Starting phenix.refine on Sat Dec 28 21:06:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2659048.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2659048.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2659048.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.50, per 1000 atoms: 0.74 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: 1.14 Conformation dependent library (CDL) restraints added in 294.5 milliseconds Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 481 0.90 - 1.17: 1162 1.17 - 1.44: 717 1.44 - 1.70: 775 1.70 - 1.97: 18 Bond restraints: 3153 Sorted by residual: bond pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 1.518 1.719 -0.201 1.00e-02 1.00e+04 4.04e+02 bond pdb=" CA LYS A 122 " pdb=" C LYS A 122 " ideal model delta sigma weight residual 1.523 1.755 -0.232 1.30e-02 5.92e+03 3.19e+02 bond pdb=" CA ALA A 178 " pdb=" C ALA A 178 " ideal model delta sigma weight residual 1.523 1.292 0.231 1.30e-02 5.92e+03 3.17e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.187 0.191 1.10e-02 8.26e+03 3.02e+02 bond pdb=" N ACYS A 53 " pdb=" CA ACYS A 53 " ideal model delta sigma weight residual 1.456 1.662 -0.205 1.20e-02 6.94e+03 2.93e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.62: 3624 5.62 - 11.25: 1728 11.25 - 16.87: 393 16.87 - 22.49: 25 22.49 - 28.11: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.91 104.91 17.00 9.80e-01 1.04e+00 3.01e+02 angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH1 ARG A 48 " ideal model delta sigma weight residual 121.50 137.32 -15.82 1.00e+00 1.00e+00 2.50e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 129.38 -10.09 6.50e-01 2.37e+00 2.41e+02 angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 105.33 13.87 9.00e-01 1.23e+00 2.37e+02 angle pdb=" C GLY A 108 " pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta sigma weight residual 119.82 105.61 14.21 9.80e-01 1.04e+00 2.10e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 19.58: 973 19.58 - 39.14: 95 39.14 - 58.70: 34 58.70 - 78.26: 8 78.26 - 97.82: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ARG A 145 " pdb=" C ARG A 145 " pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -161.22 -18.78 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 104 0.208 - 0.416: 65 0.416 - 0.624: 46 0.624 - 0.832: 21 0.832 - 1.040: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 51 " pdb=" CA VAL A 51 " pdb=" CG1 VAL A 51 " pdb=" CG2 VAL A 51 " both_signs ideal model delta sigma weight residual False -2.63 -1.59 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CA ALA A 14 " pdb=" N ALA A 14 " pdb=" C ALA A 14 " pdb=" CB ALA A 14 " both_signs ideal model delta sigma weight residual False 2.48 3.51 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CB VAL A 33 " pdb=" CA VAL A 33 " pdb=" CG1 VAL A 33 " pdb=" CG2 VAL A 33 " both_signs ideal model delta sigma weight residual False -2.63 -1.66 -0.97 2.00e-01 2.50e+01 2.37e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.044 2.00e-02 2.50e+03 6.38e-02 1.22e+02 pdb=" CG PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.096 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.026 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.137 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.045 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.112 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.005 2.00e-02 2.50e+03 5.42e-02 8.81e+01 pdb=" CG BTYR A 67 " -0.097 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.037 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.107 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.039 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.032 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.020 2.00e-02 2.50e+03 4.81e-02 6.95e+01 pdb=" CG PHE A 164 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.090 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.042 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.077 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.060 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.062 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 935 2.31 - 2.88: 8022 2.88 - 3.45: 10610 3.45 - 4.03: 15159 4.03 - 4.60: 21975 Nonbonded interactions: 56701 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.733 2.100 nonbonded pdb="HH21 ARG A 145 " pdb=" OE1 GLU A 163 " model vdw 1.834 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.858 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.870 2.450 nonbonded pdb=" H LYS A 12 " pdb=" O HOH A 396 " model vdw 1.888 2.450 ... (remaining 56696 