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_1318715.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_1318715.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1318715.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 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: 2.34, per 1000 atoms: 0.69 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: 0.86 Conformation dependent library (CDL) restraints added in 311.9 milliseconds Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 622 0.93 - 1.20: 1046 1.20 - 1.47: 791 1.47 - 1.74: 681 1.74 - 2.01: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.233 1.043 0.190 1.08e-02 8.57e+03 3.09e+02 bond pdb=" N ATYR A 67 " pdb=" CA ATYR A 67 " ideal model delta sigma weight residual 1.456 1.245 0.211 1.21e-02 6.83e+03 3.05e+02 bond pdb=" C ILE A 152 " pdb=" N ALEU A 153 " ideal model delta sigma weight residual 1.331 1.557 -0.227 1.34e-02 5.57e+03 2.87e+02 bond pdb=" C BASN A 97 " pdb=" N ARG A 98 " ideal model delta sigma weight residual 1.331 1.102 0.229 1.43e-02 4.89e+03 2.57e+02 bond pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " ideal model delta sigma weight residual 1.378 1.202 0.176 1.10e-02 8.26e+03 2.56e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 3168 4.66 - 9.33: 1865 9.33 - 13.99: 621 13.99 - 18.65: 108 18.65 - 23.31: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH1 ARG A 27 " ideal model delta sigma weight residual 121.50 140.97 -19.47 1.00e+00 1.00e+00 3.79e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.18 137.62 -14.44 1.08e+00 8.57e-01 1.79e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 131.14 -11.94 9.00e-01 1.23e+00 1.76e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.70 107.95 12.75 1.03e+00 9.43e-01 1.53e+02 angle pdb=" O GLU A 170 " pdb=" C GLU A 170 " pdb=" N ALA A 171 " ideal model delta sigma weight residual 122.09 134.96 -12.87 1.08e+00 8.57e-01 1.42e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 924 16.66 - 33.31: 136 33.31 - 49.97: 37 49.97 - 66.62: 11 66.62 - 83.28: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 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 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 106 0.225 - 0.450: 78 0.450 - 0.675: 39 0.675 - 0.900: 17 0.900 - 1.124: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 151 " pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CB LEU A 151 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.48 -1.11 2.00e-01 2.50e+01 3.06e+01 chirality pdb=" CB VAL A 169 " pdb=" CA VAL A 169 " pdb=" CG1 VAL A 169 " pdb=" CG2 VAL A 169 " both_signs ideal model delta sigma weight residual False -2.63 -3.59 0.96 2.00e-01 2.50e+01 2.32e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.110 2.00e-02 2.50e+03 6.74e-02 1.36e+02 pdb=" CG PHE A 119 " -0.090 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.131 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.050 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.078 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.048 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.096 2.00e-02 2.50e+03 6.49e-02 1.26e+02 pdb=" CG PHE A 164 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.128 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.110 2.00e-02 2.50e+03 6.12e-02 1.12e+02 pdb=" CG ATYR A 67 " 0.092 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.019 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.091 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.008 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.026 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.085 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.005 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.069 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.042 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.32: 1008 2.32 - 2.89: 8110 2.89 - 3.46: 10496 3.46 - 4.03: 15289 4.03 - 4.60: 21737 Nonbonded interactions: 56640 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.745 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.745 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.767 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.784 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.832 2.100 ... (remaining 56635 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_1318715_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2603 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787973 | | target function (ml) not normalized (work): 232254.912907 | | target function (ml) not normalized (free): 