Starting phenix.real_space_refine on Wed Aug 5 22:30:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfp_40447/08_2026/8sfp_40447.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfp_40447/08_2026/8sfp_40447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sfp_40447/08_2026/8sfp_40447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfp_40447/08_2026/8sfp_40447.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfp_40447/08_2026/8sfp_40447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfp_40447/08_2026/8sfp_40447.cif" } resolution = 3.8 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= 0.032 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 92 5.49 5 S 23 5.16 5 C 7404 2.51 5 N 2053 2.21 5 O 2490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12062 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1240, 10138 Classifications: {'peptide': 1240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1193} Chain breaks: 2 Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 826 Classifications: {'RNA': 39} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 16, 'rna3p_pyr': 16} Link IDs: {'rna2p': 6, 'rna3p': 32} Chain: "C" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 731 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 2.87, per 1000 atoms: 0.24 Number of scatterers: 12062 At special positions: 0 Unit cell: (90.8188, 99.984, 134.145, 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 23 16.00 P 92 15.00 O 2490 8.00 N 2053 7.00 C 7404 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: 1.01 Conformation dependent library (CDL) restraints added in 542.0 milliseconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 53.5% alpha, 11.0% beta 35 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.540A pdb=" N PHE A 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 66 Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 73 through 86 Processing helix chain 'A' and resid 88 through 112 removed outlier: 4.028A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 134 through 138 removed outlier: 4.195A pdb=" N LEU A 137 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 138 " --> pdb=" O ALA A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 134 through 138' Processing helix chain 'A' and resid 140 through 146 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 180 removed outlier: 3.703A pdb=" N ASN A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 215 removed outlier: 3.744A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 230 removed outlier: 3.785A pdb=" N GLU A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 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 343 Processing helix chain 'A' and resid 344 through 357 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 416 removed outlier: 3.932A pdb=" N LYS A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N HIS A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 Processing helix chain 'A' and resid 428 through 452 removed outlier: 3.836A pdb=" N SER A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.706A pdb=" N LYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 removed outlier: 5.006A pdb=" N GLU A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 522 removed outlier: 4.090A pdb=" N SER A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 612 through 622 removed outlier: 4.037A pdb=" N THR A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.590A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.654A 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 700 through 704 Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 759 through 770 removed outlier: 3.749A 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 861 through 865 Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 940 through 957 Processing helix chain 'A' and resid 964 through 987 Processing helix chain 'A' and resid 996 through 1007 Processing helix chain 'A' and resid 1013 through 1025 removed outlier: 3.896A pdb=" N LYS A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1100 removed outlier: 3.536A pdb=" N GLY A1100 " --> pdb=" O HIS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1198 through 1205 removed outlier: 4.039A pdb=" N LYS A1202 " --> pdb=" O ASN A1198 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU A1205 " --> pdb=" O PRO A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1223 removed outlier: 3.552A pdb=" N ILE A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1254 removed outlier: 3.630A pdb=" N GLN A1254 " --> pdb=" O SER A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1284 Processing helix chain 'A' and resid 1294 through 1307 