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_3675081.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_3675081.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3675081.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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 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: 0.90 Conformation dependent library (CDL) restraints added in 359.8 milliseconds Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.91: 511 0.91 - 1.15: 1100 1.15 - 1.38: 528 1.38 - 1.61: 887 1.61 - 1.85: 127 Bond restraints: 3153 Sorted by residual: bond pdb=" N LEU A 7 " pdb=" CA LEU A 7 " ideal model delta sigma weight residual 1.458 1.241 0.217 1.22e-02 6.72e+03 3.16e+02 bond pdb=" CE1 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.321 1.495 -0.174 1.00e-02 1.00e+04 3.04e+02 bond pdb=" C THR A 140 " pdb=" N TYR A 141 " ideal model delta sigma weight residual 1.330 1.091 0.239 1.38e-02 5.25e+03 3.00e+02 bond pdb=" C SER A 142 " pdb=" O SER A 142 " ideal model delta sigma weight residual 1.235 1.430 -0.195 1.22e-02 6.72e+03 2.57e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.236 1.440 -0.204 1.29e-02 6.01e+03 2.51e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 3249 4.84 - 9.68: 1840 9.68 - 14.51: 603 14.51 - 19.35: 78 19.35 - 24.18: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 91 " pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 120.95 135.23 -14.28 1.04e+00 9.25e-01 1.89e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.91 134.83 -12.92 9.80e-01 1.04e+00 1.74e+02 angle pdb=" O BGLU A 94 " pdb=" C BGLU A 94 " pdb=" N GLN A 95 " ideal model delta sigma weight residual 122.15 136.82 -14.67 1.14e+00 7.69e-01 1.66e+02 angle pdb=" O ILE A 91 " pdb=" C ILE A 91 " pdb=" N LEU A 92 " ideal model delta sigma weight residual 121.87 109.39 12.48 9.70e-01 1.06e+00 1.66e+02 angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.61 136.53 -13.92 1.09e+00 8.42e-01 1.63e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 949 17.80 - 35.59: 109 35.59 - 53.38: 41 53.38 - 71.18: 8 71.18 - 88.97: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 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 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CG PHE A 162 " pdb=" CD1 PHE A 162 " pdb=" CE1 PHE A 162 " pdb=" HE1 PHE A 162 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.189: 94 0.189 - 0.375: 57 0.375 - 0.561: 52 0.561 - 0.746: 31 0.746 - 0.932: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.44 -0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" CB THR A 160 " pdb=" CA THR A 160 " pdb=" OG1 THR A 160 " pdb=" CG2 THR A 160 " both_signs ideal model delta sigma weight residual False 2.55 1.66 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.86 0.86 2.00e-01 2.50e+01 1.85e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.120 2.00e-02 2.50e+03 6.91e-02 1.43e+02 pdb=" CG ATYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.078 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.034 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.063 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.098 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.021 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.041 2.00e-02 2.50e+03 6.81e-02 1.39e+02 pdb=" CG PHE A 162 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.094 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.025 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.106 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.162 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.050 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.017 2.00e-02 2.50e+03 5.68e-02 9.68e+01 pdb=" CG TYR A 139 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.119 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.097 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.059 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.052 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.24: 611 2.24 - 2.83: 7538 2.83 - 3.42: 10729 3.42 - 4.01: 15393 4.01 - 4.60: 22343 Nonbonded interactions: 56614 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.656 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.752 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.768 2.100 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.790 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.816 2.450 ... (remaining 56609 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_3675081_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= 0.2603 r_free= 0.1962 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789155 | | target function (ml) not normalized (work): 232353.370935 | | target function (ml) not normalized (free): 11858.993040 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3001 0.2132 7.0136 4.9469| | 2: 3.57 - 2.84 1.00 2876 122 0.2441 0.1822 4.3543 4.3487| | 3: 2.84 - 2.48 1.00 2833 165 0.2375 0.1674 4.1303 4.1674| | 4: 2.47 - 2.25 1.00 2825 136 0.2344 0.1393 3.8369 3.8323| | 5: 2.25 - 2.09 1.00 2756 127 0.2486 0.1503 3.8016 3.8201| | 6: 2.09 - 1.97 1.00 2846 113 0.2548 0.1842 3.4821 3.5635| | 7: 1.97 - 1.87 1.00 2787 165 0.2555 0.1898 3.1325 3.2439| | 8: 1.87 - 1.79 1.00 2789 144 0.2442 0.1845 3.0532 3.1635| | 9: 1.79 - 1.72 1.00 2745 138 0.2405 0.1858 2.9069 2.9737| | 10: 1.72 - 1.66 1.00 2789 158 0.2402 0.2057 2.8192 2.9288| | 11: 1.66 - 1.61 1.00 2740 147 0.2470 0.2012 2.7496 2.7921| | 12: 1.61 - 1.56 1.00 2787 146 0.2524 0.2118 2.6198 2.6834| | 13: 1.56 - 1.52 1.00 2745 130 0.2580 0.1971 2.5905 2.6117| | 14: 1.52 - 1.48 1.00 2803 134 0.2530 0.1948 2.5051 2.5353| | 15: 1.48 - 1.45 1.00 2738 128 0.2551 0.2492 2.4129 2.6088| | 16: 1.45 - 1.42 1.00 2756 161 0.2623 0.2040 2.3876 2.4096| | 17: 1.42 - 1.39 1.00 2785 139 0.2715 0.2225 2.3217 2.4309| | 18: 1.39 - 1.36 1.00 2741 179 0.2702 0.2231 2.271 2.3416| | 19: 1.36 - 1.34 1.00 2807 134 0.2660 0.2048 2.2476 2.1961| | 20: 1.34 - 1.32 1.00 2696 147 0.2654 0.2132 2.1877 2.1832| | 21: 1.32 - 1.30 1.00 2785 112 0.2688 0.2105 2.1392 2.1966| | 22: 1.29 - 1.27 1.00 2704 152 0.2748 0.2524 2.1227 2.1667| | 23: 1.27 - 1.26 1.00 2802 156 0.2733 0.2388 2.1014 2.1327| | 24: 1.26 - 1.24 1.00 2744 132 0.2800 0.2522 2.08 2.1014| | 25: 1.24 - 1.22 1.00 2734 148 0.2814 0.2438 2.0401 2.0665| | 26: 1.22 - 1.21 1.00 2727 135 0.2897 0.2430 2.0291 2.1542| | 27: 1.21 - 1.19 1.00 2814 148 0.2964 0.2783 2.0041 2.0349| | 28: 1.19 - 1.18 1.00 2671 147 0.3020 0.2760 1.988 2.0137| | 29: 1.18 - 1.16 1.00 2800 134 0.2955 0.2652 1.9631 2.0031| | 30: 1.16 - 1.15 1.00 2740 148 0.3043 0.2988 1.9288 2.0182| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.94 0.76 0.23 1487.96| | 2: 3.57 - 2.84 2876 122 0.80 26.25 1.27 0.23 1487.96| | 3: 2.84 - 2.48 2833 165 0.74 32.26 1.24 0.23 1234.68| | 4: 2.47 - 2.25 2825 136 0.81 25.80 1.26 0.25 577.37| | 5: 2.25 - 2.09 2756 127 0.77 29.58 1.28 0.25 577.37| | 6: 2.09 - 1.97 2846 113 0.83 23.03 1.29 0.25 317.68| | 7: 1.97 - 1.87 2787 165 0.89 17.27 1.29 0.25 96.20| | 8: 1.87 - 1.79 2789 144 0.85 21.85 1.25 0.25 96.20| | 9: 1.79 - 1.72 2745 138 0.88 19.13 1.23 0.25 58.82| | 10: 1.72 - 1.66 2789 158 0.86 20.83 1.22 0.25 51.34| | 11: 1.66 - 1.61 2740 147 0.85 22.09 1.24 0.25 49.55| | 12: 1.61 - 1.56 2787 146 0.88 19.01 1.24 0.25 31.40| | 13: 1.56 - 1.52 2745 130 0.86 21.08 1.24 0.25 31.40| | 14: 1.52 - 1.48 2803 134 0.86 21.45 1.23 0.25 27.92| | 15: 1.48 - 1.45 2738 128 0.87 20.45 1.22 0.25 21.55| | 16: 1.45 - 1.42 2756 161 0.85 21.95 1.23 0.25 21.55| | 17: 1.42 - 1.39 2785 139 0.86 21.14 1.24 0.25 17.85| | 18: 1.39 - 1.36 2741 179 0.86 21.22 1.24 0.25 15.71| | 19: 1.36 - 1.34 2807 134 0.85 22.10 1.22 0.25 15.71| | 20: 1.34 - 1.32 2696 147 0.87 20.53 1.21 0.25 12.62| | 21: 1.32 - 1.30 2785 112 0.86 21.68 1.21 0.24 12.40| | 22: 1.29 - 1.27 2704 152 0.86 22.05 1.22 0.24 12.12| | 23: 1.27 - 1.26 2802 156 0.86 21.88 1.20 0.24 10.68| | 24: 1.26 - 1.24 2744 132 0.85 22.40 1.20 0.24 10.68| | 25: 1.24 - 1.22 2734 148 0.85 23.24 1.20 0.23 10.28| | 26: 1.22 - 1.21 2727 135 0.84 24.11 1.20 0.23 9.84| | 27: 1.21 - 1.19 2814 148 0.83 24.98 1.20 0.23 9.84| | 28: 1.19 - 1.18 2671 147 0.82 25.88 1.18 0.23 9.45| | 29: 1.18 - 1.16 2800 134 0.82 26.15 1.16 0.22 9.31| | 30: 1.16 - 1.15 2740 148 0.80 27.82 1.15 0.22 9.31| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.31 max = 1487.96 mean = 217.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.97 mean = 22.87| |phase err.(test): min = 0.00 max = 89.90 mean = 22.51| |-----------------------------------------------------------------------------| ----------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 0.248 1557 Z= 5.357 Angle : 5.301 18.512 2118 Z= 3.705 Chirality : 0.382 0.932 243 Planarity : 0.033 0.090 284 Dihedral : 14.152 88.970 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.08 % Favored : 98.38 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 34.05 % 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: -1.90 (0.51), residues: 224 helix: -2.49 (0.38), residues: 103 sheet: -1.14 (0.76), residues: 28 loop : 0.60 (0.67), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.018 ARG A 28 TYR 0.124 0.036 TYR A 139 PHE 0.096 0.028 PHE A 164 HIS 0.086 0.041 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= 0.2603 r_free= 0.1962 