Starting phenix.real_space_refine on Sat Aug 23 12:38:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfp_40447/08_2025/8sfp_40447.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfp_40447/08_2025/8sfp_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sfp_40447/08_2025/8sfp_40447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfp_40447/08_2025/8sfp_40447.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sfp_40447/08_2025/8sfp_40447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfp_40447/08_2025/8sfp_40447.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.02, per 1000 atoms: 0.25 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: 0.99 Conformation dependent library (CDL) restraints added in 419.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.61 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: 3.21 Time building geometry restraints manager: 1.26 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=" CB LYS A 123 " pdb=" CG LYS A 123 " ideal model delta sigma weight residual 1.520 1.579 -0.059 3.00e-02 1.11e+03 3.92e+00 bond pdb=" C GLU A 651 " pdb=" N PRO A 652 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.88e+00 bond pdb=" CB ASP A 184 " pdb=" CG ASP A 184 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.63e+00 bond pdb=" CB LYS A1035 " pdb=" CG LYS A1035 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.62e+00 bond pdb=" CB GLU A 901 " pdb=" CG GLU A 901 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.51e+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 - 0.145: 1888 0.145 - 0.290: 26 0.290 - 0.434: 18 0.434 - 0.579: 0 0.579 - 0.724: 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 2.35 -3.07 -0.72 2.00e-01 2.50e+01 1.31e+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 2.35 -2.77 -0.42 2.00e-01 2.50e+01 4.43e+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 2.35 -2.76 -0.42 2.00e-01 2.50e+01 4.36e+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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.490 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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= 0.224 Angle : 1.186 24.934 17323 Z= 0.560 Chirality : 0.065 0.724 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 aren 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 covalent geometry : bond 0.00505 (12519) covalent geometry : angle 1.18571 (17323) hydrogen bonds : bond 0.13418 ( 600) hydrogen bonds : angle 5.99612 ( 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 : 0.391 Fit side-chains revert: symmetry clash 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: 0.8754 (m-80) REVERT: A 507 MET cc_start: 0.9216 (mmm) cc_final: 0.8939 (mmp) REVERT: A 1176 LEU cc_start: 0.9315 (tt) cc_final: 0.9070 (mm) outliers start: 6 outliers final: 1 residues processed: 111 average time/residue: 0.0945 time to fit residues: 15.9706 Evaluate side-chains 76 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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: 7.9990 chunk 124 optimal weight: 10.0000 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: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 HIS ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 929 GLN A1116 HIS ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1254 GLN A1265 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.036315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.026548 restraints weight = 93119.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.027748 restraints weight = 46886.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.028555 restraints weight = 30312.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.029100 restraints weight = 22569.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.029491 restraints weight = 18439.329| |-----------------------------------------------------------------------------| r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 12519 Z= 0.358 Angle : 0.769 9.322 17323 Z= 0.414 Chirality : 0.044 0.175 1933 Planarity : 0.005 0.055 1896 Dihedral : 20.490 153.821 2537 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.06 % Allowed : 22.92 % Favored : 73.01 % 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 aren not related in a simple way. whole: 0.18 (0.24), residues: 1234 helix: 0.64 (0.20), residues: 615 sheet: -0.57 (0.43), residues: 141 loop : -0.15 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 411 TYR 0.020 0.002 TYR A 61 PHE 0.020 0.002 PHE A 165 TRP 0.011 0.002 TRP A 765 HIS 0.007 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00721 (12519) covalent geometry : angle 0.76912 (17323) hydrogen bonds : bond 0.05387 ( 600) hydrogen bonds : angle 4.84056 ( 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 106 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 61 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9441 (OUTLIER) cc_final: 0.9089 (m-30) REVERT: A 203 GLU cc_start: 0.9614 (tp30) cc_final: 0.9388 (tp30) REVERT: A 353 PHE cc_start: 0.9419 (m-80) cc_final: 0.9086 (m-80) REVERT: A 507 MET cc_start: 0.9677 (mmm) cc_final: 0.9355 (mmm) REVERT: A 604 MET cc_start: 0.9338 (mmm) cc_final: 0.8973 (mmm) REVERT: A 1018 MET cc_start: 0.9441 (mmp) cc_final: 0.9157 (mmm) outliers start: 45 outliers final: 19 residues processed: 102 average time/residue: 0.0897 time to fit residues: 14.1032 Evaluate side-chains 74 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 49 GLU 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 549 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1103 PHE 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: 1.9990 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 308 GLN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN A 611 GLN A 646 ASN A 974 GLN A 977 HIS ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.037971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.028062 restraints weight = 88097.