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_7650209.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7650209.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7650209.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" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.24, per 1000 atoms: 0.66 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: 0.51 Conformation dependent library (CDL) restraints added in 201.1 milliseconds Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 512 0.91 - 1.16: 1114 1.16 - 1.40: 601 1.40 - 1.65: 859 1.65 - 1.90: 67 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 165 " pdb=" CA ALA A 165 " ideal model delta sigma weight residual 1.459 1.184 0.275 1.19e-02 7.06e+03 5.34e+02 bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.509 -0.188 1.00e-02 1.00e+04 3.52e+02 bond pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 1.332 1.489 -0.157 8.60e-03 1.35e+04 3.33e+02 bond pdb=" CA ARG A 48 " pdb=" C ARG A 48 " ideal model delta sigma weight residual 1.526 1.751 -0.225 1.28e-02 6.10e+03 3.10e+02 bond pdb=" C HIS A 126 " pdb=" O HIS A 126 " ideal model delta sigma weight residual 1.234 1.018 0.216 1.27e-02 6.20e+03 2.89e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 2849 4.17 - 8.35: 1898 8.35 - 12.52: 807 12.52 - 16.69: 201 16.69 - 20.86: 22 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 152 " pdb=" C ILE A 152 " pdb=" N ALEU A 153 " ideal model delta sigma weight residual 122.99 137.39 -14.40 1.07e+00 8.73e-01 1.81e+02 angle pdb=" CA BLEU A 153 " pdb=" C BLEU A 153 " pdb=" O BLEU A 153 " ideal model delta sigma weight residual 120.30 134.14 -13.84 1.07e+00 8.73e-01 1.67e+02 angle pdb=" OD1 ASN A 81 " pdb=" CG ASN A 81 " pdb=" ND2 ASN A 81 " ideal model delta sigma weight residual 122.60 110.15 12.45 1.00e+00 1.00e+00 1.55e+02 angle pdb=" C LEU A 77 " pdb=" N GLY A 78 " pdb=" CA GLY A 78 " ideal model delta sigma weight residual 119.94 133.62 -13.68 1.11e+00 8.12e-01 1.52e+02 angle pdb=" O LEU A 7 " pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 123.27 109.53 13.74 1.13e+00 7.83e-01 1.48e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 914 16.41 - 32.81: 139 32.81 - 49.21: 37 49.21 - 65.62: 16 65.62 - 82.02: 5 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 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 180.00 157.03 22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CD1 PHE A 119 " pdb=" CG PHE A 119 " pdb=" CD2 PHE A 119 " pdb=" HD2 PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.215: 92 0.215 - 0.424: 79 0.424 - 0.634: 44 0.634 - 0.844: 22 0.844 - 1.053: 6 Chirality restraints: 243 Sorted by residual: 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 -1.54 -1.05 2.00e-01 2.50e+01 2.77e+01 chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.49 -0.98 2.00e-01 2.50e+01 2.38e+01 chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.28e+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 7.83e-02 1.84e+02 pdb=" CG PHE A 119 " -0.167 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.113 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.058 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.043 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.089 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.066 2.00e-02 2.50e+03 6.78e-02 1.38e+02 pdb=" CG TYR A 139 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.092 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.050 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.119 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.053 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.084 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.005 2.00e-02 2.50e+03 5.59e-02 9.38e+01 pdb=" CG PHE A 164 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.080 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.052 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.086 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1035 2.32 - 2.89: 8049 2.89 - 3.46: 10545 3.46 - 4.03: 15207 4.03 - 4.60: 21803 Nonbonded interactions: 56639 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.748 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.846 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.857 2.450 nonbonded pdb=" O LEU A 92 " pdb=" H AGLU A 96 " model vdw 1.866 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.866 2.100 ... (remaining 56634 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_7650209_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= 