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_2686906.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_2686906.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2686906.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: 2.18, per 1000 atoms: 0.64 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: 0.72 Conformation dependent library (CDL) restraints added in 296.1 milliseconds Time building geometry restraints manager: 0.78 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: 531 0.91 - 1.16: 1106 1.16 - 1.41: 612 1.41 - 1.66: 849 1.66 - 1.91: 55 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.117 0.209 1.10e-02 8.26e+03 3.63e+02 bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.537 1.449 0.088 5.00e-03 4.00e+04 3.07e+02 bond pdb=" C VAL A 146 " pdb=" O VAL A 146 " ideal model delta sigma weight residual 1.236 1.409 -0.173 9.90e-03 1.02e+04 3.06e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.237 1.029 0.208 1.19e-02 7.06e+03 3.04e+02 bond pdb=" N PRO A 43 " pdb=" CD PRO A 43 " ideal model delta sigma weight residual 1.473 1.240 0.233 1.40e-02 5.10e+03 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 3001 4.29 - 8.58: 1829 8.58 - 12.86: 754 12.86 - 17.15: 172 17.15 - 21.44: 21 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.83 108.11 12.72 5.90e-01 2.87e+00 4.65e+02 angle pdb=" O LYS A 148 " pdb=" C LYS A 148 " pdb=" N ASP A 149 " ideal model delta sigma weight residual 123.31 104.50 18.81 1.17e+00 7.31e-01 2.58e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 109.20 10.09 6.50e-01 2.37e+00 2.41e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.52 120.04 -9.52 6.70e-01 2.23e+00 2.02e+02 angle pdb=" O GLY A 137 " pdb=" C GLY A 137 " pdb=" N HIS A 138 " ideal model delta sigma weight residual 122.51 133.94 -11.43 8.10e-01 1.52e+00 1.99e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 940 17.02 - 34.04: 119 34.04 - 51.06: 36 51.06 - 68.08: 13 68.08 - 85.10: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ILE A 9 " pdb=" C ILE A 9 " pdb=" N LEU A 10 " pdb=" CA LEU A 10 " ideal model delta harmonic sigma weight residual 180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.197: 98 0.197 - 0.393: 74 0.393 - 0.588: 50 0.588 - 0.784: 17 0.784 - 0.979: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 172 " pdb=" N LEU A 172 " pdb=" C LEU A 172 " pdb=" CB LEU A 172 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" CA GLU A 143 " pdb=" N GLU A 143 " pdb=" C GLU A 143 " pdb=" CB GLU A 143 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.31e+01 chirality pdb=" CA ALA A 111 " pdb=" N ALA A 111 " pdb=" C ALA A 111 " pdb=" CB ALA A 111 " both_signs ideal model delta sigma weight residual False 2.48 3.35 -0.86 2.00e-01 2.50e+01 1.86e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.114 2.00e-02 2.50e+03 6.83e-02 1.40e+02 pdb=" CG TYR A 141 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.126 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.073 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.081 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.046 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.028 2.00e-02 2.50e+03 6.07e-02 1.11e+02 pdb=" CG PHE A 164 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.081 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.068 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.076 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.114 2.00e-02 2.50e+03 6.03e-02 1.09e+02 pdb=" CG PHE A 119 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.068 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.098 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.063 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.016 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.007 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 828 2.29 - 2.87: 7894 2.87 - 3.44: 10636 3.44 - 4.02: 