Starting phenix.real_space_refine on Tue Jun 10 22:05:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfp_40447/06_2025/8sfp_40447.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfp_40447/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sfp_40447/06_2025/8sfp_40447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfp_40447/06_2025/8sfp_40447.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfp_40447/06_2025/8sfp_40447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfp_40447/06_2025/8sfp_40447.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.70, per 1000 atoms: 0.64 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: 2.97 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.31 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: 5.86 Time building geometry restraints manager: 3.56 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: 2.260 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.280 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (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 TRP 0.021 0.002 TRP A 676 HIS 0.009 0.001 HIS A1269 PHE 0.071 0.003 PHE A 683 TYR 0.054 0.002 TYR A1236 ARG 0.023 0.001 ARG A 411 Details of bonding type rmsd hydrogen bonds : bond 0.13418 ( 600) hydrogen bonds : angle 5.99612 ( 1646) covalent geometry : bond 0.00505 (12519) covalent geometry : angle 1.18571 (17323) *********************** 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 : 1.136 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: 0.2235 time to fit residues: 37.8875 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 : 1.202 ------------------------------------------------------------------------------- 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 110 optimal weight: 20.0000 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 HIS A 308 GLN A 331 GLN A 363 HIS ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 GLN A 646 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 929 GLN A 974 GLN A1116 HIS ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1254 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.037646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.027749 restraints weight = 90663.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.028988 restraints weight = 45379.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.029858 restraints weight = 29228.554| |-----------------------------------------------------------------------------| r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12519 Z= 0.240 Angle : 0.702 10.531 17323 Z= 0.369 Chirality : 0.041 0.157 1933 Planarity : 0.004 0.049 1896 Dihedral : 20.344 156.515 2537 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.16 % Allowed : 23.47 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1234 helix: 0.74 (0.21), residues: 615 sheet: -0.26 (0.45), residues: 130 loop : -0.20 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 765 HIS 0.005 0.001 HIS A1116 PHE 0.019 0.002 PHE A1015 TYR 0.014 0.002 TYR A 390 ARG 0.006 0.001 ARG A 411 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 600) hydrogen bonds : angle 4.57933 ( 1646) covalent geometry : bond 0.00497 (12519) covalent geometry : angle 0.70188 (17323) *********************** 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 98 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 63 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9435 (OUTLIER) cc_final: 0.9069 (m-30) REVERT: A 203 GLU cc_start: 0.9625 (tp30) cc_final: 0.9330 (tp30) REVERT: A 251 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.9268 (p) REVERT: A 353 PHE cc_start: 0.9420 (m-80) cc_final: 0.9098 (m-80) REVERT: A 507 MET cc_start: 0.9639 (mmm) cc_final: 0.9353 (mmm) REVERT: A 604 MET cc_start: 0.9267 (mmm) cc_final: 0.8923 (mmm) REVERT: A 965 LYS cc_start: 0.9633 (OUTLIER) cc_final: 0.9219 (mmmt) REVERT: A 1018 MET cc_start: 0.9400 (mmp) cc_final: 0.9104 (mmm) outliers start: 35 outliers final: 16 residues processed: 92 average time/residue: 0.2356 time to fit residues: 33.1717 Evaluate side-chains 81 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 178 ASN Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 251 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 779 ILE 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 965 LYS Chi-restraints excluded: chain A residue 974 GLN Chi-restraints excluded: chain A residue 1025 CYS 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 89 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN A 977 HIS ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.037884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.028005 restraints weight = 88497.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.029300 restraints weight = 44041.