Starting phenix.real_space_refine on Thu Jul 2 18:13:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d49_27178/07_2026/8d49_27178.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d49_27178/07_2026/8d49_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 { model { file = "/net/cci-nas-00/data/ceres_data/8d49_27178/07_2026/8d49_27178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d49_27178/07_2026/8d49_27178.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d49_27178/07_2026/8d49_27178.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d49_27178/07_2026/8d49_27178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d49_27178/07_2026/8d49_27178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d49_27178/07_2026/8d49_27178.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.95, per 1000 atoms: 0.21 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: 0.93 Conformation dependent library (CDL) restraints added in 312.1 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: 1.13 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: 1.80 Time building geometry restraints manager: 1.20 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: 5523 30.56 - 61.12: 192 61.12 - 91.67: 23 91.67 - 122.23: 1 122.23 - 152.79: 2 Dihedral angle restraints: 5741 sinusoidal: 2576 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 5738 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.750 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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= 0.388 Angle : 0.842 13.744 12907 Z= 0.502 Chirality : 0.052 0.296 1433 Planarity : 0.005 0.125 1570 Dihedral : 15.296 152.791 3695 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.011 0.001 ARG A 883 TYR 0.029 0.002 TYR A 579 PHE 0.040 0.003 PHE A 325 TRP 0.019 0.002 TRP A 78 HIS 0.007 0.002 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00872 / 0.39 ( 9505) covalent geometry : angle 0.84194 / 0.50 (12907) hydrogen bonds : bond 0.14121 / 9.02 ( 465) hydrogen bonds : angle 5.93566 / 4.06 ( 1344) *********************** 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 : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 47 average time/residue: 0.1325 time to fit residues: 8.4460 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 : 0.413 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN A 812 GLN A1141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.080110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.061854 restraints weight = 24630.041| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.08 r_work: 0.2906 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9505 Z= 0.161 Angle : 0.550 12.523 12907 Z= 0.292 Chirality : 0.040 0.174 1433 Planarity : 0.004 0.078 1570 Dihedral : 9.847 151.584 1466 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.21 % Allowed : 5.91 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.26), residues: 1062 helix: 1.11 (0.22), residues: 556 sheet: -1.47 (0.42), residues: 140 loop : -0.88 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 896 TYR 0.011 0.001 TYR A 157 PHE 0.034 0.001 PHE A 325 TRP 0.010 0.001 TRP A 78 HIS 0.003 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 9505) covalent geometry : angle 0.55040 / 0.29 (12907) hydrogen bonds : bond 0.04673 / 3.00 ( 465) hydrogen bonds : angle 4.49964 / 3.08 ( 1344) *********************** 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 32 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.372 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 0.1008 time to fit residues: 4.8478 Evaluate side-chains 22 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 871 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 95 optimal weight: 0.0870 chunk 77 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.080170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.061412 restraints weight = 24614.961| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.14 r_work: 0.2917 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9505 Z= 0.130 Angle : 0.474 11.286 12907 Z= 0.250 Chirality : 0.038 0.154 1433 Planarity : 0.003 0.062 1570 Dihedral : 9.552 148.489 1466 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.62 % Allowed : 7.05 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.26), residues: 1062 helix: 1.60 (0.22), residues: 556 sheet: -1.40 (0.42), residues: 140 loop : -0.73 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 896 TYR 0.015 0.001 TYR A 490 PHE 0.026 0.001 PHE A 325 TRP 0.014 0.001 TRP A 480 HIS 0.002 0.000 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9505) covalent geometry : angle 0.47418 / 0.25 (12907) hydrogen bonds : bond 0.03998 / 2.56 ( 465) hydrogen bonds : angle 4.06025 / 2.79 ( 1344) *********************** 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 31 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 386 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7403 (mp0) outliers start: 6 outliers final: 2 residues processed: 31 average time/residue: 0.0905 time to fit residues: 4.3671 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 : 0.232 ------------------------------------------------------------------------------- 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 906 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 0.0000 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 0.0670 chunk 30 optimal weight: 0.9980 