11811.889728 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3032 0.2057 7.0844 4.9424| | 2: 3.57 - 2.84 1.00 2876 122 0.2448 0.1810 4.3456 4.3452| | 3: 2.84 - 2.48 1.00 2833 165 0.2358 0.1701 4.1263 4.1635| | 4: 2.47 - 2.25 1.00 2825 136 0.2330 0.1370 3.831 3.8257| | 5: 2.25 - 2.09 1.00 2756 127 0.2477 0.1554 3.7977 3.8087| | 6: 2.09 - 1.97 1.00 2846 113 0.2532 0.1809 3.4558 3.5534| | 7: 1.97 - 1.87 1.00 2787 165 0.2522 0.1774 3.1221 3.1825| | 8: 1.87 - 1.79 1.00 2789 144 0.2459 0.1712 3.0367 3.0563| | 9: 1.79 - 1.72 1.00 2745 138 0.2398 0.1957 2.8872 2.9747| | 10: 1.72 - 1.66 1.00 2789 158 0.2423 0.1957 2.7945 2.9055| | 11: 1.66 - 1.61 1.00 2740 147 0.2505 0.1735 2.7508 2.7003| | 12: 1.61 - 1.56 1.00 2787 146 0.2485 0.2021 2.6105 2.6494| | 13: 1.56 - 1.52 1.00 2745 130 0.2541 0.1830 2.567 2.5714| | 14: 1.52 - 1.48 1.00 2803 134 0.2556 0.1987 2.5057 2.5365| | 15: 1.48 - 1.45 1.00 2738 128 0.2581 0.2295 2.4218 2.5629| | 16: 1.45 - 1.42 1.00 2756 161 0.2679 0.2239 2.3774 2.4428| | 17: 1.42 - 1.39 1.00 2785 139 0.2694 0.2006 2.3389 2.3286| | 18: 1.39 - 1.36 1.00 2741 179 0.2622 0.2525 2.258 2.4199| | 19: 1.36 - 1.34 1.00 2807 134 0.2680 0.2265 2.2502 2.2874| | 20: 1.34 - 1.32 1.00 2696 147 0.2636 0.2189 2.1901 2.206| | 21: 1.32 - 1.30 1.00 2785 112 0.2756 0.2527 2.1675 2.2638| | 22: 1.29 - 1.27 1.00 2704 152 0.2684 0.2638 2.1238 2.2227| | 23: 1.27 - 1.26 1.00 2802 156 0.2738 0.2646 2.1092 2.2182| | 24: 1.26 - 1.24 1.00 2744 132 0.2826 0.2393 2.0887 2.1212| | 25: 1.24 - 1.22 1.00 2734 148 0.2847 0.2473 2.0509 2.0506| | 26: 1.22 - 1.21 1.00 2727 135 0.2805 0.2243 2.0001 2.0746| | 27: 1.21 - 1.19 1.00 2814 148 0.2952 0.2795 2.0083 2.0495| | 28: 1.19 - 1.18 1.00 2671 147 0.2989 0.2757 1.9873 1.9892| | 29: 1.18 - 1.16 1.00 2800 134 0.2923 0.2572 1.9553 1.9777| | 30: 1.16 - 1.15 1.00 2740 148 0.3050 0.2597 1.9389 1.8963| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.80 0.76 0.23 1475.09| | 2: 3.57 - 2.84 2876 122 0.80 26.02 1.28 0.23 1475.09| | 3: 2.84 - 2.48 2833 165 0.74 31.91 1.24 0.24 1222.85| | 4: 2.47 - 2.25 2825 136 0.81 25.49 1.26 0.25 568.25| | 5: 2.25 - 2.09 2756 127 0.77 29.21 1.28 0.25 568.25| | 6: 2.09 - 1.97 2846 113 0.84 22.52 1.29 0.25 309.86| | 7: 1.97 - 1.87 2787 165 0.90 16.55 1.28 0.25 89.49| | 8: 1.87 - 1.79 2789 144 0.86 21.07 1.25 0.25 89.49| | 9: 1.79 - 1.72 2745 138 0.88 18.22 1.23 0.25 54.06| | 10: 1.72 - 1.66 2789 158 0.87 19.95 1.22 0.25 46.97| | 11: 1.66 - 1.61 2740 147 0.86 21.05 1.24 0.25 45.30| | 12: 1.61 - 1.56 2787 146 0.89 18.13 1.23 0.25 28.41| | 13: 1.56 - 1.52 2745 130 0.87 20.02 1.24 0.25 28.41| | 14: 1.52 - 1.48 2803 134 0.87 20.33 1.23 0.25 25.69| | 15: 1.48 - 1.45 2738 128 0.87 20.34 1.23 0.25 20.72| | 16: 1.45 - 1.42 2756 161 0.85 21.86 1.24 0.25 20.72| | 17: 1.42 - 1.39 2785 139 0.86 21.06 1.24 0.25 17.90| | 18: 1.39 - 1.36 2741 179 0.86 21.38 1.23 0.25 16.27| | 19: 1.36 - 1.34 2807 134 0.85 22.17 1.22 0.25 16.27| | 20: 1.34 - 1.32 2696 147 0.86 21.25 1.21 0.25 13.54| | 21: 1.32 - 1.30 2785 112 0.85 22.56 1.21 0.25 13.34| | 22: 1.29 - 1.27 2704 152 0.85 22.72 1.21 0.24 13.00| | 23: 1.27 - 1.26 2802 156 0.86 22.26 1.21 0.24 11.24| | 24: 1.26 - 1.24 2744 132 0.85 23.03 1.21 0.24 11.24| | 25: 1.24 - 1.22 2734 148 0.84 23.68 1.20 0.24 10.46| | 26: 1.22 - 1.21 2727 135 0.85 23.30 1.19 0.23 9.60| | 27: 1.21 - 1.19 2814 148 0.84 24.19 1.20 0.23 9.60| | 28: 1.19 - 1.18 2671 147 0.84 23.92 1.19 0.23 8.56| | 29: 1.18 - 1.16 2800 134 0.84 23.79 1.16 0.23 8.18| | 30: 1.16 - 1.15 2740 148 0.83 25.29 1.15 0.23 8.18| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 8.18 max = 1475.09 mean = 213.73| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.41| |phase err.(test): min = 0.00 max = 89.51 mean = 22.23| |-----------------------------------------------------------------------------| ----------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 0.261 1557 Z= 5.359 Angle : 5.264 19.467 2118 Z= 3.738 Chirality : 0.385 1.124 243 Planarity : 0.031 0.082 284 Dihedral : 13.552 83.279 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 2.48 % Allowed : 2.48 % Favored : 95.03 % Cbeta Deviations : 31.89 % 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: -2.42 (0.45), residues: 224 helix: -2.45 (0.36), residues: 108 sheet: -0.48 (0.90), residues: 28 loop : -0.50 (0.54), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.018 ARG A 98 TYR 0.107 0.039 TYR A 141 PHE 0.096 0.035 PHE A 119 HIS 0.067 0.035 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= 0.2603 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787973 | | target function (ml) not