Starting phenix.refine on Sat Dec 28 21:06:34 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9171019.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.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_9171019.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9171019.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.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 } 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 } } Starting job =============================================================================== 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: 2.27, per 1000 atoms: 0.67 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: 0.72 Conformation dependent library (CDL) restraints added in 220.7 milliseconds Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 574 0.93 - 1.20: 1102 1.20 - 1.46: 785 1.46 - 1.73: 677 1.73 - 2.00: 15 Bond restraints: 3153 Sorted by residual: bond pdb=" CA BLYS A 93 " pdb=" C BLYS A 93 " ideal model delta sigma weight residual 1.524 1.760 -0.236 1.27e-02 6.20e+03 3.45e+02 bond pdb=" N PRO A 184 " pdb=" CA PRO A 184 " ideal model delta sigma weight residual 1.470 1.246 0.224 1.22e-02 6.72e+03 3.36e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.140 0.181 1.00e-02 1.00e+04 3.27e+02 bond pdb=" C VAL A 146 " pdb=" O VAL A 146 " ideal model delta sigma weight residual 1.236 1.411 -0.175 9.90e-03 1.02e+04 3.12e+02 bond pdb=" C GLU A 143 " pdb=" N ASN A 144 " ideal model delta sigma weight residual 1.331 1.557 -0.226 1.31e-02 5.83e+03 2.97e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 3445 5.15 - 10.29: 1760 10.29 - 15.44: 505 15.44 - 20.58: 60 20.58 - 25.73: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA GLU A 143 " pdb=" C GLU A 143 " pdb=" O GLU A 143 " ideal model delta sigma weight residual 119.32 137.03 -17.71 1.19e+00 7.06e-01 2.21e+02 angle pdb=" O VAL A 25 " pdb=" C VAL A 25 " pdb=" N MET A 26 " ideal model delta sigma weight residual 121.91 107.67 14.24 9.80e-01 1.04e+00 2.11e+02 angle pdb=" O VAL A 51 " pdb=" C VAL A 51 " pdb=" N ILE A 52 " ideal model delta sigma weight residual 123.20 137.97 -14.77 1.06e+00 8.90e-01 1.94e+02 angle pdb=" OD1 ASN A 81 " pdb=" CG ASN A 81 " pdb=" ND2 ASN A 81 " ideal model delta sigma weight residual 122.60 109.16 13.44 1.00e+00 1.00e+00 1.81e+02 angle pdb=" C BCYS A 53 " pdb=" N PRO A 54 " pdb=" CA PRO A 54 " ideal model delta sigma weight residual 119.85 133.37 -13.52 1.01e+00 9.80e-01 1.79e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.89: 938 17.89 - 35.77: 128 35.77 - 53.65: 33 53.65 - 71.53: 11 71.53 - 89.41: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 155.06 24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA CYS A 106 " pdb=" C CYS A 106 " pdb=" N ALA A 107 " pdb=" CA ALA A 107 " ideal model delta harmonic sigma weight residual 180.00 158.21 21.79 0 5.00e+00 4.00e-02 1.90e+01 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 -159.33 -20.67 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.192: 98 0.192 - 0.383: 67 0.383 - 0.573: 45 0.573 - 0.764: 23 0.764 - 0.954: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA THR A 34 " pdb=" N THR A 34 " pdb=" C THR A 34 " pdb=" CB THR A 34 " both_signs ideal model delta sigma weight residual False 2.53 3.48 -0.95 2.00e-01 2.50e+01 2.28e+01 chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 1.55 0.90 2.00e-01 2.50e+01 2.01e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.113 2.00e-02 2.50e+03 6.52e-02 1.28e+02 pdb=" CG PHE A 119 " -0.179 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.020 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.035 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.071 2.00e-02 2.50e+03 5.79e-02 1.01e+02 pdb=" CG PHE A 164 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.121 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.026 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.076 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.033 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 95 " -0.043 2.00e-02 2.50e+03 9.32e-02 8.69e+01 pdb=" C GLN A 95 " 0.161 2.00e-02 2.50e+03 pdb=" O GLN A 95 " -0.060 2.00e-02 2.50e+03 pdb=" N AGLU A 96 " -0.058 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 841 2.29 - 2.87: 7976 2.87 - 3.44: 10512 3.44 - 4.02: 15324 4.02 - 4.60: 21971 Nonbonded interactions: 56624 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.712 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.765 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.795 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.834 2.450 nonbonded pdb=" O GLU A 147 " pdb=" H ATHR A 154 " model vdw 1.855 2.450 ... (remaining 56619 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 } 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 } } output { prefix = "shake_9171019_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= 0.2611 r_free= 0.1950 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790705 | | target function (ml) not normalized (work): 232482.467318 | | target function (ml) not normalized (free): 11795.170184 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3029 0.2106 7.0416 4.9513| | 2: 3.57 - 2.84 1.00 2876 122 0.2438 0.1781 4.3519 4.3346| | 3: 2.84 - 2.48 1.00 2833 165 0.2358 0.1752 4.1331 4.1646| | 4: 2.47 - 2.25 1.00 2825 136 0.2329 0.1433 3.8305 3.8236| | 5: 2.25 - 2.09 1.00 2756 127 0.2444 0.1552 3.7978 3.8101| | 6: 2.09 - 1.97 1.00 2846 113 0.2581 0.1808 3.473 3.5955| | 7: 1.97 - 1.87 1.00 2787 165 0.2557 0.1748 3.1298 3.1583| | 8: 1.87 - 1.79 1.00 2789 144 0.2545 0.1937 3.0713 3.1452| | 9: 1.79 - 1.72 1.00 2745 138 0.2389 0.1949 2.89 2.9624| | 10: 1.72 - 1.66 1.00 2789 158 0.2409 0.1997 2.8115 2.903| | 11: 1.66 - 1.61 1.00 2740 147 0.2493 0.1780 2.7495 2.7399| | 12: 1.61 - 1.56 1.00 2787 146 0.2541 0.2047 2.6375 2.6759| | 13: 1.56 - 1.52 1.00 2745 130 0.2524 0.1800 2.566 2.5474| | 14: 1.52 - 1.48 1.00 2803 134 0.2631 0.1846 2.5359 2.5143| | 15: 1.48 - 1.45 1.00 2738 128 0.2551 0.2147 2.411 2.4851| | 16: 1.45 - 1.42 1.00 2756 161 0.2636 0.2298 2.3795 2.4631| | 17: 1.42 - 1.39 1.00 2785 139 0.2690 0.2040 2.3324 2.3162| | 18: 1.39 - 1.36 1.00 2741 179 0.2685 0.1990 2.2668 2.244| | 19: 1.36 - 1.34 1.00 2807 134 0.2695 0.2313 2.2429 2.2502| | 20: 1.34 - 1.32 1.00 2696 147 0.2713 0.2259 2.1934 2.2088| | 21: 1.32 - 1.30 1.00 2785 112 0.2762 0.2320 2.1665 2.163| | 22: 1.29 - 1.27 1.00 2704 152 0.2772 0.2399 2.1311 2.19| | 23: 1.27 - 1.26 1.00 2802 156 0.2751 0.2352 2.1044 2.1419| | 24: 1.26 - 1.24 1.00 2744 132 0.2758 0.2925 2.0671 2.2806| | 25: 1.24 - 1.22 1.00 2734 148 0.2868 0.2432 2.0438 2.0371| | 26: 1.22 - 1.21 1.00 2727 135 0.2882 0.2360 2.0112 2.0887| | 27: 1.21 - 1.19 1.00 2814 148 0.2961 0.2684 2.016 2.0026| | 28: 1.19 - 1.18 1.00 2671 147 0.3005 0.2922 1.9941 2.0057| | 29: 1.18 - 1.16 1.00 2800 134 0.2944 0.2783 1.9583 2.0682| | 30: 1.16 - 1.15 1.00 2740 148 0.3056 0.2863 1.927 1.9774| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.85 0.76 0.23 1488.08| | 2: 3.57 - 2.84 2876 122 0.80 26.27 1.27 0.23 1488.08| | 3: 2.84 - 2.48 2833 165 0.74 32.01 1.24 0.24 1233.36| | 4: 2.47 - 2.25 2825 136 0.81 25.61 1.25 0.25 572.32| | 5: 2.25 - 2.09 2756 127 0.77 29.16 1.28 0.25 572.32| | 6: 2.09 - 1.97 2846 113 0.83 22.57 1.30 0.25 312.06| | 7: 1.97 - 1.87 2787 165 0.90 16.45 1.29 0.26 90.09| | 8: 1.87 - 1.79 2789 144 0.86 20.97 1.26 0.26 90.09| | 9: 1.79 - 1.72 2745 138 0.88 18.66 1.23 0.26 55.50| | 10: 1.72 - 1.66 2789 158 0.87 20.08 1.22 0.26 48.57| | 11: 1.66 - 1.61 2740 147 0.85 21.45 1.24 0.25 46.79| | 12: 1.61 - 1.56 2787 146 0.89 18.15 1.24 0.25 28.68| | 13: 1.56 - 1.52 2745 130 0.87 19.84 1.23 0.25 28.68| | 14: 1.52 - 1.48 2803 134 0.87 20.07 1.23 0.25 25.47| | 15: 1.48 - 1.45 2738 128 0.88 19.56 1.23 0.25 19.59| | 16: 1.45 - 1.42 2756 161 0.86 20.84 1.23 0.25 19.59| | 17: 1.42 - 1.39 2785 139 0.87 20.05 1.23 0.25 16.52| | 18: 1.39 - 1.36 2741 179 0.87 20.28 1.24 0.25 14.75| | 19: 1.36 - 1.34 2807 134 0.86 21.16 1.22 0.25 14.75| | 20: 1.34 - 1.32 2696 147 0.87 20.50 1.22 0.25 12.52| | 21: 1.32 - 1.30 2785 112 0.86 21.65 1.21 0.25 12.36| | 22: 1.29 - 1.27 2704 152 0.86 21.91 1.22 0.25 12.15| | 23: 1.27 - 1.26 2802 156 0.86 22.06 1.21 0.24 11.08| | 24: 1.26 - 1.24 2744 132 0.85 22.66 1.20 0.24 11.08| | 25: 1.24 - 1.22 2734 148 0.84 24.25 1.21 0.24 10.70| | 26: 1.22 - 1.21 2727 135 0.83 24.76 1.20 0.23 10.27| | 27: 1.21 - 1.19 2814 148 0.83 25.24 1.20 0.23 10.27| | 28: 1.19 - 1.18 2671 147 0.82 26.29 1.19 0.22 9.82| | 29: 1.18 - 1.16 2800 134 0.81 26.91 1.17 0.22 9.65| | 30: 1.16 - 1.15 2740 148 0.79 28.63 1.16 0.22 9.65| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.65 max = 1488.08 mean = 215.41| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.57| |phase err.