Starting phenix.real_space_refine on Sun Dec 29 02:47:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d49_27178/12_2024/8d49_27178.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d49_27178/12_2024/8d49_27178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d49_27178/12_2024/8d49_27178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d49_27178/12_2024/8d49_27178.map" model { file = "/net/cci-nas-00/data/ceres_data/8d49_27178/12_2024/8d49_27178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d49_27178/12_2024/8d49_27178.cif" } resolution = 3.2 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= 0.000 sd= 0.018 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 25 5.49 5 S 24 5.16 5 C 5812 2.51 5 N 1568 2.21 5 O 1852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9281 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8748 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 1044} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 533 Classifications: {'RNA': 26} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 5, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 19} Chain breaks: 1 Time building chain proxies: 6.16, per 1000 atoms: 0.66 Number of scatterers: 9281 At special positions: 0 Unit cell: (86.48, 96.82, 125.96, 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 24 16.00 P 25 15.00 O 1852 8.00 N 1568 7.00 C 5812 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: 2.34 Conformation dependent library (CDL) restraints added in 907.8 milliseconds 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 10 sheets defined 55.8% alpha, 11.8% beta 4 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.703A pdb=" N SER A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 79 Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 128 through 163 removed outlier: 3.601A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 197 removed outlier: 4.066A pdb=" N ILE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 201 through 205 removed outlier: 4.619A pdb=" N SER A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 removed outlier: 3.961A pdb=" N ILE A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 239 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 275 through 284 removed outlier: 3.530A pdb=" N LEU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 299 through 305 Processing helix chain 'A' and resid 310 through 319 Processing helix chain 'A' and resid 324 through 340 removed outlier: 4.386A pdb=" N HIS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLN A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.910A pdb=" N VAL A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 376 through 392 removed outlier: 3.698A pdb=" N LEU A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 4.276A pdb=" N CYS A 403 " --> pdb=" O PRO A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 438 removed outlier: 3.674A pdb=" N VAL A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 437 " --> pdb=" O ASN A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 4.134A pdb=" N LEU A 443 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 461 removed outlier: 3.766A pdb=" N PHE A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 481 Processing helix chain 'A' and resid 488 through 503 Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 531 through 559 removed outlier: 3.762A pdb=" N GLN A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 548 " --> pdb=" O TYR A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 716 through 727 Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.719A pdb=" N PHE A 757 " --> pdb=" O TRP A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 818 through 839 removed outlier: 3.825A pdb=" N GLN A 822 " --> pdb=" O ASP A 818 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP A 839 " --> pdb=" O HIS A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.727A pdb=" N SER A 886 " --> pdb=" O ARG A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 922 No H-bonds generated for 'chain 'A' and resid 920 through 922' Processing helix chain 'A' and resid 939 through 961 removed outlier: 3.535A pdb=" N THR A 960 " --> pdb=" O HIS A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 967 Processing helix chain 'A' and resid 968 through 970 No H-bonds generated for 'chain 'A' and resid 968 through 970' Processing helix chain 'A' and resid 974 