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_2659048_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= 0.2608 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788464 | | target function (ml) not normalized (work): 232295.810735 | | target function (ml) not normalized (free): 11788.995365 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3018 0.2132 7.0215 4.9572| | 2: 3.57 - 2.84 1.00 2876 122 0.2440 0.1730 4.3548 4.3242| | 3: 2.84 - 2.48 1.00 2833 165 0.2342 0.1622 4.1258 4.1573| | 4: 2.47 - 2.25 1.00 2825 136 0.2331 0.1478 3.8363 3.8311| | 5: 2.25 - 2.09 1.00 2756 127 0.2518 0.1712 3.8064 3.8307| | 6: 2.09 - 1.97 1.00 2846 113 0.2526 0.1774 3.4733 3.6178| | 7: 1.97 - 1.87 1.00 2787 165 0.2548 0.1813 3.1355 3.1668| | 8: 1.87 - 1.79 1.00 2789 144 0.2510 0.1881 3.0714 3.1255| | 9: 1.79 - 1.72 1.00 2745 138 0.2414 0.1894 2.8954 2.9345| | 10: 1.72 - 1.66 1.00 2789 158 0.2377 0.1965 2.7994 2.9017| | 11: 1.66 - 1.61 1.00 2740 147 0.2526 0.1836 2.7449 2.7523| | 12: 1.61 - 1.56 1.00 2787 146 0.2500 0.1857 2.6099 2.5798| | 13: 1.56 - 1.52 1.00 2745 130 0.2527 0.2166 2.5616 2.6939| | 14: 1.52 - 1.48 1.00 2803 134 0.2616 0.1820 2.5097 2.5619| | 15: 1.48 - 1.45 1.00 2738 128 0.2612 0.2196 2.4182 2.5277| | 16: 1.45 - 1.42 1.00 2756 161 0.2720 0.2028 2.3951 2.3901| | 17: 1.42 - 1.39 1.00 2785 139 0.2649 0.1975 2.3253 2.321| | 18: 1.39 - 1.36 1.00 2741 179 0.2677 0.2059 2.2621 2.2961| | 19: 1.36 - 1.34 1.00 2807 134 0.2636 0.2499 2.2148 2.3141| | 20: 1.34 - 1.32 1.00 2696 147 0.2699 0.1988 2.1995 2.1699| | 21: 1.32 - 1.30 1.00 2785 112 0.2675 0.2282 2.1682 2.1552| | 22: 1.29 - 1.27 1.00 2704 152 0.2695 0.2590 2.1331 2.1956| | 23: 1.27 - 1.26 1.00 2802 156 0.2792 0.2377 2.0995 2.1378| | 24: 1.26 - 1.24 1.00 2744 132 0.2790 0.2445 2.0924 2.1191| | 25: 1.24 - 1.22 1.00 2734 148 0.2874 0.2580 2.0518 2.1059| | 26: 1.22 - 1.21 1.00 2727 135 0.2904 0.2170 2.0119 2.0518| | 27: 1.21 - 1.19 1.00 2814 148 0.2983 0.2701 2.0186 2.0117| | 28: 1.19 - 1.18 1.00 2671 147 0.2989 0.2923 1.9818 2.0288| | 29: 1.18 - 1.16 1.00 2800 134 0.2974 0.2680 1.9535 1.998| | 30: 1.16 - 1.15 1.00 2740 148 0.3070 0.2773 1.9283 1.9525| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.90 0.76 0.23 1490.72| | 2: 3.57 - 2.84 2876 122 0.80 26.23 1.28 0.23 1490.72| | 3: 2.84 - 2.48 2833 165 0.74 32.16 1.24 0.23 1236.63| | 4: 2.47 - 2.25 2825 136 0.81 25.65 1.26 0.25 577.23| | 5: 2.25 - 2.09 2756 127 0.77 29.41 1.28 0.25 577.23| | 6: 2.09 - 1.97 2846 113 0.83 22.75 1.29 0.25 316.11| | 7: 1.97 - 1.87 2787 165 0.90 16.78 1.28 0.26 93.42| | 8: 1.87 - 1.79 2789 144 0.86 21.35 1.25 0.26 93.42| | 9: 1.79 - 1.72 2745 138 0.88 18.63 1.23 0.26 55.82| | 10: 1.72 - 1.66 2789 158 0.86 20.24 1.22 0.26 48.29| | 11: 1.66 - 1.61 2740 147 0.86 21.28 1.25 0.26 46.51| | 12: 1.61 - 1.56 2787 146 0.89 18.14 1.23 0.25 28.50| | 13: 1.56 - 1.52 2745 130 0.87 20.25 1.23 0.25 28.50| | 14: 1.52 - 1.48 2803 134 0.86 20.63 1.24 0.25 25.62| | 15: 1.48 - 1.45 2738 128 0.87 20.06 1.24 0.25 20.35| | 16: 1.45 - 1.42 2756 161 0.86 21.53 1.25 0.25 20.35| | 17: 1.42 - 1.39 2785 139 0.87 20.32 1.23 0.25 17.06| | 18: 1.39 - 1.36 2741 179 0.86 21.13 1.23 0.25 15.15| | 19: 1.36 - 1.34 2807 134 0.86 21.78 1.22 0.25 15.15| | 20: 1.34 - 1.32 2696 147 0.87 20.57 1.21 0.24 12.70| | 21: 1.32 - 1.30 2785 112 0.86 21.52 1.19 0.24 12.52| | 22: 1.29 - 1.27 2704 152 0.86 21.85 1.20 0.24 12.24| | 23: 1.27 - 1.26 2802 156 0.86 21.86 1.22 0.24 10.77| | 24: 1.26 - 1.24 2744 132 0.86 22.10 1.20 0.24 10.77| | 25: 1.24 - 1.22 2734 148 0.84 23.44 1.20 0.24 10.29| | 26: 1.22 - 1.21 2727 135 0.84 23.83 1.21 0.23 9.75| | 27: 1.21 - 1.19 2814 148 0.84 24.21 1.20 0.23 9.75| | 28: 1.19 - 1.18 2671 147 0.83 25.27 1.18 0.23 9.14| | 29: 1.18 - 1.16 2800 134 0.83 25.47 1.17 0.22 8.91| | 30: 1.16 - 1.15 2740 148 0.81 27.04 1.16 0.22 8.91| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 8.91 max = 1490.72 mean = 216.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 22.48| |phase err.