(test): min = 0.00 max = 89.40 mean = 22.45| |-----------------------------------------------------------------------------| ----------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 : 0.079 0.236 1557 Z= 5.337 Angle : 5.264 22.096 2118 Z= 3.767 Chirality : 0.373 0.954 243 Planarity : 0.033 0.166 284 Dihedral : 13.785 89.406 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 26.49 % 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: -2.56 (0.49), residues: 224 helix: -2.67 (0.40), residues: 102 sheet: -0.50 (0.82), residues: 38 loop : -0.62 (0.60), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.023 ARG A 28 TYR 0.090 0.032 TYR A 141 PHE 0.185 0.046 PHE A 119 HIS 0.090 0.040 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= 0.2611 r_free= 0.1950 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790705 | | target function (ml) not normalized (work): 232482.467318 | | target function (ml) not normalized (free): 11795.170184 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2570 0.2612 0.1949 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2570 0.2612 0.1949 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1987 0.1949 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2006 0.2011 0.1963 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1649 0.1643 0.1764 n_refl.: 87594 remove outliers: r(all,work,free)=0.1649 0.1643 0.1764 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 0.3916 386.423 357.323 0.671 1.002 0.407 11.894-9.307 99.02 97 4 0.1796 613.815 596.005 0.927 1.003 0.390 9.237-7.194 100.00 213 7 0.2132 502.025 493.398 0.953 1.003 0.349 7.162-5.571 100.00 427 22 0.2205 376.742 364.802 0.922 1.003 0.283 5.546-4.326 100.00 867 58 0.1286 517.173 511.067 0.967 1.003 0.214 4.315-3.360 100.00 1859 96 0.1169 491.835 487.601 1.002 1.002 0.153 3.356-2.611 100.00 3867 181 0.1434 323.110 319.835 0.999 1.002 0.057 2.608-2.026 99.99 8198 413 0.1356 214.193 212.115 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1657 104.601 104.028 1.014 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2072 46.384 45.023 1.002 0.997 0.000 1.221-1.150 99.97 13689 708 0.2574 29.225 26.997 0.977 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0431 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1643 r_free=0.1764 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 144 ASN A 173 ASN A 180 GLN Total number of N/Q/H flips: 4 r_work=0.1654 r_free=0.1787 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.531347 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2014.986186 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 0.1218 0.1473 0.0255 0.007 0.9 0.6 0.5 0.0 0 11.766 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.18 14.73 2.55 3.013 19.047 2014.986 0.017 12.41 15.44 3.03 3.173 19.544 2014.986 0.016 Individual atomic B min max mean iso aniso Overall: 8.62 118.47 21.01 2.88 0 1785 Protein: 8.62 118.47 17.87 2.88 0 1519 Water: 11.05 114.67 39.31 N/A 0 258 Other: 22.74 35.85 28.97 N/A 0 8 Chain A: 8.62 118.47 21.01 N/A 0 1785 Histogram: Values Number of atoms 8.62 - 19.61 1213 19.61 - 30.59 226 30.59 - 41.58 162 41.58 - 52.56 98 52.56 - 63.55 57 63.55 - 74.53 17 74.53 - 85.52 5 85.52 - 96.50 4 96.50 - 107.49 0 107.49 - 118.47 3 =========================== Idealize ADP of riding H ========================== r_work=0.1241 r_free=0.1544 r_work=0.1245 r_free=0.1548 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1245 r_free = 0.1548 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1246 r_free = 0.1552 target_work(ls_wunit_k1) = 0.015 | | 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= 0.1246 r_free= 0.1552 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015474 | | target function (ls_wunit_k1) not normalized (work): 1288.954312 | | target function (ls_wunit_k1) not normalized (free): 115.376211 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1260 0.1246 0.1552 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1697 0.1695 0.1771 n_refl.: 87593 remove outliers: r(all,work,free)=0.1697 0.1695 0.1771 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1720 0.1719 0.1787 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1245 0.1545 n_refl.: 87593 remove outliers: r(all,work,free)=0.1258 0.1244 0.1545 n_refl.: 87591 ======================== 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 94.79 86 5 0.3475 300.919 276.802 0.622 1.002 0.370 11.894-9.307 99.02 97 4 0.1595 478.870 467.657 0.904 1.003 0.363 9.237-7.194 100.00 213 7 0.1849 391.657 385.987 0.947 1.003 0.340 7.162-5.571 100.00 427 22 0.1720 293.917 288.428 0.922 1.003 0.253 5.546-4.326 100.00 867 58 0.0913 403.475 400.980 0.950 1.003 0.194 4.315-3.360 100.00 1859 96 0.0779 383.708 382.784 0.994 1.002 0.170 3.356-2.611 100.00 3867 181 0.1027 252.076 251.340 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0981 167.103 166.533 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1212 81.605 81.780 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1645 36.187 35.655 1.005 0.998 0.000 1.221-1.150 99.97 13689 708 0.2356 22.800 21.310 0.969 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=0.0546 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1244 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 144 ASN A 173 ASN