Starting phenix.refine on Sat Dec 28 21:06:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4023827.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4023827.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4023827.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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 =============================================================================== Symmetric amino acids flipped. Time to flip 3 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: 2.29, per 1000 atoms: 0.68 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: 0.95 Conformation dependent library (CDL) restraints added in 305.8 milliseconds Time building geometry restraints manager: 0.82 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: 502 0.91 - 1.16: 1128 1.16 - 1.41: 621 1.41 - 1.66: 847 1.66 - 1.91: 55 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 117 " pdb=" O ILE A 117 " ideal model delta sigma weight residual 1.237 1.452 -0.215 1.10e-02 8.26e+03 3.83e+02 bond pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 1.329 1.531 -0.201 1.13e-02 7.83e+03 3.18e+02 bond pdb=" C ALA A 179 " pdb=" O ALA A 179 " ideal model delta sigma weight residual 1.237 1.443 -0.207 1.16e-02 7.43e+03 3.17e+02 bond pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta sigma weight residual 1.446 1.598 -0.151 8.70e-03 1.32e+04 3.02e+02 bond pdb=" N ILE A 168 " pdb=" CA ILE A 168 " ideal model delta sigma weight residual 1.461 1.662 -0.201 1.17e-02 7.31e+03 2.94e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 3028 4.41 - 8.81: 1860 8.81 - 13.22: 705 13.22 - 17.62: 166 17.62 - 22.03: 18 Bond angle restraints: 5777 Sorted by residual: angle pdb=" N ARG A 156 " pdb=" CA ARG A 156 " pdb=" C ARG A 156 " ideal model delta sigma weight residual 113.50 132.47 -18.97 1.23e+00 6.61e-01 2.38e+02 angle pdb=" O BGLU A 90 " pdb=" C BGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 122.12 136.84 -14.72 1.06e+00 8.90e-01 1.93e+02 angle pdb=" CA MET A 134 " pdb=" C MET A 134 " pdb=" O MET A 134 " ideal model delta sigma weight residual 119.28 134.81 -15.53 1.21e+00 6.83e-01 1.65e+02 angle pdb=" CA GLY A 108 " pdb=" C GLY A 108 " pdb=" O GLY A 108 " ideal model delta sigma weight residual 119.69 111.84 7.85 6.30e-01 2.52e+00 1.55e+02 angle pdb=" O ARG A 27 " pdb=" C ARG A 27 " pdb=" N ARG A 28 " ideal model delta sigma weight residual 122.15 136.24 -14.09 1.14e+00 7.69e-01 1.53e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.43: 940 17.43 - 34.86: 122 34.86 - 52.28: 30 52.28 - 69.71: 15 69.71 - 87.14: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA BLYS A 99 " pdb=" C BLYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.235: 122 0.235 - 0.465: 71 0.465 - 0.695: 36 0.695 - 0.925: 12 0.925 - 1.155: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.67 -1.15 2.00e-01 2.50e+01 3.33e+01 chirality pdb=" CA BLEU A 153 " pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CB BLEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.45 -0.94 2.00e-01 2.50e+01 2.23e+01 chirality pdb=" CA THR A 160 " pdb=" N THR A 160 " pdb=" C THR A 160 " pdb=" CB THR A 160 " both_signs ideal model delta sigma weight residual False 2.53 1.62 0.91 2.00e-01 2.50e+01 2.06e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.012 2.00e-02 2.50e+03 6.78e-02 1.38e+02 pdb=" CG BTYR A 67 " -0.037 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.117 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.034 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.094 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.108 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.029 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.066 2.00e-02 2.50e+03 6.94e-02 1.09e+02 pdb=" CG HIS A 126 " -0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.098 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.097 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.020 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.109 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.044 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.022 2.00e-02 2.50e+03 5.55e-02 9.25e+01 pdb=" CG PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.139 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.038 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.040 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1259 2.35 - 2.91: 8260 2.91 - 3.48: 10522 3.48 - 4.04: 15154 4.04 - 4.60: 21363 Nonbonded interactions: 56558 Sorted by model distance: nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.791 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.812 2.270 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.820 