0.2611 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787888 | | target function (ml) not normalized (work): 232247.785032 | | target function (ml) not normalized (free): 11796.000060 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3036 0.2097 7.0688 4.9477| | 2: 3.57 - 2.84 1.00 2876 122 0.2439 0.1790 4.3464 4.3493| | 3: 2.84 - 2.48 1.00 2833 165 0.2375 0.1660 4.1269 4.1602| | 4: 2.47 - 2.25 1.00 2825 136 0.2310 0.1495 3.8262 3.8422| | 5: 2.25 - 2.09 1.00 2756 127 0.2476 0.1555 3.7965 3.8034| | 6: 2.09 - 1.97 1.00 2846 113 0.2572 0.1542 3.4678 3.5395| | 7: 1.97 - 1.87 1.00 2787 165 0.2554 0.1863 3.1228 3.175| | 8: 1.87 - 1.79 1.00 2789 144 0.2471 0.1745 3.0453 3.0953| | 9: 1.79 - 1.72 1.00 2745 138 0.2454 0.1734 2.9136 2.8991| | 10: 1.72 - 1.66 1.00 2789 158 0.2448 0.2087 2.7994 2.9371| | 11: 1.66 - 1.61 1.00 2740 147 0.2452 0.1793 2.7327 2.7529| | 12: 1.61 - 1.56 1.00 2787 146 0.2527 0.2128 2.6104 2.6735| | 13: 1.56 - 1.52 1.00 2745 130 0.2541 0.1943 2.5625 2.626| | 14: 1.52 - 1.48 1.00 2803 134 0.2557 0.2132 2.4906 2.592| | 15: 1.48 - 1.45 1.00 2738 128 0.2564 0.2063 2.4456 2.484| | 16: 1.45 - 1.42 1.00 2756 161 0.2638 0.2161 2.3776 2.426| | 17: 1.42 - 1.39 1.00 2785 139 0.2679 0.2082 2.3369 2.3981| | 18: 1.39 - 1.36 1.00 2741 179 0.2706 0.2127 2.2797 2.2785| | 19: 1.36 - 1.34 1.00 2807 134 0.2672 0.2308 2.2681 2.3025| | 20: 1.34 - 1.32 1.00 2696 147 0.2693 0.2125 2.1907 2.175| | 21: 1.32 - 1.30 1.00 2785 112 0.2708 0.2135 2.1717 2.1369| | 22: 1.29 - 1.27 1.00 2704 152 0.2769 0.2689 2.1375 2.2172| | 23: 1.27 - 1.26 1.00 2802 156 0.2765 0.2288 2.0942 2.1301| | 24: 1.26 - 1.24 1.00 2744 132 0.2767 0.2597 2.0598 2.2234| | 25: 1.24 - 1.22 1.00 2734 148 0.2823 0.2372 2.0304 2.0366| | 26: 1.22 - 1.21 1.00 2727 135 0.2869 0.2514 2.0022 2.1492| | 27: 1.21 - 1.19 1.00 2814 148 0.2975 0.2423 1.9982 1.9834| | 28: 1.19 - 1.18 1.00 2671 147 0.3010 0.2523 1.9909 1.9215| | 29: 1.18 - 1.16 1.00 2800 134 0.2975 0.2541 1.9587 2.0079| | 30: 1.16 - 1.15 1.00 2740 148 0.3072 0.2869 1.9282 1.9809| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.93 0.76 0.23 1476.95| | 2: 3.57 - 2.84 2876 122 0.80 26.07 1.27 0.23 1476.95| | 3: 2.84 - 2.48 2833 165 0.74 32.07 1.24 0.24 1223.23| | 4: 2.47 - 2.25 2825 136 0.81 25.44 1.25 0.25 564.79| | 5: 2.25 - 2.09 2756 127 0.77 29.10 1.28 0.25 564.79| | 6: 2.09 - 1.97 2846 113 0.84 22.43 1.30 0.25 306.31| | 7: 1.97 - 1.87 2787 165 0.90 16.03 1.28 0.26 85.86| | 8: 1.87 - 1.79 2789 144 0.86 20.34 1.25 0.26 85.86| | 9: 1.79 - 1.72 2745 138 0.89 17.99 1.24 0.25 53.18| | 10: 1.72 - 1.66 2789 158 0.87 19.78 1.23 0.25 46.63| | 11: 1.66 - 1.61 2740 147 0.86 20.92 1.24 0.25 45.09| | 12: 1.61 - 1.56 2787 146 0.88 18.55 1.24 0.25 29.42| | 13: 1.56 - 1.52 2745 130 0.86 20.52 1.24 0.25 29.42| | 14: 1.52 - 1.48 2803 134 0.86 20.94 1.24 0.25 26.42| | 15: 1.48 - 1.45 2738 128 0.87 20.11 1.22 0.25 20.94| | 16: 1.45 - 1.42 2756 161 0.86 21.66 1.24 0.25 20.94| | 17: 1.42 - 1.39 2785 139 0.86 20.94 1.23 0.25 17.69| | 18: 1.39 - 1.36 2741 179 0.86 21.44 1.23 0.25 15.81| | 19: 1.36 - 1.34 2807 134 0.86 21.88 1.21 0.25 15.81| | 20: 1.34 - 1.32 2696 147 0.87 20.99 1.21 0.24 12.82| | 21: 1.32 - 1.30 2785 112 0.86 21.68 1.20 0.24 12.61| | 22: 1.29 - 1.27 2704 152 0.86 22.11 1.22 0.24 12.34| | 23: 1.27 - 1.26 2802 156 0.86 21.77 1.22 0.24 10.95| | 24: 1.26 - 1.24 2744 132 0.85 22.88 1.21 0.24 10.95| | 25: 1.24 - 1.22 2734 148 0.84 23.43 1.20 0.24 10.29| | 26: 1.22 - 1.21 2727 135 0.85 23.39 1.21 0.24 9.55| | 27: 1.21 - 1.19 2814 148 0.84 24.05 1.21 0.24 9.55| | 28: 1.19 - 1.18 2671 147 0.84 23.97 1.18 0.23 8.58| | 29: 1.18 - 1.16 2800 134 0.84 24.19 1.17 0.23 8.22| | 30: 1.16 - 1.15 2740 148 0.83 25.56 1.16 0.23 8.22| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.22 max = 1476.95 mean = 213.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 22.31| |phase err.(test): min = 0.00 max = 89.65 mean = 22.11| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.275 1557 Z= 5.637 Angle : 5.171 17.906 2118 Z= 3.655 Chirality : 0.401 1.053 243 Planarity : 0.032 0.108 284 Dihedral : 14.076 82.020 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.08 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 34.59 % 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: -2.43 (0.46), residues: 224 helix: -2.39 (0.38), residues: 102 sheet: -0.74 (0.75), residues: 38 loop : -0.61 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.016 ARG A 156 TYR 0.061 0.025 TYR A 141 PHE 0.151 0.039 PHE A 119 HIS 0.088 0.044 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2611 