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.029363 restraints weight = 43584.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.030253 restraints weight = 27782.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.030856 restraints weight = 20380.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.031290 restraints weight = 16399.395| |-----------------------------------------------------------------------------| r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12519 Z= 0.136 Angle : 0.656 12.892 17323 Z= 0.330 Chirality : 0.040 0.155 1933 Planarity : 0.003 0.041 1896 Dihedral : 20.438 150.655 2537 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.35 % Allowed : 23.01 % 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 aren not related in a simple way. whole: 0.65 (0.24), residues: 1234 helix: 1.05 (0.21), residues: 617 sheet: -0.31 (0.44), residues: 139 loop : 0.01 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 301 TYR 0.018 0.001 TYR A 61 PHE 0.014 0.001 PHE A1015 TRP 0.007 0.001 TRP A 676 HIS 0.005 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00295 (12519) covalent geometry : angle 0.65569 (17323) hydrogen bonds : bond 0.04014 ( 600) hydrogen bonds : angle 4.39803 ( 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: 26 poor density : 71 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9387 (OUTLIER) cc_final: 0.9092 (m-30) REVERT: A 174 GLU cc_start: 0.9377 (mp0) cc_final: 0.9113 (mp0) REVERT: A 178 ASN cc_start: 0.9472 (m-40) cc_final: 0.9189 (p0) REVERT: A 202 LYS cc_start: 0.9590 (OUTLIER) cc_final: 0.8950 (ttpt) REVERT: A 203 GLU cc_start: 0.9610 (tp30) cc_final: 0.9213 (tp30) REVERT: A 251 THR cc_start: 0.9429 (OUTLIER) cc_final: 0.9198 (p) REVERT: A 307 LYS cc_start: 0.8950 (ttmt) cc_final: 0.8670 (tttm) REVERT: A 309 ILE cc_start: 0.8740 (mm) cc_final: 0.8216 (mm) REVERT: A 343 GLU cc_start: 0.9399 (OUTLIER) cc_final: 0.9083 (tm-30) REVERT: A 507 MET cc_start: 0.9671 (mmm) cc_final: 0.9358 (mmm) REVERT: A 604 MET cc_start: 0.9193 (mmm) cc_final: 0.8816 (mmm) REVERT: A 965 LYS cc_start: 0.9631 (OUTLIER) cc_final: 0.9258 (mmmt) outliers start: 26 outliers final: 13 residues processed: 94 average time/residue: 0.0973 time to fit residues: 13.8387 Evaluate side-chains 83 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU 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 235 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 343 GLU 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 932 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1294 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 108 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 105 optimal weight: 0.0270 chunk 40 optimal weight: 5.9990 chunk 99 optimal weight: 0.0770 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN ** 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 = 0.2891 r_free = 0.2891 target = 0.037541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.027660 restraints weight = 89163.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.028945 restraints weight = 43828.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.029825 restraints weight = 27855.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.030431 restraints weight = 20476.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.030822 restraints weight = 16455.574| |-----------------------------------------------------------------------------| r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12519 Z= 0.157 Angle : 0.624 12.016 17323 Z= 0.320 Chirality : 0.040 0.193 1933 Planarity : 0.003 0.039 1896 Dihedral : 20.317 150.387 2537 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.52 % Allowed : 20.40 % Favored : 76.08 % 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 aren not related in a simple way. whole: 0.91 (0.24), residues: 1234 helix: 1.25 (0.21), residues: 619 sheet: -0.23 (0.44), residues: 139 loop : 0.16 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1306 TYR 0.018 0.001 TYR A 61 PHE 0.010 0.001 PHE A1015 TRP 0.005 0.001 TRP A1258 HIS 0.003 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00331 (12519) covalent geometry : angle 0.62388 (17323) hydrogen bonds : bond 0.03873 ( 600) hydrogen bonds : angle 4.22682 ( 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 106 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 67 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9405 (OUTLIER) cc_final: 0.9140 (m-30) REVERT: A 203 GLU cc_start: 0.9616 (tp30) cc_final: 0.9254 (tp30) REVERT: A 251 THR cc_start: 0.9371 (m) cc_final: 0.9145 (p) REVERT: A 507 MET cc_start: 0.9698 (mmm) cc_final: 0.9398 (mmm) REVERT: A 604 MET cc_start: 0.9290 (mmm) cc_final: 0.8885 (mmm) REVERT: A 965 LYS cc_start: 0.9654 (OUTLIER) cc_final: 0.9438 (mppt) outliers start: 39 outliers final: 21 residues processed: 101 average time/residue: 0.0893 time to fit residues: 14.0222 Evaluate side-chains 86 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 151 THR 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 310 LEU 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 873 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE 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: 10.0000 chunk 130 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2901 r_free = 0.2901 target = 0.037869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.027982 restraints weight = 88487.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.029287 restraints weight = 44008.