Starting phenix.real_space_refine on Sat Nov 16 21:49:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfp_40447/11_2024/8sfp_40447.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfp_40447/11_2024/8sfp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfp_40447/11_2024/8sfp_40447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfp_40447/11_2024/8sfp_40447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfp_40447/11_2024/8sfp_40447.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfp_40447/11_2024/8sfp_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-5513/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: 7.74, 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: 3.32 Conformation dependent library (CDL) restraints added in 1.5 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: 4.77 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: 6.14 Time building geometry restraints manager: 3.79 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: 2.920 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.010 Find NCS groups from input model: 0.090 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.510 ------------------------------------------------------------------------------- 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 : 1.589 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: 0.2299 time to fit residues: 39.6759 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 : 1.280 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 : 1.339 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: 0.9151 (m-80) cc_final: 0.8723 (m-80) outliers start: 35 outliers final: 16 residues processed: 92 average time/residue: 0.2368 time to fit residues: 33.3644 Evaluate side-chains 77 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 151 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 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 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 66 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 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 547 ASN A 977 HIS ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12519 Z= 0.242 Angle : 0.648 10.634 17323 Z= 0.335 Chirality : 0.040 0.156 1933 Planarity : 0.004 0.040 1896 Dihedral : 20.343 153.761 2535 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.07 % Allowed : 21.75 % 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: 0.68 (0.24), residues: 1234 helix: 1.07 (0.21), residues: 617 sheet: -0.32 (0.44), residues: 139 loop : 0.03 (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 0.012 0.001 PHE A1015 TYR 0.020 0.001 TYR A 61 ARG 0.004 0.000 ARG A 341 *********************** 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: 34 poor density : 68 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1063 PHE cc_start: 0.8071 (m-80) cc_final: 0.7857 (m-10) REVERT: A 1072 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7003 (mtmt) outliers start: 34 outliers final: 21 residues processed: 96 average time/residue: 0.2383 time to fit residues: 34.7868 Evaluate side-chains 82 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 151 THR 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 373 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 974 GLN Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1294 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 611 GLN ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12519 Z= 0.347 Angle : 0.690 11.410 17323 Z= 0.365 Chirality : 0.042 0.199 1933 Planarity : 0.004 0.042 1896 Dihedral : 20.495 149.929 2535 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.33 % Allowed : 21.21 % 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: 0.55 (0.24), residues: 1234 helix: 0.96 (0.20), residues: 619 sheet: -0.47 (0.43), residues: 139 loop : -0.00 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 765 HIS 0.006 0.001 HIS A 622 PHE 0.016 0.002 PHE A1079 TYR 0.029 0.002 TYR A 61 ARG 0.004 0.001 ARG A1306 *********************** 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: 48 poor density : 56 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7745 (m-80) outliers start: 48 outliers final: 28 residues processed: 98 average time/residue: 0.2308 time to fit residues: 34.6097 Evaluate side-chains 80 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 51 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 251 THR 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 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 873 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN 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** ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12519 Z= 0.207 Angle : 0.634 11.025 17323 Z= 0.325 Chirality : 0.040 0.212 1933 Planarity : 0.003 0.039 1896 Dihedral : 20.413 146.771 2535 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.97 % Allowed : 22.02 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.24), residues: 1234 helix: 1.28 (0.21), residues: 619 sheet: -0.34 (0.44), residues: 139 loop : 0.16 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 676 HIS 0.002 0.001 HIS A 618 PHE 0.012 0.001 PHE A1015 TYR 0.019 0.001 TYR A 336 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 110 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 66 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8987 (mm) outliers start: 44 outliers final: 35 residues processed: 102 average time/residue: 0.2218 time to fit residues: 35.0537 Evaluate side-chains 96 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 60 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR 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 305 LEU Chi-restraints excluded: chain A residue 310 LEU 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 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 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 972 LEU Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 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 720 HIS A 755 HIS ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 12519 Z= 0.421 Angle : 0.747 12.515 17323 Z= 0.395 Chirality : 0.043 0.186 1933 Planarity : 0.004 0.042 1896 Dihedral : 20.614 143.879 2535 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.06 % Allowed : 23.65 % Favored : 72.29 % 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: 0.42 (0.24), residues: 1234 helix: 0.92 (0.20), residues: 618 sheet: -0.72 (0.45), residues: 128 loop : -0.11 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 765 HIS 0.007 0.001 HIS A1167 PHE 0.018 0.002 PHE A 138 TYR 0.031 0.002 TYR A 61 ARG 0.004 0.001 ARG A1094 *********************** 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 98 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 53 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7913 (m-10) outliers start: 45 outliers final: 38 residues processed: 91 average time/residue: 0.2257 time to fit residues: 31.9219 Evaluate side-chains 91 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 52 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 