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_1785239.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 { 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1785239.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1785239.pdb" } 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 1 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: 2.21, per 1000 atoms: 0.65 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: 0.58 Conformation dependent library (CDL) restraints added in 215.3 milliseconds Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.70 - 0.94: 678 0.94 - 1.18: 991 1.18 - 1.42: 612 1.42 - 1.66: 824 1.66 - 1.91: 48 Bond restraints: 3153 Sorted by residual: bond pdb=" C LEU A 58 " pdb=" N GLU A 59 " ideal model delta sigma weight residual 1.335 1.112 0.223 1.25e-02 6.40e+03 3.18e+02 bond pdb=" C ASP A 131 " pdb=" O ASP A 131 " ideal model delta sigma weight residual 1.236 1.048 0.188 1.15e-02 7.56e+03 2.67e+02 bond pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 1.236 1.047 0.189 1.16e-02 7.43e+03 2.66e+02 bond pdb=" C LYS A 148 " pdb=" O LYS A 148 " ideal model delta sigma weight residual 1.235 1.052 0.183 1.13e-02 7.83e+03 2.62e+02 bond pdb=" C BASN A 76 " pdb=" O BASN A 76 " ideal model delta sigma weight residual 1.236 1.422 -0.185 1.15e-02 7.56e+03 2.60e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.01 - 4.47: 3047 4.47 - 8.94: 1843 8.94 - 13.40: 705 13.40 - 17.87: 149 17.87 - 22.34: 33 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 107.03 12.17 9.00e-01 1.23e+00 1.83e+02 angle pdb=" O VAL A 51 " pdb=" C VAL A 51 " pdb=" N ILE A 52 " ideal model delta sigma weight residual 123.10 108.05 15.05 1.17e+00 7.31e-01 1.65e+02 angle pdb=" CA VAL A 181 " pdb=" C VAL A 181 " pdb=" N LYS A 182 " ideal model delta sigma weight residual 117.15 103.15 14.00 1.14e+00 7.69e-01 1.51e+02 angle pdb=" O SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " ideal model delta sigma weight residual 123.26 111.16 12.10 1.05e+00 9.07e-01 1.33e+02 angle pdb=" O ALA A 79 " pdb=" C ALA A 79 " pdb=" N BGLN A 80 " ideal model delta sigma weight residual 122.07 133.82 -11.75 1.03e+00 9.43e-01 1.30e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.42: 940 17.42 - 34.83: 118 34.83 - 52.24: 39 52.24 - 69.65: 11 69.65 - 87.06: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -157.80 -22.20 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta harmonic sigma weight residual 180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ARG A 156 " pdb=" C ARG A 156 " pdb=" N GLY A 157 " pdb=" CA GLY A 157 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.006 - 0.245: 107 0.245 - 0.483: 77 0.483 - 0.722: 46 0.722 - 0.960: 12 0.960 - 1.199: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -3.83 1.20 2.00e-01 2.50e+01 3.59e+01 chirality pdb=" CA BPRO A 66 " pdb=" N BPRO A 66 " pdb=" C BPRO A 66 " pdb=" CB BPRO A 66 " both_signs ideal model delta sigma weight residual False 2.72 3.66 -0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" CA ATYR A 67 " pdb=" N ATYR A 67 " pdb=" C ATYR A 67 " pdb=" CB ATYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.21e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.104 2.00e-02 2.50e+03 6.84e-02 1.40e+02 pdb=" CG PHE A 119 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.075 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.099 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.098 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.022 2.00e-02 2.50e+03 6.74e-02 1.36e+02 pdb=" CG PHE A 164 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.103 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.050 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.052 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.097 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.064 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.071 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.016 2.00e-02 2.50e+03 6.11e-02 1.12e+02 pdb=" CG TYR A 139 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.097 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.098 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.069 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.064 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.098 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.038 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 1110 2.33 - 2.90: 8216 2.90 - 3.47: 10433 3.47 - 4.03: 15222 4.03 - 4.60: 21585 Nonbonded interactions: 56566 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.767 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.794 