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789155 | | target function (ml) not normalized (work): 232353.370935 | | target function (ml) not normalized (free): 11858.993040 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2561 0.2603 0.1962 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2561 0.2603 0.1962 n_refl.: 87602 remove outliers: r(all,work,free)=0.1975 0.1978 0.1962 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2001 0.2005 0.1975 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1640 0.1633 0.1784 n_refl.: 87594 remove outliers: r(all,work,free)=0.1639 0.1632 0.1784 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 0.3775 386.247 359.668 0.666 1.004 0.401 11.894-9.307 99.02 97 4 0.1863 613.535 591.413 0.925 1.004 0.380 9.237-7.194 100.00 213 7 0.2131 501.796 490.799 0.958 1.004 0.354 7.162-5.571 100.00 427 22 0.2189 376.570 364.877 0.933 1.004 0.330 5.546-4.326 100.00 867 58 0.1270 516.938 511.290 0.960 1.004 0.226 4.315-3.360 100.00 1859 96 0.1136 491.611 487.852 1.001 1.003 0.203 3.356-2.611 100.00 3867 181 0.1455 322.963 319.506 0.996 1.002 0.109 2.608-2.026 99.99 8198 413 0.1352 214.095 211.842 1.010 1.000 0.000 2.025-1.573 100.00 17313 902 0.1626 104.553 103.929 1.013 0.998 0.000 1.573-1.221 100.00 36679 1900 0.2057 46.363 45.022 1.006 0.993 0.000 1.221-1.150 99.97 13689 708 0.2606 29.212 26.876 0.978 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0489 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1632 r_free=0.1784 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 180 GLN Total number of N/Q/H flips: 1 r_work=0.1639 r_free=0.1786 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.733505 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2037.625581 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 0.1464 0.0250 0.007 0.9 1.3 0.5 0.0 0 11.867 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 14.64 2.50 3.013 19.072 2037.626 0.017 12.35 15.28 2.93 3.052 19.469 2037.626 0.016 Individual atomic B min max mean iso aniso Overall: 8.46 118.25 20.85 2.89 0 1785 Protein: 8.46 118.25 17.76 2.89 0 1519 Water: 11.09 115.11 38.83 N/A 0 258 Other: 22.22 35.04 28.13 N/A 0 8 Chain A: 8.46 118.25 20.85 N/A 0 1785 Histogram: Values Number of atoms 8.46 - 19.44 1210 19.44 - 30.42 235 30.42 - 41.39 162 41.39 - 52.37 96 52.37 - 63.35 53 63.35 - 74.33 18 74.33 - 85.31 4 85.31 - 96.29 4 96.29 - 107.27 0 107.27 - 118.25 3 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1528 r_work=0.1239 r_free=0.1532 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1532 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 = 0.1239 r_free = 0.1536 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 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= 0.1239 r_free= 0.1536 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015438 | | target function (ls_wunit_k1) not normalized (work): 1285.915640 | | target function (ls_wunit_k1) not normalized (free): 112.038338 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1254 0.1239 0.1536 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1696 0.1695 0.1767 n_refl.: 87593 remove outliers: r(all,work,free)=0.1696 0.1695 0.1767 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1717 0.1716 0.1781 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1251 0.1237 0.1530 n_refl.: 87593 remove outliers: r(all,work,free)=0.1250 0.1236 0.1530 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 0.3461 300.843 276.150 0.679 0.924 0.370 11.894-9.307 99.02 97 4 0.1646 478.750 467.103 0.983 0.925 0.365 9.237-7.194 100.00 213 7 0.1837 391.558 386.680 1.030 0.925 0.319 7.162-5.571 100.00 427 22 0.1732 293.843 288.501 1.002 0.926 0.300 5.546-4.326 100.00 867 58 0.0929 403.374 400.640 1.028 0.927 0.214 4.315-3.360 100.00 1859 96 0.0781 383.611 382.540 1.074 0.928 0.200 3.356-2.611 100.00 3867 181 0.1023 252.013 251.294 1.076 0.929 0.120 2.608-2.026 99.99 8198 413 0.0970 167.061 166.561 1.085 0.932 0.000 2.025-1.573 100.00 17313 902 0.1194 81.584 81.790 1.085 0.937 0.000 1.573-1.221 100.00 36679 1900 0.1632 36.178 35.653 1.063 0.945 0.000 1.221-1.150 99.97 13689 708 0.2357 22.794 21.326 1.017 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=0.0483 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1530 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1239 r_free=0.1531 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1239 r_free=0.1531 | n_water=258 | time (s): 2.310 (total time: 2.310) Filter (dist) r_work=0.1249 r_free=0.1526 | n_water=252 | time (s): 26.320 (total time: 28.630) Filter (q & B) r_work=0.1252 r_free=0.1526 | n_water=249 | time (s): 3.660 (total