through 986 removed outlier: 3.829A pdb=" N GLY A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1016 removed outlier: 3.811A pdb=" N ASP A1009 " --> pdb=" O GLU A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1028 removed outlier: 3.969A pdb=" N ILE A1026 " --> pdb=" O GLU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1034 removed outlier: 4.376A pdb=" N ASN A1034 " --> pdb=" O ALA A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1054 removed outlier: 3.924A pdb=" N ALA A1041 " --> pdb=" O GLN A1037 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A1042 " --> pdb=" O GLY A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1070 Processing helix chain 'A' and resid 1090 through 1096 Processing helix chain 'A' and resid 1102 through 1119 removed outlier: 3.778A pdb=" N LYS A1119 " --> pdb=" O LYS A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1144 Processing helix chain 'A' and resid 1213 through 1232 removed outlier: 4.256A pdb=" N ALA A1217 " --> pdb=" O ASP A1213 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A1232 " --> pdb=" O LEU A1228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 removed outlier: 6.617A pdb=" N LYS A 248 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLY A 568 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR A 250 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE A 570 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 16.277A pdb=" N HIS A 566 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 13.920A pdb=" N SER A 613 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N GLY A 568 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL A 611 " --> pdb=" O GLY A 568 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 18 removed outlier: 6.617A pdb=" N LYS A 248 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLY A 568 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR A 250 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE A 570 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 123 Processing sheet with id=AA6, first strand: chain 'A' and resid 866 through 867 removed outlier: 4.462A pdb=" N VAL A 859 " --> pdb=" O LEU A 867 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 866 through 867 removed outlier: 4.462A pdb=" N VAL A 859 " --> pdb=" O LEU A 867 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU A1063 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N HIS A1159 " --> pdb=" O ALA A1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A1060 " --> pdb=" O HIS A1159 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ILE A1161 " --> pdb=" O ILE A1060 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A1062 " --> pdb=" O ILE A1161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 891 through 896 removed outlier: 5.702A pdb=" N GLN A 892 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS A 874 " --> pdb=" O GLN A 892 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N GLU A 871 " --> pdb=" O LYS A 914 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 916 " --> pdb=" O GLU A 871 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 877 through 878 Processing sheet with id=AB1, first strand: chain 'A' and resid 1120 through 1121 467 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1531 1.31 - 1.44: 2613 1.44 - 1.56: 5277 1.56 - 1.68: 49 1.68 - 1.81: 35 Bond restraints: 9505 Sorted by residual: bond pdb=" C THR A 244 " pdb=" O THR A 244 " ideal model delta sigma weight residual 1.242 1.203 0.039 9.70e-03 1.06e+04 1.63e+01 bond pdb=" C TYR A 579 " pdb=" O TYR A 579 " ideal model delta sigma weight residual 1.234 1.187 0.047 1.28e-02 6.10e+03 1.35e+01 bond pdb=" N VAL A 593 " pdb=" CA VAL A 593 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" C PRO A 245 " pdb=" O PRO A 245 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.30e-02 5.92e+03 8.64e+00 bond pdb=" CA GLY A 242 " pdb=" C GLY A 242 " ideal model delta sigma weight residual 1.512 1.488 0.024 8.70e-03 1.32e+04 7.66e+00 ... (remaining 9500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 12720 2.75 - 5.50: 169 5.50 - 8.25: 13 8.25 - 11.00: 3 11.00 - 13.74: 2 Bond angle restraints: 12907 Sorted by residual: angle pdb=" C THR A 244 " pdb=" CA THR A 244 " pdb=" CB THR A 244 " ideal model delta sigma weight residual 111.01 100.12 10.89 1.38e+00 5.25e-01 6.22e+01 angle pdb=" C ASP A 601 " pdb=" CA ASP A 601 " pdb=" CB ASP