Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2963595.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2963595.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2963595.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.68, per 1000 atoms: 0.50 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 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: 0.50 Conformation dependent library (CDL) restraints added in 217.2 milliseconds Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 528 0.91 - 1.16: 1115 1.16 - 1.42: 620 1.42 - 1.67: 851 1.67 - 1.93: 39 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.524 1.772 -0.248 1.26e-02 6.30e+03 3.87e+02 bond pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " ideal model delta sigma weight residual 1.378 1.163 0.215 1.10e-02 8.26e+03 3.82e+02 bond pdb=" N VAL A 123 " pdb=" CA VAL A 123 " ideal model delta sigma weight residual 1.456 1.240 0.215 1.11e-02 8.12e+03 3.76e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.512 -0.191 1.00e-02 1.00e+04 3.63e+02 bond pdb=" N PRO A 43 " pdb=" CA PRO A 43 " ideal model delta sigma weight residual 1.466 1.242 0.223 1.19e-02 7.06e+03 3.52e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 3338 4.85 - 9.69: 1833 9.69 - 14.54: 495 14.54 - 19.39: 105 19.39 - 24.23: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 71 " pdb=" C VAL A 71 " pdb=" N LEU A 72 " ideal model delta sigma weight residual 123.18 104.97 18.21 1.05e+00 9.07e-01 3.01e+02 angle pdb=" O SER A 47 " pdb=" C SER A 47 " pdb=" N ARG A 48 " ideal model delta sigma weight residual 122.12 138.53 -16.41 1.06e+00 8.90e-01 2.40e+02 angle pdb=" CA AGLU A 94 " pdb=" C AGLU A 94 " pdb=" O AGLU A 94 " ideal model delta sigma weight residual 119.97 104.45 15.52 1.15e+00 7.56e-01 1.82e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.35 133.76 -12.41 9.20e-01 1.18e+00 1.82e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.83 108.18 13.65 1.03e+00 9.43e-01 1.76e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 18.44: 958 18.44 - 36.87: 110 36.87 - 55.30: 30 55.30 - 73.73: 10 73.73 - 92.15: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ARG A 145 " pdb=" C ARG A 145 " pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.218: 109 0.218 - 0.430: 74 0.430 - 0.641: 31 0.641 - 0.853: 24 0.853 - 1.064: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -3.69 1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CA BLYS A 175 " pdb=" N BLYS A 175 " pdb=" C BLYS A 175 " pdb=" CB BLYS A 175 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA ILE A 117 " pdb=" N ILE A 117 " pdb=" C ILE A 117 " pdb=" CB ILE A 117 " both_signs ideal model delta sigma weight residual False 2.43 3.39 -0.95 2.00e-01 2.50e+01 2.27e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.043 2.00e-02 2.50e+03 7.35e-02 1.62e+02 pdb=" CG TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.110 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.145 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.058 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.052 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.126 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.058 2.00e-02 2.50e+03 6.04e-02 1.10e+02 pdb=" CG PHE A 119 " -0.114 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.098 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.087 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.056 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 173 " -0.002 2.00e-02 2.50e+03 7.06e-02 7.48e+01 pdb=" CG ASN A 173 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 173 " 0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN A 173 " -0.126 2.00e-02 2.50e+03 pdb="HD21 ASN A 173 " 0.010 2.00e-02 2.50e+03 pdb="HD22 ASN A 173 " 0.101 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 717 2.27 - 2.85: 7812 2.85 - 3.43: 10581 3.43 - 4.02: 15362 4.02 - 4.60: 22067 Nonbonded interactions: 56539 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.685 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.771 1.850 x-y,-y,-z-4/3 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.773 1.850 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.798 1.850 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.801 1.850 x-y,-y,-z-4/3 ... (remaining 56534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "shake_2963595_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1942 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788674 | | target function (ml) not normalized (work): 232313.244986 | | target function (ml) not normalized (free): 11816.781129 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3025 0.2109 6.9723 4.9545| | 2: 3.57 - 2.84 1.00 2876 122 0.2460 0.1880 4.3633 4.3511| | 3: 2.84 - 2.48 1.00 2833 165 0.2372 0.1637 4.1385 4.1733| | 4: 2.47 - 2.25 1.00 2825 136 0.2319 0.1416 3.8415 3.8422| | 5: 2.25 - 2.09 1.00 2756 127 0.2482 0.1609 3.8086 3.8266| | 6: 2.09 - 1.97 1.00 2846 113 0.2534 0.1688 3.4703 3.5705| | 7: 1.97 - 1.87 1.00 2787 165 0.2567 0.1663 3.1387 3.1434| | 8: 1.87 - 1.79 1.00 2789 144 0.2510 0.1820 3.0614 3.1107| | 9: 1.79 - 1.72 1.00 2745 138 0.2450 0.1938 2.8989 2.9754| | 10: 1.72 - 1.66 1.00 2789 158 0.2375 0.2054 2.795 2.9489| | 11: 1.66 - 1.61 1.00 2740 147 0.2547 0.1919 2.7728 2.7862| | 12: 1.61 - 1.56 1.00 2787 146 0.2497 0.2030 2.6228 2.6419| | 13: 1.56 - 1.52 1.00 2745 130 0.2466 0.1782 2.5546 2.5611| | 14: 1.52 - 1.48 1.00 2803 134 0.2515 0.1863 2.4862 2.4811| | 15: 1.48 - 1.45 1.00 2738 128 0.2556 0.2178 2.4115 2.554| | 16: 1.45 - 1.42 1.00 2756 161 0.2657 0.2030 2.3725 2.3647| | 17: 1.42 - 1.39 1.00 2785 139 0.2688 0.2171 2.3429 2.3967| | 18: 1.39 - 1.36 1.00 2741 179 0.2732 0.2105 2.2793 2.2733| | 19: 1.36 - 1.34 1.00 2807 134 0.2636 0.2317 2.2462 2.3025| | 20: 1.34 - 1.32 1.00 2696 147 0.2672 0.2397 2.1892 2.2274| | 21: 1.32 - 1.30 1.00 2785 112 0.2718 0.2192 2.1692 2.1198| | 22: 1.29 - 1.27 1.00 2704 152 0.2682 0.2561 2.1347 2.2004| | 23: 1.27 - 1.26 1.00 2802 156 0.2815 0.2367 2.1002 2.1509| | 24: 1.26 - 1.24 1.00 2744 132 0.2748 0.2552 2.0746 2.1784| | 25: 1.24 - 1.22 1.00 2734 148 0.2838 0.2514 2.0493 2.0718| | 26: 1.22 - 1.21 1.00 2727 135 0.2832 0.2639 2.0095 2.1379| | 27: 1.21 - 1.19 1.00 2814 148 0.2937 0.2812 2.0135 2.0714| | 28: 1.19 - 1.18 1.00 2671 147 0.3029 0.2611 2.0037 1.9786| | 29: 1.18 - 1.16 1.00 2800 134 0.2933 0.2702 1.9587 2.0116| | 30: 1.16 - 1.15 1.00 2740 148 0.3062 0.2923 1.9288 1.9827| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 19.23 0.76 0.23 1534.41| | 2: 3.57 - 2.84 2876 122 0.80 26.55 1.28 0.23 1534.41| | 3: 2.84 - 2.48 2833 165 0.73 32.66 1.25 0.23 1271.71| | 4: 2.47 - 2.25 2825 136 0.81 26.07 1.25 0.25 589.97| | 5: 2.25 - 2.09 2756 127 0.77 29.81 1.29 0.25 589.97| | 6: 2.09 - 1.97 2846 113 0.83 23.22 1.29 0.25 321.63| | 7: 1.97 - 1.87 2787 165 0.90 16.92 1.29 0.25 92.77| | 8: 1.87 - 1.79 2789 144 0.85 21.41 1.25 0.25 92.77| | 9: 1.79 - 1.72 2745 138 0.88 18.72 1.24 0.25 55.90| | 10: 1.72 - 1.66 2789 158 0.87 20.22 1.22 0.25 48.51| | 11: 1.66 - 1.61 2740 147 0.86 21.26 1.24 0.25 46.80| | 12: 1.61 - 1.56 2787 146 0.88 18.63 1.23 0.25 29.38| | 13: 1.56 - 1.52 2745 130 0.87 20.24 1.23 0.25 29.38| | 14: 1.52 - 1.48 2803 134 0.86 20.67 1.23 0.25 26.03| | 15: 1.48 - 1.45 2738 128 0.88 19.67 1.23 0.25 19.90| | 16: 1.45 - 1.42 2756 161 0.86 21.32 1.24 0.25 19.90| | 17: 1.42 - 1.39 2785 139 0.87 20.34 1.23 0.25 16.93| | 18: 1.39 - 1.36 2741 179 0.87 20.68 1.23 0.25 15.22| | 19: 1.36 - 1.34 2807 134 0.86 21.40 1.21 0.25 15.22| | 20: 1.34 - 1.32 2696 147 0.87 20.42 1.21 0.25 12.76| | 21: 1.32 - 1.30 2785 112 0.86 21.49 1.20 0.25 12.59| | 22: 1.29 - 1.27 2704 152 0.86 21.83 1.20 0.25 12.36| | 23: 1.27 - 1.26 2802 156 0.86 22.26 1.21 0.24 11.17| | 24: 1.26 - 1.24 2744 132 0.85 22.80 1.19 0.24 11.17| | 25: 1.24 - 1.22 2734 148 0.84 23.74 1.20 0.24 10.70| | 26: 1.22 - 1.21 2727 135 0.84 24.13 1.19 0.23 10.18| | 27: 1.21 - 1.19 2814 148 0.83 24.88 1.20 0.23 10.18| | 28: 1.19 - 1.18 2671 147 0.82 25.58 1.18 0.23 9.51| | 29: 1.18 - 1.16 2800 134 0.83 25.52 1.17 0.23 9.25| | 30: 1.16 - 1.15 2740 148 0.80 27.58 1.15 0.23 9.25| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 9.25 max = 1534.41 mean = 221.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 22.65| |phase err.(test): min = 0.00 max = 89.78 mean = 22.57| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.248 1557 Z= 5.538 Angle : 5.254 18.207 2118 Z= 3.716 Chirality : 0.387 1.064 243 Planarity : 0.031 0.106 284 Dihedral : 14.341 92.155 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 30.81 % Peptide Plane: Cis-proline : 18.18 % 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: -2.73 (0.47), residues: 224 helix: -2.83 (0.34), residues: 102 sheet: -0.89 (1.00), residues: 28 loop : -0.57 (0.57), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.012 ARG A 145 TYR 0.073 0.033 TYR A 139 PHE 0.119 0.037 PHE A 119 HIS 0.065 0.031 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1942 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788674 | | target function (ml) not normalized (work): 232313.244986 | | target function (ml) not normalized (free): 11816.781129 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2609 0.1943 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2609 0.1943 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1984 0.1943 n_refl.: 87594 overall B=0.23 to atoms: r(all,work,free)=0.2007 0.2011 0.1958 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1643 0.1636 0.1771 n_refl.: 87594 remove outliers: r(all,work,free)=0.1643 0.1636 0.1771 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3789 386.315 359.591 0.669 1.002 0.407 11.894-9.307 99.02 97 4 0.1818 613.643 596.067 0.930 1.003 0.390 9.237-7.194 100.00 213 7 0.2144 501.884 491.676 0.953 1.003 0.354 7.162-5.571 100.00 427 22 0.2140 376.636 365.225 0.925 1.003 0.292 5.546-4.326 100.00 867 58 0.1268 517.029 510.577 0.961 1.003 0.229 4.315-3.360 100.00 1859 96 0.1143 491.698 487.620 1.001 1.003 0.209 3.356-2.611 100.00 3867 181 0.1461 323.020 319.579 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1344 214.133 211.740 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1652 104.571 103.930 1.014 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2057 46.371 45.021 1.002 0.996 0.000 1.221-1.150 99.97 13689 708 0.2591 29.217 26.977 0.977 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0515 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1636 r_free=0.1771 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1636 r_free=0.1771 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.319442 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2020.776446 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1654 0.1764 0.0110 0.002 0.5 4.8 0.0 0.0 0 0.125 0.1503 0.1634 0.0131 0.002 0.5 3.8 0.0 0.0 0 0.250 0.1428 0.1585 