2.100 nonbonded pdb="HH21 ARG A 145 " pdb=" OE1 GLU A 163 " model vdw 1.802 2.450 nonbonded pdb=" H LEU A 72 " pdb=" O ALA A 103 " model vdw 1.808 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.816 2.100 ... (remaining 56561 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_1785239_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= 0.2609 r_free= 0.1919 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788142 | | target function (ml) not normalized (work): 232268.962612 | | target function (ml) not normalized (free): 11808.401294 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3035 0.2063 7.0951 4.9422| | 2: 3.57 - 2.84 1.00 2876 122 0.2444 0.1708 4.3471 4.323| | 3: 2.84 - 2.48 1.00 2833 165 0.2367 0.1699 4.1209 4.1518| | 4: 2.47 - 2.25 1.00 2825 136 0.2367 0.1382 3.8293 3.8216| | 5: 2.25 - 2.09 1.00 2756 127 0.2470 0.1594 3.7917 3.8128| | 6: 2.09 - 1.97 1.00 2846 113 0.2504 0.1874 3.454 3.6213| | 7: 1.97 - 1.87 1.00 2787 165 0.2523 0.1672 3.1283 3.1563| | 8: 1.87 - 1.79 1.00 2789 144 0.2476 0.1884 3.0475 3.0835| | 9: 1.79 - 1.72 1.00 2745 138 0.2473 0.1936 2.9108 2.9719| | 10: 1.72 - 1.66 1.00 2789 158 0.2409 0.1943 2.8139 2.9151| | 11: 1.66 - 1.61 1.00 2740 147 0.2521 0.1981 2.7485 2.7899| | 12: 1.61 - 1.56 1.00 2787 146 0.2464 0.1925 2.6176 2.655| | 13: 1.56 - 1.52 1.00 2745 130 0.2480 0.1804 2.5652 2.5996| | 14: 1.52 - 1.48 1.00 2803 134 0.2538 0.2004 2.4875 2.6071| | 15: 1.48 - 1.45 1.00 2738 128 0.2603 0.1908 2.4286 2.4103| | 16: 1.45 - 1.42 1.00 2756 161 0.2662 0.2062 2.3855 2.3818| | 17: 1.42 - 1.39 1.00 2785 139 0.2668 0.2013 2.3247 2.3635| | 18: 1.39 - 1.36 1.00 2741 179 0.2735 0.2254 2.267 2.3507| | 19: 1.36 - 1.34 1.00 2807 134 0.2673 0.2130 2.2328 2.2575| | 20: 1.34 - 1.32 1.00 2696 147 0.2670 0.2318 2.1899 2.2191| | 21: 1.32 - 1.30 1.00 2785 112 0.2677 0.2076 2.1446 2.139| | 22: 1.29 - 1.27 1.00 2704 152 0.2722 0.2330 2.1122 2.1499| | 23: 1.27 - 1.26 1.00 2802 156 0.2774 0.2490 2.1016 2.1578| | 24: 1.26 - 1.24 1.00 2744 132 0.2783 0.2732 2.0612 2.1993| | 25: 1.24 - 1.22 1.00 2734 148 0.2854 0.2723 2.0386 2.1507| | 26: 1.22 - 1.21 1.00 2727 135 0.2896 0.2567 2.031 2.1657| | 27: 1.21 - 1.19 1.00 2814 148 0.2960 0.2574 2.0149 2.0071| | 28: 1.19 - 1.18 1.00 2671 147 0.3034 0.2818 2.0042 2.01| | 29: 1.18 - 1.16 1.00 2800 134 0.2963 0.2405 1.9558 1.9565| | 30: 1.16 - 1.15 1.00 2740 148 0.3072 0.2814 1.9369 1.9489| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.65 0.76 0.23 1451.34| | 2: 3.57 - 2.84 2876 122 0.81 25.88 1.27 0.23 1451.34| | 3: 2.84 - 2.48 2833 165 0.74 31.79 1.24 0.23 1203.72| | 4: 2.47 - 2.25 2825 136 0.81 25.51 1.26 0.25 561.08| | 5: 2.25 - 2.09 2756 127 0.77 29.11 1.28 0.25 561.08| | 6: 2.09 - 1.97 2846 113 0.84 22.44 1.29 0.25 307.52| | 7: 1.97 - 1.87 2787 165 0.90 16.35 1.28 0.26 91.27| | 8: 1.87 - 1.79 2789 144 0.86 21.11 1.25 0.26 91.27| | 9: 1.79 - 1.72 2745 138 0.88 18.49 1.24 0.26 55.04| | 10: 1.72 - 1.66 2789 158 0.87 20.14 1.22 0.26 47.78| | 11: 1.66 - 1.61 2740 147 0.86 21.05 1.24 0.25 46.12| | 12: 1.61 - 1.56 2787 146 0.89 18.20 1.22 0.25 29.22| | 13: 1.56 - 1.52 2745 130 0.87 20.26 1.23 0.25 29.22| | 14: 1.52 - 1.48 2803 134 0.86 20.66 1.23 0.25 25.97| | 15: 1.48 - 1.45 2738 128 0.87 19.68 1.23 0.25 20.02| | 16: 1.45 - 1.42 2756 161 0.86 21.36 1.24 0.25 20.02| | 17: 1.42 - 1.39 2785 139 0.87 20.48 1.23 0.25 16.86| | 18: 1.39 - 1.36 2741 179 0.87 20.89 1.24 0.25 15.04| | 19: 1.36 - 1.34 2807 134 0.86 21.55 1.22 0.25 15.04| | 20: 1.34 - 1.32 2696 147 0.87 20.33 1.21 0.25 12.56| | 21: 1.32 - 1.30 2785 112 0.86 21.40 1.21 0.25 12.39| | 22: 1.29 - 1.27 2704 152 0.86 21.84 1.21 0.24 12.17| | 23: 1.27 - 1.26 2802 156 0.85 22.27 1.20 0.24 11.04| | 24: 1.26 - 1.24 2744 132 0.85 23.01 1.21 0.24 11.04| | 25: 1.24 - 1.22 2734 148 0.84 23.55 1.21 0.24 10.55| | 26: 1.22 - 1.21 2727 135 0.84 24.19 1.20 0.23 10.02| | 27: 1.21 - 1.19 2814 148 0.83 24.65 1.20 0.23 10.02| | 28: 1.19 - 1.18 2671 147 0.83 24.93 1.18 0.23 9.17| | 29: 1.18 - 1.16 2800 134 0.83 25.17 1.17 0.23 8.85| | 30: 1.16 - 1.15 2740 148 0.81 26.85 1.15 0.23 8.85| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.85 max = 1451.34 mean = 210.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 22.40| |phase err.