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.030177 restraints weight = 28064.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.030757 restraints weight = 20531.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.031181 restraints weight = 16560.776| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12519 Z= 0.138 Angle : 0.621 11.627 17323 Z= 0.316 Chirality : 0.039 0.170 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.190 149.968 2537 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.07 % Allowed : 21.66 % Favored : 75.27 % 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 aren not related in a simple way. whole: 1.11 (0.24), residues: 1234 helix: 1.45 (0.21), residues: 616 sheet: -0.19 (0.44), residues: 139 loop : 0.25 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 301 TYR 0.015 0.001 TYR A 61 PHE 0.013 0.001 PHE A 333 TRP 0.006 0.001 TRP A1085 HIS 0.003 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00295 (12519) covalent geometry : angle 0.62095 (17323) hydrogen bonds : bond 0.03691 ( 600) hydrogen bonds : angle 4.18881 ( 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 101 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 67 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9439 (OUTLIER) cc_final: 0.9120 (m-30) REVERT: A 203 GLU cc_start: 0.9617 (tp30) cc_final: 0.9221 (tp30) REVERT: A 251 THR cc_start: 0.9362 (m) cc_final: 0.9125 (p) REVERT: A 307 LYS cc_start: 0.8903 (ttmt) cc_final: 0.8579 (tttp) REVERT: A 507 MET cc_start: 0.9703 (mmm) cc_final: 0.9379 (mmm) REVERT: A 593 MET cc_start: 0.9562 (tmm) cc_final: 0.9244 (tmm) REVERT: A 604 MET cc_start: 0.9276 (mmm) cc_final: 0.8835 (mmm) REVERT: A 768 LEU cc_start: 0.9354 (tp) cc_final: 0.9066 (tp) REVERT: A 992 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9348 (tp) outliers start: 34 outliers final: 24 residues processed: 95 average time/residue: 0.0857 time to fit residues: 12.8722 Evaluate side-chains 89 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 310 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 480 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1025 CYS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 25 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 178 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.036794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.027084 restraints weight = 90327.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.028349 restraints weight = 44848.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.029201 restraints weight = 28562.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.029767 restraints weight = 21025.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.030184 restraints weight = 16999.558| |-----------------------------------------------------------------------------| r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12519 Z= 0.207 Angle : 0.652 12.328 17323 Z= 0.337 Chirality : 0.041 0.206 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.196 148.898 2537 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.61 % Allowed : 21.48 % Favored : 74.91 % 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 aren not related in a simple way. whole: 1.10 (0.25), residues: 1234 helix: 1.45 (0.21), residues: 616 sheet: -0.27 (0.44), residues: 139 loop : 0.26 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 301 TYR 0.021 0.001 TYR A 61 PHE 0.022 0.002 PHE A1015 TRP 0.007 0.001 TRP A 765 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00429 (12519) covalent geometry : angle 0.65181 (17323) hydrogen bonds : bond 0.04134 ( 600) hydrogen bonds : angle 4.33023 ( 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 101 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 61 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9432 (OUTLIER) cc_final: 0.9102 (m-30) REVERT: A 165 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8041 (m-80) REVERT: A 203 GLU cc_start: 0.9609 (tp30) cc_final: 0.9262 (tp30) REVERT: A 251 THR cc_start: 0.9351 (m) cc_final: 0.9112 (p) REVERT: A 507 MET cc_start: 0.9723 (mmm) cc_final: 0.9380 (mmm) REVERT: A 604 MET cc_start: 0.9316 (mmm) cc_final: 0.8873 (mmm) outliers start: 40 outliers final: 31 residues processed: 94 average time/residue: 0.0723 time to fit residues: 11.0801 Evaluate side-chains 91 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 58 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU 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 152 THR Chi-restraints excluded: chain A residue 165 PHE 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 310 LEU Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 342 ASN 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 932 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1025 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 74 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.037042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.027307 restraints weight = 89855.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.028574 restraints weight = 44539.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.029421 restraints weight = 28349.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.030013 restraints weight = 20870.