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.825 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.845 2.450 ... (remaining 56553 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_4023827_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= 0.2606 r_free= 0.1933 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791791 | | target function (ml) not normalized (work): 232572.916545 | | target function (ml) not normalized (free): 11841.897127 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3040 0.2086 7.1006 4.9525| | 2: 3.57 - 2.84 1.00 2876 122 0.2431 0.1733 4.3449 4.3358| | 3: 2.84 - 2.48 1.00 2833 165 0.2335 0.1740 4.1277 4.1603| | 4: 2.47 - 2.25 1.00 2825 136 0.2315 0.1322 3.826 3.8089| | 5: 2.25 - 2.09 1.00 2756 127 0.2433 0.1533 3.7894 3.7979| | 6: 2.09 - 1.97 1.00 2846 113 0.2574 0.1642 3.4617 3.5133| | 7: 1.97 - 1.87 1.00 2787 165 0.2620 0.1767 3.1338 3.1646| | 8: 1.87 - 1.79 1.00 2789 144 0.2495 0.1914 3.059 3.1598| | 9: 1.79 - 1.72 1.00 2745 138 0.2436 0.1825 2.889 2.9071| | 10: 1.72 - 1.66 1.00 2789 158 0.2468 0.2049 2.8012 2.8851| | 11: 1.66 - 1.61 1.00 2740 147 0.2428 0.1805 2.7349 2.7393| | 12: 1.61 - 1.56 1.00 2787 146 0.2489 0.1926 2.6127 2.6457| | 13: 1.56 - 1.52 1.00 2745 130 0.2513 0.1964 2.5695 2.636| | 14: 1.52 - 1.48 1.00 2803 134 0.2539 0.2117 2.5122 2.5984| | 15: 1.48 - 1.45 1.00 2738 128 0.2623 0.2168 2.4477 2.5408| | 16: 1.45 - 1.42 1.00 2756 161 0.2682 0.2103 2.4092 2.4674| | 17: 1.42 - 1.39 1.00 2785 139 0.2653 0.1965 2.3497 2.3627| | 18: 1.39 - 1.36 1.00 2741 179 0.2707 0.2294 2.2855 2.3433| | 19: 1.36 - 1.34 1.00 2807 134 0.2653 0.2395 2.2461 2.3107| | 20: 1.34 - 1.32 1.00 2696 147 0.2677 0.2317 2.2037 2.2586| | 21: 1.32 - 1.30 1.00 2785 112 0.2699 0.2319 2.1673 2.182| | 22: 1.29 - 1.27 1.00 2704 152 0.2734 0.2678 2.1403 2.2123| | 23: 1.27 - 1.26 1.00 2802 156 0.2791 0.2567 2.1033 2.2082| | 24: 1.26 - 1.24 1.00 2744 132 0.2742 0.2590 2.0684 2.1776| | 25: 1.24 - 1.22 1.00 2734 148 0.2844 0.2665 2.0464 2.1082| | 26: 1.22 - 1.21 1.00 2727 135 0.2835 0.2321 2.0059 2.0747| | 27: 1.21 - 1.19 1.00 2814 148 0.2967 0.2771 2.007 2.0305| | 28: 1.19 - 1.18 1.00 2671 147 0.2955 0.2633 1.9742 1.9785| | 29: 1.18 - 1.16 1.00 2800 134 0.2923 0.2778 1.9435 2.0243| | 30: 1.16 - 1.15 1.00 2740 148 0.3063 0.2749 1.9351 1.9525| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.70 0.76 0.23 1474.93| | 2: 3.57 - 2.84 2876 122 0.81 25.90 1.27 0.23 1474.93| | 3: 2.84 - 2.48 2833 165 0.74 31.83 1.24 0.24 1222.23| | 4: 2.47 - 2.25 2825 136 0.81 25.45 1.25 0.25 566.44| | 5: 2.25 - 2.09 2756 127 0.77 29.12 1.28 0.25 566.44| | 6: 2.09 - 1.97 2846 113 0.83 22.60 1.30 0.25 308.39| | 7: 1.97 - 1.87 2787 165 0.90 16.59 1.30 0.26 88.31| | 8: 1.87 - 1.79 2789 144 0.86 20.76 1.25 0.26 88.31| | 9: 1.79 - 1.72 2745 138 0.88 18.53 1.23 0.25 54.49| | 10: 1.72 - 1.66 2789 158 0.86 20.24 1.23 0.25 47.72| | 11: 1.66 - 1.61 2740 147 0.86 21.17 1.24 0.25 46.07| | 12: 1.61 - 1.56 2787 146 0.88 18.43 1.23 0.25 29.35| | 13: 1.56 - 1.52 2745 130 0.87 20.45 1.23 0.25 29.35| | 14: 1.52 - 1.48 2803 134 0.86 20.71 1.22 0.25 26.43| | 15: 1.48 - 1.45 2738 128 0.87 20.22 1.23 0.25 21.06| | 16: 1.45 - 1.42 2756 161 0.85 22.01 1.23 0.25 21.06| | 17: 1.42 - 1.39 2785 139 0.87 20.89 1.21 0.25 18.01| | 18: 1.39 - 1.36 2741 179 0.86 21.57 1.23 0.25 16.24| | 19: 1.36 - 1.34 2807 134 0.85 22.37 1.21 0.25 16.24| | 20: 1.34 - 1.32 2696 147 0.86 21.48 1.21 0.25 13.65| | 21: 1.32 - 1.30 2785 112 0.85 22.36 1.21 0.25 13.47| | 22: 1.29 - 1.27 2704 152 0.85 22.72 1.21 0.25 13.17| | 23: 1.27 - 1.26 2802 156 0.85 22.63 1.22 0.24 11.66| | 24: 1.26 - 1.24 2744 132 0.85 23.03 1.21 0.24 11.66| | 25: 1.24 - 1.22 2734 148 0.84 24.00 1.20 0.24 10.99| | 26: 1.22 - 1.21 2727 135 0.84 24.25 1.21 0.24 10.23| | 27: 1.21 - 1.19 2814 148 0.83 24.81 1.20 0.24 10.23| | 28: 1.19 - 1.18 2671 147 0.83 25.16 1.19 0.23 9.22| | 29: 1.18 - 1.16 2800 134 0.83 25.04 1.17 0.23 8.83| | 30: 1.16 - 1.15 2740 148 0.81 26.76 1.15 0.23 8.83| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.83 max = 1474.93 mean = 213.79| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.66| |phase err.