(test): min = 0.00 max = 89.91 mean = 22.29| |-----------------------------------------------------------------------------| ----------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 : 0.085 0.281 1557 Z= 5.601 Angle : 5.394 24.633 2118 Z= 3.839 Chirality : 0.390 1.040 243 Planarity : 0.031 0.098 284 Dihedral : 14.130 97.822 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.11 % Allowed : 3.73 % Favored : 93.17 % Cbeta Deviations : 30.81 % 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: -2.74 (0.46), residues: 224 helix: -2.41 (0.40), residues: 109 sheet: -1.87 (0.85), residues: 28 loop : -0.59 (0.54), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.024 ARG A 27 TYR 0.067 0.027 TYR A 139 PHE 0.111 0.037 PHE A 119 HIS 0.038 0.020 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= 0.2608 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788464 | | target function (ml) not normalized (work): 232295.810735 | | target function (ml) not normalized (free): 11788.995365 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2609 0.1942 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2609 0.1942 n_refl.: 87602 remove outliers: r(all,work,free)=0.1977 0.1981 0.1942 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2001 0.2005 0.1956 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1643 0.1637 0.1755 n_refl.: 87594 remove outliers: r(all,work,free)=0.1642 0.1637 0.1755 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 98.94 88 5 0.3899 386.379 356.693 0.668 1.004 0.407 11.894-9.307 99.02 97 4 0.1864 613.745 592.226 0.925 1.004 0.390 9.237-7.194 100.00 213 7 0.2213 501.968 489.780 0.958 1.004 0.344 7.162-5.571 100.00 427 22 0.2182 376.699 364.357 0.937 1.004 0.298 5.546-4.326 100.00 867 58 0.1270 517.114 511.706 0.963 1.004 0.233 4.315-3.360 100.00 1859 96 0.1124 491.779 488.040 1.002 1.003 0.199 3.356-2.611 100.00 3867 181 0.1439 323.074 319.850 0.999 1.002 0.048 2.608-2.026 99.99 8198 413 0.1355 214.168 211.918 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1643 104.589 103.877 1.013 0.999 0.000 1.573-1.221 99.99 36678 1900 0.2067 46.378 45.037 1.004 0.995 0.000 1.221-1.150 99.97 13689 708 0.2613 29.222 26.967 0.979 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0446 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1637 r_free=0.1755 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.1638 r_free=0.1751 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.792181 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2029.624931 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1212 0.1459 0.0247 0.007 0.9 1.0 0.5 0.0 0 12.396 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.59 2.47 3.013 19.053 2029.625 0.017 12.35 15.27 2.92 3.108 19.490 2029.625 0.016 Individual atomic B min max mean iso aniso Overall: 8.48 118.32 20.91 2.88 0 1785 Protein: 8.48 118.32 17.80 2.88 0 1519 Water: 10.97 114.88 38.99 N/A 0 258 Other: 22.50 35.38 28.55 N/A 0 8 Chain A: 8.48 118.32 20.91 N/A 0 1785 Histogram: Values Number of atoms 8.48 - 19.46 1210 19.46 - 30.44 227 30.44 - 41.43 169 41.43 - 52.41 96 52.41 - 63.40 54 63.40 - 74.38 18 74.38 - 85.36 4 85.36 - 96.35 4 96.35 - 107.33 0 107.33 - 118.32 3 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1528 r_work=0.1240 r_free=0.1531 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1240 r_free = 0.1531 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 = 0.1240 r_free = 0.1534 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1240 r_free= 0.1534 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015357 | | target function (ls_wunit_k1) not normalized (work): 1279.142366 | | target function (ls_wunit_k1) not normalized (free): 112.294083 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1254 0.1240 0.1534 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1690 0.1688 0.1760 n_refl.: 87592 remove outliers: r(all,work,free)=0.1690 0.1688 0.1760 n_refl.: 87592 overall B=0.17 to atoms: r(all,work,free)=0.1717 0.1716 0.1780 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1253 0.1238 0.1529 n_refl.: 87592 remove outliers: r(all,work,free)=0.1252 0.1238 0.1529 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3568 299.434 279.307 0.636 1.003 0.380 11.894-9.307 99.02 97 4 0.1617 479.676 467.745 0.904 1.003 0.380 9.237-7.194 100.00 213 7 0.1842 392.316 387.697 0.945 1.003 0.314 7.162-5.571 100.00 427 22 0.1714 294.411 289.383 0.925 1.003 0.258 5.546-4.326 100.00 867 58 0.0916 404.154 401.581 0.948 1.003 0.214 4.315-3.360 100.00 1859 96 0.0778 384.353 383.327 0.991 1.003 0.199 3.356-2.611 100.00 3867 181 0.1023 252.500 251.819 0.997 1.002 0.052 2.608-2.026 99.99 8198 413 0.0972 167.385 166.824 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1201 81.742 81.933 1.016 1.000 0.000 1.573-1.221 99.99 36678 1900 0.1638 36.247 35.710 1.005 0.997 0.000 1.221-1.150 99.97 13689 708 0.2353 22.839 21.342 0.970 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0380 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1238 r_free=0.1529 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=0.1238 r_free=0.1529 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1238 r_free=0.1529 | n_water=258 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1247 r_free=0.1528 | n_water=252 | time (s): 25.820 (total time: 28.200) Filter (q & B) r_work=0.1250 r_free=0.1527 | n_water=249 | time (s): 3.720 (total time: 31.920) Compute maps r_work=0.1250 r_free=0.1527 | n_water=249 | time (s): 1.870 (total time: 33.790) Filter (map) r_work=0.1270 r_free=0.1537 | n_water=235 | time (s): 3.710 (total time: 37.500) Find peaks r_work=0.1270 r_free=0.1537 | n_water=235 | time (s): 0.710 (total time: 38.210) Add new water r_work=0.1424 r_free=0.1702 | n_water=456 | time (s): 3.760 (total time: 41.970) Refine new water occ: r_work=0.1328 r_free=0.1565 adp: r_work=0.1249 r_free=0.1520 occ: r_work=0.1262 r_free=0.1508 adp: r_work=0.1227 r_free=0.1500 occ: r_work=0.1231 r_free=0.1494 adp: r_work=0.1221 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1497 r_work=0.1221 r_free=0.1497 | n_water=456 | time (s): 151.740 (total time: 193.710) Filter (q & B) r_work=0.1227 r_free=0.1502 | n_water=434 | time (s): 3.940 (total time: 197.650) Filter (dist only) r_work=0.1227 r_free=0.1502 | n_water=434 | time (s): 40.840 (total time: 238.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.481736 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1427.359617 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1228 0.1529 0.0302 0.007 0.9 1.9 0.5 0.0 0 12.241 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 15.29 3.02 3.773 23.109 1427.360 0.015 12.10 15.11 3.01 4.131 22.929 1427.360 0.015 Individual atomic B min max mean iso aniso Overall: 8.80 114.00 23.11 2.58 199 1762 Protein: 8.80 114.00 17.64 2.58 0 1519 Water: 11.02 72.36 42.14 N/A 199 235 Other: 26.30 37.45 31.19 N/A 0 8 Chain A: 8.80 114.00 20.33 N/A 0 1762 Chain S: 17.70 69.55 47.79 N/A 199 0 Histogram: Values Number of atoms 8.80 - 19.32 1206 19.32 - 29.84 254 29.84 - 40.36 194 40.36 - 50.88 139 50.88 - 61.40 103 61.40 - 71.92 53 71.92 - 82.44 6 82.44 - 92.96 3 92.96 - 103.48 1 103.48 - 114.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1511 r_work=0.1210 r_free=0.1511 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1511 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 = 0.1211 r_free = 0.1510 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1211 r_free= 0.1510 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014235 | | target function (ls_wunit_k1) not normalized (work): 1185.670303 | | target function (ls_wunit_k1) not normalized (free): 111.631718 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1226 0.1211 0.1510 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1602 0.1597 0.1732 n_refl.: 87591 remove outliers: r(all,work,free)=0.1602 0.1597 0.1732 n_refl.: 87591 overall B=0.04 to atoms: r(all,work,free)=0.1608 0.1603 0.1736 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1223 0.1208 0.1507 n_refl.: 87591 remove outliers: r(all,work,free)=0.1222 0.1207 0.1507 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 93.75 85 5 0.3446 297.991 270.559 0.634 0.940 0.368 11.894-9.307 99.02 97 4 0.1538 479.676 476.120 0.971 0.941 0.360 9.237-7.194 100.00 213 7 0.1684 392.316 392.972 1.039 0.941 0.290 7.162-5.571 100.00 427 22 0.1491 294.411 291.032 1.005 0.941 0.230 5.546-4.326 100.00 867 58 0.0853 404.154 401.468 1.019 0.941 0.210 4.315-3.360 100.00 1859 96 0.0730 384.353 383.011 1.066 0.942 0.210 3.356-2.611 100.00 3867 181 0.0967 252.500 251.773 1.072 0.942 0.067 2.608-2.026 99.99 8198 413 0.0975 167.385 166.974 1.080 0.944 0.000 2.025-1.573 100.00 17313 902 0.1188 81.742 81.961 1.085 0.946 0.000 1.573-1.221 99.99 36678 1900 0.1613 36.247 35.744 1.068 0.949 0.000 1.221-1.150 99.97 13689 708 0.2347 22.839 21.372 1.024 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0664 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1207 r_free=0.1507 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1207 r_free=0.1507 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1207 r_free=0.1507 | n_water=434 | time (s): 1.830 (total time: 1.830) Filter (dist) r_work=0.1207 r_free=0.1507 | n_water=434 | time (s): 35.090 (total time: 36.920) Filter (q & B) r_work=0.1207 r_free=0.1507 | n_water=434 | time (s): 0.990 (total time: 37.910) Compute maps r_work=0.1207 r_free=0.1507 | n_water=434 | time (s): 1.510 (total time: 39.420) Filter (map) r_work=0.1249 r_free=0.1483 | n_water=290 | time (s): 3.590 (total time: 43.010) Find peaks r_work=0.1249 r_free=0.1483 | n_water=290 | time (s): 0.490 (total time: 43.500) Add new water r_work=0.1376 r_free=0.1606 | n_water=479 | time (s): 2.700 (total time: 46.200) Refine new water occ: r_work=0.1274 r_free=0.1526 adp: r_work=0.1276 r_free=0.1526 occ: r_work=0.1252 r_free=0.1512 adp: r_work=0.1251 r_free=0.1511 occ: r_work=0.1236 r_free=0.1503 adp: r_work=0.1230 r_free=0.1500 ADP+occupancy (water only), MIN, final r_work=0.1230 r_free=0.1500 r_work=0.1230 r_free=0.1500 | n_water=479 | time (s): 154.010 (total time: 200.210) Filter (q & B) r_work=0.1236 r_free=0.1500 | n_water=443 | time (s): 3.010 (total time: 203.220) Filter (dist only) r_work=0.1236 r_free=0.1500 | n_water=443 | time (s): 34.680 (total time: 237.