Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3025539.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_3025539.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3025539.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: 2.06, per 1000 atoms: 0.61 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: 0.96 Conformation dependent library (CDL) restraints added in 223.0 milliseconds Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 578 0.92 - 1.18: 1086 1.18 - 1.43: 640 1.43 - 1.68: 822 1.68 - 1.94: 27 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " ideal model delta sigma weight residual 1.522 1.733 -0.211 1.14e-02 7.69e+03 3.42e+02 bond pdb=" N GLY A 40 " pdb=" CA GLY A 40 " ideal model delta sigma weight residual 1.447 1.643 -0.197 1.12e-02 7.97e+03 3.09e+02 bond pdb=" CA ALYS A 175 " pdb=" C ALYS A 175 " ideal model delta sigma weight residual 1.524 1.744 -0.221 1.27e-02 6.20e+03 3.02e+02 bond pdb=" N GLU A 84 " pdb=" CA GLU A 84 " ideal model delta sigma weight residual 1.456 1.685 -0.229 1.33e-02 5.65e+03 2.96e+02 bond pdb=" CA ILE A 21 " pdb=" C ILE A 21 " ideal model delta sigma weight residual 1.524 1.698 -0.173 1.05e-02 9.07e+03 2.72e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 3192 4.70 - 9.40: 1847 9.40 - 14.09: 621 14.09 - 18.79: 104 18.79 - 23.48: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 139.29 -16.69 1.00e+00 1.00e+00 2.79e+02 angle pdb=" O PHE A 162 " pdb=" C PHE A 162 " pdb=" N GLU A 163 " ideal model delta sigma weight residual 122.07 136.88 -14.81 1.03e+00 9.43e-01 2.07e+02 angle pdb=" O ALA A 179 " pdb=" C ALA A 179 " pdb=" N GLN A 180 " ideal model delta sigma weight residual 122.07 136.31 -14.24 1.03e+00 9.43e-01 1.91e+02 angle pdb=" O AGLU A 96 " pdb=" C AGLU A 96 " pdb=" N AASN A 97 " ideal model delta sigma weight residual 122.07 108.59 13.48 1.03e+00 9.43e-01 1.71e+02 angle pdb=" CD1 TYR A 141 " pdb=" CG TYR A 141 " pdb=" CD2 TYR A 141 " ideal model delta sigma weight residual 118.10 99.46 18.64 1.50e+00 4.44e-01 1.54e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.84: 948 17.84 - 35.67: 115 35.67 - 53.50: 36 53.50 - 71.33: 11 71.33 - 89.16: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CD1 PHE A 164 " pdb=" CE1 PHE A 164 " pdb=" CZ PHE A 164 " pdb=" HZ PHE A 164 " ideal model delta harmonic sigma weight residual 180.00 156.75 23.25 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.201: 107 0.201 - 0.401: 66 0.401 - 0.601: 44 0.601 - 0.800: 20 0.800 - 1.000: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 3.44 -1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CA ASP A 60 " pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CB ASP A 60 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CB VAL A 186 " pdb=" CA VAL A 186 " pdb=" CG1 VAL A 186 " pdb=" CG2 VAL A 186 " both_signs ideal model delta sigma weight residual False -2.63 -3.59 0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.042 2.00e-02 2.50e+03 7.73e-02 1.79e+02 pdb=" CG PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.142 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.111 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.153 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.053 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.083 2.00e-02 2.50e+03 5.37e-02 8.66e+01 pdb=" CG BTYR A 67 " -0.084 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.062 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.085 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.032 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.025 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.052 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.044 2.00e-02 2.50e+03 5.27e-02 8.34e+01 pdb=" CG TYR A 141 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.114 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.055 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.066 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.009 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1099 2.33 - 2.90: 8192 2.90 - 3.47: 10526 3.47 - 4.03: 15223 4.03 - 4.60: 21520 Nonbonded interactions: 56560 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.764 2.100 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.767 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.818 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.824 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.831 2.450 ... (remaining 56555 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_3025539_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= 0.2596 