(test): min = 0.00 max = 89.07 mean = 22.59| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.240 1557 Z= 5.502 Angle : 5.255 18.971 2118 Z= 3.703 Chirality : 0.369 1.155 243 Planarity : 0.033 0.120 284 Dihedral : 14.232 87.135 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 29.73 % 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: -2.63 (0.47), residues: 224 helix: -2.43 (0.40), residues: 108 sheet: -0.87 (0.81), residues: 38 loop : -0.73 (0.56), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.107 0.020 ARG A 28 TYR 0.121 0.038 TYR A 139 PHE 0.103 0.040 PHE A 162 HIS 0.071 0.039 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= 0.2606 r_free= 0.1933 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791791 | | target function (ml) not normalized (work): 232572.916545 | | target function (ml) not normalized (free): 11841.897127 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2564 0.2606 0.1933 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2564 0.2606 0.1933 n_refl.: 87602 remove outliers: r(all,work,free)=0.1974 0.1978 0.1933 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.1998 0.2003 0.1944 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1637 0.1631 0.1756 n_refl.: 87594 remove outliers: r(all,work,free)=0.1636 0.1630 0.1756 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 98.94 88 5 0.3804 386.249 357.177 0.664 1.002 0.401 11.894-9.307 98.04 96 4 0.1735 616.027 589.963 0.923 1.003 0.380 9.237-7.194 100.00 213 7 0.2168 501.798 491.721 0.955 1.003 0.370 7.162-5.571 100.00 427 22 0.2244 376.572 363.709 0.931 1.003 0.310 5.546-4.326 100.00 867 58 0.1281 516.940 512.015 0.963 1.003 0.228 4.315-3.360 100.00 1859 96 0.1145 491.613 487.823 1.006 1.003 0.199 3.356-2.611 100.00 3867 181 0.1437 322.965 319.831 0.996 1.002 0.043 2.608-2.026 99.99 8198 413 0.1326 214.096 211.719 1.004 1.001 0.000 2.025-1.573 100.00 17313 902 0.1642 104.553 104.093 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2071 46.363 45.078 1.001 0.997 0.000 1.221-1.150 99.97 13689 708 0.2555 29.212 27.012 0.978 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0463 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1630 r_free=0.1756 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** A 80 GLN A A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1637 r_free=0.1764 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.584145 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1994.625816 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 0.1214 0.1465 0.0251 0.007 0.9 1.0 0.5 0.0 0 12.792 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 14.65 2.51 3.012 19.061 1994.626 0.017 12.40 15.35 2.95 3.135 19.527 1994.626 0.015 Individual atomic B min max mean iso aniso Overall: 8.51 118.39 20.97 2.87 0 1785 Protein: 8.51 118.39 17.85 2.87 0 1519 Water: 11.02 114.70 39.07 N/A 0 258 Other: 22.79 35.83 28.94 N/A 0 8 Chain A: 8.51 118.39 20.97 N/A 0 1785 Histogram: Values Number of atoms 8.51 - 19.50 1206 19.50 - 30.49 235 30.49 - 41.48 161 41.48 - 52.47 101 52.47 - 63.45 53 63.45 - 74.44 18 74.44 - 85.43 4 85.43 - 96.42 4 96.42 - 107.41 0 107.41 - 118.39 3 =========================== Idealize ADP of riding H ========================== r_work=0.1241 r_free=0.1535 r_work=0.1245 r_free=0.1539 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1245 r_free = 0.1539 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 = 0.1245 r_free = 0.1544 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1245 r_free= 0.1544 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015306 | | target function (ls_wunit_k1) not normalized (work): 1274.909148 | | target function (ls_wunit_k1) not normalized (free): 114.072848 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1260 0.1245 0.1544 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1700 0.1699 0.1766 n_refl.: 87592 remove outliers: r(all,work,free)=0.1700 0.1699 0.1766 n_refl.: 87592 overall B=0.13 to atoms: r(all,work,free)=0.1722 0.1721 0.1781 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1257 0.1243 0.1538 n_refl.: 87592 remove outliers: r(all,work,free)=0.1257 0.1242 0.1538 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 95.83 87 5 0.3587 298.609 278.642 0.635 1.003 0.380 11.894-9.307 98.04 96 4 0.1527 480.296 469.134 0.918 1.003 0.380 9.237-7.194 100.00 213 7 0.1819 391.235 386.331 0.950 1.003 0.340 7.162-5.571 100.00 427 22 0.1740 293.600 288.375 0.924 1.003 0.290 5.546-4.326 100.00 867 58 0.0926 403.041 400.084 0.949 1.003 0.204 4.315-3.360 100.00 1859 96 0.0779 383.295 382.327 0.995 1.003 0.190 3.356-2.611 100.00 3867 181 0.1021 251.805 251.091 0.998 1.002 0.100 2.608-2.026 99.99 8198 413 0.0972 166.923 166.345 1.009 1.002 0.000 2.025-1.573 100.00 17313 902 0.1209 81.517 81.702 1.018 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1649 36.148 35.606 1.005 0.999 0.000 1.221-1.150 99.97 13689 708 0.2364 22.776 21.285 0.970 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0506 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1242 r_free=0.1538 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 A A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1244 r_free=0.1538 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1244 