.018 151.529 2509 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.95 % Allowed : 12.93 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.25), residues: 1276 helix: 2.14 (0.21), residues: 642 sheet: 0.13 (0.40), residues: 138 loop : 0.98 (0.32), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1194 TYR 0.014 0.001 TYR A 595 PHE 0.012 0.001 PHE A 198 TRP 0.010 0.001 TRP A 382 HIS 0.004 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (12867) covalent geometry : angle 0.54955 / 0.29 (17776) hydrogen bonds : bond 0.03569 / 2.40 ( 624) hydrogen bonds : angle 3.86095 / 2.78 ( 1710) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9787 (OUTLIER) cc_final: 0.9462 (tt0) REVERT: A 356 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9297 (mt) REVERT: A 387 ASN cc_start: 0.9568 (m-40) cc_final: 0.9120 (p0) REVERT: A 608 CYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9195 (t) REVERT: A 786 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8290 (mm-30) REVERT: A 911 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8415 (mt-10) REVERT: A 1018 MET cc_start: 0.9260 (mtp) cc_final: 0.9053 (mtp) REVERT: A 1260 MET cc_start: 0.9250 (mmm) cc_final: 0.8820 (mmt) outliers start: 11 outliers final: 5 residues processed: 49 average time/residue: 0.1073 time to fit residues: 8.2738 Evaluate side-chains 45 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 1051 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 133 optimal weight: 30.0000 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 HIS A1013 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.043664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.030592 restraints weight = 75088.567| |-----------------------------------------------------------------------------| r_work (start): 0.2566 rms_B_bonded: 4.08 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12867 Z= 0.201 Angle : 0.585 10.535 17776 Z= 0.310 Chirality : 0.040 0.216 1972 Planarity : 0.003 0.043 1959 Dihedral : 20.082 152.125 2509 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.13 % Allowed : 13.37 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.25), residues: 1276 helix: 2.24 (0.21), residues: 642 sheet: 0.02 (0.39), residues: 143 loop : 1.02 (0.32), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 863 TYR 0.014 0.001 TYR A 61 PHE 0.014 0.001 PHE A 198 TRP 0.013 0.001 TRP A 382 HIS 0.006 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (12867) covalent geometry : angle 0.58477 / 0.31 (17776) hydrogen bonds : bond 0.03941 / 2.68 ( 624) hydrogen bonds : angle 3.95962 / 2.87 ( 1710) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 168 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.8500 (m-80) REVERT: A 356 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9288 (mt) REVERT: A 387 ASN cc_start: 0.9590 (m-40) cc_final: 0.9144 (p0) REVERT: A 604 MET cc_start: 0.9443 (tpp) cc_final: 0.8737 (tpp) REVERT: A 608 CYS cc_start: 0.9453 (OUTLIER) cc_final: 0.9253 (t) REVERT: A 786 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8254 (mm-30) REVERT: A 798 MET cc_start: 0.8107 (tmm) cc_final: 0.7778 (tmm) REVERT: A 911 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8406 (mt-10) REVERT: A 1018 MET cc_start: 0.9329 (mtp) cc_final: 0.9109 (mtp) REVERT: A 1260 MET cc_start: 0.9232 (mmm) cc_final: 0.8763 (mmt) outliers start: 13 outliers final: 7 residues processed: 46 average time/residue: 0.0997 time to fit residues: 7.4555 Evaluate side-chains 46 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 976 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 29 optimal weight: 6.9990 chunk 62 optimal weight: 0.0370 chunk 98 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 overall best weight: 1.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1013 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.044218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.031141 restraints weight = 74893.781| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 4.15 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12867 Z= 0.119 Angle : 0.540 10.468 17776 Z= 0.288 Chirality : 0.039 0.198 1972 Planarity : 0.003 0.042 1959 Dihedral : 20.054 151.958 2509 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.87 % Allowed : 13.63 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.25), residues: 1276 helix: 2.28 (0.21), residues: 642 sheet: 0.26 (0.40), residues: 138 loop : 0.98 (0.32), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 176 TYR 0.014 0.001 TYR A 61 PHE 0.011 0.001 PHE A 198 TRP 0.010 0.001 TRP A 382 HIS 0.004 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (12867) covalent geometry : angle 0.54028 / 0.29 (17776) hydrogen bonds : bond 0.03482 / 2.34 ( 624) hydrogen bonds : angle 3.80683 / 2.75 ( 1710) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9305 (mt) REVERT: A 387 ASN cc_start: 0.9560 (m-40) cc_final: 0.9110 (p0) REVERT: A 786 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8245 (mm-30) REVERT: A 798 MET cc_start: 0.8243 (tmm) cc_final: 0.7822 (tmm) REVERT: A 911 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8383 (mt-10) REVERT: A 1013 GLN cc_start: 0.9593 (tt0) cc_final: 0.9138 (tp-100) REVERT: A 1018 MET cc_start: 0.9316 (mtp) cc_final: 0.9083 (mtp) REVERT: A 1260 MET cc_start: 0.9268 (mmm) cc_final: 0.8817 (mmt) outliers start: 10 outliers final: 6 residues processed: 47 average time/residue: 0.0947 time to fit residues: 7.0988 Evaluate