time: 32.290) Compute maps r_work=0.1252 r_free=0.1526 | n_water=249 | time (s): 1.880 (total time: 34.170) Filter (map) r_work=0.1270 r_free=0.1534 | n_water=234 | time (s): 3.860 (total time: 38.030) Find peaks r_work=0.1270 r_free=0.1534 | n_water=234 | time (s): 0.700 (total time: 38.730) Add new water r_work=0.1430 r_free=0.1686 | n_water=456 | time (s): 3.580 (total time: 42.310) Refine new water occ: r_work=0.1333 r_free=0.1559 adp: r_work=0.1251 r_free=0.1503 occ: r_work=0.1266 r_free=0.1503 adp: r_work=0.1227 r_free=0.1486 occ: r_work=0.1231 r_free=0.1480 adp: r_work=0.1221 r_free=0.1479 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1479 r_work=0.1221 r_free=0.1479 | n_water=456 | time (s): 93.910 (total time: 136.220) Filter (q & B) r_work=0.1229 r_free=0.1493 | n_water=429 | time (s): 3.850 (total time: 140.070) Filter (dist only) r_work=0.1229 r_free=0.1493 | n_water=429 | time (s): 39.710 (total time: 179.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.007883 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1619.242734 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 0.1530 0.0302 0.007 0.9 2.6 0.5 0.0 0 12.504 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 15.30 3.02 3.765 23.004 1619.243 0.015 11.99 15.06 3.07 4.069 22.833 1619.243 0.015 Individual atomic B min max mean iso aniso Overall: 8.73 114.24 23.03 2.61 195 1761 Protein: 8.73 114.24 17.59 2.61 0 1519 Water: 10.89 72.95 42.15 N/A 195 234 Other: 25.16 37.86 30.70 N/A 0 8 Chain A: 8.73 114.24 20.25 N/A 0 1761 Chain S: 20.89 67.42 48.20 N/A 195 0 Histogram: Values Number of atoms 8.73 - 19.28 1206 19.28 - 29.83 253 29.83 - 40.38 190 40.38 - 50.93 146 50.93 - 61.48 105 61.48 - 72.03 46 72.03 - 82.59 4 82.59 - 93.14 3 93.14 - 103.69 1 103.69 - 114.24 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1506 r_work=0.1199 r_free=0.1506 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1506 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 = 0.1200 r_free = 0.1502 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= 0.1502 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013884 | | target function (ls_wunit_k1) not normalized (work): 1156.505959 | | target function (ls_wunit_k1) not normalized (free): 105.857214 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1200 0.1502 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1553 0.1545 0.1721 n_refl.: 87591 remove outliers: r(all,work,free)=0.1553 0.1545 0.1721 n_refl.: 87591 overall B=0.04 to atoms: r(all,work,free)=0.1558 0.1551 0.1724 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1197 0.1500 n_refl.: 87591 remove outliers: r(all,work,free)=0.1211 0.1196 0.1500 n_refl.: 87588 ======================== 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 0.3203 291.555 279.696 0.623 0.949 0.338 11.894-9.307 99.02 97 4 0.1557 478.750 477.006 0.961 0.950 0.330 9.237-7.194 100.00 213 7 0.1675 391.558 392.780 1.034 0.950 0.270 7.162-5.571 100.00 427 22 0.1528 293.843 289.369 0.991 0.950 0.247 5.546-4.326 100.00 867 58 0.0833 403.374 400.774 1.007 0.951 0.213 4.315-3.360 100.00 1859 96 0.0710 383.611 382.572 1.055 0.951 0.206 3.356-2.611 100.00 3867 181 0.0959 252.013 251.301 1.061 0.951 0.140 2.608-2.026 99.99 8198 413 0.0970 167.061 166.749 1.070 0.952 0.000 2.025-1.573 100.00 17313 902 0.1177 81.584 81.785 1.078 0.952 0.000 1.573-1.221 100.00 36679 1900 0.1601 36.178 35.690 1.065 0.953 0.000 1.221-1.150 99.97 13689 708 0.2332 22.794 21.344 1.021 0.954 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0612 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1500 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 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1196 r_free=0.1501 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1501 | n_water=429 | time (s): 2.090 (total time: 2.090) Filter (dist) r_work=0.1197 r_free=0.1501 | n_water=426 | time (s): 37.960 (total time: 40.050) Filter (q & B) r_work=0.1197 r_free=0.1501 | n_water=426 | time (s): 0.930 (total time: 40.980) Compute maps r_work=0.1197 r_free=0.1501 | n_water=426 | time (s): 1.550 (total time: 42.530) Filter (map) r_work=0.1236 r_free=0.1493 | n_water=288 | time (s): 3.580 (total time: 46.110) Find peaks r_work=0.1236 r_free=0.1493 | n_water=288 | time (s): 0.590 (total time: 46.700) Add new water r_work=0.1367 r_free=0.1602 | n_water=485 | time (s): 3.580 (total time: 50.280) Refine new water occ: r_work=0.1264 r_free=0.1520 adp: r_work=0.1265 r_free=0.1522 occ: r_work=0.1241 r_free=0.1501 adp: r_work=0.1239 r_free=0.1502 occ: r_work=0.1226 r_free=0.1489 adp: r_work=0.1219 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1219 r_free=0.1487 r_work=0.1219 r_free=0.1487 | n_water=485 | time (s): 191.250 (total time: 241.530) Filter (q & B) r_work=0.1225 r_free=0.1488 | n_water=449 | time (s): 3.530 (total time: 245.060) Filter (dist only) r_work=0.1225 r_free=0.1488 | n_water=449 | time (s): 37.340 (total time: 282.