A 601 " ideal model delta sigma weight residual 114.40 105.14 9.26 1.25e+00 6.40e-01 5.49e+01 angle pdb=" C ASN A 240 " pdb=" CA ASN A 240 " pdb=" CB ASN A 240 " ideal model delta sigma weight residual 112.44 100.27 12.17 1.72e+00 3.38e-01 5.01e+01 angle pdb=" N PRO A 245 " pdb=" CA PRO A 245 " pdb=" CB PRO A 245 " ideal model delta sigma weight residual 103.25 96.75 6.50 1.05e+00 9.07e-01 3.83e+01 angle pdb=" C GLY A 241 " pdb=" N GLY A 242 " pdb=" CA GLY A 242 " ideal model delta sigma weight residual 121.65 117.70 3.95 6.80e-01 2.16e+00 3.38e+01 ... (remaining 12902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.56: 5577 30.56 - 61.12: 219 61.12 - 91.67: 30 91.67 - 122.23: 1 122.23 - 152.79: 2 Dihedral angle restraints: 5829 sinusoidal: 2664 harmonic: 3165 Sorted by residual: dihedral pdb=" O4' U B 14 " pdb=" C1' U B 14 " pdb=" N1 U B 14 " pdb=" C2 U B 14 " ideal model delta sinusoidal sigma weight residual 200.00 47.21 152.79 1 1.50e+01 4.44e-03 8.06e+01 dihedral pdb=" O4' C B 22 " pdb=" C1' C B 22 " pdb=" N1 C B 22 " pdb=" C2 C B 22 " ideal model delta sinusoidal sigma weight residual -128.00 6.39 -134.39 1 1.70e+01 3.46e-03 5.65e+01 dihedral pdb=" CA PHE A 325 " pdb=" C PHE A 325 " pdb=" N LEU A 326 " pdb=" CA LEU A 326 " ideal model delta harmonic sigma weight residual -180.00 -149.63 -30.37 0 5.00e+00 4.00e-02 3.69e+01 ... (remaining 5826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1138 0.059 - 0.119: 257 0.119 - 0.178: 26 0.178 - 0.237: 9 0.237 - 0.296: 3 Chirality restraints: 1433 Sorted by residual: chirality pdb=" CA LYS A 874 " pdb=" N LYS A 874 " pdb=" C LYS A 874 " pdb=" CB LYS A 874 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA THR A 244 " pdb=" N THR A 244 " pdb=" C THR A 244 " pdb=" CB THR A 244 " both_signs ideal model delta sigma weight residual False 2.53 2.78 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" P U B 33 " pdb=" OP1 U B 33 " pdb=" OP2 U B 33 " pdb=" O5' U B 33 " both_signs ideal model delta sigma weight residual True 2.41 -2.65 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1430 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 337 " -0.084 5.00e-02 4.00e+02 1.25e-01 2.50e+01 pdb=" N PRO A 338 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 325 " -0.026 2.00e-02 2.50e+03 1.84e-02 5.93e+00 pdb=" CG PHE A 325 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 325 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 325 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 325 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 325 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 325 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 596 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C ILE A 596 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE A 596 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 597 " 0.012 2.00e-02 2.50e+03 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 133 2.66 - 3.22: 8728 3.22 - 3.78: 13891 3.78 - 4.34: 19659 4.34 - 4.90: 32565 Nonbonded interactions: 74976 Sorted by model distance: nonbonded pdb=" OH TYR A 135 " pdb=" OE2 GLU A 189 " model vdw 2.098 3.040 nonbonded pdb=" OH TYR A 393 " pdb=" OD1 ASP A 426 " model vdw 2.128 3.040 nonbonded pdb=" CD1 ILE A 51 " pdb=" CG2 THR A 775 " model vdw 2.201 3.880 nonbonded pdb=" O ILE A 986 " pdb=" OH TYR A 995 " model vdw 2.219 3.040 nonbonded pdb=" OE2 GLU A 841 " pdb=" NH1 ARG A 863 " model vdw 2.225 3.120 ... (remaining 74971 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.050 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.150 Find NCS groups from input model: 0.100 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.009 0.061 9505 Z= 0.559 Angle : 0.842 13.744 12907 Z= 0.502 Chirality : 0.052 0.296 1433 Planarity : 0.005 0.125 1570 Dihedral : 16.096 152.791 3783 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 1.14 % Allowed : 0.83 % Favored : 98.03 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.72 (0.25), residues: 1062 helix: 0.32 (0.21), residues: 545 sheet: -1.42 (0.43), residues: 136 loop : -1.12 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 78 HIS 0.007 0.002 HIS A 798 PHE 0.040 0.003 PHE A 325 TYR 0.029 0.002 TYR A 579 ARG 0.011 0.001 ARG A 883 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 47 average time/residue: 0.3263 time to fit residues: 20.9514 Evaluate side-chains 27 