15268 4.02 - 4.60: 21897 Nonbonded interactions: 56523 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.711 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.751 2.450 nonbonded pdb=" H LEU A 72 " pdb=" O ALA A 103 " model vdw 1.823 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.851 2.450 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.852 2.450 ... (remaining 56518 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_2686906_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1983 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793941 | | target function (ml) not normalized (work): 232752.077972 | | target function (ml) not normalized (free): 11849.171916 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3040 0.2116 7.011 4.9419| | 2: 3.57 - 2.84 1.00 2876 122 0.2446 0.1798 4.3586 4.347| | 3: 2.84 - 2.48 1.00 2833 165 0.2333 0.1832 4.1335 4.1771| | 4: 2.47 - 2.25 1.00 2825 136 0.2361 0.1455 3.8462 3.8343| | 5: 2.25 - 2.09 1.00 2756 127 0.2458 0.1546 3.8071 3.8365| | 6: 2.09 - 1.97 1.00 2846 113 0.2549 0.1808 3.4801 3.5477| | 7: 1.97 - 1.87 1.00 2787 165 0.2570 0.1963 3.1632 3.2588| | 8: 1.87 - 1.79 1.00 2789 144 0.2475 0.2050 3.0974 3.2009| | 9: 1.79 - 1.72 1.00 2745 138 0.2403 0.1732 2.9112 2.9047| | 10: 1.72 - 1.66 1.00 2789 158 0.2429 0.2203 2.8133 2.9575| | 11: 1.66 - 1.61 1.00 2740 147 0.2454 0.1753 2.7588 2.744| | 12: 1.61 - 1.56 1.00 2787 146 0.2526 0.1847 2.6151 2.5872| | 13: 1.56 - 1.52 1.00 2745 130 0.2553 0.1947 2.5625 2.6244| | 14: 1.52 - 1.48 1.00 2803 134 0.2554 0.1927 2.5024 2.544| | 15: 1.48 - 1.45 1.00 2738 128 0.2587 0.2148 2.4293 2.4602| | 16: 1.45 - 1.42 1.00 2756 161 0.2649 0.2293 2.3795 2.4643| | 17: 1.42 - 1.39 1.00 2785 139 0.2696 0.1943 2.3285 2.3322| | 18: 1.39 - 1.36 1.00 2741 179 0.2736 0.2229 2.2812 2.3427| | 19: 1.36 - 1.34 1.00 2807 134 0.2699 0.2639 2.2692 2.3952| | 20: 1.34 - 1.32 1.00 2696 147 0.2703 0.2160 2.206 2.1867| | 21: 1.32 - 1.30 1.00 2785 112 0.2680 0.2421 2.1603 2.2414| | 22: 1.29 - 1.27 1.00 2704 152 0.2703 0.2570 2.1299 2.2129| | 23: 1.27 - 1.26 1.00 2802 156 0.2779 0.2608 2.114 2.2077| | 24: 1.26 - 1.24 1.00 2744 132 0.2725 0.2220 2.0649 2.0586| | 25: 1.24 - 1.22 1.00 2734 148 0.2841 0.2545 2.0501 2.0764| | 26: 1.22 - 1.21 1.00 2727 135 0.2832 0.2232 2.007 2.0675| | 27: 1.21 - 1.19 1.00 2814 148 0.2951 0.2793 2.0077 2.0148| | 28: 1.19 - 1.18 1.00 2671 147 0.2999 0.3147 1.9873 2.0577| | 29: 1.18 - 1.16 1.00 2800 134 0.2985 0.2751 1.9635 1.9975| | 30: 1.16 - 1.15 1.00 2740 148 0.3066 0.2797 1.9249 1.9537| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.96 0.76 0.23 1501.11| | 2: 3.57 - 2.84 2876 122 0.80 26.35 1.27 0.23 1501.11| | 3: 2.84 - 2.48 2833 165 0.74 32.23 1.24 0.23 1247.02| | 4: 2.47 - 2.25 2825 136 0.81 25.97 1.26 0.25 587.62| | 5: 2.25 - 2.09 2756 127 0.77 29.63 1.28 0.25 587.62| | 6: 2.09 - 1.97 2846 113 0.83 23.28 1.29 0.25 325.09| | 7: 1.97 - 1.87 2787 165 0.89 17.48 1.28 0.26 101.18| | 8: 1.87 - 1.79 2789 144 0.85 22.20 1.24 0.26 101.18| | 9: 1.79 - 1.72 2745 138 0.87 19.20 1.23 0.25 59.64| | 10: 1.72 - 1.66 2789 158 0.86 20.99 1.22 0.25 51.32| | 11: 1.66 - 1.61 2740 147 0.85 21.88 1.23 0.25 49.35| | 12: 1.61 - 1.56 2787 146 0.88 18.66 1.24 0.25 29.35| | 13: 1.56 - 1.52 2745 130 0.86 20.51 1.24 0.25 29.35| | 14: 1.52 - 1.48 2803 134 0.86 20.69 1.23 0.25 26.30| | 15: 1.48 - 1.45 2738 128 0.87 20.36 1.23 0.25 20.70| | 16: 1.45 - 1.42 2756 161 0.86 21.70 1.24 0.25 20.70| | 17: 1.42 - 1.39 2785 139 0.86 21.08 1.23 0.25 17.76| | 18: 1.39 - 1.36 2741 179 0.86 21.57 1.23 0.25 16.06| | 19: 1.36 - 1.34 2807 134 0.85 22.19 1.22 0.25 16.06| | 20: 1.34 - 1.32 2696 147 0.86 21.43 1.21 0.24 13.54| | 21: 1.32 - 1.30 2785 112 0.85 22.43 1.20 0.24 13.37| | 22: 1.29 - 1.27 2704 152 0.85 22.97 1.21 0.24 13.05| | 23: 1.27 - 1.26 2802 156 0.85 22.42 1.21 0.24 11.43| | 24: 1.26 - 1.24 2744 132 0.85 23.20 1.20 0.24 11.43| | 25: 1.24 - 1.22 2734 148 0.84 24.00 1.20 0.24 10.87| | 26: 1.22 - 1.21 2727 135 0.83 24.47 1.19 0.23 10.25| | 27: 1.21 - 1.19 2814 148 0.82 25.47 1.20 0.23 10.25| | 28: 1.19 - 1.18 2671 147 0.82 26.19 1.18 0.23 9.67| | 29: 1.18 - 1.16 2800 134 0.82 26.42 1.17 0.22 9.45| | 30: 1.16 - 1.15 2740 148 0.80 28.06 1.16 0.22 9.45| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.45 max = 1501.11 mean = 219.69| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.97 mean = 23.07| |phase err.