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.062284 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.401664 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 0.1241 0.1459 0.0218 0.006 0.9 1.9 0.5 0.0 0 1.031 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.41 14.59 2.18 3.605 22.040 42.402 3.730 12.35 14.22 1.88 4.177 21.834 42.402 3.662 Individual atomic B min max mean iso aniso Overall: 9.24 109.26 21.52 2.28 214 1756 Protein: 9.24 109.26 17.15 2.28 0 1519 Water: 11.55 71.09 36.43 N/A 214 229 Other: 21.59 32.99 27.43 N/A 0 8 Chain A: 9.24 109.26 19.74 N/A 0 1756 Chain S: 16.45 63.50 36.18 N/A 214 0 Histogram: Values Number of atoms 9.24 - 19.25 1235 19.25 - 29.25 279 29.25 - 39.25 220 39.25 - 49.25 129 49.25 - 59.25 73 59.25 - 69.25 21 69.25 - 79.25 7 79.25 - 89.25 3 89.25 - 99.26 1 99.26 - 109.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1423 r_work=0.1236 r_free=0.1423 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1423 target_work(ml) = 3.662 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1417 target_work(ml) = 3.660 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1230 r_free= 0.1417 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.659694 | | target function (ml) not normalized (work): 304826.928587 | | target function (ml) not normalized (free): 16095.902948 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1239 0.1230 0.1417 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1555 0.1553 0.1622 n_refl.: 87589 remove outliers: r(all,work,free)=0.1555 0.1553 0.1622 n_refl.: 87589 overall B=-0.02 to atoms: r(all,work,free)=0.1552 0.1550 0.1620 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1229 0.1221 0.1391 n_refl.: 87589 remove outliers: r(all,work,free)=0.1226 0.1217 0.1391 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 90.62 82 5 0.3988 292.110 263.206 0.473 1.000 0.302 11.894-9.307 98.04 96 4 0.2462 479.800 461.102 0.857 1.001 0.290 9.237-7.194 98.18 209 7 0.2346 383.846 383.884 0.941 1.001 0.220 7.162-5.571 100.00 427 22 0.2084 294.411 283.947 0.914 1.002 0.160 5.546-4.326 100.00 867 58 0.1119 404.154 399.302 0.952 1.002 0.155 4.315-3.360 100.00 1859 96 0.0975 384.353 381.642 0.994 1.002 0.150 3.356-2.611 100.00 3867 181 0.1185 252.500 250.464 1.001 1.001 0.057 2.608-2.026 99.99 8198 413 0.1075 167.385 166.282 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1021 81.742 81.877 1.028 1.000 0.000 1.573-1.221 99.99 36678 1900 0.1296 36.247 35.824 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2125 22.839 21.466 0.981 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0427 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1217 r_free=0.1391 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1217 r_free=0.1391 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1217 r_free=0.1391 | n_water=443 | time (s): 1.840 (total time: 1.840) Filter (dist) r_work=0.1217 r_free=0.1391 | n_water=443 | time (s): 33.170 (total time: 35.010) Filter (q & B) r_work=0.1217 r_free=0.1391 | n_water=443 | time (s): 1.090 (total time: 36.100) Compute maps r_work=0.1217 r_free=0.1391 | n_water=443 | time (s): 1.520 (total time: 37.620) Filter (map) r_work=0.1239 r_free=0.1390 | n_water=307 | time (s): 2.850 (total time: 40.470) Find peaks r_work=0.1239 r_free=0.1390 | n_water=307 | time (s): 0.480 (total time: 40.950) Add new water r_work=0.1304 r_free=0.1454 | n_water=467 | time (s): 2.730 (total time: 43.680) Refine new water occ: r_work=0.1230 r_free=0.1381 adp: r_work=0.1230 r_free=0.1383 occ: r_work=0.1217 r_free=0.1369 adp: r_work=0.1215 r_free=0.1371 occ: r_work=0.1207 r_free=0.1363 adp: r_work=0.1203 r_free=0.1362 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1362 r_work=0.1203 r_free=0.1362 | n_water=467 | time (s): 203.610 (total time: 247.290) Filter (q & B) r_work=0.1211 r_free=0.1364 | n_water=434 | time (s): 3.130 (total time: 250.420) Filter (dist only) r_work=0.1211 r_free=0.1362 | n_water=433 | time (s): 38.880 (total time: 289.