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN A 812 GLN A1141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9505 Z= 0.183 Angle : 0.536 11.742 12907 Z= 0.285 Chirality : 0.039 0.172 1433 Planarity : 0.004 0.080 1570 Dihedral : 12.861 152.107 1554 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.21 % Allowed : 5.60 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1062 helix: 1.13 (0.22), residues: 555 sheet: -1.46 (0.42), residues: 139 loop : -0.90 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 587 PHE 0.033 0.001 PHE A 325 TYR 0.010 0.001 TYR A 157 ARG 0.005 0.001 ARG A 896 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 1.075 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.2327 time to fit residues: 12.1724 Evaluate side-chains 24 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9505 Z= 0.200 Angle : 0.485 11.310 12907 Z= 0.255 Chirality : 0.038 0.155 1433 Planarity : 0.004 0.061 1570 Dihedral : 12.723 148.437 1554 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.83 % Allowed : 6.74 % Favored : 92.43 % 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: 0.61 (0.26), residues: 1062 helix: 1.63 (0.22), residues: 555 sheet: -1.36 (0.42), residues: 140 loop : -0.69 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 480 HIS 0.003 0.001 HIS A 798 PHE 0.025 0.001 PHE A 325 TYR 0.011 0.001 TYR A 579 ARG 0.004 0.000 ARG A 883 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 386 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6915 (mp0) outliers start: 8 outliers final: 3 residues processed: 34 average time/residue: 0.2653 time to fit residues: 13.3604 Evaluate side-chains 26 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 906 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 0.0170 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 87 optimal weight: 0.0370 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 HIS A1118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9505 Z= 0.142 Angle : 0.452 9.520 12907 Z= 0.238 Chirality : 0.037 0.150 1433 Planarity : 0.003 0.052 1570 Dihedral : 12.642 148.581 1553 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.52 % Allowed : 7.47 % Favored : 92.01 % 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: 0.89 (0.27), residues: 1062 helix: 1.82 (0.22), residues: 558 sheet: -1.10 (0.44), residues: 140 loop : -0.58 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.002 0.000 HIS A 566 PHE 0.037 0.001 PHE A 325 TYR 0.010 0.001 TYR A 579 ARG 0.003 0.000 ARG A1016 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 386 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6723 (mp0) outliers start: 5 outliers final: 1 residues processed: 34 average time/residue: 0.2176 time to fit residues: 11.9930 Evaluate side-chains 24 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 871 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.0970 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9505 Z= 0.238 Angle : 0.480 10.485 12907 Z= 0.249 Chirality : 0.038 0.157 1433 Planarity : 0.003 0.047 1570 Dihedral : 12.583 148.399 1553 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.62 % Allowed : 8.61 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 1062 helix: 1.91 (0.22), residues: 558 sheet: -1.07 (0.44), residues: 140 loop : -0.55 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 798 PHE 0.034 0.001 PHE A 325 TYR 0.011 0.001 TYR A 544 ARG 0.003 0.000 ARG A 883 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 1.032 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 30 average time/residue: 0.2484 time to fit residues: 11.4889 Evaluate side-chains 25 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 906 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9505 Z= 0.336 Angle : 0.544 12.705 12907 Z= 0.281 Chirality : 0.040 0.165 1433 Planarity : 0.003 0.044 1570 Dihedral : 12.562 148.461 1553 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.93 % Allowed : 9.13 % Favored : 89.94 % 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 (0.27), residues: 1062 helix: 1.90 (0.22), residues: 557 sheet: -1.16 (0.44), residues: 140 loop : -0.59 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 78 HIS 0.004 0.001 HIS A 798 PHE 0.037 0.002 PHE A 325 TYR 0.013 0.001 TYR A 544 ARG 0.002 0.000 ARG A1016 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 1.162 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 30 