Starting phenix.real_space_refine on Wed May 14 23:41:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfh_40441/05_2025/8sfh_40441.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfh_40441/05_2025/8sfh_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_40441/05_2025/8sfh_40441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfh_40441/05_2025/8sfh_40441.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfh_40441/05_2025/8sfh_40441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfh_40441/05_2025/8sfh_40441.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.72, per 1000 atoms: 0.62 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: 3.26 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.77 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: 6.42 Time building geometry restraints manager: 3.72 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 1.490 1.559 -0.069 3.00e-02 1.11e+03 5.36e+00 bond pdb=" CB THR A 16 " pdb=" CG2 THR A 16 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.02e+00 bond pdb=" CA HIS A 415 " pdb=" C HIS A 415 " ideal model delta sigma weight residual 1.522 1.552 -0.030 1.52e-02 4.33e+03 3.90e+00 bond pdb=" CA ARG A 794 " pdb=" CB ARG A 794 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.32e-02 5.74e+03 3.76e+00 bond pdb=" CG1 ILE A 979 " pdb=" CD1 ILE A 979 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.56e+00 ... (remaining 12862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 17482 3.35 - 6.70: 232 6.70 - 10.05: 43 10.05 - 13.40: 14 13.40 - 16.75: 5 Bond angle restraints: 17776 Sorted by residual: 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=" CA LEU A 310 " pdb=" CB LEU A 310 " pdb=" CG LEU A 310 " ideal model delta sigma weight residual 116.30 133.05 -16.75 3.50e+00 8.16e-02 2.29e+01 angle pdb=" CA GLN A 937 " pdb=" CB GLN A 937 " pdb=" CG GLN A 937 " ideal model delta sigma weight residual 114.10 123.35 -9.25 2.00e+00 2.50e-01 2.14e+01 angle pdb=" O3' DT D 13 " pdb=" P DA D 14 " pdb=" OP1 DA D 14 " ideal model delta sigma weight residual 108.00 121.66 -13.66 3.00e+00 1.11e-01 2.07e+01 angle pdb=" C HIS A 415 " pdb=" CA HIS A 415 " pdb=" CB HIS A 415 " ideal model delta sigma weight residual 111.35 118.75 -7.40 1.72e+00 3.38e-01 1.85e+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 - 0.092: 1768 0.092 - 0.185: 174 0.185 - 0.277: 16 0.277 - 0.369: 7 0.369 - 0.462: 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 2.35 -2.81 -0.46 2.00e-01 2.50e+01 5.33e+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 2.35 -2.80 -0.46 2.00e-01 2.50e+01 5.22e+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 2.35 -2.80 -0.46 2.00e-01 2.50e+01 5.21e+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: 5.150 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 35.660 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 0.074 12867 Z= 0.245 Angle : 1.073 16.745 17776 Z= 0.545 Chirality : 0.064 0.462 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.027 0.003 TRP A 382 HIS 0.008 0.002 HIS A 368 PHE 0.027 0.003 PHE A1253 TYR 0.037 0.003 TYR A 83 ARG 0.020 0.001 ARG A1194 Details of bonding type rmsd hydrogen bonds : bond 0.13173 ( 624) hydrogen bonds : angle 5.76391 ( 1710) covalent geometry : bond 0.00557 (12867) covalent geometry : angle 1.07275 (17776) *********************** 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 : 1.338 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 56 average time/residue: 0.2673 time to fit residues: 22.8037 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 : 1.307 ------------------------------------------------------------------------------- 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 114 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS A 206 HIS A 552 ASN A 800 HIS ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 HIS A1167 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.043580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.030485 restraints weight = 75503.335| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 4.10 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12867 Z= 0.252 Angle : 0.645 9.998 17776 Z= 0.345 Chirality : 0.042 0.147 1972 Planarity : 0.004 0.076 1959 Dihedral : 20.064 151.472 2511 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.74 % Allowed : 11.