Starting phenix.real_space_refine on Sat Jan 18 10:00:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfp_40447/01_2025/8sfp_40447.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfp_40447/01_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_40447/01_2025/8sfp_40447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfp_40447/01_2025/8sfp_40447.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfp_40447/01_2025/8sfp_40447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfp_40447/01_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-5571/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: 7.76, 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: 2.81 Conformation dependent library (CDL) restraints added in 1.1 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: 3.96 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: 6.66 Time building geometry restraints manager: 3.30 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.710 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.160 ------------------------------------------------------------------------------- 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= 0.324 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 *********************** 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 : 1.227 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: 0.2287 time to fit residues: 38.6972 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 : 1.260 ------------------------------------------------------------------------------- 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 = 0.037645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.027745 restraints weight = 90666.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.028987 restraints weight = 45414.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.029835 restraints weight = 29323.175| |-----------------------------------------------------------------------------| r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 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= 0.306 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 *********************** 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 : 1.156 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: 0.9436 (OUTLIER) cc_final: 0.9071 (m-30) REVERT: A 203 GLU cc_start: 0.9624 (tp30) cc_final: 0.9329 (tp30) REVERT: A 251 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.9269 (p) REVERT: A 353 PHE cc_start: 0.9423 (m-80) cc_final: 0.9102 (m-80) REVERT: A 507 MET cc_start: 0.9641 (mmm) cc_final: 0.9353 (mmm) REVERT: A 604 MET cc_start: 0.9265 (mmm) cc_final: 0.8922 (mmm) REVERT: A 965 LYS cc_start: 0.9632 (OUTLIER) cc_final: 0.9219 (mmmt) REVERT: A 1018 MET cc_start: 0.9401 (mmp) cc_final: 0.9105 (mmm) outliers start: 35 outliers final: 16 residues processed: 92 average time/residue: 0.2266 time to fit residues: 31.6414 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 : 1.241 ------------------------------------------------------------------------------- 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: 0.8980 chunk 119 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 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 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 = 0.2909 r_free = 0.2909 target = 0.038287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.028331 restraints weight = 87761.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.029643 restraints weight = 43623.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.030532 restraints weight = 27860.884| |-----------------------------------------------------------------------------| r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12519 Z= 0.188 Angle : 0.637 10.843 17323 Z= 0.323 Chirality : 0.040 0.152 1933 Planarity : 0.003 0.039 1896 Dihedral : 20.279 154.846 2537 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.62 % Allowed : 21.84 % Favored : 75.54 % 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: 0.71 (0.24), residues: 1234 helix: 1.09 (0.21), residues: 617 sheet: -0.26 (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 0.014 0.001 PHE A1015 TYR 0.016 0.001 TYR A 61 ARG 0.003 0.000 ARG A 411 *********************** 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 100 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9431 (OUTLIER) cc_final: 0.9040 (m-30) REVERT: A 203 GLU cc_start: 0.9648 (tp30) cc_final: 0.9277 (tp30) REVERT: A 221 HIS cc_start: 0.9598 (OUTLIER) cc_final: 0.9384 (m90) REVERT: A 251 THR cc_start: 0.9438 (OUTLIER) cc_final: 0.9208 (p) REVERT: A 307 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8634 (tttm) REVERT: A 343 GLU cc_start: 0.9391 (OUTLIER) cc_final: 0.9137 (tm-30) REVERT: A 507 MET cc_start: 0.9667 (mmm) cc_final: 0.9354 (mmm) REVERT: A 604 MET cc_start: 0.9244 (mmm) cc_final: 0.8876 (mmm) REVERT: A 965 LYS cc_start: 0.9638 (OUTLIER) cc_final: 0.9422 (mppt) outliers start: 29 outliers final: 12 residues processed: 96 average time/residue: 0.2397 time to fit residues: 34.4476 Evaluate side-chains 81 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 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 718 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 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: 10.0000 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 99 optimal weight: 0.4980 chunk 14 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** ** 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 = 0.2918 r_free = 0.2918 target = 0.038459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.028570 restraints weight = 85464.