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.030189 restraints weight = 28210.744| |-----------------------------------------------------------------------------| r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1970 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= 0.164 Angle : 0.640 10.438 17323 Z= 0.328 Chirality : 0.040 0.154 1933 Planarity : 0.003 0.039 1896 Dihedral : 20.319 154.311 2537 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.89 % Allowed : 21.93 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.24), residues: 1234 helix: 1.09 (0.21), residues: 617 sheet: -0.28 (0.44), residues: 139 loop : 0.04 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 676 HIS 0.004 0.001 HIS A 754 PHE 0.013 0.001 PHE A1015 TYR 0.018 0.001 TYR A 61 ARG 0.003 0.000 ARG A 411 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 600) hydrogen bonds : angle 4.35893 ( 1646) covalent geometry : bond 0.00348 (12519) covalent geometry : angle 0.63961 (17323) *********************** 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 102 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9415 (OUTLIER) cc_final: 0.9037 (m-30) REVERT: A 178 ASN cc_start: 0.9533 (m-40) cc_final: 0.9255 (p0) REVERT: A 203 GLU cc_start: 0.9622 (tp30) cc_final: 0.9256 (tp30) REVERT: A 221 HIS cc_start: 0.9602 (OUTLIER) cc_final: 0.9381 (m90) REVERT: A 251 THR cc_start: 0.9443 (OUTLIER) cc_final: 0.9210 (p) REVERT: A 307 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8697 (tttm) REVERT: A 343 GLU cc_start: 0.9380 (OUTLIER) cc_final: 0.9093 (tm-30) REVERT: A 507 MET cc_start: 0.9686 (mmm) cc_final: 0.9362 (mmm) REVERT: A 604 MET cc_start: 0.9217 (mmm) cc_final: 0.8864 (mmm) REVERT: A 965 LYS cc_start: 0.9644 (OUTLIER) cc_final: 0.9420 (mppt) outliers start: 32 outliers final: 15 residues processed: 97 average time/residue: 0.2417 time to fit residues: 35.4096 Evaluate side-chains 79 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 75 ASN 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 221 HIS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 549 GLU 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 972 LEU Chi-restraints excluded: chain A residue 974 GLN Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 125 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 106 optimal weight: 0.3980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** 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** ** 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 = 0.2871 r_free = 0.2871 target = 0.037007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.027265 restraints weight = 88962.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.028522 restraints weight = 44280.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.029368 restraints weight = 28352.446| |-----------------------------------------------------------------------------| r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2395 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= 0.201 Angle : 0.642 11.473 17323 Z= 0.334 Chirality : 0.040 0.205 1933 Planarity : 0.003 0.039 1896 Dihedral : 20.326 153.263 2537 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.33 % Allowed : 20.67 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.24), residues: 1234 helix: 1.18 (0.21), residues: 619 sheet: -0.29 (0.44), residues: 139 loop : 0.18 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 765 HIS 0.005 0.001 HIS A 622 PHE 0.012 0.002 PHE A 769 TYR 0.023 0.001 TYR A 61 ARG 0.007 0.000 ARG A1306 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 600) hydrogen bonds : angle 4.34416 ( 1646) covalent geometry : bond 0.00415 (12519) covalent geometry : angle 0.64181 (17323) *********************** 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 110 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 62 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9442 (OUTLIER) cc_final: 0.9132 (m-30) REVERT: A 202 LYS cc_start: 0.9591 (OUTLIER) cc_final: 0.8987 (ttmt) REVERT: A 203 GLU cc_start: 0.9640 (tp30) cc_final: 0.9274 (tp30) REVERT: A 343 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.9142 (tm-30) REVERT: A 507 MET cc_start: 0.9716 (mmm) cc_final: 0.9405 (mmm) REVERT: A 604 MET cc_start: 0.9305 (mmm) cc_final: 0.8908 (mmm) REVERT: A 965 LYS cc_start: 0.9663 (OUTLIER) cc_final: 0.9435 (mppt) outliers start: 48 outliers final: 27 residues processed: 103 average time/residue: 0.2467 time to fit residues: 39.2064 Evaluate side-chains 88 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 75 ASN Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 343 GLU 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 549 GLU 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 917 ILE 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 972 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 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 3 optimal weight: 0.0980 chunk 113 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 chunk 100 optimal weight: 0.0060 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 overall best weight: 2.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.037241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.027456 restraints weight = 88835.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.028722 restraints weight = 44066.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.029604 restraints weight = 28157.670| |-----------------------------------------------------------------------------| r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2577 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= 0.170 Angle : 0.630 11.156 17323 Z= 0.324 Chirality : 0.040 0.178 1933 Planarity : 0.003 0.037 1896 Dihedral : 20.312 151.272 2537 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.52 % Allowed : 21.