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.907282 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.825058 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 0.1378 0.0167 0.006 0.9 1.6 0.5 0.0 0 0.954 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 13.78 1.67 3.397 21.326 50.825 3.644 11.87 13.69 1.82 3.885 21.187 50.825 3.624 Individual atomic B min max mean iso aniso Overall: 9.23 104.66 20.97 2.15 206 1754 Protein: 9.23 104.66 16.81 2.15 0 1519 Water: 11.51 69.18 35.52 N/A 206 227 Other: 20.30 29.89 24.86 N/A 0 8 Chain A: 9.23 104.66 19.30 N/A 0 1754 Chain S: 15.69 63.57 35.21 N/A 206 0 Histogram: Values Number of atoms 9.23 - 18.78 1225 18.78 - 28.32 287 28.32 - 37.86 210 37.86 - 47.40 130 47.40 - 56.95 66 56.95 - 66.49 30 66.49 - 76.03 7 76.03 - 85.57 2 85.57 - 95.12 1 95.12 - 104.66 2 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1369 r_work=0.1187 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1369 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1182 r_free = 0.1363 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.19 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= 0.1182 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621914 | | target function (ml) not normalized (work): 301651.112735 | | target function (ml) not normalized (free): 15925.508553 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1182 0.1363 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1512 0.1510 0.1570 n_refl.: 87581 remove outliers: r(all,work,free)=0.1512 0.1510 0.1570 n_refl.: 87581 overall B=-0.02 to atoms: r(all,work,free)=0.1508 0.1507 0.1567 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1181 0.1361 n_refl.: 87581 remove outliers: r(all,work,free)=0.1188 0.1179 0.1361 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4051 287.488 257.439 0.460 1.000 0.314 11.894-9.307 96.08 94 4 0.2343 474.972 459.367 0.848 1.002 0.310 9.237-7.194 97.73 208 7 0.2419 384.923 376.493 0.911 1.002 0.170 7.162-5.571 100.00 427 22 0.2182 294.411 283.868 0.906 1.002 0.150 5.546-4.326 100.00 867 58 0.1168 404.154 399.362 0.952 1.002 0.140 4.315-3.360 100.00 1859 96 0.0969 384.353 381.895 0.994 1.002 0.120 3.356-2.611 100.00 3867 181 0.1153 252.500 250.708 1.001 1.002 0.090 2.608-2.026 99.99 8198 413 0.1020 167.385 166.498 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0956 81.742 82.000 1.028 1.000 0.000 1.573-1.221 99.99 36678 1900 0.1238 36.247 35.881 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2119 22.839 21.477 0.983 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0489 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1179 r_free=0.1361 After: r_work=0.1180 r_free=0.1361 ================================== NQH flips ================================== r_work=0.1180 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1180 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1180 r_free=0.1361 | n_water=433 | time (s): 1.610 (total time: 1.610) Filter (dist) r_work=0.1180 r_free=0.1361 | n_water=433 | time (s): 33.930 (total time: 35.540) Filter (q & B) r_work=0.1180 r_free=0.1361 | n_water=433 | time (s): 1.020 (total time: 36.560) Compute maps r_work=0.1180 r_free=0.1361 | n_water=433 | time (s): 1.200 (total time: 37.760) Filter (map) r_work=0.1202 r_free=0.1378 | n_water=320 | time (s): 2.730 (total time: 40.490) Find peaks r_work=0.1202 r_free=0.1378 | n_water=320 | time (s): 0.670 (total time: 41.160) Add new water r_work=0.1260 r_free=0.1432 | n_water=482 | time (s): 3.290 (total time: 44.450) Refine new water occ: r_work=0.1194 r_free=0.1357 adp: r_work=0.1195 r_free=0.1361 occ: r_work=0.1182 r_free=0.1348 adp: r_work=0.1180 r_free=0.1351 occ: r_work=0.1172 r_free=0.1346 adp: r_work=0.1169 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1169 r_free=0.1347 r_work=0.1169 r_free=0.1347 | n_water=482 | time (s): 148.820 (total time: 193.270) Filter (q & B) r_work=0.1178 r_free=0.1362 | n_water=437 | time (s): 2.950 (total time: 196.220) Filter (dist only) r_work=0.1178 r_free=0.1360 | n_water=435 | time (s): 37.120 (total time: 233.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.937209 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.452506 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 0.1204 0.1376 0.0172 0.007 1.0 3.5 0.5 0.0 0 0.969 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.76 1.72 3.258 20.917 45.453 3.630 12.06 13.75 1.68 3.360 20.877 45.453 3.625 Individual atomic B min max mean iso aniso Overall: 9.19 101.60 20.83 2.03 211 1751 Protein: 9.19 101.60 16.70 2.04 0 1519 Water: 11.52 68.75 35.18 N/A 211 224 Other: 20.33 28.75 24.66 N/A 0 8 Chain A: 9.19 101.60 19.13 N/A 0 1751 Chain S: 15.05 58.26 34.91 N/A 211 0 Histogram: Values Number of atoms 9.19 - 18.43 1218 18.43 - 27.67 291 27.67 - 36.91 202 36.91 - 46.15 140 46.15 - 