(test): min = 0.00 max = 89.93 mean = 23.06| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.248 1557 Z= 5.529 Angle : 5.240 18.808 2118 Z= 3.762 Chirality : 0.353 0.979 243 Planarity : 0.034 0.118 284 Dihedral : 13.585 85.097 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 27.03 % 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: -3.08 (0.48), residues: 224 helix: -2.85 (0.38), residues: 109 sheet: -1.23 (0.83), residues: 28 loop : -0.84 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.017 ARG A 98 TYR 0.136 0.046 TYR A 141 PHE 0.093 0.046 PHE A 119 HIS 0.062 0.030 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1983 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793941 | | target function (ml) not normalized (work): 232752.077972 | | target function (ml) not normalized (free): 11849.171916 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2570 0.2610 0.1984 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2570 0.2610 0.1984 n_refl.: 87602 remove outliers: r(all,work,free)=0.1989 0.1991 0.1984 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2014 0.2017 0.1998 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1651 0.1644 0.1788 n_refl.: 87594 remove outliers: r(all,work,free)=0.1650 0.1643 0.1788 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 0.3718 386.415 360.393 0.722 0.929 0.401 11.894-9.307 99.02 97 4 0.1850 613.801 591.909 1.000 0.930 0.380 9.237-7.194 100.00 213 7 0.2204 502.014 491.144 1.028 0.930 0.370 7.162-5.571 100.00 427 22 0.2199 376.733 364.706 1.007 0.930 0.320 5.546-4.326 100.00 867 58 0.1312 517.162 511.370 1.042 0.930 0.259 4.315-3.360 100.00 1859 96 0.1139 491.824 488.431 1.084 0.930 0.158 3.356-2.611 100.00 3867 181 0.1456 323.103 319.370 1.072 0.930 0.129 2.608-2.026 99.99 8198 413 0.1355 214.188 211.799 1.084 0.929 0.000 2.025-1.573 100.00 17313 902 0.1655 104.598 103.870 1.088 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2063 46.383 45.086 1.079 0.926 0.000 1.221-1.150 99.97 13689 708 0.2593 29.225 26.957 1.050 0.925 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0485 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1643 r_free=0.1788 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1647 r_free=0.1791 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.820522 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1983.038123 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 0.1207 0.1458 0.0251 0.008 1.0 0.6 0.5 0.0 0 13.410 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 14.58 2.51 3.013 19.071 1983.038 0.017 12.37 15.34 2.96 3.186 19.544 1983.038 0.016 Individual atomic B min max mean iso aniso Overall: 8.58 118.70 20.99 2.86 0 1785 Protein: 8.58 118.70 17.88 2.86 0 1519 Water: 11.22 114.51 39.06 N/A 0 258 Other: 22.60 36.29 29.20 N/A 0 8 Chain A: 8.58 118.70 20.99 N/A 0 1785 Histogram: Values Number of atoms 8.58 - 19.59 1211 19.59 - 30.60 225 30.60 - 41.61 167 41.61 - 52.63 101 52.63 - 63.64 51 63.64 - 74.65 18 74.65 - 85.66 5 85.66 - 96.68 4 96.68 - 107.69 0 107.69 - 118.70 3 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1534 r_work=0.1242 r_free=0.1539 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1242 r_free = 0.1539 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1243 r_free = 0.1544 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.