average time/residue: 0.2108 time to fit residues: 10.3095 Evaluate side-chains 26 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9505 Z= 0.191 Angle : 0.472 11.822 12907 Z= 0.244 Chirality : 0.038 0.155 1433 Planarity : 0.003 0.042 1570 Dihedral : 12.512 147.514 1553 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.73 % Allowed : 9.44 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.27), residues: 1062 helix: 2.02 (0.22), residues: 558 sheet: -1.20 (0.44), residues: 137 loop : -0.50 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.003 0.000 HIS A 798 PHE 0.035 0.001 PHE A 325 TYR 0.010 0.001 TYR A 579 ARG 0.003 0.000 ARG A1016 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 1.082 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 28 average time/residue: 0.1888 time to fit residues: 9.2083 Evaluate side-chains 25 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 906 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9505 Z= 0.336 Angle : 0.537 12.991 12907 Z= 0.276 Chirality : 0.040 0.181 1433 Planarity : 0.003 0.040 1570 Dihedral : 12.504 148.174 1553 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.73 % Allowed : 9.96 % Favored : 89.32 % 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: 0.97 (0.27), residues: 1062 helix: 1.96 (0.22), residues: 557 sheet: -1.20 (0.43), residues: 140 loop : -0.62 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 78 HIS 0.004 0.001 HIS A 798 PHE 0.036 0.002 PHE A 325 TYR 0.013 0.001 TYR A 544 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 1.052 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 25 average time/residue: 0.1964 time to fit residues: 8.5823 Evaluate side-chains 24 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 906 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9505 Z= 0.178 Angle : 0.460 10.660 12907 Z= 0.240 Chirality : 0.038 0.152 1433 Planarity : 0.003 0.041 1570 Dihedral : 12.440 147.254 1553 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.52 % Allowed : 10.27 % Favored : 89.21 % 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: 1.11 (0.27), residues: 1062 helix: 2.08 (0.22), residues: 558 sheet: -1.23 (0.44), residues: 137 loop : -0.51 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 480 HIS 0.002 0.000 HIS A 798 PHE 0.033 0.001 PHE A 325 TYR 0.011 0.001 TYR A 579 ARG 0.002 0.000 ARG A1016 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 1.113 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 28 average time/residue: 0.2485 time to fit residues: 11.1053 Evaluate side-chains 25 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 906 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9505 Z= 0.293 Angle : 0.514 12.082 12907 Z= 0.266 Chirality : 0.039 0.162 1433 Planarity : 0.003 0.041 1570 Dihedral : 12.411 147.926 1553 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.52 % Allowed : 10.48 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.27), residues: 1062 helix: 2.05 (0.22), residues: 557 sheet: -1.19 (0.43), residues: 140 loop : -0.62 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 78 HIS 0.003 0.001 HIS A 798 PHE 0.033 0.001 PHE A 325 TYR 0.012 0.001 TYR A 544 ARG 0.002 0.000 ARG A1016 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 1.096 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 24 average time/residue: 0.1979 time to fit residues: 8.3946 Evaluate side-chains 25 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 906 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.077010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.057324 restraints weight = 24461.615| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.55 r_work: 0.2745 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9505 Z= 0.203 Angle : 0.468 10.622 12907 Z= 0.246 Chirality : 0.038 0.156 1433 Planarity : 0.003 0.040 1570 Dihedral : 12.356 147.364 1553 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.52 % Allowed : 10.48 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.27), residues: 1062 helix: 2.10 (0.22), residues: 558 sheet: -1.17 (0.45), residues: 137 loop : -0.56 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 78 HIS 0.003 0.001 HIS A 798 PHE 0.031 0.001 PHE A 325 TYR 0.010 0.001 TYR A 544 ARG 0.003 0.000 ARG A1016 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1743.32 seconds wall clock time: 33 minutes 12.73 seconds (1992.73 seconds total)