normalized (work): 232254.912907 | | target function (ml) not normalized (free): 11811.889728 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2562 0.2604 0.1935 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2562 0.2604 0.1935 n_refl.: 87602 remove outliers: r(all,work,free)=0.1976 0.1980 0.1935 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2000 0.2005 0.1947 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1636 0.1630 0.1760 n_refl.: 87594 remove outliers: r(all,work,free)=0.1636 0.1629 0.1760 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 0.3812 386.293 357.265 0.726 0.914 0.407 11.894-9.307 99.02 97 4 0.1816 613.608 594.543 1.013 0.915 0.385 9.237-7.194 100.00 213 7 0.2171 501.856 490.119 1.054 0.916 0.369 7.162-5.571 100.00 427 22 0.2204 376.615 364.246 1.015 0.916 0.302 5.546-4.326 100.00 867 58 0.1289 517.000 511.348 1.052 0.917 0.229 4.315-3.360 100.00 1859 96 0.1149 491.670 487.816 1.098 0.918 0.209 3.356-2.611 100.00 3867 181 0.1439 323.002 319.803 1.085 0.920 0.057 2.608-2.026 99.99 8198 413 0.1357 214.121 211.917 1.092 0.923 0.000 2.025-1.573 100.00 17313 902 0.1613 104.565 103.981 1.088 0.929 0.000 1.573-1.221 100.00 36679 1900 0.2055 46.369 45.122 1.068 0.937 0.000 1.221-1.150 99.97 13689 708 0.2575 29.215 27.057 1.028 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0463 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1629 r_free=0.1760 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 80 GLN A A 180 GLN Total number of N/Q/H flips: 4 r_work=0.1640 r_free=0.1765 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.498084 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2014.701198 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 0.1213 0.1467 0.0254 0.007 0.9 1.3 0.5 0.0 0 12.249 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 14.67 2.54 3.013 19.061 2014.701 0.017 12.43 15.46 3.02 3.304 19.605 2014.701 0.016 Individual atomic B min max mean iso aniso Overall: 8.56 118.93 21.12 2.88 0 1785 Protein: 8.56 118.93 17.98 2.88 0 1519 Water: 11.07 114.50 39.29 N/A 0 258 Other: 23.02 37.10 29.87 N/A 0 8 Chain A: 8.56 118.93 21.12 N/A 0 1785 Histogram: Values Number of atoms 8.56 - 19.60 1206 19.60 - 30.64 230 30.64 - 41.67 163 41.67 - 52.71 103 52.71 - 63.75 54 63.75 - 74.78 17 74.78 - 85.82 5 85.82 - 96.86 3 96.86 - 107.89 1 107.89 - 118.93 3 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1546 r_work=0.1248 r_free=0.1548 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1248 r_free = 0.1548 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1247 r_free = 0.1549 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1247 r_free= 0.1549 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015479 | | target function (ls_wunit_k1) not normalized (work): 1289.358879 | | target function (ls_wunit_k1) not normalized (free): 114.080296 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1261 0.1247 0.1549 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1709 0.1707 0.1778 n_refl.: 87593 remove outliers: r(all,work,free)=0.1709 0.1707 0.1778 n_refl.: 87593 overall B=0.11 to atoms: r(all,work,free)=0.1728 0.1727 0.1791 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1261 0.1247 0.1543 n_refl.: 87593 remove outliers: r(all,work,free)=0.1261 0.1246 0.1543 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3630 298.332 276.835 0.628 1.002 0.374 11.894-9.307 99.02 97 4 0.1627 477.912 466.594 0.904 1.003 0.370 9.237-7.194 100.00 213 7 0.1833 390.873 385.361 0.948 1.003 0.340 7.162-5.571 100.00 427 22 0.1746 293.328 287.717 0.923 1.003 0.254 5.546-4.326 100.00 867 58 0.0912 402.667 400.062 0.949 1.003 0.214 4.315-3.360 100.00 1859 96 0.0773 382.939 381.945 0.996 1.003 0.200 3.356-2.611 100.00 3867 181 0.1021 251.571 250.885 0.999 1.002 0.052 2.608-2.026 99.99 8198 413 0.0978 166.769 166.169 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1215 81.441 81.621 1.017 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1656 36.114 35.566 1.006 0.999 0.000 1.221-1.150 99.97 13689 708 0.2365 22.755 21.271 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=0.0444 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1246 r_free=0.1543 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1248 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1248 r_free=0.1544 | n_water=258 | time (s): 2.220 (total time: 2.220) Filter (dist) r_work=0.1257 r_free=0.1544 | n_water=252 | time (s): 28.430 (total time: 30.650) Filter (q & B) r_work=0.1260 r_free=0.1543 | n_water=249 | time (s): 3.860 (total time: 34.510) Compute maps r_work=0.1260 