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787888 | | target function (ml) not normalized (work): 232247.785032 | | target function (ml) not normalized (free): 11796.000060 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2569 0.2612 0.1927 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2569 0.2612 0.1927 n_refl.: 87602 remove outliers: r(all,work,free)=0.1982 0.1987 0.1927 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2005 0.2010 0.1938 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1645 0.1639 0.1751 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1639 0.1751 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 0.3808 386.593 359.511 0.733 0.914 0.402 11.894-9.307 99.02 97 4 0.1872 614.084 595.938 1.018 0.916 0.380 9.237-7.194 100.00 213 7 0.2152 502.245 490.236 1.051 0.916 0.370 7.162-5.571 100.00 427 22 0.2198 376.907 364.878 1.024 0.917 0.340 5.546-4.326 100.00 867 58 0.1295 517.400 510.968 1.048 0.918 0.218 4.315-3.360 100.00 1859 96 0.1132 492.051 487.966 1.096 0.919 0.189 3.356-2.611 100.00 3867 181 0.1460 323.252 319.743 1.084 0.921 0.089 2.608-2.026 99.99 8198 413 0.1349 214.287 212.111 1.091 0.924 0.000 2.025-1.573 100.00 17313 902 0.1646 104.646 104.102 1.090 0.929 0.000 1.573-1.221 100.00 36679 1900 0.2066 46.405 45.082 1.066 0.937 0.000 1.221-1.150 99.97 13689 708 0.2586 29.238 27.005 1.031 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0430 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1639 r_free=0.1751 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1639 r_free=0.1751 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.464232 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2021.874566 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 0.1210 0.1464 0.0253 0.007 0.9 1.0 0.5 0.0 0 12.232 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 14.64 2.53 3.013 19.046 2021.875 0.017 12.44 15.41 2.97 3.287 19.593 2021.875 0.016 Individual atomic B min max mean iso aniso Overall: 8.58 118.70 21.11 2.88 0 1785 Protein: 8.58 118.70 17.95 2.88 0 1519 Water: 11.15 114.66 39.41 N/A 0 258 Other: 23.56 37.41 29.80 N/A 0 8 Chain A: 8.58 118.70 21.11 N/A 0 1785 Histogram: Values Number of atoms 8.58 - 19.60 1204 19.60 - 30.61 232 30.61 - 41.62 161 41.62 - 52.63 102 52.63 - 63.64 55 63.64 - 74.65 17 74.65 - 85.67 7 85.67 - 96.68 3 96.68 - 107.69 1 107.69 - 118.70 3 =========================== Idealize ADP of riding H ========================== r_work=0.1245 r_free=0.1542 r_work=0.1249 r_free=0.1547 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1249 r_free = 0.1547 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 = 0.1250 r_free = 0.1551 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1250 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015450 | | target function (ls_wunit_k1) not normalized (work): 1286.917061 | | target function (ls_wunit_k1) not normalized (free): 113.547378 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1264 0.1250 0.1551 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1706 0.1705 0.1773 n_refl.: 87593 remove outliers: r(all,work,free)=0.1706 0.1705 0.1773 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1729 0.1728 0.1789 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1262 0.1248 0.1545 n_refl.: 87593 remove outliers: r(all,work,free)=0.1262 0.1247 0.1545 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 0.3609 298.702 278.654 0.635 1.002 0.380 11.894-9.307 99.02 97 4 0.1592 478.504 466.489 0.908 1.003 0.380 9.237-7.194 100.00 213 7 0.1801 391.358 386.164 0.950 1.003 0.350 7.162-5.571 100.00 427 22 0.1710 293.692 288.299 0.922 1.003 0.258 5.546-4.326 100.00 867 58 0.0912 403.167 400.683 0.948 1.003 0.204 4.315-3.360 100.00 1859 96 0.0769 383.414 382.428 0.995 1.003 0.190 3.356-2.611 100.00 3867 181 0.1022 251.883 251.221 0.998 1.002 0.110 2.608-2.026 99.99 8198 413 0.0983 166.976 166.374 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1220 81.542 81.710 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1661 36.159 35.612 1.005 0.998 0.000 1.221-1.150 99.97 13689 708 0.2365 22.783 21.285 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=0.0553 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1247 r_free=0.1545 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** Total number of N/Q/H flips: 1 r_work=0.1249 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1249 r_free=0.1545 | n_water=258 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1258 r_free=0.1547 | n_water=252 | time (s): 