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.786432 | | target function (ml) not normalized (work): 232126.519709 | | target function (ml) not normalized (free): 11816.232051 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3013 0.2107 7.0859 4.9444| | 2: 3.57 - 2.84 1.00 2876 122 0.2418 0.1812 4.3423 4.3381| | 3: 2.84 - 2.48 1.00 2833 165 0.2343 0.1607 4.1201 4.1496| | 4: 2.47 - 2.25 1.00 2825 136 0.2313 0.1496 3.829 3.8371| | 5: 2.25 - 2.09 1.00 2756 127 0.2462 0.1593 3.7924 3.8186| | 6: 2.09 - 1.97 1.00 2846 113 0.2562 0.1849 3.4592 3.5417| | 7: 1.97 - 1.87 1.00 2787 165 0.2544 0.1677 3.1336 3.1317| | 8: 1.87 - 1.79 1.00 2789 144 0.2431 0.1927 3.0441 3.1301| | 9: 1.79 - 1.72 1.00 2745 138 0.2401 0.1750 2.8871 2.9039| | 10: 1.72 - 1.66 1.00 2789 158 0.2421 0.1904 2.7945 2.8593| | 11: 1.66 - 1.61 1.00 2740 147 0.2499 0.1773 2.7423 2.7449| | 12: 1.61 - 1.56 1.00 2787 146 0.2525 0.1877 2.6099 2.6109| | 13: 1.56 - 1.52 1.00 2745 130 0.2484 0.1823 2.5502 2.5719| | 14: 1.52 - 1.48 1.00 2803 134 0.2492 0.1856 2.4893 2.513| | 15: 1.48 - 1.45 1.00 2738 128 0.2597 0.2188 2.417 2.5088| | 16: 1.45 - 1.42 1.00 2756 161 0.2636 0.2155 2.3672 2.4595| | 17: 1.42 - 1.39 1.00 2785 139 0.2669 0.1873 2.335 2.3001| | 18: 1.39 - 1.36 1.00 2741 179 0.2692 0.2388 2.2788 2.4164| | 19: 1.36 - 1.34 1.00 2807 134 0.2675 0.2591 2.2482 2.3783| | 20: 1.34 - 1.32 1.00 2696 147 0.2686 0.2250 2.1838 2.2333| | 21: 1.32 - 1.30 1.00 2785 112 0.2738 0.2290 2.1734 2.2003| | 22: 1.29 - 1.27 1.00 2704 152 0.2763 0.2546 2.1351 2.1945| | 23: 1.27 - 1.26 1.00 2802 156 0.2796 0.2144 2.0932 2.1312| | 24: 1.26 - 1.24 1.00 2744 132 0.2809 0.2528 2.0825 2.1777| | 25: 1.24 - 1.22 1.00 2734 148 0.2844 0.2962 2.0424 2.1822| | 26: 1.22 - 1.21 1.00 2727 135 0.2839 0.2422 2.0139 2.1303| | 27: 1.21 - 1.19 1.00 2814 148 0.2954 0.2400 2.0017 1.9519| | 28: 1.19 - 1.18 1.00 2671 147 0.3026 0.2920 1.9863 2.0427| | 29: 1.18 - 1.16 1.00 2800 134 0.2985 0.2592 1.9623 2.0007| | 30: 1.16 - 1.15 1.00 2740 148 0.3046 0.2874 1.9346 1.959| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.73 0.76 0.23 1469.61| | 2: 3.57 - 2.84 2876 122 0.81 25.96 1.27 0.23 1469.61| | 3: 2.84 - 2.48 2833 165 0.74 31.84 1.25 0.24 1218.48| | 4: 2.47 - 2.25 2825 136 0.81 25.46 1.26 0.25 566.77| | 5: 2.25 - 2.09 2756 127 0.77 29.31 1.28 0.25 566.77| | 6: 2.09 - 1.97 2846 113 0.83 22.77 1.29 0.25 309.35| | 7: 1.97 - 1.87 2787 165 0.90 16.64 1.28 0.26 89.80| | 8: 1.87 - 1.79 2789 144 0.86 20.95 1.25 0.26 89.80| | 9: 1.79 - 1.72 2745 138 0.88 18.41 1.23 0.25 54.19| | 10: 1.72 - 1.66 2789 158 0.87 19.91 1.23 0.25 47.06| | 11: 1.66 - 1.61 2740 147 0.86 20.97 1.24 0.25 45.37| | 12: 1.61 - 1.56 2787 146 0.89 18.03 1.24 0.25 28.23| | 13: 1.56 - 1.52 2745 130 0.87 19.80 1.23 0.25 28.23| | 14: 1.52 - 1.48 2803 134 0.87 20.33 1.23 0.25 25.56| | 15: 1.48 - 1.45 2738 128 0.87 19.98 1.24 0.25 20.68| | 16: 1.45 - 1.42 2756 161 0.86 21.70 1.24 0.25 20.68| | 17: 1.42 - 1.39 2785 139 0.86 20.98 1.23 0.25 17.82| | 18: 1.39 - 1.36 2741 179 0.86 21.68 1.23 0.24 16.17| | 19: 1.36 - 1.34 2807 134 0.85 22.35 1.23 0.24 16.17| | 20: 1.34 - 1.32 2696 147 0.86 21.53 1.23 0.24 13.72| | 21: 1.32 - 1.30 2785 112 0.85 22.54 1.20 0.24 13.55| | 22: 1.29 - 1.27 2704 152 0.84 23.28 1.21 0.24 13.22| | 23: 1.27 - 1.26 2802 156 0.85 22.86 1.22 0.24 11.58| | 24: 1.26 - 1.24 2744 132 0.84 23.35 1.21 0.24 11.58| | 25: 1.24 - 1.22 2734 148 0.84 24.28 1.20 0.24 11.01| | 26: 1.22 - 1.21 2727 135 0.83 24.55 1.19 0.23 10.37| | 27: 1.21 - 1.19 2814 148 0.82 25.41 1.21 0.23 10.37| | 28: 1.19 - 1.18 2671 147 0.82 25.83 1.19 0.23 9.59| | 29: 1.18 - 1.16 2800 134 0.82 25.95 1.17 0.23 9.30| | 30: 1.16 - 1.15 2740 148 0.81 27.38 1.16 0.23 9.30| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.30 max = 1469.61 mean = 213.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.76| |phase err.(test): min = 0.00 max = 89.81 mean = 22.65| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.229 1557 Z= 5.385 Angle : 5.286 18.642 2118 Z= 3.693 Chirality : 0.363 1.000 243 Planarity : 0.034 0.118 284 Dihedral : 13.779 89.165 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 28.65 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.47), residues: 224 helix: -2.53 (0.38), residues: 109 sheet: -1.12 (0.81), residues: 28 loop : -0.37 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.069 0.015 ARG A 28 TYR 0.101 0.033 TYR A 141 PHE 0.107 0.047 PHE A 164 HIS 0.062 0.021 HIS A 138 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= 0.2596 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.786432 | | target function (ml) not normalized (work): 232126.519709 | | target function (ml) not normalized (free): 11816.232051 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2555 0.2597 0.1935 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2555 0.2597 0.1935 n_refl.: 87602 remove outliers: r(all,work,free)=0.1965 0.1968 0.1935 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.1987 0.1992 0.1947 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1625 0.1619 0.1756 n_refl.: 87594 remove outliers: r(all,work,free)=0.1625 0.1618 0.1756 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 0.3804 386.439 357.969 0.667 1.002 0.401 11.894-9.307 99.02 97 4 0.1806 613.839 595.171 0.934 1.003 0.380 9.237-7.194 100.00 213 7 0.2174 502.045 490.960 0.961 1.003 0.350 7.162-5.571 100.00 427 22 0.2170 376.757 364.733 0.929 1.003 0.297 5.546-4.326 100.00 867 58 0.1274 517.194 511.679 0.961 1.003 0.234 4.315-3.360 100.00 1859 96 0.1153 491.855 487.792 1.005 1.003 0.219 3.356-2.611 100.00 3867 181 0.1397 323.124 320.253 0.997 1.002 0.129 2.608-2.026 99.99 8198 413 0.1338 214.201 212.143 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1621 104.605 103.943 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2042 46.386 45.134 1.003 0.997 0.000 1.221-1.150 99.97 13689 708 0.2588 29.226 26.953 0.976 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0420 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1618 r_free=0.1756 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 173 ASN Total number of N/Q/H flips: 1 r_work=0.1619 r_free=0.1756 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.627635 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2002.636163 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 0.1212 0.1459 0.0247 0.008 1.0 1.0 0.5 0.0 0 13.314 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.59 2.47 3.013 19.042 2002.636 0.017 12.39 15.31 2.92 3.198 19.534 2002.636 0.016 Individual atomic B min max mean iso aniso Overall: 8.57 118.48 21.00 2.87 0 1785 Protein: 8.57 118.48 17.89 2.87 0 1519 Water: 11.15 114.48 39.05 N/A 0 258 Other: 22.57 35.89 28.81 N/A 0 8 Chain A: 8.57 118.48 21.00 N/A 0 1785 Histogram: Values Number of atoms 8.57 - 19.56 1206 19.56 - 30.55 230 30.55 - 41.54 166 41.54 - 52.53 102 52.53 - 63.52 52 63.52 - 74.52 17 74.52 - 85.51 5 85.51 - 96.50 4 96.50 - 107.49 0 107.49 - 118.48 3 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1531 r_work=0.1244 r_free=0.1536 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1244 r_free = 0.1536 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 = 0.1243 r_free = 0.1538 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 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= 0.1243 r_free= 0.1538 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015426 | | target function (ls_wunit_k1) not normalized (work): 1284.961425 | | target function (ls_wunit_k1) not normalized (free): 112.232647 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1257 0.1243 0.1538 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1701 0.1700 0.1771 n_refl.: 87593 remove outliers: r(all,work,free)=0.1701 0.1700 0.1771 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1722 0.1721 0.1786 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1256 0.1242 0.1535 n_refl.: 87593 remove outliers: r(all,work,free)=0.1255 0.1241 0.1535 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 0.3610 298.731 277.380 0.636 1.003 0.380 11.894-9.307 98.04 96 4 0.1501 480.492 464.159 0.910 1.003 0.380 9.237-7.194 100.00 213 7 0.1821 391.395 386.271 0.950 1.003 0.340 7.162-5.571 100.00 427 22 0.1740 293.720 288.259 0.921 1.003 0.253 5.546-4.326 100.00 867 58 0.0935 403.205 400.472 0.949 1.003 0.209 4.315-3.360 100.00 1859 96 0.0781 383.451 382.515 0.995 1.003 0.200 3.356-2.611 100.00 3867 181 0.1023 251.907 251.233 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0976 166.992 166.415 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1205 81.550 81.757 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1640 36.163 35.631 1.006 0.999 0.000 1.221-1.150 99.97 13689 708 0.2357 22.785 21.305 0.970 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0487 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1241 r_free=0.1535 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 173 ASN Total number of N/Q/H flips: 2 r_work=0.1243 r_free=0.1536 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1243 r_free=0.1536 | n_water=258 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1252 r_free=0.1534 | n_water=252 | time (s): 26.310 (total time: 28.820) Filter (q & B) r_work=0.1255 r_free=0.1534 | n_water=249 | time (s): 3.930 (total time: 32.750) Compute maps r_work=0.1255 r_free=0.1534 | n_water=249 | time (s): 1.940 (total time: 34.690) Filter (map) r_work=0.1266 r_free=0.1546 | n_water=237 | time (s): 3.910 (total time: 38.600) Find peaks r_work=0.1266 r_free=0.1546 | n_water=237 | time (s): 0.730 (total time: 39.330) Add new water r_work=0.1421 r_free=0.1709 | n_water=458 | time (s): 3.780 (total time: 43.110) Refine new water occ: r_work=0.1329 r_free=0.1558 adp: r_work=0.1254 r_free=0.1517 occ: r_work=0.1268 r_free=0.1503 adp: r_work=0.1231 r_free=0.1491 occ: r_work=0.1234 r_free=0.1480 adp: r_work=0.1223 r_free=0.1480 ADP+occupancy (water only), MIN, final r_work=0.1223 r_free=0.1480 r_work=0.1223 r_free=0.1480 | n_water=458 | time (s): 91.480 (total time: 134.590) Filter (q & B) r_work=0.1230 r_free=0.1487 | n_water=428 | time (s): 3.860 (total time: 138.450) Filter (dist only) r_work=0.1230 r_free=0.1487 | n_water=428 | time (s): 41.090 (total time: 179.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.548822 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1498.314242 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 0.1223 0.1511 0.0288 0.007 0.9 1.9 0.5 0.0 0 13.274 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.23 15.11 2.88 3.788 23.208 1498.314 0.015 12.00 14.88 2.88 4.152 23.032 1498.314 0.015 Individual atomic B min max mean iso aniso Overall: 8.67 114.59 23.24 2.61 191 1764 Protein: 8.67 114.59 17.70 2.61 0 1519 Water: 11.06 71.81 42.76 N/A 191 237 Other: 25.36 36.89 30.17 N/A 0 8 Chain A: 8.67 114.59 20.40 N/A 0 1764 Chain S: 16.14 69.13 49.46 N/A 191 0 Histogram: Values Number of atoms 8.67 - 19.26 1209 19.26 - 29.86 243 29.86 - 40.45 184 40.45 - 51.04 149 51.04 - 61.63 113 61.63 - 72.22 47 72.22 - 82.82 4 82.82 - 93.41 3 93.41 - 104.00 1 104.00 - 114.59 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1488 r_work=0.1200 r_free=0.1488 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1488 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1477 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 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= 0.1202 r_free= 0.1477 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.013867 | | target function (ls_wunit_k1) not normalized (work): 1155.049321 | | target function (ls_wunit_k1) not normalized (free): 100.657993 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1202 0.1477 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1613 0.1610 0.1710 n_refl.: 87591 remove outliers: r(all,work,free)=0.1613 0.1610 0.1710 n_refl.: 87591 overall B=0.02 to atoms: r(all,work,free)=0.1616 0.1613 0.1712 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1200 0.1472 n_refl.: 87591 remove outliers: r(all,work,free)=0.1212 0.1199 0.1472 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 92.71 84 5 0.3426 294.671 269.227 0.579 1.002 0.350 11.894-9.307 98.04 96 4 0.1540 480.492 477.196 0.919 1.003 0.337 9.237-7.194 100.00 213 7 0.1635 391.395 392.275 0.977 1.003 0.290 7.162-5.571 100.00 427 22 0.1479 293.720 289.902 0.941 1.003 0.229 5.546-4.326 100.00 867 58 0.0828 403.205 400.311 0.959 1.003 0.220 4.315-3.360 100.00 1859 96 0.0718 383.451 382.366 1.003 1.002 0.220 3.356-2.611 100.00 3867 181 0.0959 251.907 251.213 1.009 1.002 0.160 2.608-2.026 99.99 8198 413 0.0953 166.992 166.597 1.019 1.002 0.000 2.025-1.573 100.00 17313 902 0.1183 81.550 81.749 1.028 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1623 36.163 35.660 1.019 0.999 0.000 1.221-1.150 99.97 13689 708 0.2346 22.785 21.322 0.980 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0345 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1472 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1199 r_free=0.1474 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1474 | n_water=428 | time (s): 2.160 (total time: 2.160) Filter (dist) r_work=0.1198 r_free=0.1473 | n_water=426 | time (s): 38.130 (total time: 40.290) Filter (q & B) r_work=0.1198 r_free=0.1473 | n_water=426 | time (s): 1.150 (total time: 41.440) Compute maps r_work=0.1198 r_free=0.1473 | n_water=426 | time (s): 1.340 (total time: 42.780) Filter (map) r_work=0.1240 r_free=0.1485 | n_water=293 | time (s): 3.380 (total time: 46.160) Find peaks r_work=0.1240 r_free=0.1485 | n_water=293 | time (s): 0.490 (total time: 46.650) Add new water r_work=0.1373 r_free=0.1609 | n_water=490 | time (s): 2.440 (total time: 49.090) Refine new water occ: r_work=0.1270 r_free=0.1518 adp: r_work=0.1271 r_free=0.1521 occ: r_work=0.1246 r_free=0.1497 adp: r_work=0.1243 r_free=0.1498 occ: r_work=0.1229 r_free=0.1485 adp: r_work=0.1222 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1222 r_free=0.1482 r_work=0.1222 r_free=0.1482 | n_water=490 | time (s): 260.540 (total time: 309.630) Filter (q & B) r_work=0.1227 r_free=0.1484 | n_water=453 | time (s): 3.700 (total time: 313.330) Filter (dist only) r_work=0.1227 r_free=0.1484 | n_water=453 | time (s): 36.880 (total time: 350.