55.39 74 55.39 - 64.63 22 64.63 - 73.87 10 73.87 - 83.11 2 83.11 - 92.36 1 92.36 - 101.60 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1375 r_work=0.1207 r_free=0.1375 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1375 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1373 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1203 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 3.623871 | | target function (ml) not normalized (work): 301799.599546 | | target function (ml) not normalized (free): 15942.316329 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1443 0.1465 5.7095 5.6691| | 2: 3.57 - 2.84 1.00 2888 124 0.1129 0.1426 5.2169 5.2768| | 3: 2.83 - 2.48 1.00 2820 163 0.1240 0.1261 5.0219 5.0319| | 4: 2.47 - 2.25 1.00 2825 136 0.1036 0.1146 4.7209 4.7678| | 5: 2.25 - 2.09 1.00 2756 127 0.1004 0.1121 4.6643 4.7383| | 6: 2.09 - 1.97 1.00 2846 113 0.0984 0.1213 4.3665 4.4953| | 7: 1.97 - 1.87 1.00 2787 165 0.0993 0.1230 4.0829 4.1738| | 8: 1.87 - 1.79 1.00 2789 144 0.1015 0.1258 3.9901 4.0854| | 9: 1.79 - 1.72 1.00 2745 138 0.0960 0.1226 3.7145 3.8681| | 10: 1.72 - 1.66 1.00 2831 160 0.0994 0.1214 3.6259 3.739| | 11: 1.66 - 1.61 1.00 2712 147 0.0959 0.1105 3.5627 3.6102| | 12: 1.61 - 1.56 1.00 2773 144 0.0904 0.1183 3.3397 3.475| | 13: 1.56 - 1.52 1.00 2745 130 0.0970 0.1071 3.3344 3.4391| | 14: 1.52 - 1.48 1.00 2803 134 0.0980 0.1125 3.2558 3.3423| | 15: 1.48 - 1.45 1.00 2738 128 0.1003 0.1332 3.1655 3.3146| | 16: 1.45 - 1.42 1.00 2756 161 0.1061 0.1294 3.1497 3.2586| | 17: 1.42 - 1.39 1.00 2785 139 0.1117 0.1316 3.1136 3.2411| | 18: 1.39 - 1.36 1.00 2740 179 0.1143 0.1367 3.0822 3.2646| | 19: 1.36 - 1.34 1.00 2807 134 0.1205 0.1597 3.0895 3.2689| | 20: 1.34 - 1.32 1.00 2696 147 0.1310 0.1457 3.0861 3.1315| | 21: 1.32 - 1.30 1.00 2785 112 0.1406 0.1606 3.0839 3.1521| | 22: 1.29 - 1.27 1.00 2704 152 0.1461 0.1896 3.0818 3.2866| | 23: 1.27 - 1.26 1.00 2802 156 0.1575 0.1841 3.1029 3.2118| | 24: 1.26 - 1.24 1.00 2744 132 0.1624 0.1760 3.0937 3.1908| | 25: 1.24 - 1.22 1.00 2733 148 0.1793 0.2284 3.108 3.2848| | 26: 1.22 - 1.21 1.00 2727 135 0.1857 0.1741 3.1248 3.1866| | 27: 1.21 - 1.19 1.00 2814 148 0.2005 0.2096 3.1403 3.1486| | 28: 1.19 - 1.18 1.00 2671 147 0.2142 0.2309 3.1413 3.1636| | 29: 1.18 - 1.16 1.00 2800 134 0.2218 0.2372 3.1291 3.2283| | 30: 1.16 - 1.15 1.00 2739 148 0.2380 0.2484 3.1196 3.1636| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2920 171 0.94 9.35 1.00 0.97 6529.92| | 2: 3.57 - 2.84 2888 124 0.92 13.69 1.01 0.97 6529.92| | 3: 2.83 - 2.48 2820 163 0.88 17.82 0.98 0.97 5469.82| | 4: 2.47 - 2.25 2825 136 0.91 14.87 1.00 0.97 2736.15| | 5: 2.25 - 2.09 2756 127 0.89 17.15 1.01 0.97 2736.15| | 6: 2.09 - 1.97 2846 113 0.91 13.87 1.02 0.97 1600.43| | 7: 1.97 - 1.87 2787 165 0.94 10.83 1.02 0.97 631.81| | 8: 1.87 - 1.79 2789 144 0.91 14.49 1.00 0.97 631.81| | 9: 1.79 - 1.72 2745 138 0.93 11.31 0.98 0.97 336.25| | 10: 1.72 - 1.66 2831 160 0.93 12.09 0.98 0.97 277.06| | 11: 1.66 - 1.61 2712 147 0.93 12.74 0.98 0.97 264.62| | 12: 1.61 - 1.56 2773 144 0.95 9.52 0.99 0.97 147.32| | 13: 1.56 - 1.52 2745 130 0.94 11.04 1.02 0.97 147.32| | 14: 1.52 - 1.48 2803 134 0.94 11.25 1.02 0.97 131.61| | 15: 1.48 - 1.45 2738 128 0.95 10.38 1.01 0.98 102.84| | 16: 1.45 - 1.42 2756 161 0.94 11.52 1.01 0.98 102.84| | 17: 1.42 - 1.39 2785 139 0.94 11.39 1.01 0.98 92.94| | 18: 1.39 - 1.36 2740 179 0.94 11.73 1.01 0.98 87.21| | 19: 1.36 - 1.34 2807 134 0.94 12.24 1.00 0.98 87.21| | 20: 1.34 - 1.32 2696 147 0.94 12.31 0.99 0.97 81.89| | 21: 1.32 - 1.30 2785 112 0.94 13.25 0.98 0.96 81.52| | 22: 1.29 - 1.27 2704 152 0.93 13.76 0.98 0.96 81.66| | 23: 1.27 - 1.26 2802 156 0.93 14.73 0.97 0.95 82.37| | 24: 1.26 - 1.24 2744 132 0.93 14.87 0.97 0.95 82.37| | 25: 1.24 - 1.22 2733 148 0.91 16.28 0.96 0.94 84.03| | 26: 1.22 - 1.21 2727 135 0.90 17.99 1.02 0.93 85.86| | 27: 1.21 - 1.19 2814 148 0.89 18.66 1.02 0.93 85.86| | 28: 1.19 - 1.18 2671 147 0.88 20.20 1.01 0.93 89.64| | 29: 1.18 - 1.16 2800 134 0.88 20.57 0.99 0.92 91.07| | 30: 1.16 - 1.15 2739 148 0.86 21.98 0.98 0.92 91.07| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.52 max = 6529.92 mean = 1010.89| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 14.05| |phase err.