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1243 r_free= 0.1544 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015438 | | target function (ls_wunit_k1) not normalized (work): 1285.931859 | | target function (ls_wunit_k1) not normalized (free): 112.422046 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1257 0.1243 0.1544 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1705 0.1704 0.1775 n_refl.: 87593 remove outliers: r(all,work,free)=0.1705 0.1704 0.1775 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1724 0.1724 0.1789 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1255 0.1240 0.1537 n_refl.: 87593 remove outliers: r(all,work,free)=0.1255 0.1240 0.1537 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 96.88 88 5 0.3581 301.273 280.808 0.705 0.924 0.393 11.894-9.307 99.02 97 4 0.1594 478.557 466.408 0.984 0.925 0.380 9.237-7.194 100.00 213 7 0.1838 391.401 386.512 1.026 0.925 0.319 7.162-5.571 100.00 427 22 0.1709 293.725 288.142 1.003 0.926 0.263 5.546-4.326 100.00 867 58 0.0921 403.212 400.648 1.029 0.926 0.230 4.315-3.360 100.00 1859 96 0.0780 383.457 382.346 1.076 0.927 0.180 3.356-2.611 100.00 3867 181 0.1020 251.911 251.171 1.075 0.929 0.120 2.608-2.026 99.99 8198 413 0.0973 166.994 166.406 1.085 0.932 0.000 2.025-1.573 100.00 17313 902 0.1205 81.551 81.741 1.087 0.936 0.000 1.573-1.221 100.00 36679 1900 0.1644 36.163 35.631 1.065 0.943 0.000 1.221-1.150 99.97 13689 708 0.2360 22.785 21.313 1.020 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0455 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1240 r_free=0.1537 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1242 r_free=0.1539 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1242 r_free=0.1539 | n_water=258 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1251 r_free=0.1536 | n_water=252 | time (s): 27.040 (total time: 29.440) Filter (q & B) r_work=0.1254 r_free=0.1535 | n_water=249 | time (s): 3.630 (total time: 33.070) Compute maps r_work=0.1254 r_free=0.1535 | n_water=249 | time (s): 1.900 (total time: 34.970) Filter (map) r_work=0.1280 r_free=0.1551 | n_water=232 | time (s): 3.900 (total time: 38.870) Find peaks r_work=0.1280 r_free=0.1551 | n_water=232 | time (s): 0.720 (total time: 39.590) Add new water r_work=0.1440 r_free=0.1710 | n_water=458 | time (s): 3.860 (total time: 43.450) Refine new water occ: r_work=0.1335 r_free=0.1551 adp: r_work=0.1250 r_free=0.1503 occ: r_work=0.1266 r_free=0.1495 adp: r_work=0.1227 r_free=0.1481 occ: r_work=0.1230 r_free=0.1471 adp: r_work=0.1220 r_free=0.1471 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1471 r_work=0.1220 r_free=0.1471 | n_water=458 | time (s): 107.690 (total time: 151.140) Filter (q & B) r_work=0.1226 r_free=0.1477 | n_water=437 | time (s): 3.830 (total time: 154.970) Filter (dist only) r_work=0.1226 r_free=0.1477 | n_water=437 | time (s): 40.650 (total time: 195.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.741034 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1588.024390 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1227 0.1518 0.0291 0.007 0.9 2.2 0.5 0.0 0 12.371 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 15.18 2.91 3.782 23.224 1588.024 0.015 11.92 14.84 2.91 4.168 23.062 1588.024 0.014 Individual atomic B min max mean iso aniso Overall: 8.63 114.47 23.31 2.62 205 1759 Protein: 8.63 114.47 17.68 2.63 0 1519 Water: 10.87 72.34 42.75 N/A 205 232 Other: 23.65 35.22 28.86 N/A 0 8 Chain A: 8.63 114.47 20.36 N/A 0 1759 Chain S: 18.04 71.45 48.60 N/A 205 0 Histogram: Values Number of atoms 8.63 - 19.21 1199 19.21 - 29.80 256 29.80 - 40.38 186 40.38 - 50.96 147 50.96 - 61.55 114 61.55 - 72.13 50 72.13 - 82.72 6 82.72 - 93.30 3 93.30 - 103.88 1 103.88 - 114.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1484 r_work=0.1192 r_free=0.1484 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1484 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1472 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.