r_free=0.1538 | n_water=258 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1253 r_free=0.1537 | n_water=252 | time (s): 28.040 (total time: 30.510) Filter (q & B) r_work=0.1256 r_free=0.1535 | n_water=249 | time (s): 3.760 (total time: 34.270) Compute maps r_work=0.1256 r_free=0.1535 | n_water=249 | time (s): 1.920 (total time: 36.190) Filter (map) r_work=0.1265 r_free=0.1541 | n_water=238 | time (s): 3.900 (total time: 40.090) Find peaks r_work=0.1265 r_free=0.1541 | n_water=238 | time (s): 0.720 (total time: 40.810) Add new water r_work=0.1417 r_free=0.1688 | n_water=450 | time (s): 3.830 (total time: 44.640) Refine new water occ: r_work=0.1329 r_free=0.1553 adp: r_work=0.1250 r_free=0.1512 occ: r_work=0.1264 r_free=0.1499 adp: r_work=0.1229 r_free=0.1491 occ: r_work=0.1233 r_free=0.1475 adp: r_work=0.1224 r_free=0.1479 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1479 r_work=0.1224 r_free=0.1479 | n_water=450 | time (s): 154.380 (total time: 199.020) Filter (q & B) r_work=0.1229 r_free=0.1483 | n_water=429 | time (s): 3.970 (total time: 202.990) Filter (dist only) r_work=0.1229 r_free=0.1483 | n_water=429 | time (s): 39.110 (total time: 242.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.532585 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1508.671264 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 0.1225 0.1503 0.0278 0.007 0.9 1.9 0.5 0.0 0 12.266 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 15.03 2.78 3.777 23.127 1508.671 0.015 12.00 14.80 2.80 4.160 22.958 1508.671 0.015 Individual atomic B min max mean iso aniso Overall: 8.67 114.32 23.14 2.59 191 1765 Protein: 8.67 114.32 17.63 2.59 0 1519 Water: 11.01 72.90 42.54 N/A 191 238 Other: 25.01 36.05 29.88 N/A 0 8 Chain A: 8.67 114.32 20.36 N/A 0 1765 Chain S: 13.54 70.94 48.83 N/A 191 0 Histogram: Values Number of atoms 8.67 - 19.24 1202 19.24 - 29.80 253 29.80 - 40.36 187 40.36 - 50.93 140 50.93 - 61.49 109 61.49 - 72.06 54 72.06 - 82.62 5 82.62 - 93.19 3 93.19 - 103.75 1 103.75 - 114.32 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) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1477 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= 0.1201 r_free= 0.1477 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013899 | | target function (ls_wunit_k1) not normalized (work): 1157.678764 | | target function (ls_wunit_k1) not normalized (free): 103.184461 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1201 0.1477 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1607 0.1603 0.1724 n_refl.: 87591 remove outliers: r(all,work,free)=0.1607 0.1603 0.1724 n_refl.: 87591 overall B=0.04 to atoms: r(all,work,free)=0.1614 0.1609 0.1728 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1198 0.1469 n_refl.: 87591 remove outliers: r(all,work,free)=0.1210 0.1196 0.1469 n_refl.: 87587 ======================== 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 91.67 83 5 0.3223 291.314 272.163 0.580 1.003 0.350 11.894-9.307 98.04 96 4 0.1510 480.296 478.040 0.929 1.003 0.327 9.237-7.194 100.00 213 7 0.1679 391.235 393.234 0.982 1.003 0.265 7.162-5.571 100.00 427 22 0.1516 293.600 290.249 0.938 1.003 0.260 5.546-4.326 100.00 867 58 0.0845 403.041 400.104 0.959 1.003 0.215 4.315-3.360 100.00 1859 96 0.0707 383.295 382.173 1.002 1.002 0.210 3.356-2.611 100.00 3867 181 0.0957 251.805 251.053 1.009 1.002 0.140 2.608-2.026 99.99 8198 413 0.0954 166.923 166.582 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1181 81.517 81.731 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1616 36.148 35.656 1.016 0.998 0.000 1.221-1.150 99.97 13689 708 0.2340 22.776 21.308 0.975 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0652 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1469 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1469 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1469 | n_water=429 | time (s): 1.880 (total time: 1.880) Filter (dist) r_work=0.1196 r_free=0.1470 | n_water=427 | time (s): 40.800 (total time: 42.680) Filter (q & B) r_work=0.1197 r_free=0.1471 | n_water=426 | time (s): 2.980 (total time: 45.660) Compute maps r_work=0.1197 r_free=0.1471 | n_water=426 | time (s): 1.480 (total time: 47.140) Filter (map) r_work=0.1236 r_free=0.1489 | n_water=290 | time (s): 3.870 (total time: 51.010) Find peaks r_work=0.1236 r_free=0.1489 | n_water=290 | time (s): 0.540 (total time: 51.550) Add new water r_work=0.1368 r_free=0.1619 | n_water=490 | time (s): 3.660 (total time: 55.210) Refine new water occ: r_work=0.1264 r_free=0.1529 adp: r_work=0.1266 r_free=0.1530 occ: r_work=0.1242 r_free=0.1509 adp: r_work=0.1241 r_free=0.1508 occ: r_work=0.1226 r_free=0.1492 adp: r_work=0.1220 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1489 r_work=0.1220 r_free=0.1489 | n_water=490 | time (s): 182.020 (total time: 237.230) Filter (q & B) r_work=0.1227 r_free=0.1488 | n_water=449 | time (s): 2.900 (total time: 240.130) Filter (dist only) r_work=0.1227 r_free=0.1488 | n_water=449 | time (s): 33.320 (total time: 273.