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.030312 restraints weight = 16716.335| |-----------------------------------------------------------------------------| r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12519 Z= 0.172 Angle : 0.649 11.842 17323 Z= 0.331 Chirality : 0.040 0.218 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.189 147.029 2537 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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 aren not related in a simple way. whole: 1.19 (0.25), residues: 1234 helix: 1.51 (0.21), residues: 610 sheet: -0.25 (0.44), residues: 139 loop : 0.34 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.019 0.001 TYR A 61 PHE 0.014 0.001 PHE A 353 TRP 0.006 0.001 TRP A1085 HIS 0.003 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00362 (12519) covalent geometry : angle 0.64875 (17323) hydrogen bonds : bond 0.03930 ( 600) hydrogen bonds : angle 4.30565 ( 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 94 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 60 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9439 (OUTLIER) cc_final: 0.9090 (m-30) REVERT: A 165 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: A 203 GLU cc_start: 0.9604 (tp30) cc_final: 0.9236 (tp30) REVERT: A 251 THR cc_start: 0.9351 (m) cc_final: 0.9106 (p) REVERT: A 307 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8640 (tttm) REVERT: A 507 MET cc_start: 0.9724 (mmm) cc_final: 0.9354 (mmm) REVERT: A 593 MET cc_start: 0.9574 (tmm) cc_final: 0.9265 (tmm) REVERT: A 604 MET cc_start: 0.9275 (mmm) cc_final: 0.8837 (mmm) REVERT: A 768 LEU cc_start: 0.9411 (tp) cc_final: 0.9093 (tp) REVERT: A 912 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8252 (ptp90) outliers start: 34 outliers final: 29 residues processed: 90 average time/residue: 0.0796 time to fit residues: 11.5729 Evaluate side-chains 92 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU 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 152 THR Chi-restraints excluded: chain A residue 165 PHE 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 310 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 409 VAL 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 912 ARG Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 983 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A 755 HIS ** 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 = 0.2880 r_free = 0.2880 target = 0.037016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.027292 restraints weight = 89391.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.028559 restraints weight = 44570.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.029402 restraints weight = 28407.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.029952 restraints weight = 20886.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.030355 restraints weight = 16923.628| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12519 Z= 0.179 Angle : 0.660 13.250 17323 Z= 0.335 Chirality : 0.040 0.225 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.178 145.844 2537 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.25 % Allowed : 21.93 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.24), residues: 1234 helix: 1.52 (0.21), residues: 610 sheet: -0.40 (0.45), residues: 128 loop : 0.32 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 411 TYR 0.019 0.001 TYR A 61 PHE 0.024 0.001 PHE A1015 TRP 0.006 0.001 TRP A1085 HIS 0.003 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00373 (12519) covalent geometry : angle 0.65996 (17323) hydrogen bonds : bond 0.03934 ( 600) hydrogen bonds : angle 4.29984 ( 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 96 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 60 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9444 (OUTLIER) cc_final: 0.9095 (m-30) REVERT: A 165 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: A 203 GLU cc_start: 0.9608 (tp30) cc_final: 0.9254 (tp30) REVERT: A 251 THR cc_start: 0.9341 (m) cc_final: 0.9094 (p) REVERT: A 307 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8676 (tttm) REVERT: A 507 MET cc_start: 0.9732 (mmm) cc_final: 0.9357 (mmm) REVERT: A 593 MET cc_start: 0.9569 (tmm) cc_final: 0.9257 (tmm) REVERT: A 604 MET cc_start: 0.9290 (mmm) cc_final: 0.8855 (mmm) REVERT: A 768 LEU cc_start: 0.9435 (tp) cc_final: 0.9119 (tp) REVERT: A 912 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8260 (ptp90) outliers start: 36 outliers final: 30 residues processed: 91 average time/residue: 0.0850 time to fit residues: 12.4686 Evaluate side-chains 93 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU 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 152 THR Chi-restraints excluded: chain A residue 165 PHE 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 310 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 409 VAL 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 912 ARG Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1025 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 19 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** 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** A 611 GLN ** 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 = 0.2856 r_free = 0.2856 target = 0.036172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.026493 restraints weight = 92851.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.027734 restraints weight = 46235.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.028569 restraints weight = 29528.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.029131 restraints weight = 21691.