(test): min = 0.00 max = 89.25 mean = 14.16| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1203 0.1373 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1526 0.1525 0.1560 n_refl.: 87577 remove outliers: r(all,work,free)=0.1526 0.1525 0.1560 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1523 0.1523 0.1558 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1204 0.1375 n_refl.: 87577 remove outliers: r(all,work,free)=0.1212 0.1203 0.1375 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4268 287.488 248.218 0.435 1.001 0.303 11.894-9.307 95.10 93 4 0.2450 476.922 459.110 0.847 1.002 0.290 9.237-7.194 97.73 208 7 0.2546 384.923 375.764 0.899 1.002 0.140 7.162-5.571 100.00 427 22 0.2310 294.411 283.037 0.897 1.003 0.120 5.546-4.326 100.00 867 58 0.1216 404.154 399.460 0.952 1.002 0.117 4.315-3.360 100.00 1859 96 0.1002 384.353 381.780 0.995 1.002 0.107 3.356-2.611 100.00 3867 181 0.1196 252.500 250.453 1.001 1.002 0.090 2.608-2.026 99.99 8198 413 0.1049 167.385 166.424 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0977 81.742 81.990 1.028 0.999 0.000 1.573-1.221 99.99 36678 1900 0.1220 36.247 35.882 1.022 0.996 0.000 1.221-1.150 99.97 13689 708 0.2116 22.839 21.465 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0333 ================= 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 : 0.2608 0.1941 0.085 5.394 8.8 119.3 19.9 258 0.000 1_bss: 0.1637 0.1755 0.085 5.394 9.0 119.5 20.1 258 0.000 1_settarget: 0.1637 0.1755 0.085 5.394 9.0 119.5 20.1 258 0.000 1_nqh: 0.1638 0.1751 0.085 5.394 9.0 119.5 20.1 258 0.006 1_weight: 0.1638 0.1751 0.085 5.394 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1212 0.1459 0.007 0.941 9.0 119.5 20.1 258 0.131 1_adp: 0.1235 0.1528 0.007 0.941 8.5 118.3 20.9 258 0.131 1_regHadp: 0.1240 0.1531 0.007 0.941 8.5 118.3 20.9 258 0.131 1_occ: 0.1240 0.1534 0.007 0.941 8.5 118.3 20.9 258 0.131 2_bss: 0.1238 0.1529 0.007 0.941 8.6 118.5 21.1 258 0.131 2_settarget: 0.1238 0.1529 0.007 0.941 8.6 118.5 21.1 258 0.131 2_updatecdl: 0.1238 0.1529 0.007 0.954 8.6 118.5 21.1 258 0.131 2_nqh: 0.1238 0.1529 0.007 0.954 8.6 118.5 21.1 258 0.131 2_sol: 0.1227 0.1502 0.007 0.954 8.6 118.5 23.4 434 n/a 2_weight: 0.1227 0.1502 0.007 0.954 8.6 118.5 23.4 434 n/a 2_xyzrec: 0.1228 0.1529 0.007 0.877 8.6 118.5 23.4 434 n/a 2_adp: 0.1210 0.1511 0.007 0.877 8.8 114.0 23.1 434 n/a 2_regHadp: 0.1210 0.1511 0.007 0.877 8.8 114.0 23.1 434 n/a 2_occ: 0.1211 0.1510 0.007 0.877 8.8 114.0 23.1 434 n/a 3_bss: 0.1207 0.1507 0.007 0.877 8.8 114.0 23.2 434 n/a 3_settarget: 0.1207 0.1507 0.007 0.877 8.8 114.0 23.2 434 n/a 3_updatecdl: 0.1207 0.1507 0.007 0.878 8.8 114.0 23.2 434 n/a 3_nqh: 0.1207 0.1507 0.007 0.878 8.8 114.0 23.2 434 n/a 3_sol: 0.1236 0.1500 0.007 0.878 8.8 114.0 21.9 443 n/a 3_weight: 0.1236 0.1500 0.007 0.878 8.8 114.0 21.9 443 n/a 3_xyzrec: 0.1241 0.1459 0.006 0.917 8.8 114.0 21.9 443 n/a 3_adp: 0.1235 0.1423 0.006 0.917 9.2 109.3 21.5 443 n/a 3_regHadp: 0.1236 0.1423 0.006 0.917 9.2 109.3 21.5 443 n/a 3_occ: 0.1230 0.1417 0.006 0.917 9.2 109.3 21.5 443 n/a 4_bss: 0.1217 0.1391 0.006 0.917 9.2 109.2 21.5 443 n/a 4_settarget: 0.1217 0.1391 0.006 0.917 9.2 109.2 21.5 443 n/a 4_updatecdl: 0.1217 0.1391 0.006 0.915 9.2 109.2 21.5 443 n/a 4_nqh: 0.1217 0.1391 0.006 0.915 9.2 109.2 21.5 443 n/a 4_sol: 0.1211 0.1362 0.006 0.915 9.2 109.2 21.2 433 n/a 4_weight: 0.1211 0.1362 0.006 0.915 9.2 109.2 21.2 433 n/a 4_xyzrec: 0.1210 0.1378 0.006 0.947 9.2 109.2 21.2 433 n/a 4_adp: 0.1187 0.1369 0.006 0.947 9.2 104.7 21.0 433 n/a 4_regHadp: 0.1187 0.1369 0.006 0.947 9.2 104.7 21.0 433 n/a 4_occ: 0.1182 0.1363 0.006 0.947 9.2 104.7 21.0 433 n/a 5_bss: 0.1179 0.1361 0.006 0.947 9.2 104.6 21.0 433 n/a 5_settarget: 0.1179 0.1361 0.006 0.947 9.2 104.6 21.0 433 n/a 5_updatecdl: 0.1179 0.1361 0.006 0.948 9.2 104.6 21.0 433 n/a 5_setrh: 0.1180 0.1361 0.006 0.948 9.2 104.6 21.0 433 n/a 5_nqh: 0.1180 0.1361 0.006 0.948 9.2 104.6 21.0 433 n/a 5_sol: 0.1178 0.1360 0.006 0.948 9.2 104.6 20.9 435 n/a 5_weight: 0.1178 0.1360 0.006 0.948 9.2 104.6 20.9 435 n/a 5_xyzrec: 0.1204 0.1376 0.007 1.038 9.2 104.6 20.9 435 n/a 5_adp: 0.1206 0.1375 0.007 1.038 9.2 101.6 20.8 435 n/a 5_regHadp: 0.1207 0.1375 0.007 1.038 9.2 101.6 20.8 435 n/a 5_occ: 0.1203 0.1373 0.007 1.038 9.2 101.6 20.8 435 n/a end: 0.1203 0.1375 0.007 1.038 9.2 101.6 20.8 435 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2659048_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2659048_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8800 Refinement macro-cycles (run) : 3514.0700 Write final files (write_after_run_outputs) : 71.7300 Total : 3590.6800 Total CPU time: 60.48 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:20 PST -0800 (1735452680.55 s) Start R-work = 0.1637, R-free = 0.1755 Final R-work = 0.1203, R-free = 0.1375 =============================================================================== Job complete usr+sys time: 3729.88 seconds wall clock time: 66 minutes 34.12 seconds (3994.12 seconds total)