r_free=0.1543 | n_water=249 | time (s): 1.910 (total time: 36.420) Filter (map) r_work=0.1273 r_free=0.1554 | n_water=237 | time (s): 3.720 (total time: 40.140) Find peaks r_work=0.1273 r_free=0.1554 | n_water=237 | time (s): 0.690 (total time: 40.830) Add new water r_work=0.1432 r_free=0.1701 | n_water=460 | time (s): 4.100 (total time: 44.930) Refine new water occ: r_work=0.1341 r_free=0.1564 adp: r_work=0.1260 r_free=0.1512 occ: r_work=0.1272 r_free=0.1502 adp: r_work=0.1236 r_free=0.1488 occ: r_work=0.1239 r_free=0.1477 adp: r_work=0.1229 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1229 r_free=0.1482 r_work=0.1229 r_free=0.1482 | n_water=460 | time (s): 75.450 (total time: 120.380) Filter (q & B) r_work=0.1237 r_free=0.1487 | n_water=439 | time (s): 4.000 (total time: 124.380) Filter (dist only) r_work=0.1237 r_free=0.1487 | n_water=439 | time (s): 42.200 (total time: 166.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.366872 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1595.746657 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 0.1235 0.1515 0.0280 0.006 0.9 1.9 0.5 0.0 0 12.183 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.35 15.15 2.80 3.811 23.349 1595.747 0.016 12.05 14.84 2.79 4.226 23.156 1595.747 0.015 Individual atomic B min max mean iso aniso Overall: 8.79 114.99 23.36 2.63 202 1764 Protein: 8.79 114.99 17.73 2.64 0 1519 Water: 10.90 72.22 42.70 N/A 202 237 Other: 25.74 38.50 31.02 N/A 0 8 Chain A: 8.79 114.99 20.45 N/A 0 1764 Chain S: 14.73 71.76 48.83 N/A 202 0 Histogram: Values Number of atoms 8.79 - 19.41 1207 19.41 - 30.03 255 30.03 - 40.65 184 40.65 - 51.27 140 51.27 - 61.89 118 61.89 - 72.51 50 72.51 - 83.13 6 83.13 - 93.75 3 93.75 - 104.37 1 104.37 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1484 r_work=0.1205 r_free=0.1484 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1484 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 = 0.1206 r_free = 0.1483 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1206 r_free= 0.1483 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014106 | | target function (ls_wunit_k1) not normalized (work): 1174.957590 | | target function (ls_wunit_k1) not normalized (free): 100.069410 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1206 0.1483 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1603 0.1598 0.1726 n_refl.: 87592 remove outliers: r(all,work,free)=0.1603 0.1598 0.1726 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1609 0.1604 0.1729 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1217 0.1204 0.1481 n_refl.: 87592 remove outliers: r(all,work,free)=0.1216 0.1203 0.1481 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 93.75 85 5 0.3452 296.895 270.739 0.593 1.002 0.370 11.894-9.307 99.02 97 4 0.1479 477.912 475.587 0.912 1.003 0.350 9.237-7.194 100.00 213 7 0.1706 390.873 392.000 0.980 1.003 0.280 7.162-5.571 100.00 427 22 0.1505 293.328 289.629 0.939 1.003 0.225 5.546-4.326 100.00 867 58 0.0850 402.667 400.037 0.957 1.003 0.215 4.315-3.360 100.00 1859 96 0.0720 382.939 381.735 1.002 1.002 0.210 3.356-2.611 100.00 3867 181 0.0963 251.571 250.987 1.008 1.002 0.067 2.608-2.026 99.99 8198 413 0.0960 166.769 166.351 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1185 81.441 81.652 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1620 36.114 35.618 1.017 0.998 0.000 1.221-1.150 99.97 13689 708 0.2346 22.755 21.293 0.977 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0584 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1481 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=0.1203 r_free=0.1481 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1481 | n_water=439 | time (s): 2.250 (total time: 2.250) Filter (dist) r_work=0.1202 r_free=0.1480 | n_water=437 | time (s): 38.990 (total time: 41.240) Filter (q & B) r_work=0.1203 r_free=0.1483 | n_water=435 | time (s): 3.030 (total time: 44.270) Compute maps r_work=0.1203 r_free=0.1483 | n_water=435 | time (s): 1.650 (total time: 45.920) Filter (map) r_work=0.1240 r_free=0.1492 | n_water=290 | time (s): 3.120 (total time: 49.040) Find peaks r_work=0.1240 r_free=0.1492 | n_water=290 | time (s): 0.470 (total time: 49.510) Add new water r_work=0.1369 r_free=0.1620 | n_water=479 | time (s): 3.400 (total time: 52.910) Refine new water occ: r_work=0.1268 r_free=0.1534 adp: r_work=0.1269 r_free=0.1535 occ: r_work=0.1247 r_free=0.1512 adp: r_work=0.1244 r_free=0.1510 occ: r_work=0.1232 r_free=0.1496 adp: r_work=0.1224 r_free=0.1493 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1493 r_work=0.1224 r_free=0.1493 | n_water=479 | time (s): 171.270 (total time: 224.180) Filter (q & B) r_work=0.1228 r_free=0.1492 | n_water=445 | time (s): 2.950 (total time: 227.130) Filter (dist only) r_work=0.1230 r_free=0.1493 | n_water=444 | time (s): 38.840 (total time: 265.