0.0157 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1394 0.1565 0.0171 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1347 0.1533 0.0186 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1354 0.1541 0.0187 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1295 0.1508 0.0213 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1268 0.1493 0.0225 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1255 0.1486 0.0232 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1245 0.1482 0.0237 0.004 0.7 2.9 0.5 0.0 0 5.000 0.1242 0.1481 0.0239 0.004 0.8 3.2 0.5 0.0 0 6.000 0.1242 0.1479 0.0238 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1234 0.1470 0.0236 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1234 0.1475 0.0241 0.006 0.9 3.5 0.5 0.0 0 9.000 0.1234 0.1475 0.0241 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1233 0.1473 0.0240 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1227 0.1469 0.0242 0.007 0.9 3.2 0.5 0.0 0 12.000 0.1224 0.1470 0.0246 0.008 1.0 3.5 0.5 0.6 0 13.660 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1227 0.1469 0.0242 0.007 0.9 3.2 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.69 2.42 3.013 19.083 2020.776 0.017 12.27 14.68 2.41 2.989 19.083 60.623 0.017 12.33 14.66 2.33 2.669 19.082 252.597 0.017 12.67 15.27 2.60 2.751 19.245 1010.388 0.016 12.54 15.50 2.96 3.457 19.732 2020.776 0.016 12.42 15.45 3.03 3.298 19.636 3031.165 0.015 12.27 15.36 3.10 3.343 19.657 4041.553 0.015 12.18 15.30 3.11 3.202 19.555 5051.941 0.015 12.11 15.25 3.13 3.187 19.536 6062.329 0.015 12.26 15.54 3.28 3.529 19.719 7072.718 0.015 12.22 15.49 3.28 3.475 19.681 8083.106 0.015 12.17 15.45 3.29 3.480 19.673 9093.494 0.015 12.11 15.40 3.29 3.443 19.645 10103.882 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 252.597 Accepted refinement result: 12.33 14.66 2.33 2.669 19.082 252.597 0.017 Individual atomic B min max mean iso aniso Overall: 9.09 119.47 20.11 3.31 0 1785 Protein: 9.09 115.03 17.02 3.32 0 1519 Water: 11.49 119.47 38.25 N/A 0 258 Other: 19.73 26.62 22.08 N/A 0 8 Chain A: 9.09 119.47 20.11 N/A 0 1785 Histogram: Values Number of atoms 9.09 - 20.13 1272 20.13 - 31.17 227 31.17 - 42.21 125 42.21 - 53.24 94 53.24 - 64.28 42 64.28 - 75.32 11 75.32 - 86.36 7 86.36 - 97.39 4 97.39 - 108.43 1 108.43 - 119.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1466 r_work=0.1234 r_free=0.1470 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1470 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1462 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1228 r_free= 0.1462 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.016727 | | target function (ls_wunit_k1) not normalized (work): 1393.304200 | | target function (ls_wunit_k1) not normalized (free): 110.420519 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1239 0.1228 0.1462 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1676 0.1677 0.1691 n_refl.: 87593 remove outliers: r(all,work,free)=0.1676 0.1677 0.1691 n_refl.: 87593 overall B=0.02 to atoms: r(all,work,free)=0.1681 0.1682 0.1694 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1236 0.1225 0.1453 n_refl.: 87593 remove outliers: r(all,work,free)=0.1236 0.1225 0.1453 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3535 300.897 281.511 0.641 1.003 0.374 11.894-9.307 99.02 97 4 0.1651 482.020 469.075 0.920 1.003 0.370 9.237-7.194 100.00 213 7 0.1870 394.233 388.659 0.963 1.003 0.350 7.162-5.571 100.00 427 22 0.1832 295.850 289.851 0.936 1.003 0.259 5.546-4.326 100.00 867 58 0.1001 406.129 403.108 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0868 386.231 385.191 1.008 1.003 0.190 3.356-2.611 100.00 3867 181 0.1171 253.734 252.585 1.011 1.002 0.100 2.608-2.026 99.99 8198 413 0.1021 168.202 167.500 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1109 82.141 82.335 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1449 36.425 35.932 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 22.950 21.439 0.984 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0370 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1453 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1226 r_free=0.1454 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1454 | n_water=258 | time (s): 1.860 (total time: 1.860) Filter (dist) r_work=0.1236 r_free=0.1453 | n_water=251 | time (s): 22.250 (total time: 24.110) Filter (q & B) r_work=0.1238 r_free=0.1451 | n_water=248 | time (s): 2.660 (total time: 26.770) Compute maps r_work=0.1238 r_free=0.1451 | n_water=248 | time (s): 1.230 (total time: 28.000) Filter (map) r_work=0.1253 r_free=0.1455 | n_water=225 | time (s): 3.290 (total time: 31.290) Find peaks r_work=0.1253 r_free=0.1455 | n_water=225 | time (s): 0.610 (total time: 31.900) Add new water r_work=0.1399 r_free=0.1620 | n_water=434 | time (s): 2.660 (total time: 34.560) Refine new water occ: r_work=0.1304 r_free=0.1482 adp: r_work=0.1223 r_free=0.1425 occ: r_work=0.1234 r_free=0.1412 adp: r_work=0.1203 r_free=0.1396 occ: r_work=0.1206 r_free=0.1389 adp: r_work=0.1196 r_free=0.1385 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1385 r_work=0.1196 r_free=0.1385 | n_water=434 | time (s): 66.360 (total time: 100.920) Filter (q & B) r_work=0.1199 r_free=0.1391 | n_water=416 | time (s): 3.470 (total time: 104.390) Filter (dist only) r_work=0.1199 r_free=0.1390 | n_water=415 | time (s): 35.280 (total time: 139.