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.041559 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.076602 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 0.1233 0.1441 0.0209 0.006 0.9 3.2 0.5 0.0 0 1.021 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.33 14.41 2.09 3.609 22.086 41.077 3.725 12.17 14.04 1.87 4.150 21.877 41.077 3.656 Individual atomic B min max mean iso aniso Overall: 9.16 109.36 21.62 2.28 213 1763 Protein: 9.16 109.36 17.17 2.28 0 1519 Water: 11.56 71.76 36.60 N/A 213 236 Other: 20.95 31.88 26.68 N/A 0 8 Chain A: 9.16 109.36 19.87 N/A 0 1763 Chain S: 16.52 68.00 36.13 N/A 213 0 Histogram: Values Number of atoms 9.16 - 19.18 1235 19.18 - 29.20 276 29.20 - 39.22 224 39.22 - 49.24 129 49.24 - 59.26 80 59.26 - 69.28 19 69.28 - 79.30 7 79.30 - 89.32 3 89.32 - 99.34 1 99.34 - 109.36 2 =========================== Idealize ADP of riding H ========================== r_work=0.1217 r_free=0.1404 r_work=0.1219 r_free=0.1405 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1219 r_free = 0.1405 target_work(ml) = 3.656 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1212 r_free = 0.1402 target_work(ml) = 3.654 | | 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.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1212 r_free= 0.1402 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.654093 | | target function (ml) not normalized (work): 304353.031917 | | target function (ml) not normalized (free): 16051.650376 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1212 0.1402 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1535 0.1534 0.1578 n_refl.: 87587 remove outliers: r(all,work,free)=0.1535 0.1534 0.1578 n_refl.: 87587 overall B=-0.01 to atoms: r(all,work,free)=0.1533 0.1533 0.1577 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1201 0.1372 n_refl.: 87587 remove outliers: r(all,work,free)=0.1204 0.1196 0.1372 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 89.58 81 5 0.3899 287.955 258.117 0.453 1.000 0.296 11.894-9.307 94.12 92 4 0.2329 472.474 456.275 0.859 1.002 0.280 9.237-7.194 97.73 208 7 0.2423 383.862 384.573 0.939 1.002 0.180 7.162-5.571 100.00 427 22 0.2118 293.600 283.006 0.906 1.002 0.180 5.546-4.326 100.00 867 58 0.1094 403.041 398.715 0.953 1.002 0.155 4.315-3.360 100.00 1859 96 0.0929 383.295 380.415 0.993 1.002 0.150 3.356-2.611 100.00 3867 181 0.1132 251.805 249.893 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1034 166.923 166.064 1.011 1.002 0.000 2.025-1.573 100.00 17313 902 0.1017 81.517 81.669 1.025 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1303 36.148 35.727 1.018 0.999 0.000 1.221-1.150 99.97 13689 708 0.2137 22.776 21.386 0.976 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0229 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1372 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=0.1196 r_free=0.1372 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1372 | n_water=449 | time (s): 1.720 (total time: 1.720) Filter (dist) r_work=0.1196 r_free=0.1372 | n_water=448 | time (s): 37.190 (total time: 38.910) Filter (q & B) r_work=0.1195 r_free=0.1371 | n_water=447 | time (s): 2.860 (total time: 41.770) Compute maps r_work=0.1195 r_free=0.1371 | n_water=447 | time (s): 1.240 (total time: 43.010) Filter (map) r_work=0.1218 r_free=0.1386 | n_water=317 | time (s): 3.510 (total time: 46.520) Find peaks r_work=0.1218 r_free=0.1386 | n_water=317 | time (s): 0.640 (total time: 47.160) Add new water r_work=0.1284 r_free=0.1463 | n_water=481 | time (s): 2.570 (total time: 49.730) Refine new water occ: r_work=0.1217 r_free=0.1394 adp: r_work=0.1217 r_free=0.1397 occ: r_work=0.1202 r_free=0.1382 adp: r_work=0.1201 r_free=0.1384 occ: r_work=0.1192 r_free=0.1371 adp: r_work=0.1188 r_free=0.1372 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1372 r_work=0.1188 r_free=0.1372 | n_water=481 | time (s): 231.510 (total time: 281.240) Filter (q & B) r_work=0.1195 r_free=0.1373 | n_water=443 | time (s): 3.180 (total time: 284.420) Filter (dist only) r_work=0.1195 r_free=0.1372 | n_water=441 | time (s): 36.800 (total time: 321.