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.029886 restraints weight = 42541.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.030790 restraints weight = 27139.120| |-----------------------------------------------------------------------------| r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12519 Z= 0.164 Angle : 0.623 11.961 17323 Z= 0.313 Chirality : 0.039 0.186 1933 Planarity : 0.003 0.040 1896 Dihedral : 20.191 156.546 2537 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.34 % Allowed : 21.21 % Favored : 75.45 % 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: 0.95 (0.24), residues: 1234 helix: 1.30 (0.21), residues: 618 sheet: -0.16 (0.44), residues: 139 loop : 0.15 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1085 HIS 0.003 0.001 HIS A 618 PHE 0.014 0.001 PHE A1015 TYR 0.019 0.001 TYR A 336 ARG 0.008 0.000 ARG A 301 *********************** 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 104 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9415 (OUTLIER) cc_final: 0.9056 (m-30) REVERT: A 202 LYS cc_start: 0.9574 (OUTLIER) cc_final: 0.8964 (ttpt) REVERT: A 203 GLU cc_start: 0.9645 (tp30) cc_final: 0.9253 (tp30) REVERT: A 251 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.9176 (p) REVERT: A 307 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8635 (tttm) REVERT: A 507 MET cc_start: 0.9675 (mmm) cc_final: 0.9389 (mmm) REVERT: A 593 MET cc_start: 0.9556 (tmm) cc_final: 0.9234 (tmm) REVERT: A 604 MET cc_start: 0.9262 (mmm) cc_final: 0.8833 (mmm) REVERT: A 768 LEU cc_start: 0.9334 (tp) cc_final: 0.9052 (tp) outliers start: 37 outliers final: 19 residues processed: 100 average time/residue: 0.2209 time to fit residues: 33.9226 Evaluate side-chains 85 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 251 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 310 LEU 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 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 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: 2.9990 chunk 113 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 100 optimal weight: 0.0980 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: 10.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- 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** ** 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 = 0.2889 r_free = 0.2889 target = 0.037513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.027741 restraints weight = 88530.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.029020 restraints weight = 44215.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.029876 restraints weight = 28319.585| |-----------------------------------------------------------------------------| r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12519 Z= 0.230 Angle : 0.636 12.313 17323 Z= 0.329 Chirality : 0.040 0.252 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.222 157.363 2537 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.70 % Allowed : 20.67 % Favored : 75.63 % 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: 1.10 (0.24), residues: 1234 helix: 1.43 (0.21), residues: 610 sheet: -0.20 (0.44), residues: 139 loop : 0.26 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 765 HIS 0.004 0.001 HIS A 622 PHE 0.014 0.001 PHE A 333 TYR 0.019 0.001 TYR A 61 ARG 0.004 0.000 ARG A1306 *********************** 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: 41 poor density : 63 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9431 (OUTLIER) cc_final: 0.9097 (m-30) REVERT: A 202 LYS cc_start: 0.9569 (OUTLIER) cc_final: 0.8980 (ttmt) REVERT: A 203 GLU cc_start: 0.9636 (tp30) cc_final: 0.9246 (tp30) REVERT: A 251 THR cc_start: 0.9377 (m) cc_final: 0.9147 (p) REVERT: A 507 MET cc_start: 0.9714 (mmm) cc_final: 0.9390 (mmm) REVERT: A 604 MET cc_start: 0.9295 (mmm) cc_final: 0.8839 (mmm) REVERT: A 965 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8813 (mmtt) outliers start: 41 outliers final: 27 residues processed: 96 average time/residue: 0.2068 time to fit residues: 31.7203 Evaluate side-chains 88 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 178 ASN Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 96 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS ** 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 = 0.2867 r_free = 0.2867 target = 0.036735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.027064 restraints weight = 91589.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.028319 restraints weight = 45421.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.029164 restraints weight = 28993.285| |-----------------------------------------------------------------------------| r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12519 Z= 0.294 Angle : 0.657 11.052 17323 Z= 0.344 Chirality : 0.041 0.205 1933 Planarity : 0.004 0.038 1896 Dihedral : 20.268 155.850 2537 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.88 % Allowed : 21.03 % Favored : 75.09 % 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: 1.01 (0.24), residues: 1234 helix: 1.36 (0.21), residues: 616 sheet: -0.28 (0.43), residues: 139 loop : 0.22 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 765 HIS 0.004 0.001 HIS A 221 PHE 0.012 0.002 PHE A1079 TYR 0.022 0.001 TYR A 61 ARG 0.004 0.000 ARG A 176 *********************** 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 104 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 61 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9413 (OUTLIER) cc_final: 0.9067 (m-30) REVERT: A 165 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: A 202 LYS