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 29.300759 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1468.267624 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1617 0.1720 0.0102 0.002 0.4 7.7 0.0 0.0 0 0.125 0.1550 0.1664 0.0113 0.001 0.4 7.0 0.0 0.0 0 0.250 0.1425 0.1560 0.0135 0.001 0.4 5.4 0.0 0.0 0 0.500 0.1339 0.1491 0.0152 0.002 0.5 5.1 0.0 0.0 0 0.750 0.1323 0.1482 0.0159 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1331 0.1492 0.0161 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1256 0.1443 0.0186 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1223 0.1420 0.0197 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1218 0.1419 0.0201 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1210 0.1417 0.0207 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1201 0.1407 0.0207 0.005 0.7 4.8 0.5 0.0 0 6.000 0.1199 0.1409 0.0210 0.005 0.8 5.4 0.5 0.0 0 7.000 0.1196 0.1409 0.0213 0.006 0.8 5.4 0.5 0.0 0 8.000 0.1193 0.1409 0.0216 0.006 0.8 5.8 0.5 0.0 0 9.000 0.1189 0.1404 0.0214 0.006 0.9 5.4 0.5 0.0 0 10.000 0.1187 0.1411 0.0224 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1185 0.1404 0.0220 0.007 0.9 5.1 0.5 0.6 0 12.000 0.1183 0.1407 0.0224 0.008 0.9 5.4 0.5 0.6 0 13.000 0.1183 0.1408 0.0224 0.008 1.0 5.8 0.5 0.6 0 14.650 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1404 0.0214 0.006 0.9 5.4 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 14.04 2.14 3.778 21.735 1468.268 0.016 11.89 14.04 2.14 3.778 21.735 44.048 0.016 11.89 14.04 2.14 3.778 21.735 183.533 0.016 12.03 14.37 2.33 3.636 21.741 734.134 0.015 12.09 14.75 2.66 3.539 21.829 1468.268 0.015 11.93 14.72 2.80 3.450 22.166 2202.401 0.015 11.85 14.73 2.88 3.496 21.919 2936.535 0.014 11.76 14.61 2.85 3.475 22.078 3670.669 0.014 11.70 14.55 2.85 3.492 22.035 4404.803 0.014 11.66 14.69 3.03 3.496 22.117 5138.937 0.014 11.70 14.71 3.01 3.517 22.050 5873.070 0.014 11.62 14.63 3.01 3.526 22.132 6607.204 0.014 11.65 14.66 3.02 3.549 22.162 7341.338 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 183.533 Accepted refinement result: 11.89 14.04 2.14 3.778 21.735 183.533 0.016 Individual atomic B min max mean iso aniso Overall: 9.12 115.05 22.09 3.31 190 1752 Protein: 9.12 115.05 17.04 3.32 0 1519 Water: 11.51 76.70 40.58 N/A 190 225 Other: 19.76 26.65 22.10 N/A 0 8 Chain A: 9.12 115.05 19.46 N/A 0 1752 Chain S: 15.88 60.00 46.37 N/A 190 0 Histogram: Values Number of atoms 9.12 - 19.71 1260 19.71 - 30.30 248 30.30 - 40.90 165 40.90 - 51.49 129 51.49 - 62.08 117 62.08 - 72.68 12 72.68 - 83.27 5 83.27 - 93.86 4 93.86 - 104.46 0 104.46 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1404 r_work=0.1189 r_free=0.1404 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1404 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1403 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1188 r_free= 0.1403 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015068 | | target function (ls_wunit_k1) not normalized (work): 1255.088137 | | target function (ls_wunit_k1) not normalized (free): 100.962351 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1188 0.1403 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1592 0.1592 0.1629 n_refl.: 87592 remove outliers: r(all,work,free)=0.1592 0.1592 0.1629 n_refl.: 87592 overall B=0.00 to atoms: r(all,work,free)=0.1593 0.1593 0.1629 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1185 0.1395 n_refl.: 87592 remove outliers: r(all,work,free)=0.1193 0.1183 0.1395 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3398 296.808 273.864 0.592 1.002 0.350 11.894-9.307 99.02 97 4 0.1593 482.020 472.960 0.917 1.003 0.314 9.237-7.194 100.00 213 7 0.1649 394.233 395.585 0.990 1.003 0.280 7.162-5.571 100.00 427 22 0.1599 295.850 290.837 0.935 1.003 0.224 5.546-4.326 100.00 867 58 0.0879 406.129 402.741 0.961 1.003 0.205 4.315-3.360 100.00 1859 96 0.0788 386.231 385.478 1.005 1.002 0.200 3.356-2.611 100.00 3867 181 0.1077 253.734 252.841 1.011 1.002 0.100 2.608-2.026 99.99 8198 413 0.1011 168.202 167.624 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1098 82.141 82.361 1.031 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1445 36.425 35.952 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2257 22.950 21.455 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0074 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1183 r_free=0.1395 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1183 r_free=0.1395 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1395 | n_water=415 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1182 r_free=0.1394 | n_water=411 | time (s): 34.010 (total time: 36.270) Filter (q & B) r_work=0.1182 r_free=0.1394 | n_water=411 | time (s): 1.070 (total time: 37.340) Compute maps r_work=0.1182 r_free=0.1394 | n_water=411 | time (s): 1.320 (total time: 38.660) Filter (map) r_work=0.1223 r_free=0.1388 | n_water=289 | time (s): 2.630 (total time: 41.290) Find peaks r_work=0.1223 r_free=0.1388 | n_water=289 | time (s): 0.490 (total time: 41.780) Add new water r_work=0.1341 r_free=0.1506 | n_water=470 | time (s): 2.620 (total time: 44.400) Refine new water occ: r_work=0.1245 r_free=0.1424 adp: r_work=0.1247 r_free=0.1425 occ: r_work=0.1222 r_free=0.1403 adp: r_work=0.1221 r_free=0.1402 occ: r_work=0.1203 r_free=0.1387 adp: r_work=0.1198 r_free=0.1382 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1382 r_work=0.1198 r_free=0.1382 | n_water=470 | time (s): 177.350 (total time: 221.750) Filter (q & B) r_work=0.1201 r_free=0.1388 | n_water=449 | time (s): 2.900 (total time: 224.650) Filter (dist only) r_work=0.1202 r_free=0.1388 | n_water=448 | time (s): 38.890 (total time: 263.