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.056836 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.805307 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 0.1193 0.1381 0.0188 0.007 1.0 3.5 0.5 0.0 0 1.028 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.81 1.88 3.397 21.439 48.805 3.640 11.77 13.79 2.02 3.869 21.289 48.805 3.620 Individual atomic B min max mean iso aniso Overall: 9.24 104.87 21.14 2.17 207 1761 Protein: 9.24 104.87 16.83 2.17 0 1519 Water: 11.51 70.00 35.93 N/A 207 234 Other: 20.44 29.03 24.65 N/A 0 8 Chain A: 9.24 104.87 19.45 N/A 0 1761 Chain S: 15.56 68.70 35.56 N/A 207 0 Histogram: Values Number of atoms 9.24 - 18.80 1229 18.80 - 28.37 282 28.37 - 37.93 211 37.93 - 47.49 135 47.49 - 57.06 71 57.06 - 66.62 25 66.62 - 76.18 10 76.18 - 85.75 2 85.75 - 95.31 1 95.31 - 104.87 2 =========================== Idealize ADP of riding H ========================== r_work=0.1177 r_free=0.1379 r_work=0.1178 r_free=0.1380 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1178 r_free = 0.1380 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1175 r_free = 0.1376 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1175 r_free= 0.1376 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.618697 | | target function (ml) not normalized (work): 301365.104757 | | target function (ml) not normalized (free): 15932.970376 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1185 0.1175 0.1376 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1497 0.1495 0.1566 n_refl.: 87576 remove outliers: r(all,work,free)=0.1497 0.1495 0.1566 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1495 0.1493 0.1564 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1184 0.1175 0.1376 n_refl.: 87576 remove outliers: r(all,work,free)=0.1183 0.1173 0.1376 n_refl.: 87573 ======================== 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 0.4043 283.253 257.666 0.429 1.001 0.279 11.894-9.307 92.16 90 4 0.2381 476.518 449.708 0.844 1.002 0.257 9.237-7.194 97.73 208 7 0.2533 383.862 376.267 0.910 1.002 0.176 7.162-5.571 100.00 427 22 0.2213 293.600 281.630 0.900 1.002 0.143 5.546-4.326 100.00 867 58 0.1152 403.041 398.423 0.953 1.002 0.131 4.315-3.360 100.00 1859 96 0.0947 383.295 381.041 0.994 1.002 0.131 3.356-2.611 100.00 3867 181 0.1142 251.805 250.055 1.002 1.001 0.120 2.608-2.026 99.99 8198 413 0.1011 166.923 166.092 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0956 81.517 81.794 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1233 36.148 35.787 1.020 0.998 0.000 1.221-1.150 99.97 13689 708 0.2125 22.776 21.408 0.978 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0298 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1173 r_free=0.1376 After: r_work=0.1174 r_free=0.1376 ================================== NQH flips ================================== r_work=0.1174 r_free=0.1376 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=0.1174 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1174 r_free=0.1376 | n_water=441 | time (s): 1.730 (total time: 1.730) Filter (dist) r_work=0.1174 r_free=0.1376 | n_water=441 | time (s): 35.750 (total time: 37.480) Filter (q & B) r_work=0.1174 r_free=0.1378 | n_water=440 | time (s): 2.790 (total time: 40.270) Compute maps r_work=0.1174 r_free=0.1378 | n_water=440 | time (s): 1.510 (total time: 41.780) Filter (map) r_work=0.1193 r_free=0.1389 | n_water=339 | time (s): 2.610 (total time: 44.390) Find peaks r_work=0.1193 r_free=0.1389 | n_water=339 | time (s): 0.520 (total time: 44.910) Add new water r_work=0.1245 r_free=0.1430 | n_water=495 | time (s): 2.930 (total time: 47.840) Refine new water occ: r_work=0.1186 r_free=0.1362 adp: r_work=0.1186 r_free=0.1364 occ: r_work=0.1174 r_free=0.1354 adp: r_work=0.1172 r_free=0.1356 occ: r_work=0.1164 r_free=0.1350 adp: r_work=0.1161 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1161 r_free=0.1351 r_work=0.1161 r_free=0.1351 | n_water=495 | time (s): 174.770 (total time: 222.610) Filter (q & B) r_work=0.1170 r_free=0.1359 | n_water=453 | time (s): 2.870 (total time: 225.480) Filter (dist only) r_work=0.1170 r_free=0.1357 | n_water=452 | time (s): 38.600 (total time: 264.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.957476 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.220008 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 0.1194 0.1374 0.0180 0.007 1.0 5.4 0.5 0.0 0 0.979 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.74 1.80 3.270 21.102 40.220 3.623 11.98 13.72 1.75 3.319 21.074 40.220 3.619 Individual atomic B min max mean iso aniso Overall: 9.21 103.12 21.15 2.06 219 1760 Protein: 9.21 103.12 16.75 2.06 0 1519 Water: 11.56 69.78 35.85 N/A 219 233 Other: 20.79 28.84 24.75 N/A 0 8 Chain A: 9.21 103.12 19.35 N/A 0 1760 Chain S: 15.28 57.85 35.57 N/A 219 0 Histogram: Values Number of atoms 9.21 - 18.60 1225 18.60 - 27.99 289 27.99 - 37.38 202 37.38 - 46.77 144 46.77 - 56.17 77 56.17 - 65.56 27 65.56 - 74.95 11 74.95 - 84.34 1 84.34 - 93.73 1 93.73 - 103.