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.082970 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.144499 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 0.1447 0.0220 0.006 0.9 1.6 0.5 0.0 0 1.041 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.47 2.20 3.611 22.073 51.144 3.720 12.16 14.07 1.91 4.101 21.884 51.144 3.649 Individual atomic B min max mean iso aniso Overall: 9.26 109.83 21.66 2.33 218 1758 Protein: 9.26 109.83 17.17 2.34 0 1519 Water: 11.52 71.91 36.72 N/A 218 231 Other: 20.92 33.88 27.56 N/A 0 8 Chain A: 9.26 109.83 19.77 N/A 0 1758 Chain S: 16.05 65.36 36.83 N/A 218 0 Histogram: Values Number of atoms 9.26 - 19.32 1231 19.32 - 29.38 284 29.38 - 39.43 210 39.43 - 49.49 142 49.49 - 59.55 77 59.55 - 69.61 21 69.61 - 79.66 5 79.66 - 89.72 3 89.72 - 99.78 1 99.78 - 109.83 2 =========================== Idealize ADP of riding H ========================== r_work=0.1216 r_free=0.1408 r_work=0.1217 r_free=0.1408 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1217 r_free = 0.1408 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1214 r_free = 0.1408 target_work(ml) = 3.648 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1214 r_free= 0.1408 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.647852 | | target function (ml) not normalized (work): 303836.915969 | | target function (ml) not normalized (free): 16047.347065 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1223 0.1214 0.1408 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1533 0.1531 0.1591 n_refl.: 87588 remove outliers: r(all,work,free)=0.1533 0.1531 0.1591 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1530 0.1529 0.1589 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1202 0.1387 n_refl.: 87588 remove outliers: r(all,work,free)=0.1208 0.1199 0.1387 n_refl.: 87580 ======================== 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 0.3921 283.901 258.462 0.462 1.000 0.314 11.894-9.307 97.06 95 4 0.2533 482.739 461.412 0.840 1.001 0.310 9.237-7.194 98.64 210 7 0.2370 384.103 384.583 0.943 1.002 0.170 7.162-5.571 100.00 427 22 0.2097 293.843 284.271 0.910 1.002 0.160 5.546-4.326 100.00 867 58 0.1103 403.374 398.901 0.950 1.002 0.146 4.315-3.360 100.00 1859 96 0.0938 383.611 381.053 0.991 1.002 0.140 3.356-2.611 100.00 3867 181 0.1168 252.013 249.946 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1049 167.061 166.201 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.1007 81.584 81.757 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1282 36.178 35.762 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2125 22.794 21.414 0.980 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0365 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1387 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=0.1200 r_free=0.1389 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1389 | n_water=449 | time (s): 1.870 (total time: 1.870) Filter (dist) r_work=0.1200 r_free=0.1390 | n_water=448 | time (s): 41.210 (total time: 43.080) Filter (q & B) r_work=0.1200 r_free=0.1390 | n_water=448 | time (s): 0.980 (total time: 44.060) Compute maps r_work=0.1200 r_free=0.1390 | n_water=448 | time (s): 1.510 (total time: 45.570) Filter (map) r_work=0.1225 r_free=0.1394 | n_water=308 | time (s): 2.980 (total time: 48.550) Find peaks r_work=0.1225 r_free=0.1394 | n_water=308 | time (s): 0.460 (total time: 49.010) Add new water r_work=0.1290 r_free=0.1467 | n_water=473 | time (s): 3.280 (total time: 52.290) Refine new water occ: r_work=0.1214 r_free=0.1394 adp: r_work=0.1215 r_free=0.1397 occ: r_work=0.1199 r_free=0.1378 adp: r_work=0.1198 r_free=0.1380 occ: r_work=0.1189 r_free=0.1371 adp: r_work=0.1185 r_free=0.1369 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1369 r_work=0.1185 r_free=0.1369 | n_water=473 | time (s): 147.400 (total time: 199.690) Filter (q & B) r_work=0.1193 r_free=0.1376 | n_water=436 | time (s): 2.900 (total time: 202.590) Filter (dist only) r_work=0.1193 r_free=0.1376 | n_water=435 | time (s): 36.790 (total time: 239.