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 251 THR Chi-restraints excluded: chain A residue 310 LEU 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 409 VAL 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 681 ARG Chi-restraints excluded: chain A residue 714 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 917 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1167 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12519 Z= 0.242 Angle : 0.664 11.958 17323 Z= 0.341 Chirality : 0.041 0.205 1933 Planarity : 0.004 0.041 1896 Dihedral : 20.499 142.458 2535 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.88 % Allowed : 23.56 % Favored : 72.56 % 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: 0.74 (0.24), residues: 1234 helix: 1.18 (0.21), residues: 619 sheet: -0.59 (0.46), residues: 128 loop : 0.05 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 676 HIS 0.003 0.001 HIS A1210 PHE 0.012 0.001 PHE A 353 TYR 0.022 0.001 TYR A 61 ARG 0.003 0.000 ARG A1306 *********************** 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 103 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 60 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7921 (m-80) outliers start: 43 outliers final: 34 residues processed: 96 average time/residue: 0.2271 time to fit residues: 33.4814 Evaluate side-chains 89 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 54 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU 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 236 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 ARG 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 409 VAL 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 714 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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** A 974 GLN ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3132 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= 0.179 Angle : 0.681 15.487 17323 Z= 0.339 Chirality : 0.041 0.214 1933 Planarity : 0.003 0.047 1896 Dihedral : 20.361 141.109 2535 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.80 % Allowed : 24.91 % Favored : 72.29 % 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: 1.00 (0.24), residues: 1234 helix: 1.41 (0.21), residues: 618 sheet: -0.48 (0.46), residues: 128 loop : 0.16 (0.29), residues: 488 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 0.011 0.001 PHE A 353 TYR 0.015 0.001 TYR A 61 ARG 0.003 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 94 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 768 LEU cc_start: 0.8133 (tp) cc_final: 0.7901 (tp) outliers start: 31 outliers final: 27 residues processed: 90 average time/residue: 0.2317 time to fit residues: 32.0756 Evaluate side-chains 84 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 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 251 THR 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 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 714 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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** A1024 ASN ** A1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12519 Z= 0.266 Angle : 0.698 13.126 17323 Z= 0.354 Chirality : 0.042 0.243 1933 Planarity : 0.004 0.039 1896 Dihedral : 20.342 140.956 2535 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.98 % Allowed : 25.18 % Favored : 71.84 % 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: 0.94 (0.24), residues: 1234 helix: 1.38 (0.21), residues: 618 sheet: -0.55 (0.45), residues: 128 loop : 0.12 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 765 HIS 0.003 0.001 HIS A 618 PHE 0.012 0.001 PHE A1049 TYR 0.023 0.001 TYR A 61 ARG 0.003 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 90 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7855 (m-10) outliers start: 33 outliers final: 29 residues processed: 84 average time/residue: 0.2276 time to fit residues: 29.5707 Evaluate side-chains 87 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 236 SER Chi-restraints excluded: chain A residue 251 THR 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 409 VAL 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 714 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1024 ASN 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 75 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 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 3 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3296 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= 0.209 Angle : 0.702 13.112 17323 Z= 0.349 Chirality : 0.042 0.246 1933 Planarity : 0.003 0.039 1896 Dihedral : 20.317 140.725 2535 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.89 % Allowed : 25.18 % Favored : 71.93 % 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: 1.00 (0.24), residues: 1234 helix: 1.44 (0.21), residues: 618 sheet: -0.56 (0.45), residues: 128 loop : 0.16 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.004 0.001 HIS A 618 PHE 0.011 0.001 PHE A 353 TYR 0.018 0.001 TYR A 61 ARG 0.002 0.000 ARG A1306 ********************** 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 91 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: A 768 LEU cc_start: 0.8179 (tp) cc_final: 0.7938 (tp) REVERT: A 1225 MET cc_start: 0.7736 (tpp) cc_final: 0.7443 (tpp) outliers start: 32 outliers final: 29 residues processed: 86 average time/residue: 0.2183 time to fit residues: 29.6421 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 : 1.469 ------------------------------------------------------------------------------- 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 251 THR 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 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 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 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 31 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.2901 r_free = 0.2901 target = 0.037437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.027713 restraints weight = 87724.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.028995 restraints weight = 43540.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.029869 restraints weight = 27726.801| |-----------------------------------------------------------------------------| r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3273 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= 0.184 Angle : 0.695 12.910 17323 Z= 0.341 Chirality : 0.041 0.260 1933 Planarity : 0.003 0.039 1896 Dihedral : 20.150 140.491 2535 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.89 % Allowed : 25.54 % Favored : 71.57 % 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: 1.15 (0.25), residues: 1234 helix: 1.57 (0.21), residues: 612 sheet: -0.52 (0.45), residues: 128 loop : 0.24 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.004 0.001 HIS A 618 PHE 0.011 0.001 PHE A 353 TYR 0.015 0.001 TYR A 61 ARG 0.002 0.000 ARG A 725 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1986.94 seconds wall clock time: 38 minutes 7.52 seconds (2287.52 seconds total)