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.074903 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.839600 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 0.1232 0.1454 0.0223 0.006 0.9 1.6 0.5 0.0 0 1.037 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.54 2.23 3.629 22.197 46.840 3.730 12.12 14.01 1.89 4.117 22.014 46.840 3.653 Individual atomic B min max mean iso aniso Overall: 9.17 109.66 21.80 2.32 219 1761 Protein: 9.17 109.66 17.27 2.32 0 1519 Water: 11.58 70.78 36.91 N/A 219 234 Other: 20.38 32.32 26.58 N/A 0 8 Chain A: 9.17 109.66 19.92 N/A 0 1761 Chain S: 16.32 65.45 36.91 N/A 219 0 Histogram: Values Number of atoms 9.17 - 19.22 1233 19.22 - 29.26 271 29.26 - 39.31 227 39.31 - 49.36 133 49.36 - 59.41 81 59.41 - 69.46 21 69.46 - 79.51 8 79.51 - 89.56 3 89.56 - 99.61 1 99.61 - 109.66 2 =========================== Idealize ADP of riding H ========================== r_work=0.1212 r_free=0.1401 r_work=0.1213 r_free=0.1401 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1213 r_free = 0.1401 target_work(ml) = 3.653 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1396 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.12 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= 0.1206 r_free= 0.1396 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.651012 | | target function (ml) not normalized (work): 304100.090254 | | target function (ml) not normalized (free): 16058.739143 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1206 0.1396 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1539 0.1540 0.1568 n_refl.: 87588 remove outliers: r(all,work,free)=0.1539 0.1540 0.1568 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1537 0.1537 0.1566 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1197 0.1362 n_refl.: 87588 remove outliers: r(all,work,free)=0.1202 0.1194 0.1362 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3939 286.813 260.686 0.465 1.000 0.301 11.894-9.307 97.06 95 4 0.2394 480.637 464.773 0.857 1.002 0.287 9.237-7.194 97.73 208 7 0.2342 384.019 384.051 0.939 1.002 0.200 7.162-5.571 100.00 427 22 0.2083 293.720 282.373 0.909 1.002 0.175 5.546-4.326 100.00 867 58 0.1104 403.205 398.728 0.952 1.002 0.163 4.315-3.360 100.00 1859 96 0.0935 383.451 380.698 0.993 1.002 0.156 3.356-2.611 100.00 3867 181 0.1138 251.907 250.052 0.999 1.002 0.067 2.608-2.026 99.99 8198 413 0.1029 166.992 166.062 1.011 1.002 0.000 2.025-1.573 100.00 17313 902 0.1013 81.550 81.737 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1296 36.163 35.740 1.020 1.000 0.000 1.221-1.150 99.97 13689 708 0.2135 22.785 21.398 0.977 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0350 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1362 | n_water=453 | time (s): 1.850 (total time: 1.850) Filter (dist) r_work=0.1194 r_free=0.1362 | n_water=453 | time (s): 39.290 (total time: 41.140) Filter (q & B) r_work=0.1193 r_free=0.1363 | n_water=450 | time (s): 2.650 (total time: 43.790) Compute maps r_work=0.1193 r_free=0.1363 | n_water=450 | time (s): 1.350 (total time: 45.140) Filter (map) r_work=0.1218 r_free=0.1386 | n_water=304 | time (s): 2.740 (total time: 47.880) Find peaks r_work=0.1218 r_free=0.1386 | n_water=304 | time (s): 0.480 (total time: 48.360) Add new water r_work=0.1290 r_free=0.1452 | n_water=481 | time (s): 3.290 (total time: 51.650) Refine new water occ: r_work=0.1213 r_free=0.1379 adp: r_work=0.1214 r_free=0.1381 occ: r_work=0.1199 r_free=0.1368 adp: r_work=0.1197 r_free=0.1367 occ: r_work=0.1188 r_free=0.1362 adp: r_work=0.1185 r_free=0.1358 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1358 r_work=0.1185 r_free=0.1358 | n_water=481 | time (s): 188.690 (total time: 240.340) Filter (q & B) r_work=0.1190 r_free=0.1359 | n_water=445 | time (s): 3.440 (total time: 243.780) Filter (dist only) r_work=0.1190 r_free=0.1358 | n_water=443 | time (s): 39.390 (total time: 283.