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1234 helix: 1.33 (0.21), residues: 619 sheet: -0.30 (0.44), residues: 139 loop : 0.24 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1085 HIS 0.003 0.001 HIS A 622 PHE 0.014 0.001 PHE A 333 TYR 0.018 0.001 TYR A 61 ARG 0.004 0.000 ARG A1306 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 600) hydrogen bonds : angle 4.26207 ( 1646) covalent geometry : bond 0.00356 (12519) covalent geometry : angle 0.62964 (17323) *********************** 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 104 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 65 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9399 (OUTLIER) cc_final: 0.9092 (m-30) REVERT: A 165 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7962 (m-10) REVERT: A 202 LYS cc_start: 0.9568 (OUTLIER) cc_final: 0.8948 (ttmt) REVERT: A 203 GLU cc_start: 0.9609 (tp30) cc_final: 0.9224 (tp30) REVERT: A 251 THR cc_start: 0.9400 (m) cc_final: 0.9172 (p) REVERT: A 307 LYS cc_start: 0.8969 (ttmt) cc_final: 0.8685 (tttm) REVERT: A 507 MET cc_start: 0.9728 (mmm) cc_final: 0.9390 (mmm) REVERT: A 593 MET cc_start: 0.9543 (tmm) cc_final: 0.9243 (tmm) REVERT: A 604 MET cc_start: 0.9219 (mmm) cc_final: 0.8801 (mmm) outliers start: 39 outliers final: 24 residues processed: 98 average time/residue: 0.2159 time to fit residues: 32.7786 Evaluate side-chains 87 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 75 ASN Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU 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 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1294 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 96 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** ** 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 = 0.2914 r_free = 0.2914 target = 0.038256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.028338 restraints weight = 87501.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.029657 restraints weight = 43303.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.030569 restraints weight = 27527.446| |-----------------------------------------------------------------------------| r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2580 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= 0.122 Angle : 0.635 12.244 17323 Z= 0.317 Chirality : 0.041 0.381 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.127 151.251 2537 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.89 % Allowed : 22.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.24), residues: 1234 helix: 1.53 (0.21), residues: 610 sheet: -0.19 (0.44), residues: 139 loop : 0.32 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 676 HIS 0.004 0.001 HIS A 221 PHE 0.010 0.001 PHE A 333 TYR 0.015 0.001 TYR A 336 ARG 0.003 0.000 ARG A1306 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 600) hydrogen bonds : angle 4.15153 ( 1646) covalent geometry : bond 0.00261 (12519) covalent geometry : angle 0.63452 (17323) *********************** 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 105 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9399 (OUTLIER) cc_final: 0.9060 (m-30) REVERT: A 202 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.8952 (ttmt) REVERT: A 203 GLU cc_start: 0.9627 (tp30) cc_final: 0.9205 (tp30) REVERT: A 251 THR cc_start: 0.9388 (OUTLIER) cc_final: 0.9150 (p) REVERT: A 307 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8542 (tttm) REVERT: A 507 MET cc_start: 0.9709 (mmm) cc_final: 0.9378 (mmm) REVERT: A 604 MET cc_start: 0.9239 (mmm) cc_final: 0.8811 (mmm) outliers start: 32 outliers final: 24 residues processed: 99 average time/residue: 0.2185 time to fit residues: 33.0850 Evaluate side-chains 92 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 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 178 ASN Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU 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 1025 CYS 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 1210 HIS 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 39 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 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 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 611 GLN A 755 HIS ** A1024 ASN ** 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 = 0.2832 r_free = 0.2832 target = 0.035284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.025757 restraints weight = 95624.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.026955 restraints weight = 47926.