(test): min = 0.00 max = 89.72 mean = 22.22| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.262 1557 Z= 5.552 Angle : 5.304 16.410 2118 Z= 3.719 Chirality : 0.393 1.199 243 Planarity : 0.031 0.096 284 Dihedral : 13.616 87.058 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 31.35 % 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: -2.89 (0.48), residues: 224 helix: -2.45 (0.37), residues: 109 sheet: -1.32 (0.79), residues: 40 loop : -0.94 (0.66), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.074 0.019 ARG A 27 TYR 0.081 0.038 TYR A 139 PHE 0.111 0.046 PHE A 119 HIS 0.059 0.027 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= 0.2609 r_free= 0.1919 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788142 | | target function (ml) not normalized (work): 232268.962612 | | target function (ml) not normalized (free): 11808.401294 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2610 0.1920 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2610 0.1920 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1985 0.1920 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2006 0.2012 0.1935 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1639 0.1634 0.1746 n_refl.: 87594 remove outliers: r(all,work,free)=0.1638 0.1632 0.1746 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 97.87 87 5 0.3744 389.858 355.670 0.730 0.918 0.407 11.894-9.307 98.04 96 4 0.1703 616.565 591.273 1.008 0.919 0.380 9.237-7.194 100.00 213 7 0.2119 502.236 492.362 1.046 0.920 0.344 7.162-5.571 100.00 427 22 0.2174 376.900 363.940 1.013 0.920 0.320 5.546-4.326 100.00 867 58 0.1285 517.391 511.189 1.043 0.921 0.214 4.315-3.360 100.00 1859 96 0.1146 492.042 488.813 1.092 0.922 0.189 3.356-2.611 100.00 3867 181 0.1453 323.246 320.048 1.081 0.923 0.067 2.608-2.026 99.99 8198 413 0.1357 214.283 212.303 1.090 0.925 0.000 2.025-1.573 100.00 17313 902 0.1631 104.645 104.152 1.090 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2044 46.404 45.093 1.071 0.933 0.000 1.221-1.150 99.97 13689 708 0.2620 29.238 26.962 1.034 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0491 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1632 r_free=0.1746 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN B A 173 ASN Total number of N/Q/H flips: 3 r_work=0.1643 r_free=0.1758 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.977724 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2009.799467 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 0.1211 0.1462 0.0251 0.008 1.0 1.0 0.5 0.0 0 12.989 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.62 2.51 3.013 19.072 2009.799 0.017 12.38 15.39 3.02 3.114 19.525 2009.799 0.015 Individual atomic B min max mean iso aniso Overall: 8.42 118.35 20.96 2.88 0 1785 Protein: 8.42 118.35 17.84 2.88 0 1519 Water: 11.14 114.51 39.07 N/A 0 258 Other: 22.70 35.41 28.51 N/A 0 8 Chain A: 8.42 118.35 20.96 N/A 0 1785 Histogram: Values Number of atoms 8.42 - 19.42 1203 19.42 - 30.41 232 30.41 - 41.40 167 41.40 - 52.40 102 52.40 - 63.39 52 63.39 - 74.38 18 74.38 - 85.37 4 85.37 - 96.37 4 96.37 - 107.36 0 107.36 - 118.35 3 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1539 r_work=0.1242 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1242 r_free = 0.1544 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1242 r_free = 0.1547 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1242 r_free= 0.1547 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015232 | | target function (ls_wunit_k1) not normalized (work): 1268.746644 | | target function (ls_wunit_k1) not normalized (free): 114.680086 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1257 0.1242 0.1547 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1696 0.1694 0.1770 n_refl.: 87591 remove outliers: r(all,work,free)=0.1696 0.1694 0.1770 n_refl.: 87591 overall B=0.13 to atoms: r(all,work,free)=0.1718 0.1717 0.1785 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1256 0.1241 0.1543 n_refl.: 87591 remove outliers: r(all,work,free)=0.1255 0.1241 0.1543 n_refl.: 87590 ======================== 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 0.3495 300.970 280.127 0.641 1.003 0.380 11.894-9.307 98.04 96 4 0.1526 479.997 468.105 0.916 1.003 0.380 9.237-7.194 100.00 213 7 0.1832 390.991 385.873 0.949 1.003 0.340 7.162-5.571 100.00 427 22 0.1747 293.417 287.904 0.921 1.003 0.290 5.546-4.326 100.00 867 58 0.0924 402.790 399.900 0.948 1.003 0.204 4.315-3.360 100.00 1859 96 0.0777 383.056 382.115 0.994 1.003 0.190 3.356-2.611 100.00 3867 181 0.1021 251.648 250.939 0.998 1.002 0.057 2.608-2.026 99.99 8198 413 0.0971 166.819 166.245 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1206 81.466 81.643 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1648 36.125 35.587 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2363 22.761 21.265 0.970 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0522 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1241 r_free=0.1543 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B