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.715876 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 52.121395 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1237 0.1372 0.0136 0.002 0.6 4.8 0.5 0.0 0 0.086 0.1183 0.1333 0.0150 0.003 0.7 3.8 0.5 0.0 0 0.257 0.1168 0.1326 0.0159 0.004 0.8 3.5 0.5 0.0 0 0.515 0.1160 0.1324 0.0164 0.005 0.9 3.5 0.5 0.0 0 0.772 0.1155 0.1323 0.0167 0.006 1.0 3.2 0.5 0.0 0 1.030 0.1152 0.1323 0.0171 0.007 1.0 3.2 0.5 0.0 0 1.287 0.1150 0.1323 0.0172 0.007 1.1 3.5 0.5 0.0 0 1.544 0.1148 0.1319 0.0171 0.008 1.1 3.8 0.5 0.0 0 1.802 0.1157 0.1322 0.0165 0.005 0.9 3.5 0.5 0.0 0 0.858 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1148 0.1319 0.0171 0.008 1.1 3.8 0.5 0.0 0 1.802 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.48 13.19 1.71 3.780 21.305 52.121 3.615 11.48 13.19 1.71 3.780 21.305 1.564 3.615 11.48 13.19 1.70 3.770 21.305 6.515 3.615 11.55 13.30 1.74 3.717 21.287 26.061 3.610 11.56 13.35 1.79 3.743 21.256 52.121 3.609 11.48 13.32 1.84 3.766 21.246 78.182 3.602 11.44 13.31 1.87 3.783 21.239 104.243 3.599 11.40 13.30 1.90 3.798 21.228 130.303 3.596 11.39 13.32 1.92 3.817 21.219 156.364 3.595 11.37 13.28 1.92 3.827 21.216 182.425 3.593 11.35 13.26 1.92 3.833 21.217 208.486 3.591 11.34 13.25 1.91 3.841 21.214 234.546 3.590 11.33 13.25 1.93 3.846 21.216 260.607 3.590 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.564 Accepted refinement result: 11.48 13.19 1.71 3.780 21.305 1.564 3.615 Individual atomic B min max mean iso aniso Overall: 9.12 115.05 21.30 3.31 226 1749 Protein: 9.12 115.05 17.05 3.32 0 1519 Water: 11.52 76.71 35.72 N/A 226 222 Other: 19.76 26.65 22.11 N/A 0 8 Chain A: 9.12 115.05 19.42 N/A 0 1749 Chain S: 15.89 60.00 35.87 N/A 226 0 Histogram: Values Number of atoms 9.12 - 19.71 1265 19.71 - 30.31 292 30.31 - 40.90 209 40.90 - 51.49 131 51.49 - 62.09 55 62.09 - 72.68 12 72.68 - 83.27 5 83.27 - 93.87 4 93.87 - 104.46 0 104.46 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1148 r_free=0.1319 r_work=0.1148 r_free=0.1319 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1148 r_free = 0.1319 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1139 r_free = 0.1317 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1139 r_free= 0.1317 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.609778 | | target function (ml) not normalized (work): 300669.209924 | | target function (ml) not normalized (free): 15833.954604 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1148 0.1139 0.1317 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1484 0.1482 0.1549 n_refl.: 87589 remove outliers: r(all,work,free)=0.1484 0.1482 0.1549 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1483 0.1480 0.1548 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1143 0.1134 0.1304 n_refl.: 87589 remove outliers: r(all,work,free)=0.1139 0.1130 0.1304 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3938 293.537 261.070 0.472 1.000 0.297 11.894-9.307 96.08 94 4 0.2396 475.396 459.988 0.870 1.001 0.280 9.237-7.194 97.73 208 7 0.2237 386.803 386.855 0.953 1.002 0.210 7.162-5.571 100.00 427 22 0.2093 295.850 285.031 0.920 1.002 0.171 5.546-4.326 100.00 867 58 0.1101 406.129 401.473 0.964 1.002 0.160 4.315-3.360 100.00 1859 96 0.0896 386.231 384.015 1.006 1.002 0.160 3.356-2.611 100.00 3867 181 0.1107 253.734 251.646 1.009 1.002 0.038 2.608-2.026 99.99 8198 413 0.0920 168.202 167.416 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0890 82.141 82.435 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1257 36.425 36.005 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.950 21.489 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0184 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1130 r_free=0.1304 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1131 r_free=0.1304 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1131 r_free=0.1304 | n_water=448 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1134 r_free=0.1303 | n_water=445 | time (s): 48.600 (total time: 50.900) Filter (q & B) r_work=0.1134 r_free=0.1303 | n_water=445 | time (s): 1.220 (total time: 52.120) Compute maps r_work=0.1134 r_free=0.1303 | n_water=445 | time (s): 1.640 (total time: 53.760) Filter (map) r_work=0.1157 r_free=0.1302 | n_water=340 | time (s): 3.750 (total time: 57.510) Find peaks r_work=0.1157 r_free=0.1302 | n_water=340 | time (s): 0.690 (total time: 58.200) Add new water r_work=0.1222 r_free=0.1379 | n_water=494 | time (s): 3.680 (total time: 61.880) Refine new water occ: r_work=0.1159 r_free=0.1323 adp: r_work=0.1160 r_free=0.1326 occ: r_work=0.1144 r_free=0.1306 adp: r_work=0.1143 r_free=0.1308 occ: r_work=0.1133 r_free=0.1295 adp: r_work=0.1129 r_free=0.1295 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1295 r_work=0.1129 r_free=0.1295 | n_water=494 | time (s): 204.910 (total time: 266.790) Filter (q & B) r_work=0.1134 r_free=0.1301 | n_water=462 | time (s): 3.880 (total time: 270.670) Filter (dist only) r_work=0.1134 r_free=0.1301 | n_water=461 | time (s): 47.870 (total time: 318.