cc_start: 0.9566 (OUTLIER) cc_final: 0.8979 (ttmt) REVERT: A 203 GLU cc_start: 0.9608 (tp30) cc_final: 0.9238 (tp30) REVERT: A 251 THR cc_start: 0.9391 (m) cc_final: 0.9162 (p) REVERT: A 507 MET cc_start: 0.9737 (mmm) cc_final: 0.9388 (mmm) REVERT: A 593 MET cc_start: 0.9585 (tmm) cc_final: 0.9291 (tmm) REVERT: A 604 MET cc_start: 0.9270 (mmm) cc_final: 0.8846 (mmm) outliers start: 43 outliers final: 32 residues processed: 96 average time/residue: 0.2101 time to fit residues: 31.7337 Evaluate side-chains 92 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 57 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 202 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 342 ASN 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 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 858 ILE 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 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 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: 10.0000 chunk 53 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 chunk 42 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS ** A 415 HIS ** 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 = 0.2899 r_free = 0.2899 target = 0.037739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.027885 restraints weight = 88659.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.029189 restraints weight = 43899.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.030065 restraints weight = 27985.601| |-----------------------------------------------------------------------------| r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2667 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= 0.173 Angle : 0.642 13.139 17323 Z= 0.323 Chirality : 0.040 0.235 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.151 155.134 2537 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.62 % Allowed : 22.65 % Favored : 74.73 % 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: 1.51 (0.21), residues: 610 sheet: -0.17 (0.44), residues: 139 loop : 0.35 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 676 HIS 0.003 0.001 HIS A 618 PHE 0.010 0.001 PHE A1103 TYR 0.015 0.001 TYR A 61 ARG 0.004 0.000 ARG A 301 *********************** 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 95 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9400 (OUTLIER) cc_final: 0.9068 (m-30) REVERT: A 202 LYS cc_start: 0.9553 (OUTLIER) cc_final: 0.8946 (ttmt) REVERT: A 203 GLU cc_start: 0.9626 (tp30) cc_final: 0.9212 (tp30) REVERT: A 251 THR cc_start: 0.9376 (m) cc_final: 0.9136 (p) REVERT: A 307 LYS cc_start: 0.8908 (ttmt) cc_final: 0.8640 (tttm) REVERT: A 507 MET cc_start: 0.9709 (mmm) cc_final: 0.9343 (mmm) REVERT: A 604 MET cc_start: 0.9244 (mmm) cc_final: 0.8819 (mmm) outliers start: 29 outliers final: 23 residues processed: 88 average time/residue: 0.2120 time to fit residues: 29.4272 Evaluate side-chains 87 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 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 331 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 107 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 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 755 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 = 0.2872 r_free = 0.2872 target = 0.036654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.026964 restraints weight = 91403.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.028223 restraints weight = 45095.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.029080 restraints weight = 28769.201| |-----------------------------------------------------------------------------| r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2951 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= 0.259 Angle : 0.667 12.183 17323 Z= 0.341 Chirality : 0.041 0.226 1933 Planarity : 0.003 0.038 1896 Dihedral : 20.182 154.851 2537 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.34 % Allowed : 22.11 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1234 helix: 1.48 (0.21), residues: 616 sheet: -0.36 (0.45), residues: 128 loop : 0.27 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 765 HIS 0.007 0.001 HIS A1167 PHE 0.023 0.002 PHE A1015 TYR 0.022 0.001 TYR A 61 ARG 0.004 0.000 ARG A 301 *********************** 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 98 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 61 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8813 (tpt) cc_final: 0.8525 (tpt) REVERT: A 81 ASP cc_start: 0.9429 (OUTLIER) cc_final: 0.9063 (m-30) REVERT: A 165 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8073 (m-10) REVERT: A 202 LYS cc_start: 0.9568 (OUTLIER) cc_final: 0.8952 (ttmt) REVERT: A 203 GLU cc_start: 0.9626 (tp30) cc_final: 0.9240 (tp30) REVERT: A 251 THR cc_start: 0.9358 (m) cc_final: 0.9119 (p) REVERT: A 307 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8648 (tttp) REVERT: A 507 MET cc_start: 0.9732 (mmm) cc_final: 0.9370 (mmm) REVERT: A 593 MET cc_start: 0.9595 (tmm) cc_final: 0.9282 (tmm) REVERT: A 604 MET cc_start: 0.9295 (mmm) cc_final: 0.8867 (mmm) outliers start: 37 outliers final: 30 residues processed: 94 average time/residue: 0.2081 time to fit residues: 31.3017 Evaluate side-chains 94 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 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 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 423 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 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 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 109 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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** ** 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 = 0.2887 r_free = 0.2887 target = 0.037174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.027482 restraints weight = 89201.