A 180 GLN Total number of N/Q/H flips: 4 r_work=0.1248 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1248 r_free=0.1546 | n_water=258 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1255 r_free=0.1540 | n_water=254 | time (s): 26.550 (total time: 28.940) Filter (q & B) r_work=0.1258 r_free=0.1540 | n_water=251 | time (s): 3.860 (total time: 32.800) Compute maps r_work=0.1258 r_free=0.1540 | n_water=251 | time (s): 1.890 (total time: 34.690) Filter (map) r_work=0.1278 r_free=0.1549 | n_water=237 | time (s): 3.860 (total time: 38.550) Find peaks r_work=0.1278 r_free=0.1549 | n_water=237 | time (s): 0.760 (total time: 39.310) Add new water r_work=0.1428 r_free=0.1699 | n_water=465 | time (s): 3.970 (total time: 43.280) Refine new water occ: r_work=0.1333 r_free=0.1566 adp: r_work=0.1253 r_free=0.1518 occ: r_work=0.1267 r_free=0.1502 adp: r_work=0.1233 r_free=0.1492 occ: r_work=0.1236 r_free=0.1479 adp: r_work=0.1229 r_free=0.1479 ADP+occupancy (water only), MIN, final r_work=0.1229 r_free=0.1479 r_work=0.1229 r_free=0.1479 | n_water=465 | time (s): 130.210 (total time: 173.490) Filter (q & B) r_work=0.1236 r_free=0.1488 | n_water=436 | time (s): 3.830 (total time: 177.320) Filter (dist only) r_work=0.1236 r_free=0.1488 | n_water=435 | time (s): 45.950 (total time: 223.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.683432 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1534.946629 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 0.1227 0.1507 0.0280 0.007 0.9 2.6 0.5 0.0 0 12.342 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 15.07 2.80 3.789 23.219 1534.947 0.015 12.00 14.80 2.80 4.179 23.056 1534.947 0.014 Individual atomic B min max mean iso aniso Overall: 8.87 114.23 23.29 2.61 198 1764 Protein: 8.87 114.23 17.68 2.61 0 1519 Water: 11.02 73.01 42.78 N/A 198 237 Other: 23.19 35.37 28.53 N/A 0 8 Chain A: 8.87 114.23 20.46 N/A 0 1764 Chain S: 17.19 72.04 48.51 N/A 198 0 Histogram: Values Number of atoms 8.87 - 19.40 1212 19.40 - 29.94 245 29.94 - 40.48 189 40.48 - 51.01 140 51.01 - 61.55 110 61.55 - 72.09 54 72.09 - 82.62 6 82.62 - 93.16 3 93.16 - 103.70 1 103.70 - 114.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1480 r_work=0.1200 r_free=0.1479 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1479 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1475 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1200 r_free= 0.1475 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.013867 | | target function (ls_wunit_k1) not normalized (work): 1155.028229 | | target function (ls_wunit_k1) not normalized (free): 101.529608 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1200 0.1475 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1559 0.1552 0.1711 n_refl.: 87591 remove outliers: r(all,work,free)=0.1559 0.1552 0.1711 n_refl.: 87591 overall B=0.03 to atoms: r(all,work,free)=0.1564 0.1557 0.1714 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1197 0.1467 n_refl.: 87591 remove outliers: r(all,work,free)=0.1209 0.1196 0.1467 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 0.3391 294.869 279.843 0.622 0.946 0.340 11.894-9.307 99.02 97 4 0.1611 478.870 475.652 0.968 0.947 0.333 9.237-7.194 100.00 213 7 0.1695 391.657 390.166 1.034 0.947 0.269 7.162-5.571 100.00 427 22 0.1484 293.917 290.443 0.992 0.947 0.223 5.546-4.326 100.00 867 58 0.0836 403.475 401.024 1.010 0.948 0.200 4.315-3.360 100.00 1859 96 0.0716 383.708 382.329 1.058 0.948 0.184 3.356-2.611 100.00 3867 181 0.0951 252.076 251.418 1.065 0.949 0.072 2.608-2.026 99.99 8198 413 0.0953 167.103 166.626 1.073 0.949 0.000 2.025-1.573 100.00 17313 902 0.1179 81.605 81.775 1.081 0.951 0.000 1.573-1.221 100.00 36679 1900 0.1613 36.187 35.677 1.066 0.953 0.000 1.221-1.150 99.97 13689 708 0.2344 22.800 21.346 1.022 0.955 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0501 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1467 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1198 r_free=0.1467 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1467 | n_water=435 | time (s): 2.170 (total time: 2.170) Filter (dist) r_work=0.1199 r_free=0.1469 | n_water=432 | time (s): 41.940 (total time: 44.110) Filter (q & B) r_work=0.1199 r_free=0.1469 | n_water=432 | time (s): 1.020 (total time: 45.130) Compute maps r_work=0.1199 r_free=0.1469 | n_water=432 | time (s): 1.220 (total time: 46.350) Filter (map) r_work=0.1241 r_free=0.1491 | n_water=294 | time (s): 2.710 (total time: 49.060) Find peaks r_work=0.1241 r_free=0.1491 | n_water=294 | time (s): 0.490 (total time: 49.550) Add new water r_work=0.1367 r_free=0.1601 | n_water=487 | time (s): 2.480 (total time: 52.030) Refine new water occ: r_work=0.1267 r_free=0.1521 adp: r_work=0.1268 r_free=0.1521 occ: r_work=0.1244 r_free=0.1504 adp: r_work=0.1242 r_free=0.1501 occ: r_work=0.1229 r_free=0.1492 adp: r_work=0.1222 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1222 r_free=0.1485 r_work=0.1222 r_free=0.1485 | n_water=487 | time (s): 128.320 (total time: 180.350) Filter (q & B) r_work=0.1225 r_free=0.1490 | n_water=453 | time (s): 2.740 (total time: 183.090) Filter (dist only) r_work=0.1225 r_free=0.1490 | n_water=453 | time (s): 39.210 (total time: 222.