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.069607 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 58.810349 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 0.1237 0.1460 0.0223 0.006 0.9 1.6 0.5 0.0 0 1.035 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.60 2.23 3.651 22.193 58.810 3.730 12.22 14.10 1.88 4.227 21.976 58.810 3.653 Individual atomic B min max mean iso aniso Overall: 9.27 110.03 21.67 2.39 210 1761 Protein: 9.27 110.03 17.23 2.39 0 1519 Water: 11.46 70.79 36.76 N/A 210 234 Other: 21.41 34.25 27.62 N/A 0 8 Chain A: 9.27 110.03 19.91 N/A 0 1761 Chain S: 16.58 64.70 36.47 N/A 210 0 Histogram: Values Number of atoms 9.27 - 19.35 1236 19.35 - 29.42 271 29.42 - 39.50 220 39.50 - 49.57 138 49.57 - 59.65 72 59.65 - 69.73 20 69.73 - 79.80 8 79.80 - 89.88 3 89.88 - 99.96 1 99.96 - 110.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1222 r_free=0.1410 r_work=0.1223 r_free=0.1411 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1223 r_free = 0.1411 target_work(ml) = 3.654 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1217 r_free = 0.1410 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1217 r_free= 0.1410 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.651911 | | target function (ml) not normalized (work): 304182.265513 | | target function (ml) not normalized (free): 16074.785266 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1227 0.1217 0.1410 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1543 0.1542 0.1601 n_refl.: 87590 remove outliers: r(all,work,free)=0.1543 0.1542 0.1601 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1541 0.1540 0.1600 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1206 0.1376 n_refl.: 87590 remove outliers: r(all,work,free)=0.1208 0.1200 0.1376 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 0.3911 286.431 261.088 0.459 1.000 0.287 11.894-9.307 93.14 91 4 0.2307 474.054 449.478 0.844 1.001 0.263 9.237-7.194 98.18 209 7 0.2399 385.520 385.031 0.943 1.001 0.150 7.162-5.571 100.00 427 22 0.2147 293.328 282.575 0.907 1.002 0.148 5.546-4.326 100.00 867 58 0.1123 402.667 398.127 0.951 1.002 0.147 4.315-3.360 100.00 1859 96 0.0946 382.939 380.256 0.994 1.002 0.147 3.356-2.611 100.00 3867 181 0.1162 251.571 249.570 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1045 166.769 165.894 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.1010 81.441 81.618 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1283 36.114 35.694 1.019 0.999 0.000 1.221-1.150 99.97 13689 708 0.2123 22.755 21.383 0.977 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0050 b_overall=-0.0324 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1376 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1376 | n_water=444 | time (s): 2.110 (total time: 2.110) Filter (dist) r_work=0.1200 r_free=0.1376 | n_water=443 | time (s): 40.500 (total time: 42.610) Filter (q & B) r_work=0.1200 r_free=0.1375 | n_water=442 | time (s): 2.990 (total time: 45.600) Compute maps r_work=0.1200 r_free=0.1375 | n_water=442 | time (s): 1.680 (total time: 47.280) Filter (map) r_work=0.1227 r_free=0.1390 | n_water=316 | time (s): 2.980 (total time: 50.260) Find peaks r_work=0.1227 r_free=0.1390 | n_water=316 | time (s): 0.680 (total time: 50.940) Add new water r_work=0.1285 r_free=0.1446 | n_water=480 | time (s): 2.880 (total time: 53.820) Refine new water occ: r_work=0.1212 r_free=0.1377 adp: r_work=0.1212 r_free=0.1378 occ: r_work=0.1198 r_free=0.1373 adp: r_work=0.1197 r_free=0.1372 occ: r_work=0.1188 r_free=0.1374 adp: r_work=0.1185 r_free=0.1370 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1370 r_work=0.1185 r_free=0.1370 | n_water=480 | time (s): 189.750 (total time: 243.570) Filter (q & B) r_work=0.1191 r_free=0.1371 | n_water=445 | time (s): 2.820 (total time: 246.390) Filter (dist only) r_work=0.1191 r_free=0.1370 | n_water=443 | time (s): 40.260 (total time: 286.