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 removed outlier: 4.618A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 5.468A 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 532 Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 366 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 926 through 931 removed outlier: 6.555A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER A 931 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE A 915 " --> pdb=" O SER A 931 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A 905 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLU A 993 " --> pdb=" O ILE A 905 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ILE A 907 " --> pdb=" O GLU A 993 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 934 through 935 Processing sheet with id=AA7, first strand: chain 'A' and resid 1104 through 1106 Processing sheet with id=AA8, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AA9, first strand: chain 'A' and resid 1159 through 1166 removed outlier: 4.351A pdb=" N ARG A1172 " --> pdb=" O VAL A1163 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLU A1165 " --> pdb=" O THR A1170 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR A1170 " --> pdb=" O GLU A1165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1226 through 1229 524 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3142 1.34 - 1.46: 3137 1.46 - 1.58: 6018 1.58 - 1.70: 184 1.70 - 1.82: 38 Bond restraints: 12519 Sorted by residual: bond pdb=" C1' DT D 19 " pdb=" N1 DT D 19 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.43e+01 bond pdb=" C1' DC C 5 " pdb=" N1 DC C 5 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" C1' DT C 15 " pdb=" N1 DT C 15 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.39e+00 bond pdb=" C3' DA C 6 " pdb=" C2' DA C 6 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.58e+00 bond pdb=" C3' DC C 19 " pdb=" C2' DC C 19 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.83e+00 ... (remaining 12514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.99: 17137 4.99 - 9.97: 144 9.97 - 14.96: 37 14.96 - 19.95: 4 19.95 - 24.93: 1 Bond angle restraints: 17323 Sorted by residual: angle pdb=" O3' DG D 6 " pdb=" P DA D 7 " pdb=" OP1 DA D 7 " ideal model delta sigma weight residual 108.00 132.93 -24.93 3.00e+00 1.11e-01 6.91e+01 angle pdb=" CA PRO A 716 " pdb=" N PRO A 716 " pdb=" CD PRO A 716 " ideal model delta sigma weight residual 112.00 102.94 9.06 1.40e+00 5.10e-01 4.18e+01 angle pdb=" CA GLU A 901 " pdb=" CB GLU A 901 " pdb=" CG GLU A 901 " ideal model delta sigma weight residual 114.10 126.35 -12.25 2.00e+00 2.50e-01 3.75e+01 angle pdb=" CA LYS A1035 " pdb=" CB LYS A1035 " pdb=" CG LYS A1035 " ideal model delta sigma weight residual 114.10 125.46 -11.36 2.00e+00 2.50e-01 3.23e+01 angle pdb=" CA MET A1215 " pdb=" CB MET A1215 " pdb=" CG MET A1215 " ideal model delta sigma weight residual 114.10 125.21 -11.11 2.00e+00 2.50e-01 3.08e+01 ... (remaining 17318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.99: 6712 28.99 - 57.97: 655 57.97 - 86.96: 80 86.96 - 115.94: 3 115.94 - 144.93: 3 Dihedral angle restraints: 7453 sinusoidal: 3795 harmonic: 3658 Sorted by residual: 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 55.07 144.93 1 1.50e+01 4.44e-03 7.76e+01 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 58.43 141.57 1 1.50e+01 4.44e-03 7.61e+01 dihedral pdb=" CA TYR A1177 " pdb=" C TYR A1177 " pdb=" N PRO A1178 " pdb=" CA PRO A1178 " ideal model delta harmonic sigma weight residual 180.00 -158.95 -21.05 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 7450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1888 0.147 - 0.294: 26 0.294 - 0.440: 18 0.440 - 0.587: 0 0.587 - 0.734: 1 Chirality restraints: 1933 Sorted by residual: chirality pdb=" P DA D 7 " pdb=" OP1 DA D 7 " pdb=" OP2 DA D 7 " pdb=" O5' DA D 7 " both_signs ideal model delta sigma weight residual True 2.34 -3.07 -0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" P DA C 22 " pdb=" OP1 DA C 22 " pdb=" OP2 DA C 22 " pdb=" O5' DA C 22 " both_signs ideal model delta sigma weight residual True 2.34 -2.77 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" P DA C 28 " pdb=" OP1 DA C 28 " pdb=" OP2 DA C 28 " pdb=" O5' DA C 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.76 -0.43 2.00e-01 2.50e+01 4.58e+00 ... (remaining 1930 not shown) Planarity restraints: 1896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 683 " 0.023 2.00e-02 2.50e+03 3.09e-02 1.67e+01 pdb=" CG PHE A 683 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 683 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 683 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE A 683 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 683 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 683 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1079 " -0.020 2.00e-02 2.50e+03 2.99e-02 1.56e+01 pdb=" CG PHE A1079 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE A1079 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A1079 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE A1079 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A1079 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A1079 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 715 " -0.063 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO A 716 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 716 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 716 " -0.050 5.00e-02 4.00e+02 ... (remaining 1893 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2733 2.78 - 3.31: 11473 3.31 - 3.84: 22430 3.84 - 4.37: 24770 4.37 - 4.90: 39378 Nonbonded interactions: 100784 Sorted by model distance: nonbonded pdb=" O ALA A1211 " pdb=" OG1 THR A1214 " model vdw 2.256 3.040 nonbonded pdb=" O PHE A 138 " pdb=" NH2 ARG A 160 " model vdw 2.297 3.120 nonbonded pdb=" NH1 ARG A 955 " pdb=" O2' G B 30 " model vdw 2.299 3.120 nonbonded pdb=" O ILE A 294 " pdb=" OG SER A 297 " model vdw 2.302 3.040 nonbonded pdb=" OG1 THR A 151 " pdb=" OD1 ASN A 156 " model vdw 2.316 3.040 ... (remaining 100779 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.480 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.005 0.089 12519 Z= 0.332 Angle : 1.220 24.934 17323 Z= 0.684 Chirality : 0.069 0.734 1933 Planarity : 0.007 0.090 1896 Dihedral : 20.761 144.926 5085 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.54 % Allowed : 29.33 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.22), residues: 1234 helix: -0.62 (0.19), residues: 606 sheet: -0.12 (0.43), residues: 146 loop : -0.52 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 411 TYR 0.054 0.002 TYR A1236 PHE 0.071 0.003 PHE A 683 TRP 0.021 0.002 TRP A 676 HIS 0.009 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.33 (12519) covalent geometry : angle 1.22014 / 0.68 (17323) hydrogen bonds : bond 0.13418 / 9.03 ( 600) hydrogen bonds : angle 5.99612 / 4.21 ( 1646) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 PHE cc_start: 0.9096 (m-80) cc_final: 0.8755 (m-80) REVERT: A 507 MET cc_start: 0.9216 (mmm) cc_final: 0.8938 (mmp) REVERT: A 1176 LEU cc_start: 0.9315 (tt) cc_final: 0.9069 (mm) outliers start: 6 outliers final: 1 residues processed: 111 average time/residue: 0.0952 time to fit residues: 16.4385 Evaluate side-chains 75 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 24 GLN A 178 ASN ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 HIS A 308 GLN A 331 GLN A 363 HIS ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN A 929 GLN A 974 GLN A1116 HIS ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1254 GLN A1265 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.037353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.027494 restraints weight = 91809.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.028716 restraints weight = 46086.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.029548 restraints weight = 29795.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.030117 restraints weight = 22155.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.030540 restraints weight = 18030.807| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12519 Z= 0.331 Angle : 0.801 9.319 17323 Z= 0.435 Chirality : 0.046 0.270 1933 Planarity : 0.005 0.056 1896 Dihedral : 20.335 150.985 2537 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.16 % Allowed : 24.19 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.23), residues: 1234 helix: 0.50 (0.20), residues: 615 sheet: -0.43 (0.45), residues: 130 loop : -0.33 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 411 TYR 0.020 0.002 TYR A 940 PHE 0.021 0.002 PHE A 938 TRP 0.012 0.002 TRP A 765 HIS 0.007 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.33 (12519) covalent geometry : angle 0.80110 / 0.44 (17323) hydrogen bonds : bond 0.05951 / 3.96 ( 600) hydrogen bonds : angle 4.93933 / 3.51 ( 1646) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 65 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9440 (OUTLIER) cc_final: 0.9071 (m-30) REVERT: A 353 PHE cc_start: 0.9408 (m-80) cc_final: 0.9187 (m-80) REVERT: A 507 MET cc_start: 0.9676 (mmm) cc_final: 0.9373 (mmm) REVERT: A 604 MET cc_start: 0.9243 (mmm) cc_final: 0.8896 (mmm) REVERT: A 1018 MET cc_start: 0.9444 (mmp) cc_final: 0.9240 (mmp) outliers start: 35 outliers final: 16 residues processed: 94 average time/residue: 0.0890 time to fit residues: 13.0187 Evaluate side-chains 77 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.038109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.028109 restraints weight = 87632.