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.040529 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 55.297858 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 0.1446 0.0218 0.006 0.9 2.2 0.5 0.0 0 1.020 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.46 2.18 3.622 22.205 55.298 3.725 12.08 13.97 1.89 4.079 22.011 55.298 3.650 Individual atomic B min max mean iso aniso Overall: 9.22 110.06 21.82 2.35 218 1762 Protein: 9.22 110.06 17.26 2.35 0 1519 Water: 11.53 72.04 37.07 N/A 218 235 Other: 18.76 30.95 25.31 N/A 0 8 Chain A: 9.22 110.06 20.00 N/A 0 1762 Chain S: 16.35 66.50 36.52 N/A 218 0 Histogram: Values Number of atoms 9.22 - 19.31 1230 19.31 - 29.39 274 29.39 - 39.47 219 39.47 - 49.56 143 49.56 - 59.64 81 59.64 - 69.72 20 69.72 - 79.81 7 79.81 - 89.89 3 89.89 - 99.97 1 99.97 - 110.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1208 r_free=0.1397 r_work=0.1209 r_free=0.1398 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1398 target_work(ml) = 3.650 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1396 target_work(ml) = 3.648 | | occupancies: max = 1.00 min = 0.19 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= 0.1205 r_free= 0.1396 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.648287 | | target function (ml) not normalized (work): 303876.773638 | | target function (ml) not normalized (free): 16061.358724 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1205 0.1396 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1524 0.1523 0.1581 n_refl.: 87589 remove outliers: r(all,work,free)=0.1524 0.1523 0.1581 n_refl.: 87589 overall B=-0.02 to atoms: r(all,work,free)=0.1521 0.1520 0.1579 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1196 0.1376 n_refl.: 87589 remove outliers: r(all,work,free)=0.1202 0.1193 0.1376 n_refl.: 87581 ======================== 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 0.4051 291.619 261.212 0.454 1.000 0.293 11.894-9.307 96.08 94 4 0.2330 480.297 457.440 0.851 1.002 0.273 9.237-7.194 98.64 210 7 0.2384 385.214 387.668 0.945 1.002 0.150 7.162-5.571 100.00 427 22 0.2071 293.917 283.819 0.911 1.002 0.147 5.546-4.326 100.00 867 58 0.1114 403.475 399.063 0.950 1.002 0.142 4.315-3.360 100.00 1859 96 0.0934 383.708 381.062 0.993 1.002 0.140 3.356-2.611 100.00 3867 181 0.1145 252.076 250.297 1.000 1.002 0.067 2.608-2.026 99.99 8198 413 0.1035 167.103 166.192 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.1008 81.605 81.772 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1284 36.187 35.772 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2120 22.800 21.430 0.982 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0427 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1377 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=0.1193 r_free=0.1377 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1377 | n_water=453 | time (s): 1.630 (total time: 1.630) Filter (dist) r_work=0.1193 r_free=0.1378 | n_water=452 | time (s): 39.820 (total time: 41.450) Filter (q & B) r_work=0.1193 r_free=0.1378 | n_water=452 | time (s): 0.830 (total time: 42.280) Compute maps r_work=0.1193 r_free=0.1378 | n_water=452 | time (s): 1.280 (total time: 43.560) Filter (map) r_work=0.1221 r_free=0.1366 | n_water=317 | time (s): 3.310 (total time: 46.870) Find peaks r_work=0.1221 r_free=0.1366 | n_water=317 | time (s): 0.660 (total time: 47.530) Add new water r_work=0.1279 r_free=0.1432 | n_water=478 | time (s): 3.010 (total time: 50.540) Refine new water occ: r_work=0.1208 r_free=0.1362 adp: r_work=0.1209 r_free=0.1364 occ: r_work=0.1194 r_free=0.1351 adp: r_work=0.1192 r_free=0.1351 occ: r_work=0.1183 r_free=0.1346 adp: r_work=0.1180 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1344 r_work=0.1180 r_free=0.1344 | n_water=478 | time (s): 205.620 (total time: 256.160) Filter (q & B) r_work=0.1186 r_free=0.1350 | n_water=445 | time (s): 2.680 (total time: 258.840) Filter (dist only) r_work=0.1186 r_free=0.1348 | n_water=444 | time (s): 39.900 (total time: 298.