A 173 ASN Total number of N/Q/H flips: 3 r_work=0.1243 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1243 r_free=0.1543 | n_water=258 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1252 r_free=0.1541 | n_water=252 | time (s): 25.970 (total time: 28.340) Filter (q & B) r_work=0.1255 r_free=0.1540 | n_water=249 | time (s): 3.520 (total time: 31.860) Compute maps r_work=0.1255 r_free=0.1540 | n_water=249 | time (s): 1.750 (total time: 33.610) Filter (map) r_work=0.1271 r_free=0.1545 | n_water=236 | time (s): 3.480 (total time: 37.090) Find peaks r_work=0.1271 r_free=0.1545 | n_water=236 | time (s): 0.730 (total time: 37.820) Add new water r_work=0.1428 r_free=0.1700 | n_water=457 | time (s): 3.770 (total time: 41.590) Refine new water occ: r_work=0.1333 r_free=0.1561 adp: r_work=0.1253 r_free=0.1517 occ: r_work=0.1266 r_free=0.1508 adp: r_work=0.1231 r_free=0.1494 occ: r_work=0.1233 r_free=0.1483 adp: r_work=0.1222 r_free=0.1480 ADP+occupancy (water only), MIN, final r_work=0.1222 r_free=0.1480 r_work=0.1222 r_free=0.1480 | n_water=457 | time (s): 83.950 (total time: 125.540) Filter (q & B) r_work=0.1229 r_free=0.1485 | n_water=437 | time (s): 3.770 (total time: 129.310) Filter (dist only) r_work=0.1229 r_free=0.1485 | n_water=436 | time (s): 44.990 (total time: 174.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.103992 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1366.792340 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 0.1509 0.0282 0.007 0.9 2.6 0.5 0.0 0 12.552 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 15.09 2.82 3.776 23.197 1366.792 0.015 12.02 14.76 2.75 4.096 23.021 1366.792 0.015 Individual atomic B min max mean iso aniso Overall: 8.73 114.39 23.27 2.57 200 1763 Protein: 8.73 114.39 17.66 2.57 0 1519 Water: 10.86 73.70 42.71 N/A 200 236 Other: 25.15 35.55 29.48 N/A 0 8 Chain A: 8.73 114.39 20.34 N/A 0 1763 Chain S: 15.58 67.91 49.09 N/A 200 0 Histogram: Values Number of atoms 8.73 - 19.29 1208 19.29 - 29.86 247 29.86 - 40.43 190 40.43 - 50.99 138 50.99 - 61.56 121 61.56 - 72.13 48 72.13 - 82.69 5 82.69 - 93.26 3 93.26 - 103.83 1 103.83 - 114.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1476 r_work=0.1201 r_free=0.1476 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1476 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1471 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1200 r_free= 0.1471 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.014014 | | target function (ls_wunit_k1) not normalized (work): 1167.292013 | | target function (ls_wunit_k1) not normalized (free): 102.696129 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1200 0.1471 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1612 0.1608 0.1719 n_refl.: 87590 remove outliers: r(all,work,free)=0.1612 0.1608 0.1719 n_refl.: 87590 overall B=0.03 to atoms: r(all,work,free)=0.1616 0.1612 0.1722 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1197 0.1469 n_refl.: 87590 remove outliers: r(all,work,free)=0.1209 0.1196 0.1469 n_refl.: 87587 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3407 296.956 270.490 0.639 0.938 0.370 11.894-9.307 98.04 96 4 0.1379 479.997 479.480 0.991 0.938 0.370 9.237-7.194 100.00 213 7 0.1698 390.991 391.124 1.051 0.938 0.280 7.162-5.571 100.00 427 22 0.1514 293.417 290.144 1.001 0.939 0.250 5.546-4.326 100.00 867 58 0.0844 402.790 399.647 1.021 0.939 0.203 4.315-3.360 100.00 1859 96 0.0715 383.056 381.783 1.068 0.940 0.183 3.356-2.611 100.00 3867 181 0.0962 251.648 250.872 1.075 0.940 0.062 2.608-2.026 99.99 8198 413 0.0955 166.819 166.351 1.082 0.942 0.000 2.025-1.573 100.00 17313 902 0.1177 81.466 81.664 1.088 0.945 0.000 1.573-1.221 100.00 36679 1900 0.1608 36.125 35.634 1.071 0.949 0.000 1.221-1.150 99.97 13689 708 0.2339 22.761 21.314 1.025 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0462 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1469 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1196 r_free=0.1469 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1469 | n_water=436 | time (s): 2.070 (total time: 2.070) Filter (dist) r_work=0.1195 r_free=0.1470 | n_water=434 | time (s): 40.250 (total time: 42.320) Filter (q & B) r_work=0.1195 r_free=0.1470 | n_water=434 | time (s): 0.850 (total time: 43.170) Compute maps r_work=0.1195 r_free=0.1470 | n_water=434 | time (s): 1.180 (total time: 44.350) Filter (map) r_work=0.1237 r_free=0.1482 | n_water=288 | time (s): 3.220 (total time: 47.570) Find peaks r_work=0.1237 r_free=0.1482 | n_water=288 | time (s): 0.690 (total time: 48.260) Add new water r_work=0.1365 r_free=0.1611 | n_water=476 | time (s): 3.250 (total time: 51.510) Refine new water occ: r_work=0.1263 r_free=0.1519 adp: r_work=0.1264 r_free=0.1522 occ: r_work=0.1240 r_free=0.1492 adp: r_work=0.1238 r_free=0.1494 occ: r_work=0.1223 r_free=0.1473 adp: r_work=0.1217 r_free=0.1472 ADP+occupancy (water only), MIN, final r_work=0.1217 r_free=0.1472 r_work=0.1217 r_free=0.1472 | n_water=476 | time (s): 175.900 (total time: 227.410) Filter (q & B) r_work=0.1221 r_free=0.1474 | n_water=447 | time (s): 2.890 (total time: 230.300) Filter (dist only) r_work=0.1221 r_free=0.1474 | n_water=447 | time (s): 34.450 (total time: 264.