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.027766 restraints weight = 30683.444| |-----------------------------------------------------------------------------| r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 12519 Z= 0.348 Angle : 0.756 12.509 17323 Z= 0.400 Chirality : 0.044 0.235 1933 Planarity : 0.004 0.039 1896 Dihedral : 20.405 148.332 2537 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.88 % Allowed : 22.29 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.24), residues: 1234 helix: 1.05 (0.20), residues: 618 sheet: -0.66 (0.44), residues: 129 loop : 0.05 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 765 HIS 0.011 0.002 HIS A1167 PHE 0.020 0.003 PHE A 138 TYR 0.030 0.002 TYR A 61 ARG 0.004 0.001 ARG A 790 Details of bonding type rmsd hydrogen bonds : bond 0.05203 ( 600) hydrogen bonds : angle 4.68038 ( 1646) covalent geometry : bond 0.00703 (12519) covalent geometry : angle 0.75556 (17323) *********************** 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 100 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 57 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9458 (OUTLIER) cc_final: 0.9165 (m-30) REVERT: A 165 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8257 (m-10) REVERT: A 203 GLU cc_start: 0.9606 (tp30) cc_final: 0.9317 (tp30) REVERT: A 251 THR cc_start: 0.9353 (m) cc_final: 0.9106 (p) REVERT: A 507 MET cc_start: 0.9759 (mmm) cc_final: 0.9434 (mmm) REVERT: A 593 MET cc_start: 0.9603 (tmm) cc_final: 0.9315 (tmm) REVERT: A 604 MET cc_start: 0.9340 (mmm) cc_final: 0.8918 (mmm) outliers start: 43 outliers final: 34 residues processed: 92 average time/residue: 0.2013 time to fit residues: 29.6079 Evaluate side-chains 89 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 53 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 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 236 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 343 GLU 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 429 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU 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 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 1210 HIS 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 107 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 974 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 = 0.2873 r_free = 0.2873 target = 0.036741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.026969 restraints weight = 90905.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.028230 restraints weight = 45138.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.029084 restraints weight = 28739.214| |-----------------------------------------------------------------------------| r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12519 Z= 0.159 Angle : 0.658 12.652 17323 Z= 0.333 Chirality : 0.041 0.224 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.308 145.136 2537 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.16 % Allowed : 22.65 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.24), residues: 1234 helix: 1.35 (0.21), residues: 619 sheet: -0.48 (0.46), residues: 128 loop : 0.19 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 676 HIS 0.003 0.001 HIS A1210 PHE 0.011 0.001 PHE A 353 TYR 0.018 0.001 TYR A 61 ARG 0.003 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 600) hydrogen bonds : angle 4.34417 ( 1646) covalent geometry : bond 0.00336 (12519) covalent geometry : angle 0.65821 (17323) *********************** 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: 35 poor density : 61 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9484 (OUTLIER) cc_final: 0.9132 (m-30) REVERT: A 165 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: A 203 GLU cc_start: 0.9610 (tp30) cc_final: 0.9275 (tp30) REVERT: A 307 LYS cc_start: 0.8931 (ttmt) cc_final: 0.8622 (tttm) REVERT: A 507 MET cc_start: 0.9750 (mmm) cc_final: 0.9384 (mmm) REVERT: A 593 MET cc_start: 0.9609 (tmm) cc_final: 0.9305 (tmm) REVERT: A 604 MET cc_start: 0.9244 (mmm) cc_final: 0.8841 (mmm) REVERT: A 912 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8137 (ptp90) outliers start: 35 outliers final: 27 residues processed: 92 average time/residue: 0.2094 time to fit residues: 29.9368 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 : 1.139 ------------------------------------------------------------------------------- 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 146 LEU 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 236 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU 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 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 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS 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 109 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 41 optimal weight: 0.0870 chunk 123 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.2911 r_free = 0.2911 target = 0.038086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.028296 restraints weight = 86994.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.029609 restraints weight = 42885.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.030491 restraints weight = 27104.173| |-----------------------------------------------------------------------------| r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2986 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= 0.121 Angle : 0.689 15.700 17323 Z= 0.337 Chirality : 0.041 0.266 1933 Planarity : 0.003 0.039 1896 Dihedral : 20.078 144.637 2537 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.26 % Allowed : 23.65 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1234 helix: 1.50 (0.21), residues: 610 sheet: -0.34 (0.46), residues: 128 loop : 0.34 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 676 HIS 0.004 0.001 HIS A 618 PHE 0.028 0.001 PHE A1015 TYR 0.012 0.001 TYR A 595 ARG 0.003 0.000 ARG A 725 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 600) hydrogen bonds : angle 4.18328 ( 1646) covalent geometry : bond 0.00258 (12519) covalent