26.670 (total time: 29.080) Filter (q & B) r_work=0.1262 r_free=0.1546 | n_water=249 | time (s): 4.020 (total time: 33.100) Compute maps r_work=0.1262 r_free=0.1546 | n_water=249 | time (s): 1.960 (total time: 35.060) Filter (map) r_work=0.1281 r_free=0.1551 | n_water=235 | time (s): 3.990 (total time: 39.050) Find peaks r_work=0.1281 r_free=0.1551 | n_water=235 | time (s): 0.740 (total time: 39.790) Add new water r_work=0.1441 r_free=0.1696 | n_water=455 | time (s): 3.880 (total time: 43.670) Refine new water occ: r_work=0.1350 r_free=0.1570 adp: r_work=0.1266 r_free=0.1514 occ: r_work=0.1280 r_free=0.1507 adp: r_work=0.1243 r_free=0.1492 occ: r_work=0.1247 r_free=0.1484 adp: r_work=0.1237 r_free=0.1484 ADP+occupancy (water only), MIN, final r_work=0.1237 r_free=0.1484 r_work=0.1237 r_free=0.1484 | n_water=455 | time (s): 92.120 (total time: 135.790) Filter (q & B) r_work=0.1243 r_free=0.1489 | n_water=437 | time (s): 3.940 (total time: 139.730) Filter (dist only) r_work=0.1243 r_free=0.1489 | n_water=437 | time (s): 41.420 (total time: 181.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.662730 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1563.530594 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 0.1529 0.0292 0.007 0.9 2.2 0.5 0.0 0 12.831 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 15.29 2.92 3.807 23.349 1563.531 0.016 12.04 14.96 2.93 4.262 23.130 1563.531 0.015 Individual atomic B min max mean iso aniso Overall: 8.82 113.84 23.34 2.62 202 1762 Protein: 8.82 113.84 17.70 2.62 0 1519 Water: 11.21 72.33 42.84 N/A 202 235 Other: 24.63 35.92 29.37 N/A 0 8 Chain A: 8.82 113.84 20.41 N/A 0 1762 Chain S: 16.75 70.14 48.88 N/A 202 0 Histogram: Values Number of atoms 8.82 - 19.32 1212 19.32 - 29.83 238 29.83 - 40.33 193 40.33 - 50.83 139 50.83 - 61.33 111 61.33 - 71.84 58 71.84 - 82.34 7 82.34 - 92.84 3 92.84 - 103.34 1 103.34 - 113.84 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1497 r_work=0.1203 r_free=0.1496 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1496 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1495 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1203 r_free= 0.1495 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.014102 | | target function (ls_wunit_k1) not normalized (work): 1174.609867 | | target function (ls_wunit_k1) not normalized (free): 108.164709 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1203 0.1495 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1611 0.1606 0.1734 n_refl.: 87592 remove outliers: r(all,work,free)=0.1611 0.1606 0.1734 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1615 0.1610 0.1737 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1199 0.1491 n_refl.: 87592 remove outliers: r(all,work,free)=0.1212 0.1198 0.1491 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3472 295.016 271.102 0.620 0.939 0.360 11.894-9.307 99.02 97 4 0.1555 478.504 474.468 0.976 0.940 0.360 9.237-7.194 100.00 213 7 0.1695 391.358 391.669 1.047 0.940 0.290 7.162-5.571 100.00 427 22 0.1494 293.692 290.472 1.006 0.940 0.240 5.546-4.326 100.00 867 58 0.0837 403.167 400.502 1.020 0.940 0.205 4.315-3.360 100.00 1859 96 0.0712 383.414 382.317 1.066 0.941 0.200 3.356-2.611 100.00 3867 181 0.0957 251.883 251.134 1.075 0.941 0.072 2.608-2.026 99.99 8198 413 0.0968 166.976 166.570 1.082 0.942 0.000 2.025-1.573 100.00 17313 902 0.1175 81.542 81.681 1.090 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1611 36.159 35.665 1.077 0.945 0.000 1.221-1.150 99.97 13689 708 0.2338 22.783 21.341 1.033 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0402 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1491 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=0.1198 r_free=0.1491 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1491 | n_water=437 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1198 r_free=0.1490 | n_water=435 | time (s): 37.230 (total time: 39.570) Filter (q & B) r_work=0.1198 r_free=0.1490 | n_water=435 | time (s): 1.020 (total time: 40.590) Compute maps r_work=0.1198 r_free=0.1490 | n_water=435 | time (s): 1.210 (total time: 41.800) Filter (map) r_work=0.1240 r_free=0.1484 | n_water=290 | time (s): 3.300 (total time: 45.100) Find peaks r_work=0.1240 r_free=0.1484 | n_water=290 | time (s): 0.700 (total time: 45.800) Add new water r_work=0.1360 r_free=0.1597 | n_water=474 | time (s): 3.530 (total time: 49.330) Refine new water occ: r_work=0.1262 r_free=0.1524 adp: r_work=0.1263 r_free=0.1526 occ: r_work=0.1240 r_free=0.1506 adp: r_work=0.1238 r_free=0.1505 occ: r_work=0.1227 r_free=0.1495 adp: r_work=0.1219 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1219 r_free=0.1489 r_work=0.1219 r_free=0.1489 | n_water=474 | time (s): 240.790 (total time: 290.120) Filter (q & B) r_work=0.1222 r_free=0.1491 | n_water=446 | time (s): 2.740 (total time: 292.860) Filter (dist only) r_work=0.1222 r_free=0.1490 | n_water=445 | time (s): 36.750 (total time: 329.