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.915839 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.634760 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 0.1189 0.1359 0.0170 0.006 0.9 1.9 0.5 0.0 0 0.958 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.59 1.70 3.446 21.564 50.635 3.635 11.80 13.52 1.72 3.833 21.435 50.635 3.624 Individual atomic B min max mean iso aniso Overall: 9.25 105.67 21.30 2.18 210 1761 Protein: 9.25 105.67 16.97 2.18 0 1519 Water: 11.50 70.62 36.06 N/A 210 234 Other: 18.34 27.87 23.11 N/A 0 8 Chain A: 9.25 105.67 19.66 N/A 0 1761 Chain S: 16.43 60.24 35.04 N/A 210 0 Histogram: Values Number of atoms 9.25 - 18.89 1229 18.89 - 28.53 277 28.53 - 38.17 218 38.17 - 47.82 138 47.82 - 57.46 70 57.46 - 67.10 25 67.10 - 76.74 9 76.74 - 86.38 2 86.38 - 96.03 1 96.03 - 105.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.1180 r_free=0.1352 r_work=0.1180 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1180 r_free = 0.1352 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1175 r_free = 0.1349 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1175 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621971 | | target function (ml) not normalized (work): 301655.843272 | | target function (ml) not normalized (free): 15936.358709 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1183 0.1175 0.1349 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1492 0.1489 0.1562 n_refl.: 87581 remove outliers: r(all,work,free)=0.1492 0.1489 0.1562 n_refl.: 87581 overall B=-0.02 to atoms: r(all,work,free)=0.1488 0.1486 0.1560 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1184 0.1176 0.1351 n_refl.: 87581 remove outliers: r(all,work,free)=0.1183 0.1174 0.1351 n_refl.: 87578 ======================== 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 89.58 81 5 0.4201 287.005 253.363 0.437 0.999 0.289 11.894-9.307 94.12 92 4 0.2445 477.366 460.958 0.844 1.001 0.204 9.237-7.194 98.64 210 7 0.2484 385.214 379.277 0.915 1.002 0.135 7.162-5.571 100.00 427 22 0.2189 293.917 283.142 0.909 1.002 0.130 5.546-4.326 100.00 867 58 0.1142 403.475 398.900 0.950 1.002 0.120 4.315-3.360 100.00 1859 96 0.0931 383.708 380.982 0.993 1.002 0.120 3.356-2.611 100.00 3867 181 0.1134 252.076 250.400 1.001 1.002 0.083 2.608-2.026 99.99 8198 413 0.1010 167.103 166.212 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0962 81.605 81.865 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1244 36.187 35.797 1.024 0.996 0.000 1.221-1.150 99.97 13689 708 0.2128 22.800 21.414 0.983 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0453 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1174 r_free=0.1351 After: r_work=0.1175 r_free=0.1351 ================================== NQH flips ================================== r_work=0.1175 r_free=0.1351 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=0.1175 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1175 r_free=0.1351 | n_water=444 | time (s): 1.650 (total time: 1.650) Filter (dist) r_work=0.1175 r_free=0.1350 | n_water=443 | time (s): 38.350 (total time: 40.000) Filter (q & B) r_work=0.1176 r_free=0.1350 | n_water=441 | time (s): 2.660 (total time: 42.660) Compute maps r_work=0.1176 r_free=0.1350 | n_water=441 | time (s): 1.230 (total time: 43.890) Filter (map) r_work=0.1202 r_free=0.1355 | n_water=339 | time (s): 3.010 (total time: 46.900) Find peaks r_work=0.1202 r_free=0.1355 | n_water=339 | time (s): 0.680 (total time: 47.580) Add new water r_work=0.1243 r_free=0.1404 | n_water=493 | time (s): 3.230 (total time: 50.810) Refine new water occ: r_work=0.1184 r_free=0.1335 adp: r_work=0.1185 r_free=0.1338 occ: r_work=0.1173 r_free=0.1326 adp: r_work=0.1172 r_free=0.1327 occ: r_work=0.1164 r_free=0.1323 adp: r_work=0.1162 r_free=0.1322 ADP+occupancy (water only), MIN, final r_work=0.1162 r_free=0.1322 r_work=0.1162 r_free=0.1322 | n_water=493 | time (s): 177.950 (total time: 228.760) Filter (q & B) r_work=0.1172 r_free=0.1336 | n_water=448 | time (s): 3.510 (total time: 232.270) Filter (dist only) r_work=0.1172 r_free=0.1335 | n_water=447 | time (s): 39.180 (total time: 271.