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.24), residues: 1276 helix: 1.31 (0.21), residues: 645 sheet: -0.08 (0.40), residues: 141 loop : 0.75 (0.31), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 382 HIS 0.007 0.001 HIS A 415 PHE 0.017 0.002 PHE A1249 TYR 0.016 0.002 TYR A 61 ARG 0.007 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 624) hydrogen bonds : angle 4.39503 ( 1710) covalent geometry : bond 0.00536 (12867) covalent geometry : angle 0.64485 (17776) *********************** 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 57 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 1.363 Fit side-chains REVERT: A 328 GLU cc_start: 0.9754 (OUTLIER) cc_final: 0.9396 (tt0) REVERT: A 604 MET cc_start: 0.9549 (tpp) cc_final: 0.8789 (tpp) REVERT: A 766 THR cc_start: 0.9684 (OUTLIER) cc_final: 0.9461 (p) REVERT: A 911 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8431 (mt-10) REVERT: A 1014 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8779 (tm-30) REVERT: A 1260 MET cc_start: 0.9162 (mmm) cc_final: 0.8788 (mmm) outliers start: 20 outliers final: 5 residues processed: 53 average time/residue: 0.2349 time to fit residues: 19.9922 Evaluate side-chains 39 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 1051 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1290 GLN A1303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.043186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.030100 restraints weight = 75944.856| |-----------------------------------------------------------------------------| r_work (start): 0.2549 rms_B_bonded: 4.12 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12867 Z= 0.208 Angle : 0.582 9.452 17776 Z= 0.312 Chirality : 0.040 0.137 1972 Planarity : 0.004 0.059 1959 Dihedral : 20.065 153.822 2509 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.74 % Allowed : 11.81 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.25), residues: 1276 helix: 1.75 (0.21), residues: 647 sheet: -0.13 (0.40), residues: 143 loop : 0.90 (0.32), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 382 HIS 0.007 0.001 HIS A 415 PHE 0.014 0.001 PHE A 198 TYR 0.017 0.001 TYR A 595 ARG 0.004 0.000 ARG A1194 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 624) hydrogen bonds : angle 4.12217 ( 1710) covalent geometry : bond 0.00446 (12867) covalent geometry : angle 0.58246 (17776) *********************** 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 55 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 35 time to evaluate : 1.340 Fit side-chains REVERT: A 328 GLU cc_start: 0.9756 (OUTLIER) cc_final: 0.9415 (tt0) REVERT: A 356 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9292 (mt) REVERT: A 604 MET cc_start: 0.9601 (tpp) cc_final: 0.8851 (tpp) REVERT: A 766 THR cc_start: 0.9687 (OUTLIER) cc_final: 0.9477 (p) REVERT: A 795 MET cc_start: 0.9038 (tpp) cc_final: 0.8807 (mmm) REVERT: A 806 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6445 (ttm) REVERT: A 911 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8417 (mt-10) REVERT: A 1014 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8758 (tm-30) REVERT: A 1260 MET cc_start: 0.9248 (mmm) cc_final: 0.8984 (mmt) outliers start: 20 outliers final: 6 residues processed: 53 average time/residue: 0.2473 time to fit residues: 20.6635 Evaluate side-chains 42 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 328 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 766 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 75 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.043578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.030386 restraints weight = 75737.947| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 4.15 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12867 Z= 0.167 Angle : 0.549 11.791 17776 Z= 0.292 Chirality : 0.039 0.132 1972 Planarity : 0.003 0.051 1959 Dihedral : 19.926 152.478 2509 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.65 % Allowed : 12.41 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.25), residues: 1276 helix: 2.05 (0.21), residues: 643 sheet: 0.30 (0.41), residues: 136 loop : 0.91 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 382 HIS 0.006 0.001 HIS A 415 PHE 0.011 0.001 PHE A 198 TYR 0.016 0.001 TYR A 595 ARG 0.003 0.000 ARG A1194 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 624) hydrogen bonds : angle 3.87809 ( 1710) covalent geometry : bond 