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.028764 restraints weight = 43772.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.029624 restraints weight = 27709.798| |-----------------------------------------------------------------------------| r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2926 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= 0.198 Angle : 0.661 12.464 17323 Z= 0.330 Chirality : 0.041 0.243 1933 Planarity : 0.003 0.039 1896 Dihedral : 20.150 154.132 2537 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.98 % Allowed : 22.65 % 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 (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: 1.24 (0.25), residues: 1234 helix: 1.57 (0.21), residues: 610 sheet: -0.34 (0.45), residues: 128 loop : 0.36 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 676 HIS 0.003 0.001 HIS A 618 PHE 0.010 0.001 PHE A 353 TYR 0.018 0.001 TYR A 61 ARG 0.004 0.000 ARG A 301 *********************** 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 95 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8805 (tpt) cc_final: 0.8505 (tpt) REVERT: A 165 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: A 203 GLU cc_start: 0.9615 (tp30) cc_final: 0.9209 (tp30) REVERT: A 251 THR cc_start: 0.9372 (m) cc_final: 0.9138 (p) REVERT: A 307 LYS cc_start: 0.8895 (ttmt) cc_final: 0.8633 (tttm) REVERT: A 507 MET cc_start: 0.9727 (mmm) cc_final: 0.9347 (mmm) REVERT: A 593 MET cc_start: 0.9604 (tmm) cc_final: 0.9276 (tmm) REVERT: A 604 MET cc_start: 0.9246 (mmm) cc_final: 0.8825 (mmm) outliers start: 33 outliers final: 29 residues processed: 92 average time/residue: 0.2005 time to fit residues: 29.4769 Evaluate side-chains 90 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 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 423 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 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 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 0 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 100 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** ** 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 = 0.2891 r_free = 0.2891 target = 0.037310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.027578 restraints weight = 88730.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.028852 restraints weight = 44127.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.029715 restraints weight = 28033.592| |-----------------------------------------------------------------------------| r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2985 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= 0.202 Angle : 0.675 15.824 17323 Z= 0.335 Chirality : 0.041 0.250 1933 Planarity : 0.003 0.039 1896 Dihedral : 20.089 154.181 2535 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.98 % Allowed : 22.92 % 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: 1.25 (0.25), residues: 1234 helix: 1.56 (0.21), residues: 610 sheet: -0.35 (0.45), residues: 128 loop : 0.40 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1085 HIS 0.003 0.001 HIS A 618 PHE 0.027 0.001 PHE A1015 TYR 0.017 0.001 TYR A 61 ARG 0.004 0.000 ARG A 301 ********************** 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 94 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: A 203 GLU cc_start: 0.9622 (tp30) cc_final: 0.9377 (tp30) REVERT: A 307 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8661 (tttm) REVERT: A 507 MET cc_start: 0.9727 (mmm) cc_final: 0.9346 (mmm) REVERT: A 593 MET cc_start: 0.9595 (tmm) cc_final: 0.9263 (tmm) REVERT: A 604 MET cc_start: 0.9253 (mmm) cc_final: 0.8826 (mmm) REVERT: A 1018 MET cc_start: 0.9641 (mmm) cc_final: 0.9160 (mpp) outliers start: 33 outliers final: 31 residues processed: 90 average time/residue: 0.1948 time to fit residues: 28.6379 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 : 1.260 ------------------------------------------------------------------------------- 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 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 423 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 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 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: 0.9980 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.2882 r_free = 0.2882 target = 0.036941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.027253 restraints weight = 89689.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.028511 restraints weight = 44584.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.029374 restraints weight = 28441.798| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3105 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= 0.227 Angle : 0.673 13.794 17323 Z= 0.337 Chirality : 0.041 0.245 1933 Planarity : 0.003 0.039 1896 Dihedral : 20.105 154.019 2535 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.80 % Allowed : 23.01 % 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: 1.24 (0.25), residues: 1234 helix: 1.56 (0.21), residues: 610 sheet: -0.41 (0.46), residues: 128 loop : 0.39 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1085 HIS 0.003 0.001 HIS A 618 PHE 0.012 0.001 PHE A1117 TYR 0.019 0.001 TYR A 61 ARG 0.004 0.000 ARG A 301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3055.82 seconds wall clock time: 56 minutes 28.67 seconds (3388.67 seconds total)