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.034712 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 54.256033 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 0.1229 0.1454 0.0225 0.006 0.9 2.2 0.5 0.0 0 1.017 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.54 2.25 3.605 22.091 54.256 3.725 12.17 14.07 1.90 4.250 21.854 54.256 3.649 Individual atomic B min max mean iso aniso Overall: 9.27 109.44 21.55 2.33 213 1761 Protein: 9.27 109.44 17.12 2.33 0 1519 Water: 11.65 72.30 36.53 N/A 213 234 Other: 20.56 31.00 25.67 N/A 0 8 Chain A: 9.27 109.44 19.78 N/A 0 1761 Chain S: 15.72 65.06 36.19 N/A 213 0 Histogram: Values Number of atoms 9.27 - 19.29 1240 19.29 - 29.31 280 29.31 - 39.32 220 39.32 - 49.34 126 49.34 - 59.36 73 59.36 - 69.38 23 69.38 - 79.39 6 79.39 - 89.41 3 89.41 - 99.43 1 99.43 - 109.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1217 r_free=0.1407 r_work=0.1218 r_free=0.1409 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1218 r_free = 0.1409 target_work(ml) = 3.650 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1401 target_work(ml) = 3.646 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1210 r_free= 0.1401 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.645682 | | target function (ml) not normalized (work): 303652.520993 | | target function (ml) not normalized (free): 16047.764617 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1210 0.1401 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1546 0.1545 0.1585 n_refl.: 87587 remove outliers: r(all,work,free)=0.1546 0.1545 0.1585 n_refl.: 87587 overall B=-0.02 to atoms: r(all,work,free)=0.1542 0.1542 0.1583 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1201 0.1365 n_refl.: 87587 remove outliers: r(all,work,free)=0.1206 0.1198 0.1365 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 89.58 81 5 0.3774 293.735 260.766 0.479 1.000 0.319 11.894-9.307 97.06 95 4 0.2232 473.291 464.775 0.868 1.002 0.270 9.237-7.194 98.18 209 7 0.2362 382.550 384.377 0.941 1.002 0.195 7.162-5.571 100.00 427 22 0.2128 293.417 283.487 0.911 1.002 0.168 5.546-4.326 100.00 867 58 0.1115 402.790 397.960 0.952 1.002 0.154 4.315-3.360 100.00 1859 96 0.0935 383.056 380.484 0.993 1.002 0.143 3.356-2.611 100.00 3867 181 0.1173 251.648 249.620 0.999 1.002 0.120 2.608-2.026 99.99 8198 413 0.1057 166.819 165.805 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1004 81.466 81.588 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1276 36.125 35.681 1.023 0.998 0.000 1.221-1.150 99.97 13689 708 0.2124 22.761 21.366 0.983 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0491 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1365 | n_water=447 | time (s): 1.410 (total time: 1.410) Filter (dist) r_work=0.1198 r_free=0.1365 | n_water=446 | time (s): 38.600 (total time: 40.010) Filter (q & B) r_work=0.1198 r_free=0.1365 | n_water=446 | time (s): 1.560 (total time: 41.570) Compute maps r_work=0.1198 r_free=0.1365 | n_water=446 | time (s): 1.380 (total time: 42.950) Filter (map) r_work=0.1221 r_free=0.1376 | n_water=308 | time (s): 3.230 (total time: 46.180) Find peaks r_work=0.1221 r_free=0.1376 | n_water=308 | time (s): 0.600 (total time: 46.780) Add new water r_work=0.1292 r_free=0.1458 | n_water=473 | time (s): 3.090 (total time: 49.870) Refine new water occ: r_work=0.1219 r_free=0.1383 adp: r_work=0.1220 r_free=0.1385 occ: r_work=0.1203 r_free=0.1367 adp: r_work=0.1203 r_free=0.1369 occ: r_work=0.1191 r_free=0.1356 adp: r_work=0.1188 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1356 r_work=0.1188 r_free=0.1356 | n_water=473 | time (s): 209.120 (total time: 258.990) Filter (q & B) r_work=0.1195 r_free=0.1359 | n_water=436 | time (s): 2.810 (total time: 261.800) Filter (dist only) r_work=0.1195 r_free=0.1357 | n_water=435 | time (s): 37.060 (total time: 298.