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.363037 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.049513 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 0.1191 0.1368 0.0178 0.006 1.0 4.2 0.5 0.0 0 1.182 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.68 1.78 3.433 21.523 50.050 3.634 11.76 13.66 1.90 3.902 21.364 50.050 3.618 Individual atomic B min max mean iso aniso Overall: 9.29 105.04 21.16 2.17 212 1758 Protein: 9.29 105.04 16.92 2.17 0 1519 Water: 11.51 69.26 35.65 N/A 212 231 Other: 18.17 29.02 23.33 N/A 0 8 Chain A: 9.29 105.04 19.48 N/A 0 1758 Chain S: 15.39 66.10 35.10 N/A 212 0 Histogram: Values Number of atoms 9.29 - 18.86 1235 18.86 - 28.44 283 28.44 - 38.01 202 38.01 - 47.59 133 47.59 - 57.16 79 57.16 - 66.74 25 66.74 - 76.31 8 76.31 - 85.89 2 85.89 - 95.46 1 95.46 - 105.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1176 r_free=0.1366 r_work=0.1177 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1177 r_free = 0.1366 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1172 r_free = 0.1363 target_work(ml) = 3.616 | | 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.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1172 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.616121 | | target function (ml) not normalized (work): 301161.418834 | | target function (ml) not normalized (free): 15918.039652 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1181 0.1172 0.1363 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1502 0.1500 0.1560 n_refl.: 87579 remove outliers: r(all,work,free)=0.1502 0.1500 0.1560 n_refl.: 87579 overall B=-0.02 to atoms: r(all,work,free)=0.1499 0.1497 0.1558 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1180 0.1171 0.1368 n_refl.: 87579 remove outliers: r(all,work,free)=0.1179 0.1170 0.1368 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 89.58 81 5 0.4189 286.813 249.298 0.435 1.001 0.308 11.894-9.307 95.10 93 4 0.2395 477.751 461.865 0.846 1.002 0.246 9.237-7.194 97.73 208 7 0.2492 384.019 377.198 0.905 1.002 0.165 7.162-5.571 100.00 427 22 0.2227 293.720 281.882 0.898 1.002 0.137 5.546-4.326 100.00 867 58 0.1158 403.205 398.302 0.954 1.002 0.137 4.315-3.360 100.00 1859 96 0.0953 383.451 380.946 0.994 1.002 0.117 3.356-2.611 100.00 3867 181 0.1133 251.907 249.914 1.002 1.002 0.043 2.608-2.026 99.99 8198 413 0.0997 166.992 166.176 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0948 81.550 81.826 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1234 36.163 35.790 1.023 0.998 0.000 1.221-1.150 99.97 13689 708 0.2122 22.785 21.415 0.982 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0462 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1170 r_free=0.1368 After: r_work=0.1170 r_free=0.1368 ================================== NQH flips ================================== r_work=0.1170 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1170 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1170 r_free=0.1368 | n_water=443 | time (s): 1.990 (total time: 1.990) Filter (dist) r_work=0.1170 r_free=0.1368 | n_water=443 | time (s): 33.280 (total time: 35.270) Filter (q & B) r_work=0.1171 r_free=0.1370 | n_water=440 | time (s): 2.680 (total time: 37.950) Compute maps r_work=0.1171 r_free=0.1370 | n_water=440 | time (s): 1.560 (total time: 39.510) Filter (map) r_work=0.1186 r_free=0.1370 | n_water=334 | time (s): 3.350 (total time: 42.860) Find peaks r_work=0.1186 r_free=0.1370 | n_water=334 | time (s): 0.440 (total time: 43.300) Add new water r_work=0.1229 r_free=0.1406 | n_water=481 | time (s): 2.500 (total time: 45.800) Refine new water occ: r_work=0.1175 r_free=0.1347 adp: r_work=0.1175 r_free=0.1349 occ: r_work=0.1166 r_free=0.1340 adp: r_work=0.1164 r_free=0.1341 occ: r_work=0.1159 r_free=0.1336 adp: r_work=0.1156 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1156 r_free=0.1335 r_work=0.1156 r_free=0.1335 | n_water=481 | time (s): 220.820 (total time: 266.620) Filter (q & B) r_work=0.1163 r_free=0.1339 | n_water=441 | time (s): 3.420 (total time: 270.040) Filter (dist only) r_work=0.1163 r_free=0.1338 | n_water=440 | time (s): 40.060 (total time: 310.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.952534 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 33.846566 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 0.1190 0.1370 0.0180 0.007 1.1 4.5 0.5 0.0 0 0.976 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.70 1.80 3.290 21.048 33.847 3.625 11.94 13.68 1.75 3.314 21.033 33.847 3.622 Individual atomic B min max mean iso aniso Overall: 9.28 104.14 20.99 2.11 209 1758 Protein: 9.28 104.14 16.87 2.11 0 1519 Water: 11.52 69.15 35.14 N/A 209 231 Other: 18.14 27.93 23.21 N/A 0 8 Chain A: 9.28 104.14 19.43 N/A 0 1758 Chain S: 15.24 56.26 34.09 N/A 209 0 Histogram: Values Number of atoms 9.28 - 18.77 1232 18.77 - 28.25 291 28.25 - 37.74 198 37.74 - 47.23 141 47.23 - 56.71 69 56.71 - 66.20 21 66.20 - 75.68 10 