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.029488 restraints weight = 17512.814| |-----------------------------------------------------------------------------| r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12519 Z= 0.238 Angle : 0.696 12.273 17323 Z= 0.360 Chirality : 0.042 0.228 1933 Planarity : 0.004 0.038 1896 Dihedral : 20.303 142.981 2537 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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 aren not related in a simple way. whole: 1.03 (0.24), residues: 1234 helix: 1.41 (0.21), residues: 610 sheet: -0.40 (0.44), residues: 137 loop : 0.24 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1094 TYR 0.024 0.002 TYR A 61 PHE 0.014 0.002 PHE A 769 TRP 0.008 0.001 TRP A 765 HIS 0.004 0.001 HIS A1210 Details of bonding type rmsd covalent geometry : bond 0.00489 (12519) covalent geometry : angle 0.69600 (17323) hydrogen bonds : bond 0.04364 ( 600) hydrogen bonds : angle 4.42986 ( 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 94 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 59 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8778 (tpt) cc_final: 0.8447 (tpt) REVERT: A 165 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8167 (m-10) REVERT: A 203 GLU cc_start: 0.9592 (tp30) cc_final: 0.9268 (tp30) REVERT: A 507 MET cc_start: 0.9749 (mmm) cc_final: 0.9379 (mmm) REVERT: A 604 MET cc_start: 0.9303 (mmm) cc_final: 0.8876 (mmm) REVERT: A 912 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8199 (ptp90) outliers start: 35 outliers final: 28 residues processed: 89 average time/residue: 0.0784 time to fit residues: 11.5124 Evaluate side-chains 89 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 PHE 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 310 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 409 VAL 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 902 THR Chi-restraints excluded: chain A residue 912 ARG Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1025 CYS 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 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: 6.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A 720 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 = 0.2840 r_free = 0.2840 target = 0.035619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.026076 restraints weight = 94017.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.027274 restraints weight = 47223.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.028061 restraints weight = 30413.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.028614 restraints weight = 22618.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.028989 restraints weight = 18295.771| |-----------------------------------------------------------------------------| r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12519 Z= 0.273 Angle : 0.720 11.963 17323 Z= 0.372 Chirality : 0.042 0.227 1933 Planarity : 0.004 0.038 1896 Dihedral : 20.371 142.159 2535 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.80 % Allowed : 23.29 % 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 aren not related in a simple way. whole: 0.83 (0.24), residues: 1234 helix: 1.23 (0.21), residues: 620 sheet: -0.53 (0.45), residues: 137 loop : 0.14 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 176 TYR 0.025 0.002 TYR A 61 PHE 0.024 0.002 PHE A1015 TRP 0.008 0.001 TRP A 765 HIS 0.005 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00556 (12519) covalent geometry : angle 0.72023 (17323) hydrogen bonds : bond 0.04530 ( 600) hydrogen bonds : angle 4.53774 ( 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 90 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8778 (tpt) cc_final: 0.8529 (tpt) REVERT: A 165 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: A 203 GLU cc_start: 0.9559 (tp30) cc_final: 0.9251 (tp30) REVERT: A 251 THR cc_start: 0.9326 (m) cc_final: 0.9115 (p) REVERT: A 507 MET cc_start: 0.9771 (mmm) cc_final: 0.9391 (mmm) REVERT: A 593 MET cc_start: 0.9544 (tmm) cc_final: 0.9246 (tmm) REVERT: A 604 MET cc_start: 0.9265 (mmm) cc_final: 0.8872 (mmm) REVERT: A 912 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8151 (ptp90) outliers start: 31 outliers final: 27 residues processed: 86 average time/residue: 0.0824 time to fit residues: 11.6399 Evaluate side-chains 87 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 PHE 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 310 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 409 VAL 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 912 ARG 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 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1123 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 84 optimal weight: 0.0060 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 GLN ** 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 = 0.2878 r_free = 0.2878 target = 0.036871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.027129 restraints weight = 89628.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.028407 restraints weight = 44502.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.029249 restraints weight = 28367.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.029830 restraints weight = 20789.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.030209 restraints weight = 16735.778| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3240 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= 0.146 Angle : 0.676 12.481 17323 Z= 0.338 Chirality : 0.041 0.243 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.259 141.217 2535 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.44 % Allowed : 23.92 % Favored : 73.65 % 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 aren not related in a simple way. whole: 1.14 (0.25), residues: 1234 helix: 1.49 (0.21), residues: 610 sheet: -0.35 (0.45), residues: 137 loop : 0.30 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.017 0.001 TYR A 61 PHE 0.012 0.001 PHE A1117 TRP 0.011 0.001 TRP A 382 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00310 (12519) covalent geometry : angle 0.67583 (17323) hydrogen bonds : bond 0.03797 ( 600) hydrogen bonds : angle 4.30556 ( 1646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1690.66 seconds wall clock time: 30 minutes 20.30 seconds (1820.30 seconds total)