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.017007 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.338117 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 0.1189 0.1339 0.0150 0.007 1.0 4.8 0.5 0.0 0 1.009 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.39 1.50 3.306 21.236 43.338 3.627 11.93 13.43 1.50 3.476 21.179 43.338 3.622 Individual atomic B min max mean iso aniso Overall: 9.30 101.94 21.18 2.05 214 1760 Protein: 9.30 101.94 16.82 2.05 0 1519 Water: 11.53 69.95 35.99 N/A 214 233 Other: 18.33 26.27 22.47 N/A 0 8 Chain A: 9.30 101.94 19.48 N/A 0 1760 Chain S: 15.91 60.15 35.21 N/A 214 0 Histogram: Values Number of atoms 9.30 - 18.56 1220 18.56 - 27.83 283 27.83 - 37.09 201 37.09 - 46.36 151 46.36 - 55.62 74 55.62 - 64.89 29 64.89 - 74.15 11 74.15 - 83.41 2 83.41 - 92.68 1 92.68 - 101.94 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1343 r_work=0.1194 r_free=0.1343 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1343 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1342 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1191 r_free= 0.1342 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.620981 | | target function (ml) not normalized (work): 301562.514441 | | target function (ml) not normalized (free): 15940.679005 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1409 0.1371 5.682 5.6578| | 2: 3.57 - 2.84 1.00 2888 124 0.1105 0.1389 5.1957 5.2503| | 3: 2.83 - 2.48 1.00 2820 163 0.1213 0.1229 5.0034 5.0228| | 4: 2.47 - 2.25 1.00 2825 136 0.1018 0.1098 4.7057 4.7336| | 5: 2.25 - 2.09 1.00 2756 127 0.0993 0.1063 4.6491 4.7078| | 6: 2.09 - 1.97 1.00 2846 113 0.0971 0.1189 4.3491 4.4791| | 7: 1.97 - 1.87 1.00 2787 165 0.0981 0.1223 4.0623 4.1786| | 8: 1.87 - 1.79 1.00 2789 144 0.1014 0.1238 3.981 4.0672| | 9: 1.79 - 1.72 1.00 2745 138 0.0948 0.1259 3.7112 3.8882| | 10: 1.72 - 1.66 1.00 2831 160 0.0996 0.1235 3.6287 3.7537| | 11: 1.66 - 1.61 1.00 2712 147 0.0951 0.1071 3.5615 3.6024| | 12: 1.61 - 1.56 1.00 2773 144 0.0913 0.1189 3.3442 3.4851| | 13: 1.56 - 1.52 1.00 2745 130 0.0982 0.1112 3.3373 3.448| | 14: 1.52 - 1.48 1.00 2803 134 0.1002 0.1096 3.2635 3.3369| | 15: 1.48 - 1.45 1.00 2738 128 0.1009 0.1351 3.1703 3.3315| | 16: 1.45 - 1.42 1.00 2756 161 0.1072 0.1295 3.1535 3.2633| | 17: 1.42 - 1.39 1.00 2785 139 0.1125 0.1294 3.1185 3.2389| | 18: 1.39 - 1.36 1.00 2741 179 0.1157 0.1380 3.0907 3.2658| | 19: 1.36 - 1.34 1.00 2807 134 0.1219 0.1619 3.0975 3.2739| | 20: 1.34 - 1.32 1.00 2696 147 0.1319 0.1507 3.0916 3.1504| | 21: 1.32 - 1.30 1.00 2785 112 0.1418 0.1614 3.0921 3.1578| | 22: 1.29 - 1.27 1.00 2704 152 0.1474 0.1913 3.0883 3.2874| | 23: 1.27 - 1.26 1.00 2802 156 0.1574 0.1873 3.1044 3.2174| | 24: 1.26 - 1.24 1.00 2744 132 0.1621 0.1773 3.0944 3.2007| | 25: 1.24 - 1.22 1.00 2733 148 0.1793 0.2307 3.1122 3.2904| | 26: 1.22 - 1.21 1.00 2727 135 0.1860 0.1770 3.1225 3.1962| | 27: 1.21 - 1.19 1.00 2814 148 0.2014 0.2075 3.1401 3.1471| | 28: 1.19 - 1.18 1.00 2671 147 0.2147 0.2304 3.1405 3.1653| | 29: 1.18 - 1.16 1.00 2800 134 0.2214 0.2367 3.1275 3.2259| | 30: 1.16 - 1.15 1.00 2739 148 0.2373 0.2500 3.1162 3.1661| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2920 171 0.95 9.13 1.00 0.97 6295.33| | 2: 3.57 - 2.84 2888 124 0.92 13.34 1.01 0.97 6295.33| | 3: 2.83 - 2.48 2820 163 0.89 17.48 0.99 0.98 5273.89| | 4: 2.47 - 2.25 2825 136 0.91 14.58 1.00 0.98 2639.92| | 5: 2.25 - 2.09 2756 127 0.89 16.78 1.01 0.98 2639.92| | 6: 2.09 - 1.97 2846 113 0.92 13.53 1.02 0.98 1546.21| | 7: 1.97 - 1.87 2787 165 0.94 10.65 1.02 0.98 613.43| | 8: 1.87 - 1.79 2789 144 0.91 14.23 1.00 0.98 613.43| | 9: 1.79 - 1.72 2745 138 0.94 11.23 0.98 0.97 333.70| | 10: 1.72 - 1.66 2831 160 0.93 12.14 0.98 0.97 277.68| | 11: 1.66 - 1.61 2712 147 0.93 12.78 0.98 0.97 265.22| | 12: 1.61 - 1.56 2773 144 0.95 9.56 0.99 0.97 147.77| | 13: 1.56 - 1.52 2745 130 0.94 11.07 1.02 0.97 147.77| | 14: 1.52 - 1.48 2803 134 0.94 11.35 1.02 0.98 132.41| | 15: 1.48 - 1.45 2738 128 0.95 10.48 1.01 0.98 104.28| | 16: 1.45 - 1.42 2756 161 0.94 11.66 1.02 0.98 104.28| | 17: 1.42 - 1.39 2785 139 0.94 11.57 1.01 0.99 94.39| | 18: 1.39 - 1.36 2741 179 0.94 11.95 1.01 0.99 88.67| | 19: 1.36 - 1.34 2807 134 0.94 12.43 1.00 0.99 88.67| | 20: 1.34 - 1.32 2696 147 0.94 12.54 0.99 0.97 83.62| | 21: 1.32 - 1.30 2785 112 0.93 13.50 0.99 0.97 83.26| | 22: 1.29 - 1.27 2704 152 0.93 14.01 0.99 0.97 83.33| | 23: 1.27 - 1.26 2802 156 0.92 14.89 0.98 0.95 83.67| | 24: 1.26 - 1.24 2744 132 0.92 15.02 0.97 0.95 83.67| | 25: 1.24 - 1.22 2733 148 0.91 16.41 0.96 0.94 85.10| | 26: 1.22 - 1.21 2727 135 0.90 18.14 1.02 0.94 86.68| | 27: 1.21 - 1.19 2814 148 0.89 18.79 1.02 0.94 86.68| | 28: 1.19 - 1.18 2671 147 0.88 20.27 1.01 0.93 90.02| | 29: 1.18 - 1.16 2800 134 0.88 20.64 0.99 0.93 91.27| | 30: 1.16 - 1.15 2739 148 0.86 22.00 0.98 0.93 91.27| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 83.26 max = 6295.33 mean = 978.98| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 14.06| |phase err.