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.354476 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.413456 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 0.1385 0.0195 0.006 1.0 3.5 0.5 0.0 0 1.177 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.85 1.95 3.457 21.486 49.413 3.632 11.79 13.79 2.00 3.699 21.398 49.413 3.620 Individual atomic B min max mean iso aniso Overall: 9.20 106.04 21.25 2.22 213 1757 Protein: 9.20 106.04 17.05 2.22 0 1519 Water: 11.56 69.97 35.55 N/A 213 230 Other: 21.07 31.74 26.75 N/A 0 8 Chain A: 9.20 106.04 19.61 N/A 0 1757 Chain S: 16.33 64.91 34.73 N/A 213 0 Histogram: Values Number of atoms 9.20 - 18.88 1227 18.88 - 28.57 284 28.57 - 38.25 209 38.25 - 47.94 151 47.94 - 57.62 62 57.62 - 67.30 23 67.30 - 76.99 9 76.99 - 86.67 2 86.67 - 96.36 1 96.36 - 106.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1179 r_free=0.1379 r_work=0.1180 r_free=0.1379 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1180 r_free = 0.1379 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1177 r_free = 0.1378 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1177 r_free= 0.1378 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.619767 | | target function (ml) not normalized (work): 301454.232232 | | target function (ml) not normalized (free): 15945.930027 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1187 0.1177 0.1378 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1490 0.1488 0.1556 n_refl.: 87576 remove outliers: r(all,work,free)=0.1490 0.1488 0.1556 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1488 0.1486 0.1555 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1187 0.1177 0.1381 n_refl.: 87576 remove outliers: r(all,work,free)=0.1186 0.1176 0.1381 n_refl.: 87574 ======================== 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 0.4148 286.431 254.081 0.439 0.998 0.295 11.894-9.307 91.18 89 4 0.2205 469.701 452.616 0.850 1.000 0.192 9.237-7.194 98.18 209 7 0.2474 385.520 378.677 0.917 1.000 0.120 7.162-5.571 100.00 427 22 0.2165 293.328 283.383 0.901 1.001 0.120 5.546-4.326 100.00 867 58 0.1133 402.667 397.554 0.950 1.001 0.118 4.315-3.360 100.00 1859 96 0.0951 382.939 380.508 0.995 1.001 0.117 3.356-2.611 100.00 3867 181 0.1155 251.571 249.591 1.000 1.001 0.100 2.608-2.026 99.99 8198 413 0.1017 166.769 165.932 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0961 81.441 81.742 1.026 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1239 36.114 35.751 1.017 1.002 0.000 1.221-1.150 99.97 13689 708 0.2117 22.755 21.343 0.971 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0327 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1176 r_free=0.1381 After: r_work=0.1177 r_free=0.1380 ================================== NQH flips ================================== r_work=0.1177 r_free=0.1380 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=0.1177 r_free=0.1380 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1177 r_free=0.1380 | n_water=443 | time (s): 1.900 (total time: 1.900) Filter (dist) r_work=0.1177 r_free=0.1380 | n_water=443 | time (s): 38.220 (total time: 40.120) Filter (q & B) r_work=0.1177 r_free=0.1380 | n_water=443 | time (s): 0.900 (total time: 41.020) Compute maps r_work=0.1177 r_free=0.1380 | n_water=443 | time (s): 1.410 (total time: 42.430) Filter (map) r_work=0.1201 r_free=0.1391 | n_water=345 | time (s): 3.340 (total time: 45.770) Find peaks r_work=0.1201 r_free=0.1391 | n_water=345 | time (s): 0.640 (total time: 46.410) Add new water r_work=0.1245 r_free=0.1421 | n_water=500 | time (s): 2.660 (total time: 49.070) Refine new water occ: r_work=0.1186 r_free=0.1367 adp: r_work=0.1186 r_free=0.1368 occ: r_work=0.1174 r_free=0.1361 adp: r_work=0.1173 r_free=0.1363 occ: r_work=0.1166 r_free=0.1359 adp: r_work=0.1163 r_free=0.1359 ADP+occupancy (water only), MIN, final r_work=0.1163 r_free=0.1359 r_work=0.1163 r_free=0.1359 | n_water=500 | time (s): 190.730 (total time: 239.800) Filter (q & B) r_work=0.1171 r_free=0.1363 | n_water=455 | time (s): 2.640 (total time: 242.440) Filter (dist only) r_work=0.1171 r_free=0.1361 | n_water=453 | time (s): 40.450 (total time: 282.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.968149 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.163071 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 0.1379 0.0184 0.006 1.0 2.6 0.5 0.0 0 0.984 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.79 1.84 3.345 21.270 37.163 3.629 11.98 13.80 1.81 3.397 21.242 37.163 3.628 Individual atomic B min max mean iso aniso Overall: 9.27 104.69 21.18 2.14 223 1757 Protein: 9.27 104.69 16.98 2.14 0 1519 Water: 11.53 69.80 35.20 N/A 223 230 Other: 21.15 31.25 26.58 N/A 0 8 Chain A: 9.27 104.69 19.54 N/A 0 1757 Chain S: 16.03 56.82 34.13 N/A 223 0 Histogram: Values Number of atoms 9.27 - 18.82 1233 18.82 - 28.36 285 28.36 - 37.90 208 37.90 - 47.44 153 47.44 - 56.98 64 56.98 - 66.52 21 66.52 - 76.07 11 76.07 - 85.61 2 85.61 - 95.15 1 95.15 - 104.69 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1380 r_work=0.1198 r_free=0.1380 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1380 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1378 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1196 r_free= 0.1378 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.627690 | | target function (ml) not normalized (work): 302106.735100 | | target function (ml) not normalized (free): 15973.598983 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1391 0.1454 5.6513 5.6715| | 2: 3.57 - 2.84 1.00 2888 124 0.1118 0.1478 5.2139 5.2965| | 3: 2.83 - 2.48 1.00 2820 163 0.1212 0.1183 5.0204 5.0177| | 4: 2.47 - 2.25 1.00 2825 136 0.1019 0.1148 4.7183 4.7731| | 5: 2.25 - 2.09 1.00 2756 127 0.1003 0.1144 4.6674 4.748| | 6: 2.09 - 1.97 1.00 2846 113 0.0982 0.1182 4.3614 4.4806| | 7: 1.97 - 1.87 1.00 2787 165 0.0998 0.1224 4.077 4.1721| | 8: 1.87 - 1.79 1.00 2789 144 0.1016 0.1275 3.9879 4.0875| | 9: 1.79 - 1.72 1.00 2745 138 0.0962 0.1345 3.7197 3.93| | 10: 1.72 - 1.66 1.00 2831 160 0.1015 0.1264 3.6425 3.7655| | 11: 1.66 - 1.61 1.00 2712 147 0.0981 0.1097 3.5774 3.6125| | 12: 1.61 - 1.56 1.00 2773 144 0.0928 0.1129 3.3565 3.4608| | 13: 1.56 - 1.52 1.00 2745 130 0.0990 0.1102 3.3467 3.4426| | 14: 1.52 - 1.48 1.00 2803 134 0.0997 0.1141 3.2671 3.3553| | 15: 1.48 - 1.45 1.00 2738 128 0.1033 0.1379 3.1816 3.349| | 16: 1.45 - 1.42 1.00 2756 161 0.1084 0.1282 3.1625 3.2553| | 17: 1.42 - 1.39 1.00 2785 139 0.1128 0.1298 3.1252 3.2367| | 18: 1.39 - 1.36 1.00 2741 179 0.1165 0.1429 3.0982 3.2975| | 19: 1.36 - 1.34 1.00 2807 134 0.1231 0.1618 3.1044 3.2868| | 20: 1.34 - 1.32 1.00 2696 147 0.1334 0.1474 3.0959 3.1412| | 21: 1.32 - 1.30 1.00 2785 112 0.1423 0.1644 3.0941 3.1776| | 22: 1.29 - 1.27 1.00 2704 152 0.1486 0.1962 3.0915 3.2841| | 23: 1.27 - 1.26 1.00 2802 156 0.1593 0.1864 3.1109 3.2105| | 24: 1.26 - 1.24 1.00 2744 132 0.1644 0.1793 3.1006 3.197| | 25: 1.24 - 1.22 1.00 2733 148 0.1807 0.2301 3.1126 3.2897| | 26: 1.22 - 1.21 1.00 2727 135 0.1872 0.1789 3.1285 3.2022| | 27: 1.21 - 1.19 1.00 2814 148 0.2020 0.2119 3.1427 3.1511| | 28: 1.19 - 1.18 1.00 2671 147 0.2149 0.2319 3.1397 3.1592| | 29: 1.18 - 1.16 1.00 2800 134 0.2220 0.2357 3.1275 3.2172| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2483 3.1162 3.1637| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2916 171 0.94 9.45 1.00 0.97 6674.70| | 2: 3.57 - 2.84 2888 124 0.92 13.91 1.01 0.97 6674.70| | 3: 2.83 - 2.48 2820 163 0.88 18.07 0.99 0.97 5584.52| | 4: 2.47 - 2.25 2825 136 0.91 15.04 1.00 0.98 2773.31| | 5: 2.25 - 2.09 2756 127 0.89 17.37 1.01 0.98 2773.31| | 6: 2.09 - 1.97 2846 113 0.91 13.88 1.02 0.97 1611.80| | 7: 1.97 - 1.87 2787 165 0.94 10.78 1.02 0.97 621.19| | 8: 1.87 - 1.79 2789 144 0.91 14.35 0.99 0.97 621.19| | 9: 1.79 - 1.72 2745 138 0.93 11.44 0.98 0.97 341.02| | 10: 1.72 - 1.66 2831 160 0.93 12.31 0.98 0.97 284.91| | 11: 1.66 - 1.61 2712 147 0.93 12.97 0.98 0.97 271.93| | 12: 1.61 - 1.56 2773 144 0.95 9.58 0.99 0.97 149.55| | 13: 1.56 - 1.52 2745 130 0.94 11.21 1.02 0.97 149.55| | 14: 1.52 - 1.48 2803 134 0.94 11.37 1.02 0.97 134.04| | 15: 1.48 - 1.45 2738 128 0.95 10.61 1.01 0.98 105.63| | 16: 1.45 - 1.42 2756 161 0.94 11.82 1.02 0.98 105.63| | 17: 1.42 - 1.39 2785 139 0.94 11.61 1.01 0.98 95.80| | 18: 1.39 - 1.36 2741 179 0.94 12.03 1.01 0.98 90.11| | 19: 1.36 - 1.34 2807 134 0.94 12.58 1.00 0.98 90.11| | 20: 1.34 - 1.32 2696 147 0.94 12.69 0.99 0.96 84.43| | 21: 1.32 - 1.30 2785 112 0.93 13.61 0.98 0.96 84.03| | 22: 1.29 - 1.27 2704 152 0.93 14.08 0.98 0.96 84.03| | 23: 1.27 - 1.26 2802 156 0.92 14.97 0.97 0.95 84.03| | 24: 1.26 - 1.24 2744 132 0.92 15.14 0.96 0.95 84.03| | 25: 1.24 - 1.22 2733 148 0.91 16.45 0.96 0.94 85.04| | 26: 1.22 - 1.21 2727 135 0.90 18.15 1.03 0.93 86.15| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.93 86.15| | 28: 1.19 - 1.18 2671 147 0.88 20.16 1.01 0.93 88.74| | 29: 1.18 - 1.16 2800 134 0.88 20.41 0.99 0.93 89.72| | 30: 1.16 - 1.15 2739 148 0.87 21.80 0.98 0.93 89.72| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 84.03 max = 6674.70 mean = 1028.41| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 14.21| |phase err.