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.104026 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.752098 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 0.1195 0.1387 0.0192 0.006 1.0 1.6 0.5 0.0 0 1.052 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.87 1.92 3.421 21.375 45.752 3.636 11.86 13.81 1.95 3.723 21.273 45.752 3.626 Individual atomic B min max mean iso aniso Overall: 9.28 105.27 21.08 2.16 206 1756 Protein: 9.28 105.27 16.95 2.16 0 1519 Water: 11.64 70.96 35.41 N/A 206 229 Other: 20.81 30.88 26.10 N/A 0 8 Chain A: 9.28 105.27 19.49 N/A 0 1756 Chain S: 15.79 65.63 34.68 N/A 206 0 Histogram: Values Number of atoms 9.28 - 18.88 1230 18.88 - 28.48 280 28.48 - 38.08 212 38.08 - 47.68 137 47.68 - 57.28 63 57.28 - 66.88 27 66.88 - 76.48 8 76.48 - 86.07 2 86.07 - 95.67 1 95.67 - 105.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.1186 r_free=0.1382 r_work=0.1187 r_free=0.1382 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1382 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1184 r_free = 0.1380 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1184 r_free= 0.1380 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.625103 | | target function (ml) not normalized (work): 301913.113182 | | target function (ml) not normalized (free): 15964.950758 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1184 0.1380 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1522 0.1521 0.1587 n_refl.: 87580 remove outliers: r(all,work,free)=0.1522 0.1521 0.1587 n_refl.: 87580 overall B=-0.02 to atoms: r(all,work,free)=0.1519 0.1517 0.1584 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1184 0.1381 n_refl.: 87580 remove outliers: r(all,work,free)=0.1192 0.1183 0.1381 n_refl.: 87577 ======================== 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 87.50 79 5 0.3931 286.068 242.723 0.429 1.000 0.314 11.894-9.307 96.08 94 4 0.2369 484.762 465.580 0.848 1.002 0.250 9.237-7.194 98.18 209 7 0.2526 383.105 376.927 0.908 1.002 0.174 7.162-5.571 100.00 427 22 0.2222 293.843 283.818 0.906 1.002 0.155 5.546-4.326 100.00 867 58 0.1154 403.374 398.705 0.951 1.002 0.128 4.315-3.360 100.00 1859 96 0.0953 383.611 381.239 0.993 1.002 0.124 3.356-2.611 100.00 3867 181 0.1164 252.013 250.053 1.001 1.002 0.100 2.608-2.026 99.99 8198 413 0.1020 167.061 166.250 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0963 81.584 81.879 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1240 36.178 35.813 1.023 0.998 0.000 1.221-1.150 99.97 13689 708 0.2123 22.794 21.429 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=-0.0478 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1183 r_free=0.1381 After: r_work=0.1183 r_free=0.1381 ================================== NQH flips ================================== r_work=0.1183 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1183 r_free=0.1382 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1382 | n_water=435 | time (s): 1.690 (total time: 1.690) Filter (dist) r_work=0.1183 r_free=0.1382 | n_water=435 | time (s): 35.320 (total time: 37.010) Filter (q & B) r_work=0.1183 r_free=0.1382 | n_water=435 | time (s): 0.960 (total time: 37.970) Compute maps r_work=0.1183 r_free=0.1382 | n_water=435 | time (s): 1.280 (total time: 39.250) Filter (map) r_work=0.1209 r_free=0.1390 | n_water=325 | time (s): 2.810 (total time: 42.060) Find peaks r_work=0.1209 r_free=0.1390 | n_water=325 | time (s): 0.450 (total time: 42.510) Add new water r_work=0.1261 r_free=0.1432 | n_water=477 | time (s): 2.560 (total time: 45.070) Refine new water occ: r_work=0.1196 r_free=0.1371 adp: r_work=0.1197 r_free=0.1373 occ: r_work=0.1186 r_free=0.1360 adp: r_work=0.1185 r_free=0.1362 occ: r_work=0.1178 r_free=0.1354 adp: r_work=0.1175 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1175 r_free=0.1353 r_work=0.1175 r_free=0.1353 | n_water=477 | time (s): 100.270 (total time: 145.340) Filter (q & B) r_work=0.1183 r_free=0.1360 | n_water=440 | time (s): 3.350 (total time: 148.690) Filter (dist only) r_work=0.1183 r_free=0.1359 | n_water=439 | time (s): 35.990 (total time: 184.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.956789 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.544251 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 0.1206 0.1380 0.0174 0.006 1.1 2.9 0.5 0.0 0 0.978 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.80 1.74 3.297 21.089 41.544 3.633 12.14 13.83 1.69 3.578 20.991 41.544 3.629 Individual atomic B min max mean iso aniso Overall: 9.29 100.80 20.85 2.00 211 1755 Protein: 9.29 100.80 16.72 2.00 0 1519 Water: 11.45 70.02 35.06 N/A 211 228 Other: 21.21 29.56 25.62 N/A 0 8 Chain A: 9.29 100.80 19.23 N/A 0 1755 Chain S: 14.99 65.84 34.30 N/A 211 0 Histogram: Values Number of atoms 9.29 - 18.44 1221 18.44 - 27.59 280 27.59 - 36.74 208 36.74 - 45.89 150 45.89 - 55.04 65 55.04 - 64.19 26 64.19 - 73.35 12 73.35 - 82.50 1 82.50 - 91.65 1 91.65 - 100.80 