0.00359 (12867) covalent geometry : angle 0.54901 (17776) *********************** 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 56 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 1.235 Fit side-chains REVERT: A 141 LYS cc_start: 0.9594 (mmtt) cc_final: 0.9377 (mmtt) REVERT: A 328 GLU cc_start: 0.9772 (OUTLIER) cc_final: 0.9454 (tt0) REVERT: A 356 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9292 (mt) REVERT: A 604 MET cc_start: 0.9566 (tpp) cc_final: 0.8831 (tpp) REVERT: A 911 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8440 (mt-10) REVERT: A 1260 MET cc_start: 0.9280 (mmm) cc_final: 0.8958 (mmt) outliers start: 19 outliers final: 7 residues processed: 53 average time/residue: 0.2186 time to fit residues: 18.5985 Evaluate side-chains 41 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 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 82 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.043423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.030328 restraints weight = 73874.347| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 4.05 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12867 Z= 0.180 Angle : 0.551 11.010 17776 Z= 0.293 Chirality : 0.039 0.132 1972 Planarity : 0.003 0.046 1959 Dihedral : 19.955 152.489 2509 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.39 % Allowed : 13.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.25), residues: 1276 helix: 2.20 (0.21), residues: 641 sheet: 0.13 (0.40), residues: 143 loop : 1.01 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 382 HIS 0.005 0.001 HIS A1269 PHE 0.012 0.001 PHE A 198 TYR 0.016 0.001 TYR A 595 ARG 0.003 0.000 ARG A1194 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 624) hydrogen bonds : angle 3.85203 ( 1710) covalent geometry : bond 0.00386 (12867) covalent geometry : angle 0.55128 (17776) *********************** 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 48 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9772 (OUTLIER) cc_final: 0.9472 (tt0) REVERT: A 356 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9293 (mt) REVERT: A 604 MET cc_start: 0.9541 (tpp) cc_final: 0.8806 (tpp) REVERT: A 911 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8446 (mt-10) REVERT: A 1260 MET cc_start: 0.9248 (mmm) cc_final: 0.8868 (mmt) outliers start: 16 outliers final: 11 residues processed: 46 average time/residue: 0.2163 time to fit residues: 16.4136 Evaluate side-chains 43 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 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 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 976 ILE 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 86 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 133 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS A 977 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.044517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.031359 restraints weight = 75277.815| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 4.19 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 12867 Z= 0.109 Angle : 0.520 10.414 17776 Z= 0.272 Chirality : 0.038 0.132 1972 Planarity : 0.003 0.043 1959 Dihedral : 19.793 149.428 2509 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.39 % Allowed : 13.02 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.25), residues: 1276 helix: 2.40 (0.21), residues: 636 sheet: 0.41 (0.41), residues: 138 loop : 0.99 (0.31), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.004 0.001 HIS A 107 PHE 0.009 0.001 PHE A 871 TYR 0.025 0.001 TYR A 173 ARG 0.002 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.03103 ( 624) hydrogen bonds : angle 3.64038 ( 1710) covalent geometry : bond 0.00233 (12867) covalent geometry : angle 0.51992 (17776) *********************** 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 55 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9788 (OUTLIER) cc_final: 0.9354 (tm-30) REVERT: A 356 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9302 (mt) REVERT: A 387 ASN cc_start: 0.9571 (m-40) cc_final: 0.9151 (p0) REVERT: A 539 THR cc_start: 0.9351 (p) cc_final: 0.9088 (p) REVERT: A 911 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8419 (mt-10) REVERT: A 1260 MET cc_start: 0.9317 (mmm) cc_final: 0.9004 (mmt) REVERT: A 1307 ASN cc_start: 0.9415 (t0) cc_final: 0.9102 (p0) outliers start: 16 outliers final: 