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.381121 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.172881 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 0.1365 0.0171 0.006 1.0 4.5 0.5 0.0 0 1.191 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.65 1.71 3.403 21.335 43.173 3.630 11.86 13.64 1.77 3.616 21.268 43.173 3.620 Individual atomic B min max mean iso aniso Overall: 9.28 105.58 21.16 2.14 203 1759 Protein: 9.28 105.58 16.96 2.15 0 1519 Water: 11.48 71.51 35.77 N/A 203 232 Other: 20.00 28.89 24.66 N/A 0 8 Chain A: 9.28 105.58 19.55 N/A 0 1759 Chain S: 15.71 65.33 35.10 N/A 203 0 Histogram: Values Number of atoms 9.28 - 18.91 1233 18.91 - 28.54 281 28.54 - 38.17 204 38.17 - 47.80 135 47.80 - 57.43 70 57.43 - 67.06 24 67.06 - 76.69 10 76.69 - 86.32 2 86.32 - 95.95 1 95.95 - 105.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.1186 r_free=0.1364 r_work=0.1187 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1364 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1184 r_free = 0.1362 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1184 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.619125 | | target function (ml) not normalized (work): 301415.237581 | | target function (ml) not normalized (free): 15936.489856 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1184 0.1362 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1518 0.1518 0.1555 n_refl.: 87580 remove outliers: r(all,work,free)=0.1518 0.1518 0.1555 n_refl.: 87580 overall B=-0.02 to atoms: r(all,work,free)=0.1514 0.1514 0.1553 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1184 0.1362 n_refl.: 87580 remove outliers: r(all,work,free)=0.1191 0.1182 0.1362 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 88.54 80 5 0.3955 289.105 260.964 0.452 0.999 0.289 11.894-9.307 96.08 94 4 0.2406 477.140 458.022 0.847 1.001 0.239 9.237-7.194 97.73 208 7 0.2500 383.623 377.294 0.910 1.001 0.178 7.162-5.571 100.00 427 22 0.2221 293.417 282.691 0.907 1.001 0.147 5.546-4.326 100.00 867 58 0.1172 402.790 397.892 0.953 1.001 0.130 4.315-3.360 100.00 1859 96 0.0958 383.056 380.318 0.992 1.001 0.120 3.356-2.611 100.00 3867 181 0.1157 251.648 249.662 1.001 1.001 0.100 2.608-2.026 99.99 8198 413 0.1026 166.819 165.901 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0963 81.466 81.776 1.028 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1233 36.125 35.774 1.021 1.002 0.000 1.221-1.150 99.97 13689 708 0.2116 22.761 21.371 0.976 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0559 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1182 r_free=0.1362 After: r_work=0.1183 r_free=0.1362 ================================== NQH flips ================================== r_work=0.1183 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1183 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1362 | n_water=435 | time (s): 2.210 (total time: 2.210) Filter (dist) r_work=0.1183 r_free=0.1362 | n_water=435 | time (s): 34.870 (total time: 37.080) Filter (q & B) r_work=0.1184 r_free=0.1363 | n_water=431 | time (s): 2.690 (total time: 39.770) Compute maps r_work=0.1184 r_free=0.1363 | n_water=431 | time (s): 1.480 (total time: 41.250) Filter (map) r_work=0.1208 r_free=0.1378 | n_water=324 | time (s): 2.500 (total time: 43.750) Find peaks r_work=0.1208 r_free=0.1378 | n_water=324 | time (s): 0.510 (total time: 44.260) Add new water r_work=0.1264 r_free=0.1429 | n_water=497 | time (s): 3.150 (total time: 47.410) Refine new water occ: r_work=0.1193 r_free=0.1362 adp: r_work=0.1194 r_free=0.1365 occ: r_work=0.1180 r_free=0.1353 adp: r_work=0.1178 r_free=0.1354 occ: r_work=0.1169 r_free=0.1351 adp: r_work=0.1166 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1166 r_free=0.1349 r_work=0.1166 r_free=0.1349 | n_water=497 | time (s): 202.390 (total time: 249.800) Filter (q & B) r_work=0.1174 r_free=0.1354 | n_water=456 | time (s): 2.740 (total time: 252.540) Filter (dist only) r_work=0.1174 r_free=0.1353 | n_water=455 | time (s): 39.440 (total time: 291.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.876649 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.733329 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1377 0.0174 0.007 1.1 3.5 0.5 0.0 0 0.938 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.77 1.74 3.291 21.195 50.733 3.629 12.00 13.78 1.78 3.664 21.080 50.733 3.619 Individual atomic B min max mean iso aniso Overall: 9.28 100.78 21.01 2.04 225 1757 Protein: 9.28 100.78 16.67 2.04 0 1519 Water: 11.62 69.97 35.48 N/A 225 230 Other: 20.25 27.74 23.88 N/A 0 8 Chain A: 9.28 100.78 19.21 N/A 0 1757 Chain S: 14.68 65.91 35.12 N/A 225 0 Histogram: Values Number of atoms 9.28 - 18.43 1222 18.43 - 27.58 280 27.58 - 36.73 214 36.73 - 45.88 154 45.88 - 55.03 67 55.03 - 64.18 28 64.18 - 73.33 12 73.33 - 82.48 2 82.48 - 91.63 1 91.63 - 100.