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.012218 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 53.985449 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 0.1453 0.0224 0.006 0.9 1.9 0.5 0.0 0 1.006 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.53 2.24 3.634 22.137 53.985 3.724 12.08 14.04 1.96 4.174 21.952 53.985 3.650 Individual atomic B min max mean iso aniso Overall: 9.28 108.87 21.70 2.34 213 1759 Protein: 9.28 108.87 17.24 2.34 0 1519 Water: 11.62 70.97 36.82 N/A 213 232 Other: 20.22 31.92 25.85 N/A 0 8 Chain A: 9.28 108.87 19.91 N/A 0 1759 Chain S: 15.64 69.08 36.48 N/A 213 0 Histogram: Values Number of atoms 9.28 - 19.24 1234 19.24 - 29.20 266 29.20 - 39.16 223 39.16 - 49.12 140 49.12 - 59.07 73 59.07 - 69.03 22 69.03 - 78.99 8 78.99 - 88.95 3 88.95 - 98.91 1 98.91 - 108.87 2 =========================== Idealize ADP of riding H ========================== r_work=0.1208 r_free=0.1404 r_work=0.1209 r_free=0.1405 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1405 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1402 target_work(ml) = 3.648 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1203 r_free= 0.1402 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.648405 | | target function (ml) not normalized (work): 303886.588721 | | target function (ml) not normalized (free): 16051.619392 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1203 0.1402 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1547 0.1546 0.1599 n_refl.: 87589 remove outliers: r(all,work,free)=0.1547 0.1546 0.1599 n_refl.: 87589 overall B=-0.02 to atoms: r(all,work,free)=0.1543 0.1542 0.1597 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1196 0.1385 n_refl.: 87589 remove outliers: r(all,work,free)=0.1201 0.1192 0.1385 n_refl.: 87581 ======================== 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 0.3742 291.618 261.241 0.483 1.001 0.330 11.894-9.307 98.04 96 4 0.2412 471.840 463.525 0.853 1.002 0.330 9.237-7.194 98.64 210 7 0.2406 383.906 382.628 0.945 1.002 0.190 7.162-5.571 100.00 427 22 0.2101 293.692 282.812 0.910 1.002 0.169 5.546-4.326 100.00 867 58 0.1086 403.167 398.834 0.949 1.003 0.154 4.315-3.360 100.00 1859 96 0.0922 383.414 380.646 0.993 1.002 0.147 3.356-2.611 100.00 3867 181 0.1144 251.883 249.974 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1042 166.976 166.001 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1003 81.542 81.686 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1290 36.159 35.733 1.022 0.999 0.000 1.221-1.150 99.97 13689 708 0.2130 22.783 21.399 0.982 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0465 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1385 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=0.1192 r_free=0.1385 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1385 | n_water=445 | time (s): 1.820 (total time: 1.820) Filter (dist) r_work=0.1192 r_free=0.1382 | n_water=444 | time (s): 38.380 (total time: 40.200) Filter (q & B) r_work=0.1192 r_free=0.1381 | n_water=443 | time (s): 2.530 (total time: 42.730) Compute maps r_work=0.1192 r_free=0.1381 | n_water=443 | time (s): 1.410 (total time: 44.140) Filter (map) r_work=0.1219 r_free=0.1373 | n_water=311 | time (s): 3.470 (total time: 47.610) Find peaks r_work=0.1219 r_free=0.1373 | n_water=311 | time (s): 0.590 (total time: 48.200) Add new water r_work=0.1287 r_free=0.1435 | n_water=468 | time (s): 2.960 (total time: 51.160) Refine new water occ: r_work=0.1211 r_free=0.1372 adp: r_work=0.1212 r_free=0.1372 occ: r_work=0.1195 r_free=0.1360 adp: r_work=0.1194 r_free=0.1359 occ: r_work=0.1184 r_free=0.1357 adp: r_work=0.1179 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1353 r_work=0.1179 r_free=0.1353 | n_water=468 | time (s): 134.300 (total time: 185.460) Filter (q & B) r_work=0.1186 r_free=0.1354 | n_water=438 | time (s): 3.180 (total time: 188.640) Filter (dist only) r_work=0.1193 r_free=0.1351 | n_water=436 | time (s): 38.900 (total time: 227.