Starting phenix.real_space_refine on Fri Jul 3 05:47:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfh_40441/07_2026/8sfh_40441.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfh_40441/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sfh_40441/07_2026/8sfh_40441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfh_40441/07_2026/8sfh_40441.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfh_40441/07_2026/8sfh_40441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfh_40441/07_2026/8sfh_40441.cif" } 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-dev-6108/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: 2.59, per 1000 atoms: 0.21 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: 1.09 Conformation dependent library (CDL) restraints added in 473.2 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: 1.67 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: 2.94 Time building geometry restraints manager: 1.45 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: 17478 3.35 - 6.70: 236 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: 1767 0.094 - 0.189: 179 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.930 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.150 ------------------------------------------------------------------------------- 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= 0.359 Angle : 1.097 16.745 17776 Z= 0.642 Chirality : 0.066 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 0.00597 / 0.36 (12867) covalent geometry : angle 1.09677 / 0.64 (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 : 0.504 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 56 average time/residue: 0.1148 time to fit residues: 9.7493 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 : 0.444 ------------------------------------------------------------------------------- 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 = 0.3170 r_free = 0.3170 target = 0.045837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.032748 restraints weight = 72842.088| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 4.15 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12867 Z= 0.139 Angle : 0.635 10.893 17776 Z= 0.345 Chirality : 0.043 0.277 1972 Planarity : 0.004 0.075 1959 Dihedral : 20.078 147.237 2511 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.30 % Allowed : 11.81 % Favored : 86.89 % 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: 0.93 (0.24), residues: 1276 helix: 1.00 (0.21), 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 0.007 0.001 ARG A1194 TYR 0.015 0.001 TYR A 827 PHE 0.012 0.001 PHE A 198 TRP 0.013 0.001 TRP A 382 HIS 0.008 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (12867) covalent geometry : angle 0.63504 / 0.35 (17776) hydrogen bonds : bond 0.04463 / 2.99 ( 624) hydrogen bonds : angle 4.48011 / 3.23 ( 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 : 0.466 Fit side-chains REVERT: A 132 LEU cc_start: 0.9783 (tp) cc_final: 0.9535 (tp) REVERT: A 328 GLU cc_start: 0.9751 (OUTLIER) cc_final: 0.9434 (tt0) REVERT: A 458 LEU cc_start: 0.9345 (mt) cc_final: 0.9144 (mm) REVERT: A 911 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: A 1014 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8525 (tm-30) REVERT: A 1260 MET cc_start: 0.9217 (mmm) cc_final: 0.9000 (mmm) outliers start: 15 outliers final: 2 residues processed: 51 average time/residue: 0.1124 time to fit residues: 8.9133 Evaluate side-chains 39 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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: 2.9990 chunk 125 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 34 optimal weight: 0.0770 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1105 HIS A1290 GLN A1303 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.044482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.031346 restraints weight = 75064.941| |-----------------------------------------------------------------------------| r_work (start): 0.2584 rms_B_bonded: 4.14 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12867 Z= 0.177 Angle : 0.588 9.852 17776 Z= 0.320 Chirality : 0.041 0.195 1972 Planarity : 0.004 0.056 1959 Dihedral : 20.144 149.291 2509 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.56 % Allowed : 11.28 % Favored : 87.15 % 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: 1.54 (0.24), residues: 1276 helix: 1.58 (0.21), residues: 645 sheet: -0.19 (0.39), residues: 143 loop : 0.86 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1194 TYR 0.016 0.001 TYR A 173 PHE 0.018 0.001 PHE A 138 TRP 0.013 0.001 TRP A 382 HIS 0.006 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (12867) covalent geometry : angle 0.58768 / 0.32 (17776) hydrogen bonds : bond 0.04251 / 2.87 ( 624) hydrogen bonds : angle 4.19454 / 3.03 ( 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 57 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9760 (OUTLIER) cc_final: 0.9443 (tt0) REVERT: A 356 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9303 (mt) REVERT: A 539 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9095 (p) REVERT: A 608 CYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9176 (t) REVERT: A 786 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8256 (mm-30) REVERT: A 911 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8388 (mt-10) REVERT: A 1014 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8583 (tm-30) REVERT: A 1260 MET cc_start: 0.9198 (mmm) cc_final: 0.8853 (mmt) outliers start: 18 outliers final: 4 residues processed: 54 average time/residue: 0.1024 time to fit residues: 8.9780 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 : 0.476 ------------------------------------------------------------------------------- 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: 6.9990 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 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: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3123 r_free = 0.3123 target = 0.043834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.030631 restraints weight = 75800.516| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 4.13 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12867 Z= 0.200 Angle : 0.586 11.333 17776 Z= 0.315 Chirality : 0.042 0.405 1972 Planarity : 0.003 0.051 1959 Dihedral : 20.228 152.161 2509 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.22 % Allowed : 11.63 % Favored : 87.15 % 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: 1.81 (0.25), residues: 1276 helix: 1.83 (0.21), residues: 646 sheet: -0.11 (0.40), residues: 143 loop : 0.96 (0.32), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 386 TYR 0.016 0.002 TYR A 61 PHE 0.015 0.001 PHE A 198 TRP 0.015 0.001 TRP A 382 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (12867) covalent geometry : angle 0.58577 / 0.32 (17776) hydrogen bonds : bond 0.04080 / 2.74 ( 624) hydrogen bonds : angle 4.11133 / 2.97 ( 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 53 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9761 (OUTLIER) cc_final: 0.9443 (tt0) REVERT: A 356 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9275 (mt) REVERT: A 786 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8255 (mm-30) REVERT: A 806 MET cc_start: 0.6700 (OUTLIER) cc_final: 0.6192 (ttm) REVERT: A 911 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: A 1014 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8762 (tm-30) REVERT: A 1260 MET cc_start: 0.9217 (mmm) cc_final: 0.8833 (mmt) outliers start: 14 outliers final: 4 residues processed: 49 average time/residue: 0.1095 time to fit residues: 8.5551 Evaluate side-chains 46 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain A residue 1051 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 125 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 31 optimal weight: 0.0870 chunk 73 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 824 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.044537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.031401 restraints weight = 74946.101| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 4.14 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12867 Z= 0.116 Angle : 0.530 10.644 17776 Z= 0.288 Chirality : 0.039 0.187 1972 Planarity : 0.003 0.046 1959 Dihedral : 20.113 151.420 2509 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.22 % Allowed : 12.59 % Favored : 86.20 % 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: 1.96 (0.25), residues: 1276 helix: 2.01 (0.21), residues: 646 sheet: 0.05 (0.40), residues: 138 loop : 0.90 (0.32), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.014 0.001 TYR A 595 PHE 0.011 0.001 PHE A 138 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 0.00230 / 0.12 (12867) covalent geometry : angle 0.52994 / 0.29 (17776) hydrogen bonds : bond 0.03572 / 2.39 ( 624) hydrogen bonds : angle 3.87297 / 2.79 ( 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: 14 poor density : 43 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9774 (OUTLIER) cc_final: 0.9440 (tt0) REVERT: A 356 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9299 (mt) REVERT: A 387 ASN cc_start: 0.9581 (m-40) cc_final: 0.9152 (p0) REVERT: A 786 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8314 (mm-30) REVERT: A 911 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8401 (mt-10) REVERT: A 1260 MET cc_start: 0.9273 (mmm) cc_final: 0.8865 (mmt) outliers start: 14 outliers final: 5 residues processed: 54 average time/residue: 0.1109 time to fit residues: 9.3398 Evaluate side-chains 44 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 72 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 18 optimal weight: 0.0470 chunk 83 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 overall best weight: 1.4284 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.044386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.031341 restraints weight = 75117.420| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 4.12 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12867 Z= 0.124 Angle : 0.542 10.902 17776 Z= 0.290 Chirality : 0.040 0.353 1972 Planarity : 0.003 0.044 1959 Dihedral : 20.076 150.686 2509 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.04 % Allowed : 12.93 % Favored : 86.02 % 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: 2.09 (0.25), residues: 1276 helix: 2.14 (0.21), residues: 642 sheet: 0.08 (0.40), residues: 138 loop : 0.94 (0.31), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.018 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 A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (12867) covalent geometry : angle 0.54158 / 0.29 (17776) hydrogen bonds : bond 0.03540 / 2.37 ( 624) hydrogen bonds : angle 3.84737 / 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 50 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9788 (OUTLIER) cc_final: 0.9471 (tt0) REVERT: A 356 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9299 (mt) REVERT: A 387 ASN cc_start: 0.9561 (m-40) cc_final: 0.9356 (m-40) REVERT: A 786 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8288 (mm-30) REVERT: A 798 MET cc_start: 0.7995 (tmm) cc_final: 0.7514 (tmm) REVERT: A 911 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8409 (mt-10) REVERT: A 1260 MET cc_start: 0.9258 (mmm) cc_final: 0.8853 (mmt) outliers start: 12 outliers final: 8 residues processed: 48 average time/residue: 0.1077 time to fit residues: 8.1906 Evaluate side-chains 45 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 328 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 806 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 133 optimal weight: 30.0000 chunk 92 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 HIS A 856 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.043374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.030399 restraints weight = 74020.565| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 4.01 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12867 Z= 0.227 Angle : 0.590 10.150 17776 Z= 0.314 Chirality : 0.040 0.194 1972 Planarity : 0.003 0.042 1959 Dihedral : 20.156 152.168 2509 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.30 % Allowed : 13.37 % Favored : 85.33 % 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: 2.16 (0.25), residues: 1276 helix: 2.22 (0.21), residues: 642 sheet: -0.03 (0.39), residues: 143 loop : 1.00 (0.32), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 863 TYR 0.016 0.001 TYR A 595 PHE 0.014 0.001 PHE A 198 TRP 0.012 0.001 TRP A 382 HIS 0.006 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.23 (12867) covalent geometry : angle 0.58955 / 0.31 (17776) hydrogen bonds : bond 0.03999 / 2.71 ( 624) hydrogen bonds : angle 3.97619 / 2.89 ( 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 49 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9296 (mt) REVERT: A 604 MET cc_start: 0.9425 (tpp) cc_final: 0.8755 (tpp) REVERT: A 798 MET cc_start: 0.8220 (tmm) cc_final: 0.7905 (tmm) REVERT: A 806 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6410 (ttm) REVERT: A 911 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8368 (mt-10) REVERT: A 1260 MET cc_start: 0.9253 (mmm) cc_final: 0.8790 (mmt) outliers start: 15 outliers final: 10 residues processed: 47 average time/residue: 0.1016 time to fit residues: 7.8558 Evaluate side-chains 45 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 165 PHE 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 806 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 Chi-restraints excluded: chain A residue 1051 SER 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: 0.7980 chunk 98 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 HIS A 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.043956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.030879 restraints weight = 75056.438| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 4.11 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2289 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= 0.136 Angle : 0.542 9.882 17776 Z= 0.290 Chirality : 0.039 0.184 1972 Planarity : 0.003 0.041 1959 Dihedral : 20.150 152.108 2509 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.04 % Allowed : 13.98 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.25), residues: 1276 helix: 2.25 (0.21), residues: 642 sheet: 0.25 (0.40), residues: 138 loop : 0.99 (0.32), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.017 0.001 TYR A 595 PHE 0.011 0.001 PHE A 198 TRP 0.008 0.001 TRP A 382 HIS 0.004 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (12867) covalent geometry : angle 0.54163 / 0.29 (17776) hydrogen bonds : bond 0.03564 / 2.40 ( 624) hydrogen bonds : angle 3.87776 / 2.82 ( 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 45 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9302 (mt) REVERT: A 604 MET cc_start: 0.9419 (tpp) cc_final: 0.8746 (tpp) REVERT: A 798 MET cc_start: 0.8248 (tmm) cc_final: 0.7864 (tmm) REVERT: A 806 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6302 (ttm) REVERT: A 911 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8402 (mt-10) REVERT: A 1260 MET cc_start: 0.9238 (mmm) cc_final: 0.8786 (mmt) outliers start: 12 outliers final: 9 residues processed: 43 average time/residue: 0.1025 time to fit residues: 7.1651 Evaluate side-chains 44 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 806 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 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: 2.9990 chunk 81 