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1378 r_work=0.1200 r_free=0.1378 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1378 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1374 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1195 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.617297 | | target function (ml) not normalized (work): 301252.103911 | | target function (ml) not normalized (free): 15940.262580 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1419 0.1442 5.6705 5.6588| | 2: 3.57 - 2.84 1.00 2888 124 0.1128 0.1405 5.2059 5.2611| | 3: 2.83 - 2.48 1.00 2820 163 0.1240 0.1288 5.0205 5.0391| | 4: 2.47 - 2.25 1.00 2825 136 0.1029 0.1161 4.7157 4.7604| | 5: 2.25 - 2.09 1.00 2756 127 0.0989 0.1091 4.6556 4.714| | 6: 2.09 - 1.97 1.00 2846 113 0.0980 0.1198 4.3581 4.4729| | 7: 1.97 - 1.87 1.00 2787 165 0.0978 0.1282 4.0694 4.2137| | 8: 1.87 - 1.79 1.00 2789 144 0.1014 0.1283 3.9879 4.0894| | 9: 1.79 - 1.72 1.00 2745 138 0.0944 0.1316 3.7086 3.8887| | 10: 1.72 - 1.66 1.00 2831 160 0.0988 0.1278 3.6272 3.7787| | 11: 1.66 - 1.61 1.00 2712 147 0.0946 0.1081 3.5598 3.6144| | 12: 1.61 - 1.56 1.00 2773 144 0.0906 0.1099 3.3361 3.4425| | 13: 1.56 - 1.52 1.00 2745 130 0.0974 0.1076 3.3255 3.4426| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1135 3.2513 3.3455| | 15: 1.48 - 1.45 1.00 2738 128 0.1001 0.1322 3.1584 3.3073| | 16: 1.45 - 1.42 1.00 2756 161 0.1058 0.1235 3.1416 3.2328| | 17: 1.42 - 1.39 1.00 2785 139 0.1110 0.1295 3.1073 3.2229| | 18: 1.39 - 1.36 1.00 2741 179 0.1129 0.1397 3.0724 3.2708| | 19: 1.36 - 1.34 1.00 2807 134 0.1213 0.1598 3.0875 3.2726| | 20: 1.34 - 1.32 1.00 2696 147 0.1307 0.1471 3.0807 3.1342| | 21: 1.32 - 1.30 1.00 2785 112 0.1406 0.1571 3.0812 3.147| | 22: 1.29 - 1.27 1.00 2704 152 0.1465 0.1948 3.0771 3.2967| | 23: 1.27 - 1.26 1.00 2802 156 0.1568 0.1854 3.0988 3.2032| | 24: 1.26 - 1.24 1.00 2744 132 0.1620 0.1780 3.0898 3.1946| | 25: 1.24 - 1.22 1.00 2733 148 0.1793 0.2302 3.106 3.2787| | 26: 1.22 - 1.21 1.00 2727 135 0.1854 0.1797 3.119 3.1965| | 27: 1.21 - 1.19 1.00 2814 148 0.2002 0.2118 3.1367 3.1529| | 28: 1.19 - 1.18 1.00 2671 147 0.2139 0.2287 3.136 3.164| | 29: 1.18 - 1.16 1.00 2800 134 0.2222 0.2384 3.1257 3.2195| | 30: 1.16 - 1.15 1.00 2739 148 0.2376 0.2472 3.1131 3.1598| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.95 9.18 1.00 0.97 6456.69| | 2: 3.57 - 2.84 2888 124 0.92 13.77 1.01 0.97 6456.69| | 3: 2.83 - 2.48 2820 163 0.88 17.78 0.99 0.97 5409.34| | 4: 2.47 - 2.25 2825 136 0.91 14.83 1.00 0.98 2708.57| | 5: 2.25 - 2.09 2756 127 0.89 17.08 1.01 0.98 2708.57| | 6: 2.09 - 1.97 2846 113 0.91 13.79 1.02 0.97 1585.65| | 7: 1.97 - 1.87 2787 165 0.94 10.84 1.02 0.97 627.96| | 8: 1.87 - 1.79 2789 144 0.91 14.44 0.99 0.97 627.96| | 9: 1.79 - 1.72 2745 138 0.93 11.44 0.98 0.97 339.50| | 10: 1.72 - 1.66 2831 160 0.93 12.28 0.98 0.97 281.74| | 11: 1.66 - 1.61 2712 147 0.93 12.90 0.98 0.97 268.70| | 12: 1.61 - 1.56 2773 144 0.95 9.47 0.99 0.97 145.72| | 13: 1.56 - 1.52 2745 130 0.94 11.10 1.02 0.97 145.72| | 14: 1.52 - 1.48 2803 134 0.94 11.15 1.02 0.97 130.19| | 15: 1.48 - 1.45 2738 128 0.95 10.28 1.01 0.98 101.76| | 16: 1.45 - 1.42 2756 161 0.94 11.46 1.02 0.98 101.76| | 17: 1.42 - 1.39 2785 139 0.94 11.37 1.01 0.98 92.14| | 18: 1.39 - 1.36 2741 179 0.94 11.67 1.01 0.98 86.57| | 19: 1.36 - 1.34 2807 134 0.94 12.25 1.00 0.98 86.57| | 20: 1.34 - 1.32 2696 147 0.94 12.40 0.99 0.96 81.80| | 21: 1.32 - 1.30 2785 112 0.94 13.29 0.98 0.96 81.46| | 22: 1.29 - 1.27 2704 152 0.93 13.85 0.98 0.96 81.64| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.97 0.94 82.55| | 24: 1.26 - 1.24 2744 132 0.92 14.96 0.97 0.94 82.55| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 84.10| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.02 0.93 85.82| | 27: 1.21 - 1.19 2814 148 0.89 18.72 1.02 0.93 85.82| | 28: 1.19 - 1.18 2671 147 0.88 20.20 1.01 0.93 89.04| | 29: 1.18 - 1.16 2800 134 0.88 20.54 0.99 0.92 90.25| | 30: 1.16 - 1.15 2739 148 0.86 21.92 0.98 0.92 90.25| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.46 max = 6456.69 mean = 1001.09| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.94 mean = 14.06| |phase err.