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1372 r_work=0.1198 r_free=0.1372 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1372 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1370 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87573 (all), 4.91 % free)------------| | | | r_work= 0.1195 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.618396 | | target function (ml) not normalized (work): 301329.133482 | | target function (ml) not normalized (free): 15913.220098 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2915 171 0.1421 0.1449 5.6957 5.6418| | 2: 3.57 - 2.84 1.00 2888 124 0.1118 0.1442 5.1943 5.2499| | 3: 2.83 - 2.48 1.00 2820 163 0.1205 0.1295 4.9945 5.0219| | 4: 2.47 - 2.25 1.00 2825 136 0.1019 0.1125 4.701 4.7473| | 5: 2.25 - 2.09 1.00 2756 127 0.0994 0.1089 4.6445 4.7047| | 6: 2.09 - 1.97 1.00 2846 113 0.0973 0.1242 4.3509 4.492| | 7: 1.97 - 1.87 1.00 2787 165 0.1006 0.1207 4.081 4.1728| | 8: 1.87 - 1.79 1.00 2789 144 0.1023 0.1260 3.9929 4.0904| | 9: 1.79 - 1.72 1.00 2745 138 0.0956 0.1304 3.7153 3.9199| | 10: 1.72 - 1.66 1.00 2831 160 0.1008 0.1199 3.6333 3.7336| | 11: 1.66 - 1.61 1.00 2712 147 0.0959 0.1118 3.5598 3.6084| | 12: 1.61 - 1.56 1.00 2773 144 0.0916 0.1125 3.3401 3.4476| | 13: 1.56 - 1.52 1.00 2745 130 0.0976 0.1043 3.3312 3.4145| | 14: 1.52 - 1.48 1.00 2803 134 0.0983 0.1099 3.2525 3.3342| | 15: 1.48 - 1.45 1.00 2738 128 0.1003 0.1309 3.1577 3.2997| | 16: 1.45 - 1.42 1.00 2756 161 0.1060 0.1223 3.141 3.2384| | 17: 1.42 - 1.39 1.00 2785 139 0.1113 0.1278 3.1067 3.2293| | 18: 1.39 - 1.36 1.00 2741 179 0.1151 0.1370 3.0806 3.2517| | 19: 1.36 - 1.34 1.00 2807 134 0.1209 0.1599 3.0859 3.2789| | 20: 1.34 - 1.32 1.00 2696 147 0.1324 0.1469 3.0834 3.1259| | 21: 1.32 - 1.30 1.00 2785 112 0.1416 0.1635 3.0835 3.1671| | 22: 1.29 - 1.27 1.00 2704 152 0.1471 0.1900 3.0807 3.2703| | 23: 1.27 - 1.26 1.00 2802 156 0.1577 0.1831 3.101 3.1959| | 24: 1.26 - 1.24 1.00 2744 132 0.1628 0.1769 3.0929 3.195| | 25: 1.24 - 1.22 1.00 2733 148 0.1799 0.2307 3.1087 3.2904| | 26: 1.22 - 1.21 1.00 2727 135 0.1870 0.1766 3.1258 3.192| | 27: 1.21 - 1.19 1.00 2814 148 0.2012 0.2085 3.142 3.1417| | 28: 1.19 - 1.18 1.00 2671 147 0.2141 0.2311 3.1395 3.1613| | 29: 1.18 - 1.16 1.00 2800 134 0.2220 0.2397 3.1276 3.2269| | 30: 1.16 - 1.15 1.00 2739 148 0.2375 0.2498 3.1155 3.1698| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2915 171 0.95 9.01 1.00 0.97 6149.67| | 2: 3.57 - 2.84 2888 124 0.92 13.19 1.01 0.97 6149.67| | 3: 2.83 - 2.48 2820 163 0.89 17.33 0.99 0.97 5160.69| | 4: 2.47 - 2.25 2825 136 0.91 14.51 1.00 0.98 2610.43| | 5: 2.25 - 2.09 2756 127 0.89 16.75 1.01 0.98 2610.43| | 6: 2.09 - 1.97 2846 113 0.92 13.66 1.02 0.97 1542.47| | 7: 1.97 - 1.87 2787 165 0.94 10.93 1.02 0.97 631.64| | 8: 1.87 - 1.79 2789 144 0.91 14.45 1.00 0.97 631.64| | 9: 1.79 - 1.72 2745 138 0.93 11.39 0.98 0.97 336.70| | 10: 1.72 - 1.66 2831 160 0.93 12.13 0.98 0.97 277.63| | 11: 1.66 - 1.61 2712 147 0.93 12.80 0.98 0.97 264.82| | 12: 1.61 - 1.56 2773 144 0.95 9.36 0.99 0.97 144.02| | 13: 1.56 - 1.52 2745 130 0.94 10.91 1.02 0.97 144.02| | 14: 1.52 - 1.48 2803 134 0.94 11.06 1.02 0.97 128.57| | 15: 1.48 - 1.45 2738 128 0.95 10.21 1.01 0.98 100.28| | 16: 1.45 - 1.42 2756 161 0.94 11.32 1.02 0.98 100.28| | 17: 1.42 - 1.39 2785 139 0.95 11.27 1.01 0.98 90.91| | 18: 1.39 - 1.36 2741 179 0.94 11.58 1.01 0.98 85.49| | 19: 1.36 - 1.34 2807 134 0.94 12.10 1.00 0.98 85.49| | 20: 1.34 - 1.32 2696 147 0.94 12.35 0.99 0.96 81.01| | 21: 1.32 - 1.30 2785 112 0.94 13.21 0.98 0.96 80.69| | 22: 1.29 - 1.27 2704 152 0.93 13.73 0.98 0.96 80.87| | 23: 1.27 - 1.26 2802 156 0.92 14.75 0.97 0.94 81.78| | 24: 1.26 - 1.24 2744 132 0.93 14.83 0.97 0.94 81.78| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 83.57| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.02 0.93 85.56| | 27: 1.21 - 1.19 2814 148 0.89 18.71 1.02 0.93 85.56| | 28: 1.19 - 1.18 2671 147 0.88 20.28 1.01 0.92 89.50| | 29: 1.18 - 1.16 2800 134 0.88 20.60 0.99 0.92 90.99| | 30: 1.16 - 1.15 2739 148 0.86 22.02 0.98 0.92 90.99| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 80.69 max = 6149.67 mean = 962.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.95| |phase err.