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.891340 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 52.170389 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 0.1363 0.0168 0.006 0.9 1.9 0.5 0.0 0 0.946 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.63 1.68 3.431 21.482 52.170 3.636 11.87 13.59 1.72 3.786 21.371 52.170 3.621 Individual atomic B min max mean iso aniso Overall: 9.27 105.07 21.22 2.19 209 1754 Protein: 9.27 105.07 16.98 2.19 0 1519 Water: 11.60 69.62 35.93 N/A 209 227 Other: 19.20 29.16 24.15 N/A 0 8 Chain A: 9.27 105.07 19.52 N/A 0 1754 Chain S: 15.11 58.49 35.45 N/A 209 0 Histogram: Values Number of atoms 9.27 - 18.85 1223 18.85 - 28.43 280 28.43 - 38.01 209 38.01 - 47.59 144 47.59 - 57.17 69 57.17 - 66.75 24 66.75 - 76.33 9 76.33 - 85.91 2 85.91 - 95.49 1 95.49 - 105.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1359 r_work=0.1188 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1359 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1183 r_free = 0.1360 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1183 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.620369 | | target function (ml) not normalized (work): 301522.468468 | | target function (ml) not normalized (free): 15934.681720 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1183 0.1360 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1516 0.1515 0.1561 n_refl.: 87581 remove outliers: r(all,work,free)=0.1516 0.1515 0.1561 n_refl.: 87581 overall B=-0.02 to atoms: r(all,work,free)=0.1513 0.1512 0.1559 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1183 0.1362 n_refl.: 87581 remove outliers: r(all,work,free)=0.1191 0.1182 0.1362 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4031 291.618 254.642 0.455 0.999 0.320 11.894-9.307 97.06 95 4 0.2441 469.318 458.282 0.840 1.001 0.320 9.237-7.194 98.18 209 7 0.2391 382.908 378.081 0.919 1.001 0.140 7.162-5.571 100.00 427 22 0.2143 293.692 283.345 0.900 1.001 0.140 5.546-4.326 100.00 867 58 0.1134 403.167 398.646 0.951 1.001 0.132 4.315-3.360 100.00 1859 96 0.0950 383.414 380.679 0.994 1.001 0.127 3.356-2.611 100.00 3867 181 0.1162 251.883 249.972 1.001 1.002 0.110 2.608-2.026 99.99 8198 413 0.1035 166.976 166.079 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0967 81.542 81.797 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1239 36.159 35.777 1.019 1.001 0.000 1.221-1.150 99.97 13689 708 0.2121 22.783 21.358 0.975 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0417 ============================ 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=436 | time (s): 1.990 (total time: 1.990) Filter (dist) r_work=0.1183 r_free=0.1362 | n_water=436 | time (s): 34.420 (total time: 36.410) Filter (q & B) r_work=0.1183 r_free=0.1363 | n_water=435 | time (s): 2.760 (total time: 39.170) Compute maps r_work=0.1183 r_free=0.1363 | n_water=435 | time (s): 1.580 (total time: 40.750) Filter (map) r_work=0.1211 r_free=0.1366 | n_water=324 | time (s): 3.550 (total time: 44.300) Find peaks r_work=0.1211 r_free=0.1366 | n_water=324 | time (s): 0.690 (total time: 44.990) Add new water r_work=0.1258 r_free=0.1410 | n_water=469 | time (s): 3.280 (total time: 48.270) Refine new water occ: r_work=0.1196 r_free=0.1354 adp: r_work=0.1196 r_free=0.1356 occ: r_work=0.1184 r_free=0.1344 adp: r_work=0.1183 r_free=0.1345 occ: r_work=0.1174 r_free=0.1341 adp: r_work=0.1172 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1172 r_free=0.1339 r_work=0.1172 r_free=0.1339 | n_water=469 | time (s): 172.290 (total time: 220.560) Filter (q & B) r_work=0.1180 r_free=0.1344 | n_water=435 | time (s): 3.590 (total time: 224.150) Filter (dist only) r_work=0.1180 r_free=0.1343 | n_water=434 | time (s): 38.100 (total time: 262.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.872530 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.511819 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 0.1210 0.1372 0.0163 0.007 1.0 3.5 0.5 0.0 0 0.936 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 13.72 1.63 3.307 21.145 39.512 3.630 12.11 13.67 1.56 3.356 21.118 39.512 3.626 Individual atomic B min max mean iso aniso Overall: 9.26 103.60 21.07 2.11 208 1753 Protein: 9.26 103.60 16.91 2.11 0 1519 Water: 11.49 69.43 35.61 N/A 208 226 Other: 19.68 28.40 24.12 N/A 0 8 Chain A: 9.26 103.60 19.42 N/A 0 1753 Chain S: 15.05 58.44 35.00 N/A 208 0 Histogram: Values Number of atoms 9.26 - 18.70 1222 18.70 - 28.13 284 28.13 - 37.56 198 37.56 - 47.00 152 47.00 - 56.43 65 56.43 - 65.86 23 65.86 - 75.30 12 75.30 - 84.73 2 84.73 - 94.16 1 94.16 - 103.60 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1367 r_work=0.1211 