75.68 - 85.17 2 85.17 - 94.66 1 94.66 - 104.14 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1368 r_work=0.1194 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1368 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1369 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1190 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621446 | | target function (ml) not normalized (work): 301597.657911 | | target function (ml) not normalized (free): 15931.424259 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1400 0.1448 5.6662 5.6486| | 2: 3.57 - 2.84 1.00 2888 124 0.1114 0.1431 5.2015 5.2833| | 3: 2.83 - 2.48 1.00 2820 163 0.1189 0.1268 5.0088 5.0362| | 4: 2.47 - 2.25 1.00 2825 136 0.1018 0.1154 4.7098 4.7589| | 5: 2.25 - 2.09 1.00 2756 127 0.0989 0.1103 4.6561 4.7243| | 6: 2.09 - 1.97 1.00 2846 113 0.0962 0.1215 4.3534 4.4769| | 7: 1.97 - 1.87 1.00 2787 165 0.0994 0.1180 4.0719 4.1647| | 8: 1.87 - 1.79 1.00 2789 144 0.1012 0.1266 3.9841 4.0865| | 9: 1.79 - 1.72 1.00 2745 138 0.0961 0.1265 3.7183 3.9275| | 10: 1.72 - 1.66 1.00 2831 160 0.1008 0.1295 3.6387 3.7789| | 11: 1.66 - 1.61 1.00 2712 147 0.0971 0.1077 3.569 3.6037| | 12: 1.61 - 1.56 1.00 2773 144 0.0923 0.1139 3.3485 3.4539| | 13: 1.56 - 1.52 1.00 2745 130 0.0984 0.1048 3.3346 3.4151| | 14: 1.52 - 1.48 1.00 2803 134 0.0991 0.1109 3.2568 3.3324| | 15: 1.48 - 1.45 1.00 2738 128 0.1016 0.1314 3.1658 3.2977| | 16: 1.45 - 1.42 1.00 2756 161 0.1072 0.1245 3.1473 3.2374| | 17: 1.42 - 1.39 1.00 2785 139 0.1120 0.1273 3.111 3.2153| | 18: 1.39 - 1.36 1.00 2741 179 0.1153 0.1382 3.0826 3.2547| | 19: 1.36 - 1.34 1.00 2807 134 0.1215 0.1562 3.0913 3.2729| | 20: 1.34 - 1.32 1.00 2696 147 0.1322 0.1452 3.0851 3.127| | 21: 1.32 - 1.30 1.00 2785 112 0.1419 0.1634 3.0869 3.1674| | 22: 1.29 - 1.27 1.00 2704 152 0.1484 0.1916 3.0866 3.2797| | 23: 1.27 - 1.26 1.00 2802 156 0.1594 0.1821 3.1085 3.2022| | 24: 1.26 - 1.24 1.00 2744 132 0.1632 0.1786 3.0964 3.1971| | 25: 1.24 - 1.22 1.00 2733 148 0.1801 0.2319 3.1118 3.2907| | 26: 1.22 - 1.21 1.00 2727 135 0.1866 0.1795 3.1263 3.192| | 27: 1.21 - 1.19 1.00 2814 148 0.2016 0.2098 3.1422 3.1438| | 28: 1.19 - 1.18 1.00 2671 147 0.2155 0.2349 3.142 3.1681| | 29: 1.18 - 1.16 1.00 2800 134 0.2225 0.2376 3.1297 3.2216| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2518 3.1184 3.1757| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.31 1.00 0.97 6476.38| | 2: 3.57 - 2.84 2888 124 0.92 13.62 1.01 0.97 6476.38| | 3: 2.83 - 2.48 2820 163 0.89 17.66 0.99 0.97 5423.13| | 4: 2.47 - 2.25 2825 136 0.91 14.79 1.00 0.98 2707.14| | 5: 2.25 - 2.09 2756 127 0.89 17.06 1.01 0.98 2707.14| | 6: 2.09 - 1.97 2846 113 0.92 13.69 1.02 0.98 1580.87| | 7: 1.97 - 1.87 2787 165 0.94 10.76 1.02 0.97 620.31| | 8: 1.87 - 1.79 2789 144 0.91 14.36 1.00 0.97 620.31| | 9: 1.79 - 1.72 2745 138 0.93 11.42 0.98 0.97 338.78| | 10: 1.72 - 1.66 2831 160 0.93 12.30 0.98 0.97 282.40| | 11: 1.66 - 1.61 2712 147 0.93 12.88 0.98 0.97 269.26| | 12: 1.61 - 1.56 2773 144 0.95 9.42 0.99 0.97 145.42| | 13: 1.56 - 1.52 2745 130 0.94 11.00 1.02 0.97 145.42| | 14: 1.52 - 1.48 2803 134 0.94 11.10 1.02 0.98 129.66| | 15: 1.48 - 1.45 2738 128 0.95 10.19 1.01 0.98 100.82| | 16: 1.45 - 1.42 2756 161 0.94 11.36 1.02 0.98 100.82| | 17: 1.42 - 1.39 2785 139 0.95 11.25 1.01 0.99 91.11| | 18: 1.39 - 1.36 2741 179 0.94 11.54 1.01 0.99 85.49| | 19: 1.36 - 1.34 2807 134 0.94 12.09 1.00 0.99 85.49| | 20: 1.34 - 1.32 2696 147 0.94 12.28 0.99 0.97 81.05| | 21: 1.32 - 1.30 2785 112 0.94 13.19 0.98 0.97 80.74| | 22: 1.29 - 1.27 2704 152 0.93 13.75 0.98 0.96 80.95| | 23: 1.27 - 1.26 2802 156 0.92 14.80 0.98 0.95 82.04| | 24: 1.26 - 1.24 2744 132 0.92 14.91 0.97 0.95 82.04| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.94 83.94| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.02 0.93 86.05| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.02 0.93 86.05| | 28: 1.19 - 1.18 2671 147 0.88 20.35 1.01 0.93 90.11| | 29: 1.18 - 1.16 2800 134 0.88 20.68 0.99 0.93 91.64| | 30: 1.16 - 1.15 2739 148 0.86 22.13 0.98 0.93 91.64| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 80.74 max = 6476.38 mean = 1002.00| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 14.02| |phase err.