(test): min = 0.00 max = 88.63 mean = 14.02| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1195 0.1370 n_refl.: 87573 re-set all scales: r(all,work,free)=0.1505 0.1503 0.1564 n_refl.: 87573 remove outliers: r(all,work,free)=0.1505 0.1503 0.1564 n_refl.: 87573 overall B=-0.01 to atoms: r(all,work,free)=0.1504 0.1502 0.1563 n_refl.: 87573 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1195 0.1373 n_refl.: 87573 remove outliers: r(all,work,free)=0.1202 0.1194 0.1373 n_refl.: 87570 ======================== 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 0.4161 283.253 254.543 0.423 0.999 0.281 11.894-9.307 90.20 88 4 0.2384 466.209 452.623 0.851 1.000 0.192 9.237-7.194 97.27 207 7 0.2534 383.389 375.770 0.903 1.001 0.130 7.162-5.571 100.00 427 22 0.2278 293.600 281.078 0.893 1.001 0.120 5.546-4.326 100.00 867 58 0.1188 403.041 398.208 0.954 1.001 0.120 4.315-3.360 100.00 1859 96 0.0981 383.295 380.706 0.995 1.001 0.117 3.356-2.611 100.00 3867 181 0.1181 251.805 249.811 1.002 1.001 0.100 2.608-2.026 99.99 8198 413 0.1032 166.923 165.919 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0981 81.517 81.755 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1226 36.148 35.787 1.018 1.000 0.000 1.221-1.150 99.97 13689 708 0.2119 22.776 21.368 0.972 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0232 ================= 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 : 0.2606 0.1933 0.083 5.255 8.8 119.3 19.9 258 0.000 1_bss: 0.1630 0.1756 0.083 5.255 9.0 119.5 20.1 258 0.000 1_settarget: 0.1630 0.1756 0.083 5.255 9.0 119.5 20.1 258 0.000 1_nqh: 0.1637 0.1764 0.083 5.255 9.0 119.5 20.1 258 0.010 1_weight: 0.1637 0.1764 0.083 5.255 9.0 119.5 20.1 258 0.010 1_xyzrec: 0.1214 0.1465 0.007 0.947 9.0 119.5 20.1 258 0.134 1_adp: 0.1241 0.1535 0.007 0.947 8.5 118.4 21.0 258 0.134 1_regHadp: 0.1245 0.1539 0.007 0.947 8.5 118.4 21.0 258 0.134 1_occ: 0.1245 0.1544 0.007 0.947 8.5 118.4 21.0 258 0.134 2_bss: 0.1242 0.1538 0.007 0.947 8.6 118.5 21.1 258 0.134 2_settarget: 0.1242 0.1538 0.007 0.947 8.6 118.5 21.1 258 0.134 2_updatecdl: 0.1242 0.1538 0.007 0.957 8.6 118.5 21.1 258 0.134 2_nqh: 0.1244 0.1538 0.007 0.957 8.6 118.5 21.1 258 0.128 2_sol: 0.1229 0.1483 0.007 0.957 8.6 118.5 23.4 429 n/a 2_weight: 0.1229 0.1483 0.007 0.957 8.6 118.5 23.4 429 n/a 2_xyzrec: 0.1225 0.1503 0.007 0.869 8.6 118.5 23.4 429 n/a 2_adp: 0.1200 0.1480 0.007 0.869 8.7 114.3 23.1 429 n/a 2_regHadp: 0.1200 0.1479 0.007 0.869 8.7 114.3 23.1 429 n/a 2_occ: 0.1201 0.1477 0.007 0.869 8.7 114.3 23.1 429 n/a 3_bss: 0.1196 0.1469 0.007 0.869 8.7 114.4 23.2 429 n/a 3_settarget: 0.1196 0.1469 0.007 0.869 8.7 114.4 23.2 429 n/a 3_updatecdl: 0.1196 0.1469 0.007 0.870 8.7 114.4 23.2 429 n/a 3_nqh: 0.1196 0.1469 0.007 0.870 8.7 114.4 23.2 429 n/a 3_sol: 0.1227 0.1488 0.007 0.870 8.7 114.4 22.0 449 n/a 3_weight: 0.1227 0.1488 0.007 0.870 8.7 114.4 22.0 449 n/a 3_xyzrec: 0.1233 0.1441 0.006 0.927 8.7 114.4 22.0 449 n/a 3_adp: 0.1217 0.1404 0.006 0.927 9.2 109.4 21.6 449 n/a 3_regHadp: 0.1219 0.1405 0.006 0.927 9.2 109.4 21.6 449 n/a 3_occ: 0.1212 0.1402 0.006 0.927 9.2 109.4 21.6 449 n/a 4_bss: 0.1196 0.1372 0.006 0.927 9.2 109.4 21.6 449 n/a 4_settarget: 0.1196 0.1372 0.006 0.927 9.2 109.4 21.6 449 n/a 4_updatecdl: 0.1196 0.1372 0.006 0.928 9.2 109.4 21.6 449 n/a 4_nqh: 0.1196 0.1372 0.006 0.928 9.2 109.4 21.6 449 n/a 4_sol: 0.1195 0.1372 0.006 0.928 9.2 109.4 21.4 441 n/a 4_weight: 0.1195 0.1372 0.006 0.928 9.2 109.4 21.4 441 n/a 4_xyzrec: 0.1193 0.1381 0.007 0.962 9.2 109.4 21.4 441 n/a 4_adp: 0.1177 0.1379 0.007 0.962 9.2 104.9 21.1 441 n/a 4_regHadp: 0.1178 0.1380 0.007 0.962 9.2 104.9 21.1 441 n/a 4_occ: 0.1175 0.1376 0.007 0.962 9.2 104.9 21.1 441 n/a 5_bss: 0.1173 0.1376 0.007 0.962 9.2 104.9 21.1 441 n/a 5_settarget: 0.1173 0.1376 0.007 0.962 9.2 104.9 21.1 441 n/a 5_updatecdl: 0.1173 0.1376 0.007 0.963 9.2 104.9 21.1 441 n/a 5_setrh: 0.1174 0.1376 0.007 0.963 9.2 104.9 21.1 441 n/a 5_nqh: 0.1174 0.1376 0.007 0.963 9.2 104.9 21.1 441 n/a 5_sol: 0.1170 0.1357 0.007 0.963 9.2 104.9 21.2 452 n/a 5_weight: 0.1170 0.1357 0.007 0.963 9.2 104.9 21.2 452 n/a 5_xyzrec: 0.1194 0.1374 0.007 1.046 9.2 104.9 21.2 452 n/a 5_adp: 0.1198 0.1372 0.007 1.046 9.2 103.1 21.1 452 n/a 5_regHadp: 0.1198 0.1372 0.007 1.046 9.2 103.1 21.1 452 n/a 5_occ: 0.1195 0.1370 0.007 1.046 9.2 103.1 21.1 452 n/a end: 0.1194 0.1373 0.007 1.046 9.2 103.1 21.1 452 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4023827_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4023827_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9000 Refinement macro-cycles (run) : 3573.1600 Write final files (write_after_run_outputs) : 66.5800 Total : 3644.6400 Total CPU time: 61.36 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:18 PST -0800 (1735452738.83 s) Start R-work = 0.1630, R-free = 0.1756 Final R-work = 0.1194, R-free = 0.1373 =============================================================================== Job complete usr+sys time: 3785.77 seconds wall clock time: 67 minutes 35.10 seconds (4055.10 seconds total)