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.723084 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.568024 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1348 0.0145 0.002 0.6 4.8 0.5 0.0 0 0.086 0.1162 0.1317 0.0155 0.003 0.7 3.8 0.5 0.0 0 0.258 0.1147 0.1307 0.0160 0.004 0.9 4.5 0.5 0.0 0 0.517 0.1140 0.1303 0.0163 0.006 0.9 4.2 0.5 0.0 0 0.775 0.1136 0.1303 0.0167 0.006 1.0 3.8 0.5 0.0 0 1.034 0.1133 0.1302 0.0170 0.007 1.0 3.8 0.5 0.0 0 1.292 0.1131 0.1301 0.0169 0.008 1.1 3.8 0.5 0.0 0 1.551 0.1130 0.1300 0.0170 0.008 1.1 3.8 0.5 0.0 0 1.809 0.1138 0.1303 0.0165 0.006 1.0 4.2 0.5 0.0 0 0.862 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1130 0.1300 0.0170 0.008 1.1 3.8 0.5 0.0 0 1.809 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 13.00 1.70 3.781 21.292 45.568 3.603 11.30 13.00 1.70 3.781 21.292 1.367 3.603 11.30 13.00 1.70 3.771 21.292 5.696 3.602 11.36 13.09 1.73 3.713 21.279 22.784 3.600 11.34 13.13 1.79 3.741 21.262 45.568 3.598 11.32 13.15 1.83 3.761 21.241 68.352 3.594 11.27 13.14 1.86 3.778 21.236 91.136 3.590 11.25 13.12 1.87 3.788 21.232 113.920 3.587 11.22 13.11 1.88 3.799 21.230 136.704 3.585 11.22 13.13 1.91 3.817 21.220 159.488 3.585 11.21 13.12 1.91 3.826 21.217 182.272 3.584 11.20 13.10 1.90 3.833 21.215 205.056 3.582 11.19 13.10 1.91 3.840 21.214 227.840 3.582 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.696 Accepted refinement result: 11.30 13.00 1.70 3.771 21.292 5.696 3.602 Individual atomic B min max mean iso aniso Overall: 9.13 114.93 21.28 3.28 242 1746 Protein: 9.13 114.93 17.04 3.28 0 1519 Water: 11.52 76.70 35.25 N/A 242 219 Other: 19.71 26.60 22.09 N/A 0 8 Chain A: 9.13 114.93 19.36 N/A 0 1746 Chain S: 15.87 60.00 35.13 N/A 242 0 Histogram: Values Number of atoms 9.13 - 19.71 1264 19.71 - 30.29 302 30.29 - 40.87 218 40.87 - 51.45 132 51.45 - 62.03 50 62.03 - 72.61 11 72.61 - 83.19 5 83.19 - 93.77 4 93.77 - 104.35 0 104.35 - 114.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.1130 r_free=0.1300 r_work=0.1130 r_free=0.1300 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1130 r_free = 0.1300 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1126 r_free = 0.1295 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1126 r_free= 0.1295 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600060 | | target function (ml) not normalized (work): 299823.838618 | | target function (ml) not normalized (free): 15797.231232 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1134 0.1126 0.1295 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1456 0.1455 0.1513 n_refl.: 87579 remove outliers: r(all,work,free)=0.1456 0.1455 0.1513 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1455 0.1453 0.1512 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1133 0.1124 0.1298 n_refl.: 87579 remove outliers: r(all,work,free)=0.1132 0.1123 0.1298 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4060 295.796 255.124 0.448 0.998 0.314 11.894-9.307 95.10 93 4 0.2436 469.182 457.297 0.851 1.001 0.244 9.237-7.194 97.73 208 7 0.2294 386.803 381.412 0.924 1.001 0.164 7.162-5.571 100.00 427 22 0.2101 295.850 285.113 0.902 1.002 0.143 5.546-4.326 100.00 867 58 0.1121 406.129 401.243 0.957 1.002 0.137 4.315-3.360 100.00 1859 96 0.0891 386.231 384.270 0.994 1.002 0.107 3.356-2.611 100.00 3867 181 0.1099 253.734 251.815 1.001 1.002 0.029 2.608-2.026 99.99 8198 413 0.0903 168.202 167.609 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0880 82.141 82.489 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.425 36.029 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.950 21.506 0.981 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0245 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1123 r_free=0.1298 After: r_work=0.1125 r_free=0.1298 ================================== NQH flips ================================== r_work=0.1125 r_free=0.1298 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1125 r_free=0.1298 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1125 r_free=0.1298 | n_water=461 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1125 r_free=0.1298 | n_water=459 | time (s): 49.880 (total time: 52.240) Filter (q & B) r_work=0.1126 r_free=0.1297 | n_water=455 | time (s): 3.880 (total time: 56.120) Compute maps r_work=0.1126 r_free=0.1297 | n_water=455 | time (s): 1.810 (total time: 57.930) Filter (map) r_work=0.1147 r_free=0.1298 | n_water=362 | time (s): 3.780 (total time: 61.710) Find peaks r_work=0.1147 r_free=0.1298 | n_water=362 | time (s): 0.680 (total time: 62.390) Add new water r_work=0.1193 r_free=0.1332 | n_water=504 | time (s): 3.610 (total time: 66.000) Refine new water occ: r_work=0.1141 r_free=0.1289 adp: r_work=0.1141 r_free=0.1290 occ: r_work=0.1131 r_free=0.1280 adp: r_work=0.1129 r_free=0.1280 occ: r_work=0.1124 r_free=0.1275 adp: r_work=0.1120 r_free=0.1274 ADP+occupancy (water only), MIN, final r_work=0.1120 r_free=0.1274 r_work=0.1120 r_free=0.1274 | n_water=504 | time (s): 234.090 (total time: 300.090) Filter (q & B) r_work=0.1125 r_free=0.1280 | n_water=472 | time (s): 3.810 (total time: 303.900) Filter (dist only) r_work=0.1125 r_free=0.1279 | n_water=471 | time (s): 49.460 (total time: 353.