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.029394 restraints weight = 43618.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.030292 restraints weight = 27904.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.030858 restraints weight = 20502.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.031295 restraints weight = 16639.894| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12519 Z= 0.161 Angle : 0.670 10.962 17323 Z= 0.355 Chirality : 0.043 0.261 1933 Planarity : 0.004 0.042 1896 Dihedral : 20.375 151.520 2537 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.62 % Allowed : 23.10 % Favored : 74.28 % 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: 0.54 (0.24), residues: 1234 helix: 0.98 (0.21), residues: 613 sheet: -0.38 (0.44), residues: 139 loop : -0.06 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 411 TYR 0.019 0.001 TYR A1236 PHE 0.013 0.001 PHE A1015 TRP 0.006 0.001 TRP A 765 HIS 0.006 0.001 HIS A 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (12519) covalent geometry : angle 0.66990 / 0.36 (17323) hydrogen bonds : bond 0.04705 / 3.13 ( 600) hydrogen bonds : angle 4.54943 / 3.24 ( 1646) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9403 (OUTLIER) cc_final: 0.9038 (m-30) REVERT: A 203 GLU cc_start: 0.9604 (tp30) cc_final: 0.9387 (tp30) REVERT: A 353 PHE cc_start: 0.9397 (m-80) cc_final: 0.9067 (m-80) REVERT: A 507 MET cc_start: 0.9660 (mmm) cc_final: 0.9373 (mmm) REVERT: A 604 MET cc_start: 0.9210 (mmm) cc_final: 0.8893 (mmm) outliers start: 29 outliers final: 12 residues processed: 92 average time/residue: 0.0961 time to fit residues: 13.7505 Evaluate side-chains 75 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 108 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 HIS ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.037838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.027967 restraints weight = 89079.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.029278 restraints weight = 44007.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.030166 restraints weight = 28004.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.030785 restraints weight = 20477.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.031151 restraints weight = 16347.755| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12519 Z= 0.169 Angle : 0.644 11.269 17323 Z= 0.342 Chirality : 0.042 0.259 1933 Planarity : 0.003 0.040 1896 Dihedral : 20.305 151.261 2537 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.07 % Allowed : 22.29 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.24), residues: 1234 helix: 1.06 (0.21), residues: 618 sheet: -0.34 (0.43), residues: 139 loop : 0.07 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1306 TYR 0.016 0.001 TYR A 61 PHE 0.010 0.001 PHE A 241 TRP 0.006 0.001 TRP A 765 HIS 0.004 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (12519) covalent geometry : angle 0.64357 / 0.34 (17323) hydrogen bonds : bond 0.04520 / 3.01 ( 600) hydrogen bonds : angle 4.43243 / 3.17 ( 1646) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9423 (OUTLIER) cc_final: 0.9050 (m-30) REVERT: A 203 GLU cc_start: 0.9619 (tp30) cc_final: 0.9276 (tp30) REVERT: A 353 PHE cc_start: 0.9386 (m-80) cc_final: 0.9167 (m-80) REVERT: A 507 MET cc_start: 0.9704 (mmm) cc_final: 0.9397 (mmm) REVERT: A 604 MET cc_start: 0.9256 (mmm) cc_final: 0.8894 (mmm) outliers start: 34 outliers final: 22 residues processed: 91 average time/residue: 0.0862 time to fit residues: 12.6099 Evaluate side-chains 84 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1294 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 GLN ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.036766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.026927 restraints weight = 92065.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.028211 restraints weight = 45270.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.029067 restraints weight = 28775.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.029661 restraints weight = 21158.