2 =========================== Idealize ADP of riding H ========================== r_work=0.1214 r_free=0.1383 r_work=0.1214 r_free=0.1383 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1214 r_free = 0.1383 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1211 r_free = 0.1379 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1211 r_free= 0.1379 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.627678 | | target function (ml) not normalized (work): 302116.652897 | | target function (ml) not normalized (free): 15972.662926 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1444 0.1468 5.6905 5.6887| | 2: 3.57 - 2.84 1.00 2888 124 0.1146 0.1462 5.2305 5.2955| | 3: 2.83 - 2.48 1.00 2820 163 0.1254 0.1256 5.0402 5.0526| | 4: 2.47 - 2.25 1.00 2825 136 0.1048 0.1184 4.7363 4.7897| | 5: 2.25 - 2.09 1.00 2756 127 0.1003 0.1117 4.6751 4.7391| | 6: 2.09 - 1.97 1.00 2846 113 0.0982 0.1113 4.3667 4.48| | 7: 1.97 - 1.87 1.00 2787 165 0.0995 0.1196 4.0758 4.1698| | 8: 1.87 - 1.79 1.00 2789 144 0.1032 0.1263 3.989 4.0821| | 9: 1.79 - 1.72 1.00 2745 138 0.0943 0.1268 3.7092 3.8881| | 10: 1.72 - 1.66 1.00 2831 160 0.1005 0.1263 3.6338 3.7735| | 11: 1.66 - 1.61 1.00 2712 147 0.0956 0.1117 3.5653 3.6172| | 12: 1.61 - 1.56 1.00 2773 144 0.0924 0.1188 3.3519 3.4886| | 13: 1.56 - 1.52 1.00 2745 130 0.0981 0.1066 3.3403 3.4277| | 14: 1.52 - 1.48 1.00 2803 134 0.0988 0.1158 3.2624 3.3632| | 15: 1.48 - 1.45 1.00 2738 128 0.1015 0.1376 3.1719 3.344| | 16: 1.45 - 1.42 1.00 2756 161 0.1074 0.1251 3.1566 3.2482| | 17: 1.42 - 1.39 1.00 2785 139 0.1120 0.1286 3.1201 3.231| | 18: 1.39 - 1.36 1.00 2741 179 0.1161 0.1366 3.0925 3.2649| | 19: 1.36 - 1.34 1.00 2807 134 0.1222 0.1619 3.099 3.2806| | 20: 1.34 - 1.32 1.00 2696 147 0.1322 0.1517 3.0915 3.1593| | 21: 1.32 - 1.30 1.00 2785 112 0.1414 0.1608 3.0895 3.1584| | 22: 1.29 - 1.27 1.00 2704 152 0.1483 0.1923 3.0874 3.2868| | 23: 1.27 - 1.26 1.00 2802 156 0.1568 0.1876 3.1007 3.2086| | 24: 1.26 - 1.24 1.00 2744 132 0.1635 0.1768 3.0969 3.1907| | 25: 1.24 - 1.22 1.00 2733 148 0.1803 0.2297 3.1115 3.2815| | 26: 1.22 - 1.21 1.00 2727 135 0.1860 0.1813 3.1232 3.2069| | 27: 1.21 - 1.19 1.00 2814 148 0.2014 0.2080 3.1416 3.1485| | 28: 1.19 - 1.18 1.00 2671 147 0.2146 0.2306 3.1398 3.1606| | 29: 1.18 - 1.16 1.00 2800 134 0.2221 0.2390 3.1281 3.2276| | 30: 1.16 - 1.15 1.00 2739 148 0.2375 0.2483 3.1162 3.165| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2919 171 0.94 9.73 1.00 0.97 6869.96| | 2: 3.57 - 2.84 2888 124 0.91 14.11 1.01 0.97 6869.96| | 3: 2.83 - 2.48 2820 163 0.88 18.33 0.98 0.97 5742.87| | 4: 2.47 - 2.25 2825 136 0.91 15.22 1.00 0.98 2836.47| | 5: 2.25 - 2.09 2756 127 0.89 17.55 1.01 0.98 2836.47| | 6: 2.09 - 1.97 2846 113 0.91 13.89 1.02 0.97 1639.92| | 7: 1.97 - 1.87 2787 165 0.94 10.74 1.02 0.97 619.42| | 8: 1.87 - 1.79 2789 144 0.91 14.33 1.00 0.97 619.42| | 9: 1.79 - 1.72 2745 138 0.93 11.39 0.98 0.97 337.42| | 10: 1.72 - 1.66 2831 160 0.93 12.25 0.98 0.97 280.95| | 11: 1.66 - 1.61 2712 147 0.93 12.88 0.98 0.97 268.35| | 12: 1.61 - 1.56 2773 144 0.95 9.59 0.99 0.97 149.52| | 13: 1.56 - 1.52 2745 130 0.94 11.23 1.02 0.97 149.52| | 14: 1.52 - 1.48 2803 134 0.94 11.38 1.02 0.97 133.82| | 15: 1.48 - 1.45 2738 128 0.95 10.53 1.01 0.98 105.06| | 16: 1.45 - 1.42 2756 161 0.94 11.75 1.02 0.98 105.06| | 17: 1.42 - 1.39 2785 139 0.94 11.56 1.01 0.98 94.80| | 18: 1.39 - 1.36 2741 179 0.94 11.88 1.01 0.98 88.87| | 19: 1.36 - 1.34 2807 134 0.94 12.49 1.00 0.98 88.87| | 20: 1.34 - 1.32 2696 147 0.94 12.55 0.99 0.96 83.48| | 21: 1.32 - 1.30 2785 112 0.93 13.48 0.98 0.96 83.10| | 22: 1.29 - 1.27 2704 152 0.93 14.01 0.98 0.96 83.15| | 23: 1.27 - 1.26 2802 156 0.92 14.87 0.98 0.95 83.43| | 24: 1.26 - 1.24 2744 132 0.92 15.04 0.97 0.95 83.43| | 25: 1.24 - 1.22 2733 148 0.91 16.38 0.96 0.94 84.87| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.02 0.93 86.47| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.93 86.47| | 28: 1.19 - 1.18 2671 147 0.88 20.28 1.01 0.93 89.72| | 29: 1.18 - 1.16 2800 134 0.88 20.60 0.99 0.92 90.94| | 30: 1.16 - 1.15 2739 148 0.86 21.97 0.98 0.92 90.94| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 83.10 max = 6869.96 mean = 1052.13| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 14.22| |phase err.(test): min = 0.00 max = 89.92 mean = 14.