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.712364 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.525741 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1228 0.1345 0.0118 0.004 0.7 6.1 0.0 0.0 0 0.086 0.1174 0.1308 0.0134 0.004 0.8 5.8 0.0 0.0 0 0.257 0.1150 0.1293 0.0143 0.005 0.9 6.1 0.5 0.0 0 0.514 0.1142 0.1288 0.0146 0.006 1.0 6.1 0.5 0.0 0 0.771 0.1134 0.1282 0.0148 0.006 1.0 5.8 0.5 0.0 0 1.027 0.1131 0.1281 0.0149 0.007 1.1 5.8 0.5 0.0 0 1.284 0.1127 0.1279 0.0152 0.008 1.1 6.1 0.5 0.0 0 1.541 0.1125 0.1279 0.0154 0.008 1.1 6.1 0.5 0.0 0 1.798 0.1140 0.1287 0.0146 0.006 1.0 6.4 0.5 0.0 0 0.856 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1125 0.1279 0.0154 0.008 1.1 6.1 0.5 0.0 0 1.798 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.25 12.79 1.54 3.765 21.307 36.526 3.600 11.25 12.79 1.54 3.765 21.307 1.096 3.600 11.25 12.79 1.54 3.765 21.307 4.566 3.600 11.27 12.82 1.55 3.701 21.301 18.263 3.595 11.27 12.90 1.63 3.719 21.288 36.526 3.595 11.27 12.96 1.69 3.745 21.262 54.789 3.594 11.24 12.96 1.72 3.759 21.256 73.051 3.590 11.20 12.94 1.73 3.771 21.252 91.314 3.587 11.17 12.91 1.73 3.779 21.253 109.577 3.585 11.16 12.91 1.75 3.789 21.248 127.840 3.583 11.17 12.96 1.78 3.808 21.237 146.103 3.584 11.15 12.93 1.78 3.815 21.236 164.366 3.582 11.14 12.92 1.78 3.822 21.236 182.629 3.581 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.096 Accepted refinement result: 11.25 12.79 1.54 3.765 21.307 1.096 3.600 Individual atomic B min max mean iso aniso Overall: 9.12 114.92 21.32 3.28 252 1746 Protein: 9.12 114.92 17.03 3.28 0 1519 Water: 11.51 76.69 35.14 N/A 252 219 Other: 19.71 26.59 22.08 N/A 0 8 Chain A: 9.12 114.92 19.35 N/A 0 1746 Chain S: 15.86 59.99 34.94 N/A 252 0 Histogram: Values Number of atoms 9.12 - 19.70 1264 19.70 - 30.28 307 30.28 - 40.86 224 40.86 - 51.44 129 51.44 - 62.02 52 62.02 - 72.60 11 72.60 - 83.18 5 83.18 - 93.76 4 93.76 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1125 r_free=0.1279 r_work=0.1125 r_free=0.1279 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1125 r_free = 0.1279 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1123 r_free = 0.1278 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1123 r_free= 0.1278 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.599162 | | target function (ml) not normalized (work): 299738.229779 | | target function (ml) not normalized (free): 15788.306977 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1317 0.1344 5.6324 5.6074| | 2: 3.57 - 2.84 1.00 2888 124 0.1041 0.1332 5.1377 5.1829| | 3: 2.83 - 2.48 1.00 2820 163 0.1084 0.1188 4.9312 4.9547| | 4: 2.47 - 2.25 1.00 2825 136 0.0889 0.0952 4.6158 4.6407| | 5: 2.25 - 2.09 1.00 2756 127 0.0862 0.0944 4.5636 4.6146| | 6: 2.09 - 1.97 1.00 2846 113 0.0853 0.1018 4.2594 4.3426| | 7: 1.97 - 1.87 1.00 2787 165 0.0875 0.1106 3.9715 4.0838| | 8: 1.87 - 1.79 1.00 2789 144 0.0899 0.1095 3.8814 3.9891| | 9: 1.79 - 1.72 1.00 2745 138 0.0874 0.1187 3.6434 3.8318| | 10: 1.72 - 1.66 1.00 2831 160 0.0912 0.1214 3.5594 3.7166| | 11: 1.66 - 1.61 1.00 2712 147 0.0865 0.1051 3.4943 3.5748| | 12: 1.61 - 1.56 1.00 2773 144 0.0906 0.1134 3.3282 3.4484| | 13: 1.56 - 1.52 1.00 2745 130 0.0938 0.1032 3.3038 3.3972| | 14: 1.52 - 1.48 1.00 2803 134 0.0983 0.1046 3.2388 3.3134| | 15: 1.48 - 1.45 1.00 2738 128 0.1006 0.1220 3.1524 3.2607| | 16: 1.45 - 1.42 1.00 2756 161 0.1058 0.1257 3.1341 3.2475| | 17: 1.42 - 1.39 1.00 2785 139 0.1142 0.1312 3.1171 3.2312| | 18: 1.39 - 1.36 1.00 2741 179 0.1197 0.1311 3.1012 3.223| | 19: 1.36 - 1.34 1.00 2807 134 0.1257 0.1565 3.1098 3.268| | 20: 1.34 - 1.32 1.00 2696 147 0.1369 0.1457 3.1122 3.1507| | 21: 1.32 - 1.30 1.00 2785 112 0.1470 0.1522 3.1133 3.1058| | 22: 1.29 - 1.27 1.00 2704 152 0.1563 0.1995 3.123 3.2966| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1806 3.1317 3.2044| | 24: 1.26 - 1.24 1.00 2744 132 0.1708 0.1827 3.1258 3.223| | 25: 1.24 - 1.22 1.00 2733 148 0.1880 0.2137 3.1414 3.254| | 26: 1.22 - 1.21 1.00 2727 135 0.1907 0.1765 3.1466 3.2023| | 27: 1.21 - 1.19 1.00 2814 148 0.2077 0.2180 3.17 3.1657| | 28: 1.19 - 1.18 1.00 2671 147 0.2201 0.2311 3.1647 3.1737| | 29: 1.18 - 1.16 1.00 2800 134 0.2268 0.2391 3.1477 3.2279| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2462 3.1418 3.1674| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2918 171 0.95 8.36 1.00 0.98 5536.44| | 2: 3.57 - 2.84 2888 124 0.93 12.33 1.01 0.98 5536.44| | 3: 2.83 - 2.48 2820 163 0.90 16.18 0.99 0.98 4628.30| | 4: 2.47 - 2.25 2825 136 0.92 13.23 1.00 0.99 2286.49| | 5: 2.25 - 2.09 2756 127 0.91 15.34 1.01 0.99 2286.49| | 6: 2.09 - 1.97 2846 113 0.93 12.23 1.02 0.99 1326.47| | 7: 1.97 - 1.87 2787 165 0.95 9.26 1.02 0.98 507.70| | 8: 1.87 - 1.79 2789 144 0.93 12.61 0.99 0.98 507.70| | 9: 1.79 - 1.72 2745 138 0.94 10.08 0.98 0.98 289.08| | 10: 1.72 - 1.66 2831 160 0.94 11.15 0.98 0.98 245.30| | 11: 1.66 - 1.61 2712 147 0.93 11.79 0.98 0.98 234.95| | 12: 1.61 - 1.56 2773 144 0.96 8.89 0.99 0.98 137.32| | 13: 1.56 - 1.52 2745 130 0.95 10.41 1.02 0.98 137.32| | 14: 1.52 - 1.48 2803 134 0.94 10.79 1.02 0.99 123.07| | 15: 1.48 - 1.45 2738 128 0.95 9.86 1.02 0.99 96.97| | 16: 1.45 - 1.42 2756 161 0.94 11.06 1.02 0.99 96.97| | 17: 1.42 - 1.39 2785 139 0.95 10.90 1.01 0.99 88.40| | 18: 1.39 - 1.36 2741 179 0.94 11.50 1.01 0.99 83.44| | 19: 1.36 - 1.34 2807 134 0.94 11.82 0.99 0.99 83.44| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.97 79.78| | 21: 1.32 - 1.30 2785 112 0.94 13.06 0.98 0.97 79.52| | 22: 1.29 - 1.27 2704 152 0.93 13.65 0.98 0.97 79.97| | 23: 1.27 - 1.26 2802 156 0.92 14.86 0.97 0.95 82.25| | 24: 1.26 - 1.24 2744 132 0.92 14.88 0.96 0.95 82.25| | 25: 1.24 - 1.22 2733 148 0.91 16.39 0.96 0.95 84.28| | 26: 1.22 - 1.21 2727 135 0.90 18.14 1.02 0.94 86.52| | 27: 1.21 - 1.19 2814 148 0.89 18.83 1.02 0.94 86.52| | 28: 1.19 - 1.18 2671 147 0.88 20.45 1.01 0.93 90.26| | 29: 1.18 - 1.16 2800 134 0.88 20.55 0.99 0.93 91.67| | 30: 1.16 - 1.15 2739 148 0.86 22.09 0.98 0.93 91.67| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.52 max = 5536.44 mean = 859.