9 residues processed: 53 average time/residue: 0.2371 time to fit residues: 20.4581 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 : 1.281 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 18 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 HIS ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.042763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.029786 restraints weight = 74883.593| |-----------------------------------------------------------------------------| r_work (start): 0.2536 rms_B_bonded: 4.04 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12867 Z= 0.254 Angle : 0.600 9.794 17776 Z= 0.314 Chirality : 0.040 0.138 1972 Planarity : 0.003 0.041 1959 Dihedral : 20.087 153.842 2509 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.22 % Allowed : 13.54 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.25), residues: 1276 helix: 2.34 (0.21), residues: 646 sheet: 0.26 (0.41), residues: 143 loop : 1.09 (0.32), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 382 HIS 0.007 0.001 HIS A1269 PHE 0.015 0.001 PHE A 198 TYR 0.025 0.002 TYR A 173 ARG 0.004 0.000 ARG A 794 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 624) hydrogen bonds : angle 3.89344 ( 1710) covalent geometry : bond 0.00543 (12867) covalent geometry : angle 0.59963 (17776) *********************** 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 45 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: A 174 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8818 (pp20) REVERT: A 328 GLU cc_start: 0.9780 (OUTLIER) cc_final: 0.9476 (tt0) REVERT: A 356 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9261 (mt) REVERT: A 604 MET cc_start: 0.9526 (tpp) cc_final: 0.8760 (tpp) REVERT: A 911 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8470 (mt-10) REVERT: A 1260 MET cc_start: 0.9216 (mmm) cc_final: 0.8805 (mmt) REVERT: A 1307 ASN cc_start: 0.9452 (t0) cc_final: 0.9232 (t0) outliers start: 14 outliers final: 7 residues processed: 43 average time/residue: 0.2341 time to fit residues: 16.3974 Evaluate side-chains 41 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 174 GLU 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 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 43 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.043247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.030239 restraints weight = 74306.575| |-----------------------------------------------------------------------------| r_work (start): 0.2552 rms_B_bonded: 4.05 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12867 Z= 0.186 Angle : 0.559 10.273 17776 Z= 0.291 Chirality : 0.039 0.132 1972 Planarity : 0.003 0.040 1959 Dihedral : 20.069 152.471 2509 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.22 % Allowed : 14.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.25), residues: 1276 helix: 2.49 (0.21), residues: 636 sheet: 0.28 (0.41), residues: 143 loop : 0.99 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 382 HIS 0.006 0.001 HIS A1269 PHE 0.012 0.001 PHE A 198 TYR 0.023 0.001 TYR A 173 ARG 0.002 0.000 ARG A 794 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 624) hydrogen bonds : angle 3.78955 ( 1710) covalent geometry : bond 0.00402 (12867) covalent geometry : angle 0.55921 (17776) *********************** 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 46 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9780 (OUTLIER) cc_final: 0.9473 (tt0) REVERT: A 356 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9279 (mt) REVERT: A 604 MET cc_start: 0.9512 (tpp) cc_final: 0.8754 (tpp) REVERT: A 1260 MET cc_start: 0.9208 (mmm) cc_final: 0.8804 (mmt) REVERT: A 1307 ASN cc_start: 0.9435 (t0) cc_final: 0.9219 (t0) outliers start: 14 outliers final: 8 residues processed: 44 average time/residue: 0.2149 time to fit residues: 16.0951 Evaluate side-chains 40 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.044102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.031047 restraints weight = 74558.941| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 4.13 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12867 Z= 0.121 Angle : 0.536 11.488 17776 Z= 0.276 Chirality : 0.038 0.274 1972 Planarity : 0.003 0.040 1959 Dihedral : 19.907 149.488 2509 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.04 % Allowed : 14.50 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.25), residues: 