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1211 0.1379 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1528 0.1527 0.1585 n_refl.: 87577 remove outliers: r(all,work,free)=0.1528 0.1527 0.1585 n_refl.: 87577 overall B=-0.02 to atoms: r(all,work,free)=0.1525 0.1524 0.1583 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1219 0.1211 0.1381 n_refl.: 87577 remove outliers: r(all,work,free)=0.1219 0.1211 0.1381 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 87.50 79 5 0.4076 286.068 248.278 0.437 1.001 0.307 11.894-9.307 96.08 94 4 0.2447 484.762 468.351 0.860 1.002 0.248 9.237-7.194 97.73 208 7 0.2620 382.628 374.418 0.898 1.002 0.172 7.162-5.571 100.00 427 22 0.2300 293.843 282.315 0.902 1.002 0.152 5.546-4.326 100.00 867 58 0.1204 403.374 399.065 0.951 1.002 0.119 4.315-3.360 100.00 1859 96 0.1011 383.611 380.639 0.995 1.002 0.113 3.356-2.611 100.00 3867 181 0.1216 252.013 249.851 1.001 1.001 0.048 2.608-2.026 99.99 8198 413 0.1057 167.061 166.041 1.014 1.000 0.000 2.025-1.573 100.00 17313 902 0.0979 81.584 81.825 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1231 36.178 35.809 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2117 22.794 21.434 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0429 ================= 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 : 0.2603 0.1962 0.083 5.301 8.8 119.3 19.9 258 0.000 1_bss: 0.1632 0.1784 0.083 5.301 9.1 119.5 20.1 258 0.000 1_settarget: 0.1632 0.1784 0.083 5.301 9.1 119.5 20.1 258 0.000 1_nqh: 0.1639 0.1786 0.083 5.301 9.1 119.5 20.1 258 0.003 1_weight: 0.1639 0.1786 0.083 5.301 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1214 0.1464 0.007 0.936 9.1 119.5 20.1 258 0.128 1_adp: 0.1235 0.1528 0.007 0.936 8.5 118.3 20.9 258 0.128 1_regHadp: 0.1239 0.1532 0.007 0.936 8.5 118.3 20.9 258 0.128 1_occ: 0.1239 0.1536 0.007 0.936 8.5 118.3 20.9 258 0.128 2_bss: 0.1236 0.1530 0.007 0.936 8.6 118.4 21.0 258 0.128 2_settarget: 0.1236 0.1530 0.007 0.936 8.6 118.4 21.0 258 0.128 2_updatecdl: 0.1236 0.1530 0.007 0.944 8.6 118.4 21.0 258 0.128 2_nqh: 0.1239 0.1531 0.007 0.944 8.6 118.4 21.0 258 0.128 2_sol: 0.1229 0.1493 0.007 0.944 8.6 118.4 23.3 429 n/a 2_weight: 0.1229 0.1493 0.007 0.944 8.6 118.4 23.3 429 n/a 2_xyzrec: 0.1228 0.1530 0.007 0.873 8.6 118.4 23.3 429 n/a 2_adp: 0.1199 0.1506 0.007 0.873 8.7 114.2 23.0 429 n/a 2_regHadp: 0.1199 0.1506 0.007 0.873 8.7 114.2 23.0 429 n/a 2_occ: 0.1200 0.1502 0.007 0.873 8.7 114.2 23.0 429 n/a 3_bss: 0.1196 0.1500 0.007 0.873 8.8 114.3 23.1 429 n/a 3_settarget: 0.1196 0.1500 0.007 0.873 8.8 114.3 23.1 429 n/a 3_updatecdl: 0.1196 0.1500 0.007 0.875 8.8 114.3 23.1 429 n/a 3_nqh: 0.1196 0.1501 0.007 0.875 8.8 114.3 23.1 429 n/a 3_sol: 0.1225 0.1488 0.007 0.875 8.8 114.3 22.0 449 n/a 3_weight: 0.1225 0.1488 0.007 0.875 8.8 114.3 22.0 449 n/a 3_xyzrec: 0.1227 0.1447 0.006 0.924 8.8 114.3 22.0 449 n/a 3_adp: 0.1216 0.1408 0.006 0.924 9.3 109.8 21.7 449 n/a 3_regHadp: 0.1217 0.1408 0.006 0.924 9.3 109.8 21.7 449 n/a 3_occ: 0.1214 0.1408 0.006 0.924 9.3 109.8 21.7 449 n/a 4_bss: 0.1199 0.1387 0.006 0.924 9.2 109.8 21.6 449 n/a 4_settarget: 0.1199 0.1387 0.006 0.924 9.2 109.8 21.6 449 n/a 4_updatecdl: 0.1199 0.1387 0.006 0.921 9.2 109.8 21.6 449 n/a 4_nqh: 0.1200 0.1389 0.006 0.921 9.2 109.8 21.6 449 n/a 4_sol: 0.1193 0.1376 0.006 0.921 9.2 109.8 21.3 435 n/a 4_weight: 0.1193 0.1376 0.006 0.921 9.2 109.8 21.3 435 n/a 4_xyzrec: 0.1195 0.1387 0.006 0.956 9.2 109.8 21.3 435 n/a 4_adp: 0.1186 0.1382 0.006 0.956 9.3 105.3 21.1 435 n/a 4_regHadp: 0.1187 0.1382 0.006 0.956 9.3 105.3 21.1 435 n/a 4_occ: 0.1184 0.1380 0.006 0.956 9.3 105.3 21.1 435 n/a 5_bss: 0.1183 0.1381 0.006 0.956 9.3 105.3 21.1 435 n/a 5_settarget: 0.1183 0.1381 0.006 0.956 9.3 105.3 21.1 435 n/a 5_updatecdl: 0.1183 0.1381 0.006 0.960 9.3 105.3 21.1 435 n/a 5_setrh: 0.1183 0.1381 0.006 0.960 9.3 105.3 21.1 435 n/a 5_nqh: 0.1183 0.1382 0.006 0.960 9.3 105.3 21.1 435 n/a 5_sol: 0.1183 0.1359 0.006 0.960 9.3 105.3 21.0 439 n/a 5_weight: 0.1183 0.1359 0.006 0.960 9.3 105.3 21.0 439 n/a 5_xyzrec: 0.1206 0.1380 0.006 1.075 9.3 105.3 21.0 439 n/a 5_adp: 0.1214 0.1383 0.006 1.075 9.3 100.8 20.8 439 n/a 5_regHadp: 0.1214 0.1383 0.006 1.075 9.3 100.8 20.8 439 n/a 5_occ: 0.1211 0.1379 0.006 1.075 9.3 100.8 20.8 439 n/a end: 0.1211 0.1381 0.006 1.075 9.3 100.8 20.8 439 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3675081_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3675081_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8000 Refinement macro-cycles (run) : 3311.0900 Write final files (write_after_run_outputs) : 70.4100 Total : 3386.3000 Total CPU time: 57.05 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:08:45 PST -0800 (1735452525.06 s) Start R-work = 0.1632, R-free = 0.1784 Final R-work = 0.1211, R-free = 0.1381 =============================================================================== Job complete usr+sys time: 3541.50 seconds wall clock time: 64 minutes 16.64 seconds (3856.64 seconds total)