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.41| |phase err.(test): min = 0.00 max = 89.64 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1130 0.1123 0.1278 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1447 0.1446 0.1490 n_refl.: 87576 remove outliers: r(all,work,free)=0.1447 0.1446 0.1490 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1446 0.1445 0.1490 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1130 0.1123 0.1277 n_refl.: 87576 remove outliers: r(all,work,free)=0.1128 0.1121 0.1277 n_refl.: 87572 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 85.42 77 5 0.3933 289.679 250.738 0.438 0.998 0.293 11.894-9.307 94.12 92 4 0.2444 465.342 451.706 0.857 1.001 0.224 9.237-7.194 97.73 208 7 0.2311 386.803 380.816 0.921 1.001 0.170 7.162-5.571 100.00 427 22 0.2084 295.850 285.501 0.914 1.002 0.140 5.546-4.326 100.00 867 58 0.1111 406.129 400.770 0.965 1.002 0.120 4.315-3.360 100.00 1859 96 0.0894 386.231 384.253 1.004 1.002 0.120 3.356-2.611 100.00 3867 181 0.1089 253.734 251.873 1.011 1.002 0.019 2.608-2.026 99.99 8198 413 0.0901 168.202 167.641 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0882 82.141 82.490 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.425 36.022 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.950 21.495 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0137 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2608 0.1942 0.082 5.254 8.8 119.3 19.9 258 0.000 1_bss: 0.1636 0.1771 0.082 5.254 9.1 119.5 20.1 258 0.000 1_settarget: 0.1636 0.1771 0.082 5.254 9.1 119.5 20.1 258 0.000 1_nqh: 0.1636 0.1771 0.082 5.254 9.1 119.5 20.1 258 0.000 1_weight: 0.1636 0.1771 0.082 5.254 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1227 0.1469 0.007 0.937 9.1 119.5 20.1 258 0.131 1_adp: 0.1233 0.1466 0.007 0.937 9.1 119.5 20.1 258 0.131 1_regHadp: 0.1234 0.1470 0.007 0.937 9.1 119.5 20.1 258 0.131 1_occ: 0.1228 0.1462 0.007 0.937 9.1 119.5 20.1 258 0.131 2_bss: 0.1225 0.1453 0.007 0.937 9.1 119.5 20.1 258 0.131 2_settarget: 0.1225 0.1453 0.007 0.937 9.1 119.5 20.1 258 0.131 2_updatecdl: 0.1225 0.1453 0.007 0.941 9.1 119.5 20.1 258 0.131 2_nqh: 0.1226 0.1454 0.007 0.941 9.1 119.5 20.1 258 0.134 2_sol: 0.1199 0.1390 0.007 0.941 9.1 115.1 22.1 415 n/a 2_weight: 0.1199 0.1390 0.007 0.941 9.1 115.1 22.1 415 n/a 2_xyzrec: 0.1189 0.1404 0.006 0.858 9.1 115.1 22.1 415 n/a 2_adp: 0.1189 0.1404 0.006 0.858 9.1 115.0 22.1 415 n/a 2_regHadp: 0.1189 0.1404 0.006 0.858 9.1 115.0 22.1 415 n/a 2_occ: 0.1188 0.1403 0.006 0.858 9.1 115.0 22.1 415 n/a 3_bss: 0.1183 0.1395 0.006 0.858 9.1 115.1 22.1 415 n/a 3_settarget: 0.1183 0.1395 0.006 0.858 9.1 115.1 22.1 415 n/a 3_updatecdl: 0.1183 0.1395 0.006 0.858 9.1 115.1 22.1 415 n/a 3_nqh: 0.1183 0.1395 0.006 0.858 9.1 115.1 22.1 415 n/a 3_sol: 0.1202 0.1388 0.006 0.858 9.1 115.1 21.3 448 n/a 3_weight: 0.1202 0.1388 0.006 0.858 9.1 115.1 21.3 448 n/a 3_xyzrec: 0.1148 0.1319 0.008 1.083 9.1 115.1 21.3 448 n/a 3_adp: 0.1148 0.1319 0.008 1.083 9.1 115.1 21.3 448 n/a 3_regHadp: 0.1148 0.1319 0.008 1.083 9.1 115.1 21.3 448 n/a 3_occ: 0.1139 0.1317 0.008 1.083 9.1 115.1 21.3 448 n/a 4_bss: 0.1130 0.1304 0.008 1.083 9.1 115.0 21.3 448 n/a 4_settarget: 0.1130 0.1304 0.008 1.083 9.1 115.0 21.3 448 n/a 4_updatecdl: 0.1130 0.1304 0.008 1.085 9.1 115.0 21.3 448 n/a 4_nqh: 0.1131 0.1304 0.008 1.085 9.1 115.0 21.3 448 n/a 4_sol: 0.1134 0.1301 0.008 1.085 9.1 115.0 21.3 461 n/a 4_weight: 0.1134 0.1301 0.008 1.085 9.1 115.0 21.3 461 n/a 4_xyzrec: 0.1130 0.1300 0.008 1.122 9.1 115.0 21.3 461 n/a 4_adp: 0.1130 0.1300 0.008 1.122 9.1 114.9 21.3 461 n/a 4_regHadp: 0.1130 0.1300 0.008 1.122 9.1 114.9 21.3 461 n/a 4_occ: 0.1126 0.1295 0.008 1.122 9.1 114.9 21.3 461 n/a 5_bss: 0.1123 0.1298 0.008 1.122 9.1 114.9 21.3 461 n/a 5_settarget: 0.1123 0.1298 0.008 1.122 9.1 114.9 21.3 461 n/a 5_updatecdl: 0.1123 0.1298 0.008 1.122 9.1 114.9 21.3 461 n/a 5_setrh: 0.1125 0.1298 0.008 1.122 9.1 114.9 21.3 461 n/a 5_nqh: 0.1125 0.1298 0.008 1.122 9.1 114.9 21.3 461 n/a 5_sol: 0.1125 0.1279 0.008 1.122 9.1 114.9 21.3 471 n/a 5_weight: 0.1125 0.1279 0.008 1.122 9.1 114.9 21.3 471 n/a 5_xyzrec: 0.1125 0.1279 0.008 1.143 9.1 114.9 21.3 471 n/a 5_adp: 0.1125 0.1279 0.008 1.143 9.1 114.9 21.3 471 n/a 5_regHadp: 0.1125 0.1279 0.008 1.143 9.1 114.9 21.3 471 n/a 5_occ: 0.1123 0.1278 0.008 1.143 9.1 114.9 21.3 471 n/a end: 0.1121 0.1277 0.008 1.143 9.1 114.9 21.3 471 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2963595_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2963595_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0900 Refinement macro-cycles (run) : 13324.4900 Write final files (write_after_run_outputs) : 94.0100 Total : 13421.5900 Total CPU time: 3.74 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:02:29 PST -0800 (1735365749.02 s) Start R-work = 0.1636, R-free = 0.1771 Final R-work = 0.1121, R-free = 0.1277 =============================================================================== Job complete usr+sys time: 13603.74 seconds wall clock time: 246 minutes 55.39 seconds (14815.39 seconds total)