(test): min = 0.00 max = 89.97 mean = 14.14| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1190 0.1369 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1518 0.1517 0.1571 n_refl.: 87577 remove outliers: r(all,work,free)=0.1518 0.1517 0.1571 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1516 0.1514 0.1569 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1191 0.1370 n_refl.: 87577 remove outliers: r(all,work,free)=0.1199 0.1190 0.1370 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 0.4183 286.813 250.807 0.433 1.001 0.298 11.894-9.307 94.12 92 4 0.2399 477.842 453.528 0.845 1.002 0.238 9.237-7.194 97.73 208 7 0.2523 384.019 376.722 0.903 1.002 0.157 7.162-5.571 100.00 427 22 0.2207 293.720 282.392 0.893 1.003 0.127 5.546-4.326 100.00 867 58 0.1167 403.205 398.607 0.953 1.003 0.115 4.315-3.360 100.00 1859 96 0.0977 383.451 381.029 0.995 1.002 0.107 3.356-2.611 100.00 3867 181 0.1170 251.907 250.027 1.002 1.002 0.090 2.608-2.026 99.99 8198 413 0.1029 166.992 166.134 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0976 81.550 81.822 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1232 36.163 35.797 1.023 0.996 0.000 1.221-1.150 99.97 13689 708 0.2124 22.785 21.406 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0395 ================= 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 : 0.2596 0.1934 0.081 5.286 8.8 119.3 19.9 258 0.000 1_bss: 0.1618 0.1756 0.081 5.286 9.0 119.5 20.1 258 0.000 1_settarget: 0.1618 0.1756 0.081 5.286 9.0 119.5 20.1 258 0.000 1_nqh: 0.1619 0.1756 0.081 5.286 9.0 119.5 20.1 258 0.003 1_weight: 0.1619 0.1756 0.081 5.286 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1212 0.1459 0.008 0.971 9.0 119.5 20.1 258 0.122 1_adp: 0.1239 0.1531 0.008 0.971 8.6 118.5 21.0 258 0.122 1_regHadp: 0.1244 0.1536 0.008 0.971 8.6 118.5 21.0 258 0.122 1_occ: 0.1243 0.1538 0.008 0.971 8.6 118.5 21.0 258 0.122 2_bss: 0.1241 0.1535 0.008 0.971 8.7 118.6 21.1 258 0.122 2_settarget: 0.1241 0.1535 0.008 0.971 8.7 118.6 21.1 258 0.122 2_updatecdl: 0.1241 0.1535 0.008 0.978 8.7 118.6 21.1 258 0.122 2_nqh: 0.1243 0.1536 0.008 0.978 8.7 118.6 21.1 258 0.122 2_sol: 0.1230 0.1487 0.008 0.978 8.7 118.6 23.6 428 n/a 2_weight: 0.1230 0.1487 0.008 0.978 8.7 118.6 23.6 428 n/a 2_xyzrec: 0.1223 0.1511 0.007 0.903 8.7 118.6 23.6 428 n/a 2_adp: 0.1200 0.1488 0.007 0.903 8.7 114.6 23.2 428 n/a 2_regHadp: 0.1200 0.1488 0.007 0.903 8.7 114.6 23.2 428 n/a 2_occ: 0.1202 0.1477 0.007 0.903 8.7 114.6 23.2 428 n/a 3_bss: 0.1199 0.1472 0.007 0.903 8.7 114.6 23.3 428 n/a 3_settarget: 0.1199 0.1472 0.007 0.903 8.7 114.6 23.3 428 n/a 3_updatecdl: 0.1199 0.1472 0.007 0.905 8.7 114.6 23.3 428 n/a 3_nqh: 0.1199 0.1474 0.007 0.905 8.7 114.6 23.3 428 n/a 3_sol: 0.1227 0.1484 0.007 0.905 8.7 114.6 22.1 453 n/a 3_weight: 0.1227 0.1484 0.007 0.905 8.7 114.6 22.1 453 n/a 3_xyzrec: 0.1232 0.1454 0.006 0.930 8.7 114.6 22.1 453 n/a 3_adp: 0.1212 0.1401 0.006 0.930 9.2 109.7 21.8 453 n/a 3_regHadp: 0.1213 0.1401 0.006 0.930 9.2 109.7 21.8 453 n/a 3_occ: 0.1206 0.1396 0.006 0.930 9.2 109.7 21.8 453 n/a 4_bss: 0.1194 0.1362 0.006 0.930 9.2 109.7 21.8 453 n/a 4_settarget: 0.1194 0.1362 0.006 0.930 9.2 109.7 21.8 453 n/a 4_updatecdl: 0.1194 0.1362 0.006 0.927 9.2 109.7 21.8 453 n/a 4_nqh: 0.1194 0.1362 0.006 0.927 9.2 109.7 21.8 453 n/a 4_sol: 0.1190 0.1358 0.006 0.927 9.2 109.7 21.4 443 n/a 4_weight: 0.1190 0.1358 0.006 0.927 9.2 109.7 21.4 443 n/a 4_xyzrec: 0.1191 0.1368 0.006 0.979 9.2 109.7 21.4 443 n/a 4_adp: 0.1176 0.1366 0.006 0.979 9.3 105.0 21.2 443 n/a 4_regHadp: 0.1177 0.1366 0.006 0.979 9.3 105.0 21.2 443 n/a 4_occ: 0.1172 0.1363 0.006 0.979 9.3 105.0 21.2 443 n/a 5_bss: 0.1170 0.1368 0.006 0.979 9.3 105.0 21.1 443 n/a 5_settarget: 0.1170 0.1368 0.006 0.979 9.3 105.0 21.1 443 n/a 5_updatecdl: 0.1170 0.1368 0.006 0.980 9.3 105.0 21.1 443 n/a 5_setrh: 0.1170 0.1368 0.006 0.980 9.3 105.0 21.1 443 n/a 5_nqh: 0.1170 0.1368 0.006 0.980 9.3 105.0 21.1 443 n/a 5_sol: 0.1163 0.1338 0.006 0.980 9.3 105.0 21.0 440 n/a 5_weight: 0.1163 0.1338 0.006 0.980 9.3 105.0 21.0 440 n/a 5_xyzrec: 0.1190 0.1370 0.007 1.056 9.3 105.0 21.0 440 n/a 5_adp: 0.1194 0.1368 0.007 1.056 9.3 104.1 21.0 440 n/a 5_regHadp: 0.1194 0.1368 0.007 1.056 9.3 104.1 21.0 440 n/a 5_occ: 0.1190 0.1369 0.007 1.056 9.3 104.1 21.0 440 n/a end: 0.1190 0.1370 0.007 1.056 9.3 104.1 21.0 440 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3025539_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3025539_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.0000 Refinement macro-cycles (run) : 3578.8300 Write final files (write_after_run_outputs) : 61.1900 Total : 3645.0200 Total CPU time: 61.35 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:32 PST -0800 (1735452752.28 s) Start R-work = 0.1618, R-free = 0.1756 Final R-work = 0.1190, R-free = 0.1370 =============================================================================== Job complete usr+sys time: 3779.71 seconds wall clock time: 67 minutes 44.28 seconds (4064.28 seconds total)