(test): min = 0.00 max = 89.71 mean = 14.19| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1191 0.1342 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1499 0.1497 0.1565 n_refl.: 87578 remove outliers: r(all,work,free)=0.1499 0.1497 0.1565 n_refl.: 87578 overall B=-0.02 to atoms: r(all,work,free)=0.1496 0.1493 0.1563 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1191 0.1346 n_refl.: 87578 remove outliers: r(all,work,free)=0.1198 0.1190 0.1346 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 0.4049 283.558 255.577 0.438 0.998 0.292 11.894-9.307 94.12 92 4 0.2471 477.366 458.610 0.848 1.001 0.191 9.237-7.194 98.18 209 7 0.2529 386.293 378.674 0.904 1.001 0.110 7.162-5.571 100.00 427 22 0.2258 293.917 282.614 0.901 1.001 0.110 5.546-4.326 100.00 867 58 0.1174 403.475 398.714 0.951 1.001 0.110 4.315-3.360 100.00 1859 96 0.0971 383.708 381.007 0.995 1.001 0.120 3.356-2.611 100.00 3867 181 0.1172 252.076 250.337 1.001 1.001 0.057 2.608-2.026 99.99 8198 413 0.1033 167.103 166.181 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0970 81.605 81.868 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1230 36.187 35.822 1.022 0.999 0.000 1.221-1.150 99.97 13689 708 0.2117 22.800 21.407 0.979 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0467 ================= 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 : 0.2611 0.1950 0.079 5.264 8.8 119.3 19.9 258 0.000 1_bss: 0.1643 0.1764 0.079 5.264 9.0 119.5 20.1 258 0.000 1_settarget: 0.1643 0.1764 0.079 5.264 9.0 119.5 20.1 258 0.000 1_nqh: 0.1654 0.1787 0.079 5.264 9.0 119.5 20.1 258 0.013 1_weight: 0.1654 0.1787 0.079 5.264 9.0 119.5 20.1 258 0.013 1_xyzrec: 0.1218 0.1473 0.007 0.926 9.0 119.5 20.1 258 0.136 1_adp: 0.1241 0.1544 0.007 0.926 8.6 118.5 21.0 258 0.136 1_regHadp: 0.1245 0.1548 0.007 0.926 8.6 118.5 21.0 258 0.136 1_occ: 0.1246 0.1552 0.007 0.926 8.6 118.5 21.0 258 0.136 2_bss: 0.1244 0.1545 0.007 0.926 8.8 118.6 21.2 258 0.136 2_settarget: 0.1244 0.1545 0.007 0.926 8.8 118.6 21.2 258 0.136 2_updatecdl: 0.1244 0.1545 0.007 0.940 8.8 118.6 21.2 258 0.136 2_nqh: 0.1248 0.1546 0.007 0.940 8.8 118.6 21.2 258 0.130 2_sol: 0.1236 0.1488 0.007 0.940 8.8 118.6 23.6 435 n/a 2_weight: 0.1236 0.1488 0.007 0.940 8.8 118.6 23.6 435 n/a 2_xyzrec: 0.1227 0.1507 0.007 0.875 8.8 118.6 23.6 435 n/a 2_adp: 0.1200 0.1480 0.007 0.875 8.9 114.2 23.3 435 n/a 2_regHadp: 0.1200 0.1479 0.007 0.875 8.9 114.2 23.3 435 n/a 2_occ: 0.1200 0.1475 0.007 0.875 8.9 114.2 23.3 435 n/a 3_bss: 0.1196 0.1467 0.007 0.875 8.9 114.3 23.3 435 n/a 3_settarget: 0.1196 0.1467 0.007 0.875 8.9 114.3 23.3 435 n/a 3_updatecdl: 0.1196 0.1467 0.007 0.875 8.9 114.3 23.3 435 n/a 3_nqh: 0.1198 0.1467 0.007 0.875 8.9 114.3 23.3 435 n/a 3_sol: 0.1225 0.1490 0.007 0.875 8.9 114.3 22.2 453 n/a 3_weight: 0.1225 0.1490 0.007 0.875 8.9 114.3 22.2 453 n/a 3_xyzrec: 0.1228 0.1446 0.006 0.914 8.9 114.3 22.2 453 n/a 3_adp: 0.1208 0.1397 0.006 0.914 9.2 110.1 21.8 453 n/a 3_regHadp: 0.1209 0.1398 0.006 0.914 9.2 110.1 21.8 453 n/a 3_occ: 0.1205 0.1396 0.006 0.914 9.2 110.1 21.8 453 n/a 4_bss: 0.1193 0.1377 0.006 0.914 9.2 110.0 21.8 453 n/a 4_settarget: 0.1193 0.1377 0.006 0.914 9.2 110.0 21.8 453 n/a 4_updatecdl: 0.1193 0.1377 0.006 0.913 9.2 110.0 21.8 453 n/a 4_nqh: 0.1193 0.1377 0.006 0.913 9.2 110.0 21.8 453 n/a 4_sol: 0.1186 0.1348 0.006 0.913 9.2 110.0 21.5 444 n/a 4_weight: 0.1186 0.1348 0.006 0.913 9.2 110.0 21.5 444 n/a 4_xyzrec: 0.1189 0.1359 0.006 0.939 9.2 110.0 21.5 444 n/a 4_adp: 0.1180 0.1352 0.006 0.939 9.2 105.7 21.3 444 n/a 4_regHadp: 0.1180 0.1352 0.006 0.939 9.2 105.7 21.3 444 n/a 4_occ: 0.1175 0.1349 0.006 0.939 9.2 105.7 21.3 444 n/a 5_bss: 0.1174 0.1351 0.006 0.939 9.2 105.7 21.3 444 n/a 5_settarget: 0.1174 0.1351 0.006 0.939 9.2 105.7 21.3 444 n/a 5_updatecdl: 0.1174 0.1351 0.006 0.940 9.2 105.7 21.3 444 n/a 5_setrh: 0.1175 0.1351 0.006 0.940 9.2 105.7 21.3 444 n/a 5_nqh: 0.1175 0.1351 0.006 0.940 9.2 105.7 21.3 444 n/a 5_sol: 0.1172 0.1335 0.006 0.940 9.2 105.7 21.3 447 n/a 5_weight: 0.1172 0.1335 0.006 0.940 9.2 105.7 21.3 447 n/a 5_xyzrec: 0.1189 0.1339 0.007 1.024 9.2 105.7 21.3 447 n/a 5_adp: 0.1193 0.1343 0.007 1.024 9.3 101.9 21.2 447 n/a 5_regHadp: 0.1194 0.1343 0.007 1.024 9.3 101.9 21.2 447 n/a 5_occ: 0.1191 0.1342 0.007 1.024 9.3 101.9 21.2 447 n/a end: 0.1190 0.1346 0.007 1.024 9.3 101.9 21.2 447 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_9171019_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_9171019_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8700 Refinement macro-cycles (run) : 3490.2400 Write final files (write_after_run_outputs) : 70.4400 Total : 3565.5500 Total CPU time: 60.05 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:14 PST -0800 (1735452674.03 s) Start R-work = 0.1643, R-free = 0.1764 Final R-work = 0.1190, R-free = 0.1346 =============================================================================== Job complete usr+sys time: 3702.58 seconds wall clock time: 66 minutes 25.40 seconds (3985.40 seconds total)