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1211 r_free = 0.1367 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1364 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1207 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.625050 | | target function (ml) not normalized (work): 301905.054955 | | target function (ml) not normalized (free): 15934.172631 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1423 0.1400 5.6904 5.6338| | 2: 3.57 - 2.84 1.00 2888 124 0.1133 0.1468 5.2041 5.2715| | 3: 2.83 - 2.48 1.00 2820 163 0.1237 0.1255 5.0089 5.0176| | 4: 2.47 - 2.25 1.00 2825 136 0.1035 0.1105 4.7069 4.7386| | 5: 2.25 - 2.09 1.00 2756 127 0.1007 0.1154 4.6475 4.7268| | 6: 2.09 - 1.97 1.00 2846 113 0.0992 0.1169 4.3559 4.4622| | 7: 1.97 - 1.87 1.00 2787 165 0.1001 0.1226 4.0772 4.1836| | 8: 1.87 - 1.79 1.00 2789 144 0.1030 0.1236 3.991 4.0736| | 9: 1.79 - 1.72 1.00 2745 138 0.0968 0.1260 3.723 3.8767| | 10: 1.72 - 1.66 1.00 2831 160 0.1011 0.1320 3.6405 3.8236| | 11: 1.66 - 1.61 1.00 2712 147 0.0983 0.1096 3.5768 3.6008| | 12: 1.61 - 1.56 1.00 2773 144 0.0929 0.1177 3.3529 3.4725| | 13: 1.56 - 1.52 1.00 2745 130 0.0997 0.1083 3.3457 3.4237| | 14: 1.52 - 1.48 1.00 2803 134 0.1002 0.1081 3.2668 3.3346| | 15: 1.48 - 1.45 1.00 2738 128 0.1025 0.1322 3.174 3.3188| | 16: 1.45 - 1.42 1.00 2756 161 0.1070 0.1266 3.1512 3.2569| | 17: 1.42 - 1.39 1.00 2785 139 0.1128 0.1306 3.119 3.2461| | 18: 1.39 - 1.36 1.00 2741 179 0.1174 0.1356 3.0951 3.2609| | 19: 1.36 - 1.34 1.00 2807 134 0.1224 0.1602 3.0963 3.2726| | 20: 1.34 - 1.32 1.00 2696 147 0.1320 0.1451 3.0887 3.1284| | 21: 1.32 - 1.30 1.00 2785 112 0.1423 0.1619 3.0897 3.1613| | 22: 1.29 - 1.27 1.00 2704 152 0.1479 0.1930 3.0871 3.2746| | 23: 1.27 - 1.26 1.00 2802 156 0.1579 0.1840 3.1057 3.2108| | 24: 1.26 - 1.24 1.00 2744 132 0.1630 0.1794 3.0961 3.1911| | 25: 1.24 - 1.22 1.00 2733 148 0.1800 0.2321 3.111 3.2964| | 26: 1.22 - 1.21 1.00 2727 135 0.1876 0.1750 3.1272 3.1861| | 27: 1.21 - 1.19 1.00 2814 148 0.2019 0.2110 3.1429 3.149| | 28: 1.19 - 1.18 1.00 2671 147 0.2143 0.2299 3.1406 3.1583| | 29: 1.18 - 1.16 1.00 2800 134 0.2219 0.2367 3.1269 3.2227| | 30: 1.16 - 1.15 1.00 2739 148 0.2372 0.2504 3.1166 3.1673| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2921 171 0.95 9.02 1.00 0.97 6193.92| | 2: 3.57 - 2.84 2888 124 0.92 13.22 1.01 0.97 6193.92| | 3: 2.83 - 2.48 2820 163 0.89 17.40 0.99 0.97 5192.79| | 4: 2.47 - 2.25 2825 136 0.91 14.50 1.00 0.98 2611.20| | 5: 2.25 - 2.09 2756 127 0.90 16.68 1.01 0.98 2611.20| | 6: 2.09 - 1.97 2846 113 0.92 13.62 1.02 0.98 1535.67| | 7: 1.97 - 1.87 2787 165 0.94 10.73 1.02 0.98 618.39| | 8: 1.87 - 1.79 2789 144 0.91 14.29 1.00 0.98 618.39| | 9: 1.79 - 1.72 2745 138 0.93 11.42 0.98 0.97 338.79| | 10: 1.72 - 1.66 2831 160 0.93 12.26 0.98 0.97 282.80| | 11: 1.66 - 1.61 2712 147 0.93 12.90 0.98 0.97 269.73| | 12: 1.61 - 1.56 2773 144 0.95 9.48 0.99 0.97 146.47| | 13: 1.56 - 1.52 2745 130 0.94 11.02 1.02 0.97 146.47| | 14: 1.52 - 1.48 2803 134 0.94 11.18 1.02 0.98 130.91| | 15: 1.48 - 1.45 2738 128 0.95 10.31 1.01 0.98 102.41| | 16: 1.45 - 1.42 2756 161 0.94 11.48 1.02 0.98 102.41| | 17: 1.42 - 1.39 2785 139 0.94 11.40 1.01 0.98 92.61| | 18: 1.39 - 1.36 2741 179 0.94 11.69 1.01 0.99 86.94| | 19: 1.36 - 1.34 2807 134 0.94 12.24 1.00 0.99 86.94| | 20: 1.34 - 1.32 2696 147 0.94 12.41 0.99 0.97 82.08| | 21: 1.32 - 1.30 2785 112 0.94 13.36 0.98 0.97 81.74| | 22: 1.29 - 1.27 2704 152 0.93 13.82 0.98 0.96 81.89| | 23: 1.27 - 1.26 2802 156 0.92 14.79 0.98 0.95 82.66| | 24: 1.26 - 1.24 2744 132 0.92 14.94 0.97 0.95 82.66| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 84.14| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.03 0.94 85.79| | 27: 1.21 - 1.19 2814 148 0.89 18.69 1.02 0.94 85.79| | 28: 1.19 - 1.18 2671 147 0.88 20.16 1.01 0.93 89.03| | 29: 1.18 - 1.16 2800 134 0.88 20.47 0.99 0.93 90.25| | 30: 1.16 - 1.15 2739 148 0.86 21.85 0.99 0.93 90.25| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 81.74 max = 6193.92 mean = 966.92| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.98| |phase err.