geometry : angle 0.68892 (17323) *********************** 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 91 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9473 (OUTLIER) cc_final: 0.9113 (m-30) REVERT: A 165 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: A 203 GLU cc_start: 0.9611 (tp30) cc_final: 0.9240 (tp30) REVERT: A 251 THR cc_start: 0.9323 (m) cc_final: 0.9121 (p) REVERT: A 307 LYS cc_start: 0.8822 (ttmt) cc_final: 0.8491 (tttm) REVERT: A 507 MET cc_start: 0.9708 (mmm) cc_final: 0.9326 (mmm) REVERT: A 593 MET cc_start: 0.9581 (tmm) cc_final: 0.9244 (tmm) REVERT: A 604 MET cc_start: 0.9200 (mmm) cc_final: 0.8775 (mmm) REVERT: A 912 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8108 (ptp90) outliers start: 25 outliers final: 20 residues processed: 87 average time/residue: 0.2207 time to fit residues: 29.8572 Evaluate side-chains 87 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 165 PHE Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 205 CYS 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 408 LYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 912 ARG 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 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS 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 0 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 100 optimal weight: 0.0870 chunk 110 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 96 optimal weight: 0.3980 chunk 6 optimal weight: 0.0970 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 ** 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 = 0.2933 r_free = 0.2933 target = 0.038726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.028889 restraints weight = 85911.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.030218 restraints weight = 42561.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.031107 restraints weight = 26915.522| |-----------------------------------------------------------------------------| r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3000 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= 0.118 Angle : 0.691 14.551 17323 Z= 0.334 Chirality : 0.041 0.274 1933 Planarity : 0.003 0.039 1896 Dihedral : 19.884 147.766 2537 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.08 % Allowed : 23.47 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1234 helix: 1.55 (0.21), residues: 610 sheet: -0.30 (0.45), residues: 128 loop : 0.35 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 676 HIS 0.004 0.000 HIS A 618 PHE 0.011 0.001 PHE A 353 TYR 0.012 0.001 TYR A 595 ARG 0.003 0.000 ARG A 725 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 600) hydrogen bonds : angle 4.14828 ( 1646) covalent geometry : bond 0.00252 (12519) covalent geometry : angle 0.69146 (17323) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9454 (OUTLIER) cc_final: 0.9059 (m-30) REVERT: A 165 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8041 (m-80) REVERT: A 203 GLU cc_start: 0.9577 (tp30) cc_final: 0.9194 (tp30) REVERT: A 307 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8529 (tttm) REVERT: A 507 MET cc_start: 0.9696 (mmm) cc_final: 0.9314 (mmm) REVERT: A 593 MET cc_start: 0.9544 (tmm) cc_final: 0.9207 (tmm) REVERT: A 604 MET cc_start: 0.9191 (mmm) cc_final: 0.8753 (mmm) REVERT: A 768 LEU cc_start: 0.9325 (tp) cc_final: 0.9067 (tp) REVERT: A 912 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8074 (ptp90) outliers start: 23 outliers final: 17 residues processed: 89 average time/residue: 0.2132 time to fit residues: 29.3712 Evaluate side-chains 86 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 165 PHE Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 912 ARG Chi-restraints excluded: chain A residue 944 LEU 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 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 54 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 A1126 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 = 0.2883 r_free = 0.2883 target = 0.036907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.027266 restraints weight = 90872.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.028539 restraints weight = 45470.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.029384 restraints weight = 29086.367| |-----------------------------------------------------------------------------| r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.3234 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= 0.205 Angle : 0.700 13.303 17323 Z= 0.351 Chirality : 0.042 0.355 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.040 148.540 2537 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.26 % Allowed : 23.47 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1234 helix: 1.55 (0.21), residues: 610 sheet: -0.46 (0.45), residues: 129 loop : 0.39 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 765 HIS 0.004 0.001 HIS A 447 PHE 0.023 0.002 PHE A1015 TYR 0.021 0.001 TYR A 61 ARG 0.002 0.000 ARG A1094 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 600) hydrogen bonds : angle 4.31220 ( 1646) covalent geometry : bond 0.00426 (12519) covalent geometry : angle 0.70048 (17323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3901.16 seconds wall clock time: 69 minutes 58.88 seconds (4198.88 seconds total)