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.030021 restraints weight = 17024.054| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12519 Z= 0.248 Angle : 0.672 11.301 17323 Z= 0.364 Chirality : 0.044 0.423 1933 Planarity : 0.004 0.041 1896 Dihedral : 20.333 150.563 2537 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.43 % Allowed : 22.56 % Favored : 74.01 % 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: 0.67 (0.24), residues: 1234 helix: 1.09 (0.21), residues: 616 sheet: -0.47 (0.43), residues: 139 loop : 0.05 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1306 TYR 0.021 0.002 TYR A 61 PHE 0.013 0.002 PHE A 165 TRP 0.007 0.001 TRP A 765 HIS 0.005 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.25 (12519) covalent geometry : angle 0.67159 / 0.36 (17323) hydrogen bonds : bond 0.04931 / 3.30 ( 600) hydrogen bonds : angle 4.52512 / 3.24 ( 1646) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 60 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9426 (OUTLIER) cc_final: 0.9144 (m-30) REVERT: A 202 LYS cc_start: 0.9621 (OUTLIER) cc_final: 0.9004 (ttmt) REVERT: A 203 GLU cc_start: 0.9628 (tp30) cc_final: 0.9320 (tp30) REVERT: A 353 PHE cc_start: 0.9413 (m-80) cc_final: 0.9188 (m-80) REVERT: A 507 MET cc_start: 0.9718 (mmm) cc_final: 0.9411 (mmm) REVERT: A 604 MET cc_start: 0.9336 (mmm) cc_final: 0.8980 (mmm) REVERT: A 714 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9410 (pp) outliers start: 38 outliers final: 27 residues processed: 91 average time/residue: 0.0854 time to fit residues: 12.1659 Evaluate side-chains 86 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 56 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1294 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 178 ASN A 221 HIS ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.037951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.027994 restraints weight = 87696.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.029309 restraints weight = 43412.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.030217 restraints weight = 27636.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.030796 restraints weight = 20230.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.031208 restraints weight = 16332.936| |-----------------------------------------------------------------------------| r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12519 Z= 0.123 Angle : 0.644 12.668 17323 Z= 0.335 Chirality : 0.042 0.252 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.294 149.603 2537 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.89 % Allowed : 23.19 % Favored : 73.92 % 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: 0.85 (0.24), residues: 1234 helix: 1.17 (0.21), residues: 615 sheet: -0.31 (0.44), residues: 139 loop : 0.21 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1306 TYR 0.018 0.001 TYR A 61 PHE 0.011 0.001 PHE A1103 TRP 0.006 0.001 TRP A 676 HIS 0.005 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (12519) covalent geometry : angle 0.64427 / 0.34 (17323) hydrogen bonds : bond 0.04192 / 2.79 ( 600) hydrogen bonds : angle 4.31590 / 3.07 ( 1646) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9393 (OUTLIER) cc_final: 0.9102 (m-30) REVERT: A 202 LYS cc_start: 0.9596 (OUTLIER) cc_final: 0.8966 (ttmt) REVERT: A 203 GLU cc_start: 0.9615 (tp30) cc_final: 0.9236 (tp30) REVERT: A 507 MET cc_start: 0.9720 (mmm) cc_final: 0.9380 (mmm) REVERT: A 593 MET cc_start: 0.9583 (tmm) cc_final: 0.9298 (tmm) REVERT: A 604 MET cc_start: 0.9222 (mmm) cc_final: 0.8807 (mmm) REVERT: A 965 LYS cc_start: 0.9652 (OUTLIER) cc_final: 0.9245 (mmmm) REVERT: A 1063 PHE cc_start: 0.9352 (m-80) cc_final: 0.9106 (m-10) outliers start: 32 outliers final: 19 residues processed: 90 average time/residue: 0.0807 time to fit residues: 11.2660 Evaluate side-chains 85 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1294 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.0040 chunk 122 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 127 optimal weight: 40.0000 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.038259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.028351 restraints weight = 87917.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.029680 restraints weight = 43443.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.030592 restraints weight = 27612.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.031190 restraints weight = 20123.