(test): min = 0.00 max = 87.95 mean = 14.17| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1195 0.1374 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1517 0.1515 0.1574 n_refl.: 87577 remove outliers: r(all,work,free)=0.1517 0.1515 0.1574 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1514 0.1513 0.1572 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1195 0.1375 n_refl.: 87577 remove outliers: r(all,work,free)=0.1204 0.1195 0.1375 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4011 289.105 253.680 0.444 1.000 0.304 11.894-9.307 95.10 93 4 0.2361 471.036 457.193 0.843 1.001 0.223 9.237-7.194 97.73 208 7 0.2530 383.623 377.282 0.909 1.001 0.150 7.162-5.571 100.00 427 22 0.2209 293.417 283.689 0.901 1.002 0.140 5.546-4.326 100.00 867 58 0.1201 402.790 397.973 0.952 1.002 0.116 4.315-3.360 100.00 1859 96 0.0996 383.056 380.260 0.993 1.002 0.110 3.356-2.611 100.00 3867 181 0.1199 251.648 249.366 1.001 1.001 0.048 2.608-2.026 99.99 8198 413 0.1044 166.819 165.842 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0966 81.466 81.725 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1217 36.125 35.764 1.021 1.000 0.000 1.221-1.150 99.97 13689 708 0.2111 22.761 21.365 0.975 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0397 ================= 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 : 0.2609 0.1919 0.082 5.304 8.8 119.3 19.9 258 0.000 1_bss: 0.1632 0.1746 0.082 5.304 9.1 119.5 20.1 258 0.000 1_settarget: 0.1632 0.1746 0.082 5.304 9.1 119.5 20.1 258 0.000 1_nqh: 0.1643 0.1758 0.082 5.304 9.1 119.5 20.1 258 0.010 1_weight: 0.1643 0.1758 0.082 5.304 9.1 119.5 20.1 258 0.010 1_xyzrec: 0.1211 0.1462 0.008 0.966 9.1 119.5 20.1 258 0.128 1_adp: 0.1238 0.1539 0.008 0.966 8.4 118.4 21.0 258 0.128 1_regHadp: 0.1242 0.1544 0.008 0.966 8.4 118.4 21.0 258 0.128 1_occ: 0.1242 0.1547 0.008 0.966 8.4 118.4 21.0 258 0.128 2_bss: 0.1241 0.1543 0.008 0.966 8.6 118.5 21.1 258 0.128 2_settarget: 0.1241 0.1543 0.008 0.966 8.6 118.5 21.1 258 0.128 2_updatecdl: 0.1241 0.1543 0.008 0.971 8.6 118.5 21.1 258 0.128 2_nqh: 0.1243 0.1543 0.008 0.971 8.6 118.5 21.1 258 0.125 2_sol: 0.1229 0.1485 0.008 0.971 8.6 118.5 23.6 436 n/a 2_weight: 0.1229 0.1485 0.008 0.971 8.6 118.5 23.6 436 n/a 2_xyzrec: 0.1227 0.1509 0.007 0.889 8.6 118.5 23.6 436 n/a 2_adp: 0.1202 0.1476 0.007 0.889 8.7 114.4 23.3 436 n/a 2_regHadp: 0.1201 0.1476 0.007 0.889 8.7 114.4 23.3 436 n/a 2_occ: 0.1200 0.1471 0.007 0.889 8.7 114.4 23.3 436 n/a 3_bss: 0.1196 0.1469 0.007 0.889 8.8 114.4 23.3 436 n/a 3_settarget: 0.1196 0.1469 0.007 0.889 8.8 114.4 23.3 436 n/a 3_updatecdl: 0.1196 0.1469 0.007 0.887 8.8 114.4 23.3 436 n/a 3_nqh: 0.1196 0.1469 0.007 0.887 8.8 114.4 23.3 436 n/a 3_sol: 0.1221 0.1474 0.007 0.887 8.8 114.4 22.0 447 n/a 3_weight: 0.1221 0.1474 0.007 0.887 8.8 114.4 22.0 447 n/a 3_xyzrec: 0.1229 0.1454 0.006 0.917 8.8 114.4 22.0 447 n/a 3_adp: 0.1217 0.1407 0.006 0.917 9.3 109.4 21.5 447 n/a 3_regHadp: 0.1218 0.1409 0.006 0.917 9.3 109.4 21.5 447 n/a 3_occ: 0.1210 0.1401 0.006 0.917 9.3 109.4 21.5 447 n/a 4_bss: 0.1198 0.1365 0.006 0.917 9.3 109.4 21.5 447 n/a 4_settarget: 0.1198 0.1365 0.006 0.917 9.3 109.4 21.5 447 n/a 4_updatecdl: 0.1198 0.1365 0.006 0.915 9.3 109.4 21.5 447 n/a 4_nqh: 0.1198 0.1365 0.006 0.915 9.3 109.4 21.5 447 n/a 4_sol: 0.1195 0.1357 0.006 0.915 9.3 109.4 21.3 435 n/a 4_weight: 0.1195 0.1357 0.006 0.915 9.3 109.4 21.3 435 n/a 4_xyzrec: 0.1195 0.1365 0.006 0.980 9.3 109.4 21.3 435 n/a 4_adp: 0.1186 0.1364 0.006 0.980 9.3 105.6 21.2 435 n/a 4_regHadp: 0.1187 0.1364 0.006 0.980 9.3 105.6 21.2 435 n/a 4_occ: 0.1184 0.1362 0.006 0.980 9.3 105.6 21.2 435 n/a 5_bss: 0.1182 0.1362 0.006 0.980 9.3 105.6 21.1 435 n/a 5_settarget: 0.1182 0.1362 0.006 0.980 9.3 105.6 21.1 435 n/a 5_updatecdl: 0.1182 0.1362 0.006 0.983 9.3 105.6 21.1 435 n/a 5_setrh: 0.1183 0.1362 0.006 0.983 9.3 105.6 21.1 435 n/a 5_nqh: 0.1183 0.1362 0.006 0.983 9.3 105.6 21.1 435 n/a 5_sol: 0.1174 0.1353 0.006 0.983 9.3 105.6 21.2 455 n/a 5_weight: 0.1174 0.1353 0.006 0.983 9.3 105.6 21.2 455 n/a 5_xyzrec: 0.1203 0.1377 0.007 1.072 9.3 105.6 21.2 455 n/a 5_adp: 0.1200 0.1378 0.007 1.072 9.3 100.8 21.0 455 n/a 5_regHadp: 0.1200 0.1378 0.007 1.072 9.3 100.8 21.0 455 n/a 5_occ: 0.1195 0.1374 0.007 1.072 9.3 100.8 21.0 455 n/a end: 0.1195 0.1375 0.007 1.072 9.3 100.8 21.0 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1785239_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1785239_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8500 Refinement macro-cycles (run) : 3450.5200 Write final files (write_after_run_outputs) : 74.9500 Total : 3530.3200 Total CPU time: 59.45 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:10:17 PST -0800 (1735452617.69 s) Start R-work = 0.1632, R-free = 0.1746 Final R-work = 0.1195, R-free = 0.1375 =============================================================================== Job complete usr+sys time: 3675.97 seconds wall clock time: 65 minutes 39.30 seconds (3939.30 seconds total)