(test): min = 0.00 max = 88.84 mean = 14.08| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1207 0.1364 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1537 0.1538 0.1557 n_refl.: 87579 remove outliers: r(all,work,free)=0.1537 0.1538 0.1557 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1535 0.1536 0.1555 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1208 0.1363 n_refl.: 87579 remove outliers: r(all,work,free)=0.1215 0.1207 0.1363 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 0.4034 291.618 254.609 0.453 0.999 0.314 11.894-9.307 96.08 94 4 0.2441 471.206 451.499 0.829 1.001 0.254 9.237-7.194 97.73 208 7 0.2559 382.432 376.035 0.905 1.001 0.178 7.162-5.571 100.00 427 22 0.2257 293.692 283.499 0.895 1.001 0.159 5.546-4.326 100.00 867 58 0.1192 403.167 398.250 0.952 1.002 0.126 4.315-3.360 100.00 1859 96 0.1002 383.414 380.926 0.996 1.002 0.120 3.356-2.611 100.00 3867 181 0.1191 251.883 250.162 1.002 1.002 0.048 2.608-2.026 99.99 8198 413 0.1055 166.976 166.005 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0988 81.542 81.809 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1237 36.159 35.805 1.020 1.000 0.000 1.221-1.150 99.97 13689 708 0.2121 22.783 21.387 0.977 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0392 ================= 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 : 0.2611 0.1926 0.084 5.171 8.8 119.3 19.9 258 0.000 1_bss: 0.1639 0.1751 0.084 5.171 9.0 119.5 20.1 258 0.000 1_settarget: 0.1639 0.1751 0.084 5.171 9.0 119.5 20.1 258 0.000 1_nqh: 0.1639 0.1751 0.084 5.171 9.0 119.5 20.1 258 0.000 1_weight: 0.1639 0.1751 0.084 5.171 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1210 0.1464 0.007 0.938 9.0 119.5 20.1 258 0.125 1_adp: 0.1245 0.1542 0.007 0.938 8.6 118.7 21.1 258 0.125 1_regHadp: 0.1249 0.1547 0.007 0.938 8.6 118.7 21.1 258 0.125 1_occ: 0.1250 0.1551 0.007 0.938 8.6 118.7 21.1 258 0.125 2_bss: 0.1247 0.1545 0.007 0.938 8.7 118.8 21.3 258 0.125 2_settarget: 0.1247 0.1545 0.007 0.938 8.7 118.8 21.3 258 0.125 2_updatecdl: 0.1247 0.1545 0.007 0.945 8.7 118.8 21.3 258 0.125 2_nqh: 0.1249 0.1545 0.007 0.945 8.7 118.8 21.3 258 0.128 2_sol: 0.1243 0.1489 0.007 0.945 8.7 118.8 23.7 437 n/a 2_weight: 0.1243 0.1489 0.007 0.945 8.7 118.8 23.7 437 n/a 2_xyzrec: 0.1237 0.1529 0.007 0.880 8.7 118.8 23.7 437 n/a 2_adp: 0.1204 0.1497 0.007 0.880 8.8 113.8 23.3 437 n/a 2_regHadp: 0.1203 0.1496 0.007 0.880 8.8 113.8 23.3 437 n/a 2_occ: 0.1203 0.1495 0.007 0.880 8.8 113.8 23.3 437 n/a 3_bss: 0.1198 0.1491 0.007 0.880 8.8 113.9 23.4 437 n/a 3_settarget: 0.1198 0.1491 0.007 0.880 8.8 113.9 23.4 437 n/a 3_updatecdl: 0.1198 0.1491 0.007 0.880 8.8 113.9 23.4 437 n/a 3_nqh: 0.1198 0.1491 0.007 0.880 8.8 113.9 23.4 437 n/a 3_sol: 0.1222 0.1490 0.007 0.880 8.8 113.9 22.0 445 n/a 3_weight: 0.1222 0.1490 0.007 0.880 8.8 113.9 22.0 445 n/a 3_xyzrec: 0.1229 0.1453 0.006 0.914 8.8 113.9 22.0 445 n/a 3_adp: 0.1208 0.1404 0.006 0.914 9.3 108.9 21.7 445 n/a 3_regHadp: 0.1209 0.1405 0.006 0.914 9.3 108.9 21.7 445 n/a 3_occ: 0.1203 0.1402 0.006 0.914 9.3 108.9 21.7 445 n/a 4_bss: 0.1192 0.1385 0.006 0.914 9.3 108.9 21.7 445 n/a 4_settarget: 0.1192 0.1385 0.006 0.914 9.3 108.9 21.7 445 n/a 4_updatecdl: 0.1192 0.1385 0.006 0.914 9.3 108.9 21.7 445 n/a 4_nqh: 0.1192 0.1385 0.006 0.914 9.3 108.9 21.7 445 n/a 4_sol: 0.1193 0.1351 0.006 0.914 9.3 108.9 21.4 436 n/a 4_weight: 0.1193 0.1351 0.006 0.914 9.3 108.9 21.4 436 n/a 4_xyzrec: 0.1195 0.1363 0.006 0.945 9.3 108.9 21.4 436 n/a 4_adp: 0.1187 0.1359 0.006 0.945 9.3 105.1 21.2 436 n/a 4_regHadp: 0.1188 0.1359 0.006 0.945 9.3 105.1 21.2 436 n/a 4_occ: 0.1183 0.1360 0.006 0.945 9.3 105.1 21.2 436 n/a 5_bss: 0.1182 0.1362 0.006 0.945 9.3 105.1 21.2 436 n/a 5_settarget: 0.1182 0.1362 0.006 0.945 9.3 105.1 21.2 436 n/a 5_updatecdl: 0.1182 0.1362 0.006 0.946 9.3 105.1 21.2 436 n/a 5_setrh: 0.1183 0.1362 0.006 0.946 9.3 105.1 21.2 436 n/a 5_nqh: 0.1183 0.1362 0.006 0.946 9.3 105.1 21.2 436 n/a 5_sol: 0.1180 0.1343 0.006 0.946 9.3 105.1 21.1 434 n/a 5_weight: 0.1180 0.1343 0.006 0.946 9.3 105.1 21.1 434 n/a 5_xyzrec: 0.1210 0.1372 0.007 1.050 9.3 105.1 21.1 434 n/a 5_adp: 0.1211 0.1367 0.007 1.050 9.3 103.6 21.1 434 n/a 5_regHadp: 0.1211 0.1367 0.007 1.050 9.3 103.6 21.1 434 n/a 5_occ: 0.1207 0.1364 0.007 1.050 9.3 103.6 21.1 434 n/a end: 0.1207 0.1363 0.007 1.050 9.2 103.6 21.1 434 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7650209_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7650209_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7600 Refinement macro-cycles (run) : 3576.4500 Write final files (write_after_run_outputs) : 61.2100 Total : 3642.4200 Total CPU time: 61.32 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:22 PST -0800 (1735452742.77 s) Start R-work = 0.1639, R-free = 0.1751 Final R-work = 0.1207, R-free = 0.1363 =============================================================================== Job complete usr+sys time: 3774.73 seconds wall clock time: 67 minutes 31.06 seconds (4051.06 seconds total)