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.079531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.060720 restraints weight = 24779.335| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.20 r_work: 0.2896 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1768 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= 0.153 Angle : 0.475 11.441 12907 Z= 0.249 Chirality : 0.038 0.157 1433 Planarity : 0.003 0.053 1570 Dihedral : 9.428 148.579 1465 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.83 % Allowed : 7.26 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.27), residues: 1062 helix: 1.75 (0.22), residues: 557 sheet: -1.14 (0.44), residues: 140 loop : -0.70 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 896 TYR 0.010 0.001 TYR A 579 PHE 0.038 0.001 PHE A 325 TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9505) covalent geometry : angle 0.47450 / 0.25 (12907) hydrogen bonds : bond 0.03926 / 2.50 ( 465) hydrogen bonds : angle 3.98834 / 2.73 ( 1344) *********************** 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 31 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 386 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: A 768 GLU cc_start: 0.8615 (pm20) cc_final: 0.8390 (pm20) outliers start: 8 outliers final: 3 residues processed: 30 average time/residue: 0.0611 time to fit residues: 2.9419 Evaluate side-chains 25 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 871 GLU Chi-restraints excluded: chain A residue 906 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.077973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.059366 restraints weight = 24565.936| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.12 r_work: 0.2901 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1961 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= 0.158 Angle : 0.479 11.263 12907 Z= 0.248 Chirality : 0.038 0.158 1433 Planarity : 0.003 0.048 1570 Dihedral : 9.346 148.047 1465 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.83 % Allowed : 8.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.27), residues: 1062 helix: 1.90 (0.22), residues: 557 sheet: -1.13 (0.45), residues: 137 loop : -0.63 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1016 TYR 0.010 0.001 TYR A 544 PHE 0.035 0.001 PHE A 325 TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 9505) covalent geometry : angle 0.47922 / 0.25 (12907) hydrogen bonds : bond 0.03826 / 2.44 ( 465) hydrogen bonds : angle 3.89087 / 2.67 ( 1344) *********************** 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 34 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.9049 (tt0) cc_final: 0.8809 (pp20) outliers start: 8 outliers final: 5 residues processed: 33 average time/residue: 0.0803 time to fit residues: 4.2070 Evaluate side-chains 30 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.078657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.060216 restraints weight = 24569.267| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.13 r_work: 0.2913 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9505 Z= 0.128 Angle : 0.462 10.592 12907 Z= 0.240 Chirality : 0.037 0.155 1433 Planarity : 0.003 0.045 1570 Dihedral : 9.249 147.596 1465 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.62 % Allowed : 9.23 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.27), residues: 1062 helix: 2.02 (0.22), residues: 557 sheet: -1.07 (0.45), residues: 137 loop : -0.56 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 896 TYR 0.009 0.001 TYR A 544 PHE 0.026 0.001 PHE A 325 TRP 0.010 0.001 TRP A 480 HIS 0.002 0.000 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9505) covalent geometry : angle 0.46189 / 0.24 (12907) hydrogen bonds : bond 0.03631 / 2.32 ( 465) hydrogen bonds : angle 3.77964 / 2.60 ( 1344) *********************** 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 34 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.9037 (tt0) cc_final: 0.8797 (pp20) outliers start: 6 outliers final: 3 residues processed: 32 average time/residue: 0.1010 time to fit residues: 4.8204 Evaluate side-chains 27 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 771 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 0.2980 chunk 96 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.076233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.056737 restraints weight = 24628.398| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.39 r_work: 0.2767 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9505 Z= 0.192 Angle : 0.513 12.944 12907 Z= 0.264 Chirality : 0.039 0.160 1433 Planarity : 0.003 0.042 1570 Dihedral : 9.258 148.028 1465 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.83 % Allowed : 9.44 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.27), residues: 1062 helix: 2.03 (0.22), residues: 557 sheet: -1.07 (0.44), residues: 140 loop : -0.64 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 849 TYR 0.012 0.001 TYR A 544 PHE 0.027 0.001 PHE A 325 TRP 0.011 0.001 TRP A 78 HIS 0.004 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 9505) covalent geometry : angle 0.51325 / 0.26 (12907) hydrogen bonds : bond 0.03862 / 2.46 ( 465) hydrogen bonds : angle 3.86671 / 2.66 ( 1344) *********************** 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 32 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8955 (tt0) cc_final: 0.8606 (pp20) outliers start: 8 outliers final: 5 residues processed: 31 average time/residue: 0.0862 time to fit residues: 4.3019 Evaluate