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.031617 restraints weight = 16208.043| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12519 Z= 0.125 Angle : 0.641 12.832 17323 Z= 0.331 Chirality : 0.042 0.336 1933 Planarity : 0.003 0.037 1896 Dihedral : 20.207 149.110 2537 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.26 % Allowed : 23.29 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.98 (0.24), residues: 1234 helix: 1.27 (0.21), residues: 616 sheet: -0.25 (0.44), residues: 139 loop : 0.29 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1306 TYR 0.014 0.001 TYR A 61 PHE 0.009 0.001 PHE A1103 TRP 0.005 0.001 TRP A1085 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (12519) covalent geometry : angle 0.64150 / 0.33 (17323) hydrogen bonds : bond 0.04112 / 2.71 ( 600) hydrogen bonds : angle 4.24737 / 3.02 ( 1646) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9385 (OUTLIER) cc_final: 0.9089 (m-30) REVERT: A 202 LYS cc_start: 0.9590 (OUTLIER) cc_final: 0.8953 (ttmt) REVERT: A 203 GLU cc_start: 0.9618 (tp30) cc_final: 0.9241 (tp30) REVERT: A 251 THR cc_start: 0.9357 (m) cc_final: 0.9129 (p) REVERT: A 507 MET cc_start: 0.9728 (mmm) cc_final: 0.9384 (mmm) REVERT: A 604 MET cc_start: 0.9264 (mmm) cc_final: 0.8840 (mmm) REVERT: A 965 LYS cc_start: 0.9649 (OUTLIER) cc_final: 0.9237 (mmmm) REVERT: A 1063 PHE cc_start: 0.9353 (m-80) cc_final: 0.9111 (m-10) outliers start: 25 outliers final: 19 residues processed: 84 average time/residue: 0.0960 time to fit residues: 12.3598 Evaluate side-chains 83 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1294 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 8.9990 chunk 129 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.037816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.027984 restraints weight = 88213.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.029294 restraints weight = 43822.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.030159 restraints weight = 27898.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.030769 restraints weight = 20527.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.031131 restraints weight = 16471.020| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12519 Z= 0.156 Angle : 0.641 12.221 17323 Z= 0.334 Chirality : 0.041 0.241 1933 Planarity : 0.003 0.037 1896 Dihedral : 20.215 149.246 2537 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.16 % Allowed : 22.47 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.24), residues: 1234 helix: 1.39 (0.21), residues: 615 sheet: -0.30 (0.44), residues: 139 loop : 0.28 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1306 TYR 0.014 0.001 TYR A 61 PHE 0.009 0.001 PHE A 133 TRP 0.005 0.001 TRP A1085 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (12519) covalent geometry : angle 0.64119 / 0.33 (17323) hydrogen bonds : bond 0.04191 / 2.79 ( 600) hydrogen bonds : angle 4.28740 / 3.05 ( 1646) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9403 (OUTLIER) cc_final: 0.9092 (m-30) REVERT: A 202 LYS cc_start: 0.9591 (OUTLIER) cc_final: 0.8973 (ttmt) REVERT: A 203 GLU cc_start: 0.9618 (tp30) cc_final: 0.9227 (tp30) REVERT: A 251 THR cc_start: 0.9345 (m) cc_final: 0.9112 (p) REVERT: A 507 MET cc_start: 0.9733 (mmm) cc_final: 0.9387 (mmm) REVERT: A 593 MET cc_start: 0.9577 (tmm) cc_final: 0.9273 (tmm) REVERT: A 604 MET cc_start: 0.9288 (mmm) cc_final: 0.8846 (mmm) REVERT: A 965 LYS cc_start: 0.9644 (OUTLIER) cc_final: 0.9258 (mmmm) REVERT: A 1009 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8830 (ttpp) REVERT: A 1063 PHE cc_start: 0.9345 (m-80) cc_final: 0.9109 (m-10) outliers start: 35 outliers final: 25 residues processed: 89 average time/residue: 0.0817 time to fit residues: 11.2292 Evaluate side-chains 90 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1294 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 19 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 124 optimal weight: 30.0000 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.037937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.028073 restraints weight = 88533.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.029387 restraints weight = 43808.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.030251 restraints weight = 27856.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.030875 restraints weight = 20496.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.031305 restraints weight = 16451.152| |-----------------------------------------------------------------------------| r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12519 Z= 0.138 Angle : 0.661 13.967 17323 Z= 0.338 Chirality : 0.041 0.244 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.217 148.955 2537 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.98 % Allowed : 22.74 % Favored : 74.28 % 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: 1.08 (0.24), residues: 1234 helix: 1.38 (0.21), residues: 615 sheet: -0.27 (0.44), residues: 139 loop : 0.32 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1306 TYR 0.016 0.001 TYR A 61 PHE 0.016 0.001 PHE A1015 TRP 0.006 0.001 TRP A1258 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (12519) covalent geometry : angle 0.66091 / 0.34 (17323) hydrogen bonds : bond 0.04103 / 2.74 ( 600) hydrogen bonds : angle 4.27413 / 3.04 ( 1646) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 63 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9394 (OUTLIER) cc_final: 0.9078 (m-30) REVERT: A 202 LYS cc_start: 0.9584 (OUTLIER) cc_final: 0.8945 (ttmt) REVERT: A 203 GLU cc_start: 0.9616 (tp30) cc_final: 0.9214 (tp30) REVERT: A 251 THR cc_start: 0.9356 (m) cc_final: 0.9120 (p) REVERT: A 507 MET cc_start: 0.9731 (mmm) cc_final: 0.9380 (mmm) REVERT: A 593 MET cc_start: 0.9567 (tmm) cc_final: 0.9256 (tmm) REVERT: A 604 MET cc_start: 0.9279 (mmm) cc_final: 0.8852 (mmm) REVERT: A 965 LYS cc_start: 0.9547 (OUTLIER) cc_final: 0.9266 (mmmm) REVERT: A 1063 PHE cc_start: 0.9333 (m-80) cc_final: 0.9109 (m-10) outliers start: 33 outliers final: 24 residues processed: 89 average time/residue: 0.0859 time to fit residues: 11.7561 Evaluate side-chains 88 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 117 optimal weight: 0.0170 chunk 44 optimal weight: 8.9990 chunk 60 optimal weight: 0.2980 chunk 98 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.038377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.028466 restraints weight = 87324.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.029787 restraints weight = 43260.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.030696 restraints weight = 27564.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.031290 restraints weight = 20117.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.031713 restraints weight = 16211.500| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 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 0.042 12519 Z= 0.122 Angle : 0.669 12.807 17323 Z= 0.336 Chirality : 0.042 0.255 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.187 148.656 2537 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.53 % Allowed : 23.29 % Favored : 74.19 % 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: 1.14 (0.24), residues: 1234 helix: 1.42 (0.21), residues: 609 sheet: -0.20 (0.44), residues: 139 loop : 0.37 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1306 TYR 0.014 0.001 TYR A 61 PHE 0.010 0.001 PHE A1103 TRP 0.006 0.001 TRP A 676 HIS 0.008 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (12519) covalent geometry : angle 0.66910 / 0.34 (17323) hydrogen bonds : bond 0.03961 / 2.63 ( 600) hydrogen bonds : angle 4.24835 / 3.02 ( 1646) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9391 (OUTLIER) cc_final: 0.9071 (m-30) REVERT: A 202 LYS cc_start: 0.9584 (OUTLIER) cc_final: 0.8952 (ttmt) REVERT: A 203 GLU cc_start: 0.9620 (tp30) cc_final: 0.9205 (tp30) REVERT: A 251 THR cc_start: 0.9344 (m) cc_final: 0.9099 (p) REVERT: A 305 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9276 (mm) REVERT: A 507 MET cc_start: 0.9723 (mmm) cc_final: 0.9365 (mmm) REVERT: A 604 MET cc_start: 0.9253 (mmm) cc_final: 0.8810 (mmm) REVERT: A 965 LYS cc_start: 0.9535 (OUTLIER) cc_final: 0.9276 (mmmm) REVERT: A 1063 PHE cc_start: 0.9306 (m-80) cc_final: 0.9099 (m-10) outliers start: 28 outliers final: 21 residues processed: 86 average time/residue: 0.0899 time to fit residues: 12.0235 Evaluate side-chains 88 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 39 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.037892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.028048 restraints weight = 88556.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.029357 restraints weight = 43743.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.030230 restraints weight = 27827.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.030844 restraints weight = 20418.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.031273 restraints weight = 16343.516| |-----------------------------------------------------------------------------| r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12519 Z= 0.147 Angle : 0.677 15.688 17323 Z= 0.342 Chirality : 0.042 0.321 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.188 148.601 2537 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.53 % Allowed : 23.47 % Favored : 74.01 % 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: 1.17 (0.24), residues: 1234 helix: 1.45 (0.21), residues: 609 sheet: -0.19 (0.44), residues: 139 loop : 0.37 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1306 TYR 0.016 0.001 TYR A 61 PHE 0.019 0.001 PHE A1015 TRP 0.006 0.001 TRP A1085 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (12519) covalent geometry : angle 0.67747 / 0.34 (17323) hydrogen bonds : bond 0.04110 / 2.74 ( 600) hydrogen bonds : angle 4.26383 / 3.03 ( 1646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1677.59 seconds wall clock time: 30 minutes 3.02 seconds (1803.02 seconds total)