1276 helix: 2.56 (0.21), residues: 636 sheet: 0.39 (0.40), residues: 141 loop : 1.01 (0.32), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.003 0.001 HIS A1269 PHE 0.009 0.001 PHE A 198 TYR 0.021 0.001 TYR A 173 ARG 0.003 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 624) hydrogen bonds : angle 3.63355 ( 1710) covalent geometry : bond 0.00265 (12867) covalent geometry : angle 0.53596 (17776) *********************** 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 45 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9693 (tp) cc_final: 0.9329 (pp) REVERT: A 328 GLU cc_start: 0.9790 (OUTLIER) cc_final: 0.9374 (tm-30) REVERT: A 356 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9286 (mt) REVERT: A 539 THR cc_start: 0.9355 (p) cc_final: 0.9076 (p) REVERT: A 604 MET cc_start: 0.9508 (tpp) cc_final: 0.8727 (tpp) REVERT: A 798 MET cc_start: 0.8269 (tmm) cc_final: 0.7809 (tmm) REVERT: A 1260 MET cc_start: 0.9292 (mmm) cc_final: 0.8949 (mmt) REVERT: A 1307 ASN cc_start: 0.9427 (t0) cc_final: 0.9179 (t0) outliers start: 12 outliers final: 9 residues processed: 43 average time/residue: 0.1979 time to fit residues: 14.6502 Evaluate side-chains 43 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 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 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 94 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 0.0170 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.042496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.029593 restraints weight = 75107.847| |-----------------------------------------------------------------------------| r_work (start): 0.2533 rms_B_bonded: 4.04 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12867 Z= 0.261 Angle : 0.610 11.940 17776 Z= 0.317 Chirality : 0.040 0.229 1972 Planarity : 0.003 0.040 1959 Dihedral : 20.173 153.393 2509 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.95 % Allowed : 14.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.25), residues: 1276 helix: 2.41 (0.21), residues: 647 sheet: 0.22 (0.41), residues: 145 loop : 0.98 (0.32), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 382 HIS 0.006 0.001 HIS A1269 PHE 0.015 0.001 PHE A 198 TYR 0.028 0.002 TYR A 173 ARG 0.004 0.000 ARG A 386 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 624) hydrogen bonds : angle 3.92836 ( 1710) covalent geometry : bond 0.00556 (12867) covalent geometry : angle 0.61008 (17776) ********************** 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 40 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9788 (OUTLIER) cc_final: 0.9485 (tt0) REVERT: A 356 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9252 (mt) REVERT: A 604 MET cc_start: 0.9487 (tpp) cc_final: 0.8705 (tpp) REVERT: A 1260 MET cc_start: 0.9184 (mmm) cc_final: 0.8759 (mmt) REVERT: A 1307 ASN cc_start: 0.9462 (t0) cc_final: 0.9250 (t0) outliers start: 11 outliers final: 8 residues processed: 38 average time/residue: 0.1995 time to fit residues: 13.1195 Evaluate side-chains 39 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 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 19 optimal weight: 4.9990 chunk 86 optimal weight: 0.0370 chunk 81 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.043481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.030538 restraints weight = 73666.862| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 4.05 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.3138 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= 0.142 Angle : 0.554 12.722 17776 Z= 0.284 Chirality : 0.038 0.227 1972 Planarity : 0.003 0.039 1959 Dihedral : 20.067 151.099 2509 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.95 % Allowed : 14.58 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.25), residues: 1276 helix: 2.56 (0.21), residues: 637 sheet: 0.43 (0.41), residues: 141 loop : 0.98 (0.31), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 382 HIS 0.005 0.001 HIS A1269 PHE 0.011 0.001 PHE A 198 TYR 0.021 0.001 TYR A 173 ARG 0.005 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 624) hydrogen bonds : angle 3.74311 ( 1710) covalent geometry : bond 0.00310 (12867) covalent geometry : angle 0.55398 (17776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3965.64 seconds wall clock time: 70 minutes 34.01 seconds (4234.01 seconds total)