side-chains 26 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 771 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 84 optimal weight: 0.0570 chunk 60 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.077396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.057695 restraints weight = 24514.445| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.49 r_work: 0.2770 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9505 Z= 0.104 Angle : 0.453 10.251 12907 Z= 0.237 Chirality : 0.037 0.156 1433 Planarity : 0.003 0.041 1570 Dihedral : 9.095 147.005 1465 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.52 % Allowed : 9.96 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.27), residues: 1062 helix: 2.11 (0.22), residues: 558 sheet: -0.99 (0.45), residues: 137 loop : -0.53 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1016 TYR 0.010 0.001 TYR A 579 PHE 0.022 0.001 PHE A 325 TRP 0.009 0.001 TRP A 480 HIS 0.002 0.000 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 9505) covalent geometry : angle 0.45339 / 0.24 (12907) hydrogen bonds : bond 0.03463 / 2.21 ( 465) hydrogen bonds : angle 3.69721 / 2.54 ( 1344) *********************** 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 31 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8854 (tt0) cc_final: 0.8474 (pp20) REVERT: A 725 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8426 (mm-30) outliers start: 5 outliers final: 5 residues processed: 30 average time/residue: 0.0893 time to fit residues: 4.3064 Evaluate side-chains 30 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 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 19 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.077037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.057579 restraints weight = 24299.150| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.41 r_work: 0.2787 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9505 Z= 0.155 Angle : 0.476 10.979 12907 Z= 0.247 Chirality : 0.038 0.157 1433 Planarity : 0.003 0.041 1570 Dihedral : 9.060 147.484 1465 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.73 % Allowed : 9.85 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.27), residues: 1062 helix: 2.15 (0.22), residues: 557 sheet: -1.00 (0.44), residues: 140 loop : -0.57 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1016 TYR 0.011 0.001 TYR A 544 PHE 0.023 0.001 PHE A 325 TRP 0.009 0.001 TRP A 78 HIS 0.003 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 9505) covalent geometry : angle 0.47578 / 0.25 (12907) hydrogen bonds : bond 0.03661 / 2.33 ( 465) hydrogen bonds : angle 3.75857 / 2.59 ( 1344) *********************** 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 33 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8951 (tt0) cc_final: 0.8589 (pp20) outliers start: 7 outliers final: 5 residues processed: 32 average time/residue: 0.0920 time to fit residues: 4.7415 Evaluate side-chains 27 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.077552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.057784 restraints weight = 24400.686| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.57 r_work: 0.2758 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2401 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= 0.125 Angle : 0.459 10.025 12907 Z= 0.240 Chirality : 0.038 0.154 1433 Planarity : 0.003 0.040 1570 Dihedral : 8.962 147.139 1465 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.52 % Allowed : 9.96 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.27), residues: 1062 helix: 2.19 (0.22), residues: 558 sheet: -1.00 (0.45), residues: 137 loop : -0.54 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1016 TYR 0.009 0.001 TYR A 544 PHE 0.021 0.001 PHE A 325 TRP 0.008 0.001 TRP A 480 HIS 0.002 0.000 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 9505) covalent geometry : angle 0.45932 / 0.24 (12907) hydrogen bonds : bond 0.03508 / 2.24 ( 465) hydrogen bonds : angle 3.68816 / 2.54 ( 1344) ********************** 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 32 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8796 (tt0) cc_final: 0.8447 (pp20) outliers start: 5 outliers final: 5 residues processed: 32 average time/residue: 0.1135 time to fit residues: 5.4330 Evaluate side-chains 26 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 64 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.057249 restraints weight = 24467.429| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.59 r_work: 0.2752 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2422 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= 0.136 Angle : 0.469 10.111 12907 Z= 0.245 Chirality : 0.038 0.155 1433 Planarity : 0.003 0.040 1570 Dihedral : 8.909 147.187 1465 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.62 % Allowed : 10.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.27), residues: 1062 helix: 2.21 (0.22), residues: 558 sheet: -0.98 (0.44), residues: 140 loop : -0.57 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1016 TYR 0.010 0.001 TYR A 544 PHE 0.020 0.001 PHE A 325 TRP 0.009 0.001 TRP A 480 HIS 0.002 0.000 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9505) covalent geometry : angle 0.46864 / 0.25 (12907) hydrogen bonds : bond 0.03551 / 2.27 ( 465) hydrogen bonds : angle 3.69533 / 2.54 ( 1344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1886.89 seconds wall clock time: 33 minutes 12.45 seconds (1992.45 seconds total)