side-chains 43 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1051 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 102 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 104 optimal weight: 0.3980 chunk 93 optimal weight: 0.0470 chunk 23 optimal weight: 0.0770 chunk 116 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.044246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.031239 restraints weight = 75308.972| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 4.12 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12867 Z= 0.126 Angle : 0.539 11.286 17776 Z= 0.287 Chirality : 0.039 0.164 1972 Planarity : 0.003 0.041 1959 Dihedral : 20.000 150.952 2509 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.95 % Allowed : 13.89 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.25), residues: 1276 helix: 2.37 (0.21), residues: 634 sheet: 0.36 (0.41), residues: 136 loop : 0.96 (0.31), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.014 0.001 TYR A 595 PHE 0.011 0.001 PHE A 198 TRP 0.009 0.001 TRP A 382 HIS 0.004 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (12867) covalent geometry : angle 0.53881 / 0.29 (17776) hydrogen bonds : bond 0.03446 / 2.32 ( 624) hydrogen bonds : angle 3.77091 / 2.72 ( 1710) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9313 (mt) REVERT: A 387 ASN cc_start: 0.9553 (m-40) cc_final: 0.9103 (p0) REVERT: A 539 THR cc_start: 0.9366 (p) cc_final: 0.9098 (p) REVERT: A 786 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8248 (mm-30) REVERT: A 795 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8742 (mmm) REVERT: A 798 MET cc_start: 0.8238 (tmm) cc_final: 0.7826 (tmm) REVERT: A 911 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: A 1013 GLN cc_start: 0.9597 (tt0) cc_final: 0.9078 (tp-100) REVERT: A 1018 MET cc_start: 0.9292 (mtp) cc_final: 0.9065 (mtp) REVERT: A 1260 MET cc_start: 0.9275 (mmm) cc_final: 0.8850 (mmt) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.1100 time to fit residues: 7.9795 Evaluate side-chains 45 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 976 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 68 optimal weight: 0.0020 chunk 36 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.9994 ------------------------------------------------------------------------------- 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 = 0.3144 r_free = 0.3144 target = 0.044293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.031251 restraints weight = 75637.877| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 4.22 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12867 Z= 0.141 Angle : 0.549 11.978 17776 Z= 0.289 Chirality : 0.039 0.158 1972 Planarity : 0.003 0.041 1959 Dihedral : 20.010 151.233 2509 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.87 % Allowed : 14.06 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.25), residues: 1276 helix: 2.39 (0.21), residues: 635 sheet: 0.18 (0.40), residues: 143 loop : 1.03 (0.32), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.015 0.001 TYR A 595 PHE 0.012 0.001 PHE A 198 TRP 0.010 0.001 TRP A 382 HIS 0.004 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (12867) covalent geometry : angle 0.54864 / 0.29 (17776) hydrogen bonds : bond 0.03464 / 2.32 ( 624) hydrogen bonds : angle 3.76644 / 2.72 ( 1710) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9308 (mt) REVERT: A 387 ASN cc_start: 0.9573 (m-40) cc_final: 0.9127 (p0) REVERT: A 539 THR cc_start: 0.9373 (p) cc_final: 0.9109 (p) REVERT: A 798 MET cc_start: 0.8289 (tmm) cc_final: 0.7963 (tmm) REVERT: A 806 MET cc_start: 0.6303 (ttt) cc_final: 0.6100 (tpp) REVERT: A 911 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8390 (mt-10) REVERT: A 1013 GLN cc_start: 0.9597 (tt0) cc_final: 0.9070 (tp-100) REVERT: A 1260 MET cc_start: 0.9273 (mmm) cc_final: 0.8829 (mmt) outliers start: 10 outliers final: 7 residues processed: 42 average time/residue: 0.0913 time to fit residues: 6.3839 Evaluate side-chains 42 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 976 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 6.9990 chunk 133 optimal weight: 30.0000 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 127 optimal weight: 0.0370 chunk 64 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 130 optimal weight: 50.0000 chunk 8 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.043804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.030794 restraints weight = 75436.450| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 4.17 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12867 Z= 0.176 Angle : 0.572 11.628 17776 Z= 0.300 Chirality : 0.039 0.156 1972 Planarity : 0.003 0.041 1959 Dihedral : 20.074 151.852 2509 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.22 % Allowed : 13.72 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.25), residues: 1276 helix: 2.44 (0.21), residues: 635 sheet: 0.24 (0.40), residues: 143 loop : 0.99 (0.32), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 797 TYR 0.015 0.001 TYR A 595 PHE 0.014 0.001 PHE A 198 TRP 0.012 0.001 TRP A 382 HIS 0.005 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (12867) covalent geometry : angle 0.57249 / 0.30 (17776) hydrogen bonds : bond 0.03683 / 2.48 ( 624) hydrogen bonds : angle 3.80657 / 2.75 ( 1710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1774.82 seconds wall clock time: 31 minutes 33.02 seconds (1893.02 seconds total)