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 HIS A 191 HIS 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 = 0.044257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.031091 restraints weight = 75260.522| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 4.14 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2428 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= 0.130 Angle : 0.539 11.301 17776 Z= 0.286 Chirality : 0.039 0.183 1972 Planarity : 0.003 0.040 1959 Dihedral : 20.068 150.918 2509 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 2.34 (0.25), residues: 1276 helix: 2.38 (0.21), residues: 634 sheet: 0.43 (0.41), residues: 136 loop : 0.94 (0.31), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.016 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 0.00267 / 0.13 (12867) covalent geometry : angle 0.53915 / 0.29 (17776) hydrogen bonds : bond 0.03423 / 2.30 ( 624) hydrogen bonds : angle 3.80451 / 2.75 ( 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 51 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9672 (OUTLIER) cc_final: 0.9305 (mt) REVERT: A 539 THR cc_start: 0.9352 (p) cc_final: 0.9079 (p) REVERT: A 798 MET cc_start: 0.8326 (tmm) cc_final: 0.8080 (tmm) REVERT: A 911 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8389 (mt-10) REVERT: A 1260 MET cc_start: 0.9258 (mmm) cc_final: 0.8826 (mmt) outliers start: 14 outliers final: 10 residues processed: 49 average time/residue: 0.0887 time to fit residues: 7.2498 Evaluate side-chains 46 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 806 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 Chi-restraints excluded: chain A residue 1051 SER 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: 1.9990 chunk 127 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 112 optimal weight: 0.0070 chunk 111 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- 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 = 0.3150 r_free = 0.3150 target = 0.044472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.031310 restraints weight = 75626.316| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 4.16 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2499 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= 0.117 Angle : 0.539 11.732 17776 Z= 0.285 Chirality : 0.039 0.183 1972 Planarity : 0.003 0.040 1959 Dihedral : 20.048 150.967 2509 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.78 % Allowed : 14.67 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.25), residues: 1276 helix: 2.43 (0.21), residues: 634 sheet: 0.27 (0.40), residues: 141 loop : 1.02 (0.32), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 909 TYR 0.016 0.001 TYR A 595 PHE 0.010 0.001 PHE A 198 TRP 0.007 0.001 TRP A1258 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (12867) covalent geometry : angle 0.53862 / 0.29 (17776) hydrogen bonds : bond 0.03337 / 2.23 ( 624) hydrogen bonds : angle 3.76437 / 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 45 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9702 (tp) cc_final: 0.9318 (pp) REVERT: A 356 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9303 (mt) REVERT: A 539 THR cc_start: 0.9355 (p) cc_final: 0.9093 (p) REVERT: A 795 MET cc_start: 0.9043 (tpp) cc_final: 0.8840 (mmp) REVERT: A 1260 MET cc_start: 0.9268 (mmm) cc_final: 0.8855 (mmt) REVERT: A 1307 ASN cc_start: 0.9421 (t0) cc_final: 0.9074 (p0) outliers start: 9 outliers final: 8 residues processed: 43 average time/residue: 0.1001 time to fit residues: 6.9891 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 : 0.544 ------------------------------------------------------------------------------- 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 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1051 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 4.9990 chunk 133 optimal weight: 30.0000 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 40 optimal weight: 0.1980 chunk 39 optimal weight: 7.9990 chunk 130 optimal weight: 50.0000 chunk 8 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- 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 = 0.3115 r_free = 0.3115 target = 0.043423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.030432 restraints weight = 74582.156| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 4.03 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12867 Z= 0.236 Angle : 0.606 11.507 17776 Z= 0.318 Chirality : 0.040 0.181 1972 Planarity : 0.004 0.040 1959 Dihedral : 20.179 152.267 2509 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.04 % Allowed : 14.67 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.25), residues: 1276 helix: 2.40 (0.21), residues: 641 sheet: 0.26 (0.41), residues: 141 loop : 0.98 (0.32), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 909 TYR 0.022 0.002 TYR A 173 PHE 0.016 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 0.00492 / 0.24 (12867) covalent geometry : angle 0.60606 / 0.32 (17776) hydrogen bonds : bond 0.04093 / 2.76 ( 624) hydrogen bonds : angle 3.93445 / 2.86 ( 1710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2038.99 seconds wall clock time: 36 minutes 14.38 seconds (2174.38 seconds total)