(test): min = 0.00 max = 88.49 mean = 14.32| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1196 0.1378 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1498 0.1497 0.1561 n_refl.: 87574 remove outliers: r(all,work,free)=0.1498 0.1497 0.1561 n_refl.: 87574 overall B=-0.01 to atoms: r(all,work,free)=0.1497 0.1495 0.1560 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1196 0.1380 n_refl.: 87574 remove outliers: r(all,work,free)=0.1204 0.1195 0.1380 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4225 282.990 248.142 0.414 1.001 0.283 11.894-9.307 91.18 89 4 0.2269 469.701 449.379 0.840 1.002 0.187 9.237-7.194 98.18 209 7 0.2481 385.520 379.291 0.915 1.002 0.107 7.162-5.571 100.00 427 22 0.2194 293.328 283.340 0.895 1.002 0.103 5.546-4.326 100.00 867 58 0.1167 402.667 398.322 0.951 1.002 0.100 4.315-3.360 100.00 1859 96 0.0979 382.939 380.336 0.996 1.002 0.100 3.356-2.611 100.00 3867 181 0.1185 251.571 249.418 1.000 1.001 0.048 2.608-2.026 99.99 8198 413 0.1036 166.769 165.830 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0982 81.441 81.680 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1241 36.114 35.735 1.022 0.996 0.000 1.221-1.150 99.97 13689 708 0.2124 22.755 21.376 0.979 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0273 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2603 0.1934 0.081 5.264 8.8 119.3 19.9 258 0.000 1_bss: 0.1629 0.1760 0.081 5.264 9.0 119.5 20.1 258 0.000 1_settarget: 0.1629 0.1760 0.081 5.264 9.0 119.5 20.1 258 0.000 1_nqh: 0.1640 0.1765 0.081 5.264 9.0 119.5 20.1 258 0.013 1_weight: 0.1640 0.1765 0.081 5.264 9.0 119.5 20.1 258 0.013 1_xyzrec: 0.1213 0.1467 0.007 0.927 9.0 119.5 20.1 258 0.136 1_adp: 0.1244 0.1546 0.007 0.927 8.6 118.9 21.1 258 0.136 1_regHadp: 0.1248 0.1548 0.007 0.927 8.6 118.9 21.1 258 0.136 1_occ: 0.1247 0.1549 0.007 0.927 8.6 118.9 21.1 258 0.136 2_bss: 0.1246 0.1543 0.007 0.927 8.7 119.0 21.2 258 0.136 2_settarget: 0.1246 0.1543 0.007 0.927 8.7 119.0 21.2 258 0.136 2_updatecdl: 0.1246 0.1543 0.007 0.947 8.7 119.0 21.2 258 0.136 2_nqh: 0.1248 0.1544 0.007 0.947 8.7 119.0 21.2 258 0.130 2_sol: 0.1237 0.1487 0.007 0.947 8.7 119.0 23.7 439 n/a 2_weight: 0.1237 0.1487 0.007 0.947 8.7 119.0 23.7 439 n/a 2_xyzrec: 0.1235 0.1515 0.006 0.862 8.7 119.0 23.7 439 n/a 2_adp: 0.1205 0.1484 0.006 0.862 8.8 115.0 23.4 439 n/a 2_regHadp: 0.1205 0.1484 0.006 0.862 8.8 115.0 23.4 439 n/a 2_occ: 0.1206 0.1483 0.006 0.862 8.8 115.0 23.4 439 n/a 3_bss: 0.1203 0.1481 0.006 0.862 8.8 115.0 23.4 439 n/a 3_settarget: 0.1203 0.1481 0.006 0.862 8.8 115.0 23.4 439 n/a 3_updatecdl: 0.1203 0.1481 0.006 0.861 8.8 115.0 23.4 439 n/a 3_nqh: 0.1203 0.1481 0.006 0.861 8.8 115.0 23.4 439 n/a 3_sol: 0.1230 0.1493 0.006 0.861 8.8 115.0 22.1 444 n/a 3_weight: 0.1230 0.1493 0.006 0.861 8.8 115.0 22.1 444 n/a 3_xyzrec: 0.1237 0.1460 0.006 0.918 8.8 115.0 22.1 444 n/a 3_adp: 0.1222 0.1410 0.006 0.918 9.3 110.0 21.7 444 n/a 3_regHadp: 0.1223 0.1411 0.006 0.918 9.3 110.0 21.7 444 n/a 3_occ: 0.1217 0.1410 0.006 0.918 9.3 110.0 21.7 444 n/a 4_bss: 0.1200 0.1376 0.006 0.918 9.3 110.0 21.7 444 n/a 4_settarget: 0.1200 0.1376 0.006 0.918 9.3 110.0 21.7 444 n/a 4_updatecdl: 0.1200 0.1376 0.006 0.917 9.3 110.0 21.7 444 n/a 4_nqh: 0.1200 0.1376 0.006 0.917 9.3 110.0 21.7 444 n/a 4_sol: 0.1191 0.1370 0.006 0.917 9.3 110.0 21.4 443 n/a 4_weight: 0.1191 0.1370 0.006 0.917 9.3 110.0 21.4 443 n/a 4_xyzrec: 0.1190 0.1385 0.006 0.972 9.3 110.0 21.4 443 n/a 4_adp: 0.1179 0.1379 0.006 0.972 9.2 106.0 21.2 443 n/a 4_regHadp: 0.1180 0.1379 0.006 0.972 9.2 106.0 21.2 443 n/a 4_occ: 0.1177 0.1378 0.006 0.972 9.2 106.0 21.2 443 n/a 5_bss: 0.1176 0.1381 0.006 0.972 9.2 106.0 21.2 443 n/a 5_settarget: 0.1176 0.1381 0.006 0.972 9.2 106.0 21.2 443 n/a 5_updatecdl: 0.1176 0.1381 0.006 0.975 9.2 106.0 21.2 443 n/a 5_setrh: 0.1177 0.1380 0.006 0.975 9.2 106.0 21.2 443 n/a 5_nqh: 0.1177 0.1380 0.006 0.975 9.2 106.0 21.2 443 n/a 5_sol: 0.1171 0.1361 0.006 0.975 9.2 106.0 21.2 453 n/a 5_weight: 0.1171 0.1361 0.006 0.975 9.2 106.0 21.2 453 n/a 5_xyzrec: 0.1195 0.1379 0.006 1.023 9.2 106.0 21.2 453 n/a 5_adp: 0.1198 0.1380 0.006 1.023 9.3 104.7 21.2 453 n/a 5_regHadp: 0.1198 0.1380 0.006 1.023 9.3 104.7 21.2 453 n/a 5_occ: 0.1196 0.1378 0.006 1.023 9.3 104.7 21.2 453 n/a end: 0.1195 0.1380 0.006 1.023 9.3 104.7 21.2 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1318715_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1318715_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.1200 Refinement macro-cycles (run) : 3453.8300 Write final files (write_after_run_outputs) : 74.4800 Total : 3533.4300 Total CPU time: 59.52 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:10:43 PST -0800 (1735452643.72 s) Start R-work = 0.1629, R-free = 0.1760 Final R-work = 0.1195, R-free = 0.1380 =============================================================================== Job complete usr+sys time: 3679.70 seconds wall clock time: 66 minutes 4.91 seconds (3964.91 seconds total)