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1195 r_free= 0.1472 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013668 | | target function (ls_wunit_k1) not normalized (work): 1138.539036 | | target function (ls_wunit_k1) not normalized (free): 99.238733 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1195 0.1472 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1610 0.1607 0.1713 n_refl.: 87593 remove outliers: r(all,work,free)=0.1610 0.1607 0.1713 n_refl.: 87593 overall B=0.02 to atoms: r(all,work,free)=0.1614 0.1611 0.1715 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1192 0.1474 n_refl.: 87593 remove outliers: r(all,work,free)=0.1205 0.1191 0.1474 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3422 297.296 272.886 0.611 1.002 0.380 11.894-9.307 99.02 97 4 0.1528 478.557 475.085 0.916 1.003 0.370 9.237-7.194 100.00 213 7 0.1567 391.401 392.546 0.977 1.003 0.254 7.162-5.571 100.00 427 22 0.1462 293.725 290.167 0.948 1.003 0.229 5.546-4.326 100.00 867 58 0.0823 403.212 401.076 0.957 1.003 0.220 4.315-3.360 100.00 1859 96 0.0707 383.457 382.412 1.002 1.003 0.201 3.356-2.611 100.00 3867 181 0.0957 251.911 251.333 1.008 1.002 0.072 2.608-2.026 99.99 8198 413 0.0961 166.994 166.561 1.018 1.002 0.000 2.025-1.573 100.00 17313 902 0.1174 81.551 81.756 1.029 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1603 36.163 35.673 1.019 0.999 0.000 1.221-1.150 99.97 13689 708 0.2334 22.785 21.325 0.980 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0363 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1474 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1474 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1474 | n_water=437 | time (s): 2.220 (total time: 2.220) Filter (dist) r_work=0.1191 r_free=0.1474 | n_water=437 | time (s): 36.960 (total time: 39.180) Filter (q & B) r_work=0.1191 r_free=0.1474 | n_water=437 | time (s): 1.040 (total time: 40.220) Compute maps r_work=0.1191 r_free=0.1474 | n_water=437 | time (s): 1.860 (total time: 42.080) Filter (map) r_work=0.1231 r_free=0.1479 | n_water=296 | time (s): 3.260 (total time: 45.340) Find peaks r_work=0.1231 r_free=0.1479 | n_water=296 | time (s): 0.530 (total time: 45.870) Add new water r_work=0.1364 r_free=0.1617 | n_water=500 | time (s): 3.420 (total time: 49.290) Refine new water occ: r_work=0.1261 r_free=0.1529 adp: r_work=0.1263 r_free=0.1532 occ: r_work=0.1238 r_free=0.1502 adp: r_work=0.1237 r_free=0.1504 occ: r_work=0.1223 r_free=0.1479 adp: r_work=0.1216 r_free=0.1479 ADP+occupancy (water only), MIN, final r_work=0.1216 r_free=0.1479 r_work=0.1216 r_free=0.1479 | n_water=500 | time (s): 185.440 (total time: 234.730) Filter (q & B) r_work=0.1220 r_free=0.1482 | n_water=460 | time (s): 3.330 (total time: 238.060) Filter (dist only) r_work=0.1219 r_free=0.1479 | n_water=459 | time (s): 37.980 (total time: 276.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.120400 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.617940 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 0.1226 0.1436 0.0210 0.006 0.9 1.6 0.5 0.0 0 1.060 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.36 2.10 3.630 22.167 51.618 3.719 12.12 13.92 1.80 4.083 21.996 51.618 3.649 Individual atomic B min max mean iso aniso Overall: 9.16 109.93 21.80 2.35 228 1758 Protein: 9.16 109.93 17.28 2.36 0 1519 Water: 11.47 71.35 36.67 N/A 228 231 Other: 19.16 31.21 25.86 N/A 0 8 Chain A: 9.16 109.93 19.93 N/A 0 1758 Chain S: 16.85 60.89 36.15 N/A 228 0 Histogram: Values Number of atoms 9.16 - 19.24 1231 19.24 - 29.32 278 29.32 - 39.39 227 39.39 - 49.47 141 49.47 - 59.55 78 59.55 - 69.62 18 69.62 - 79.70 7 79.70 - 89.78 3 89.78 - 99.85 1 99.85 - 109.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.1212 r_free=0.1392 r_work=0.1213 r_free=0.1392 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1213 r_free = 0.1392 target_work(ml) = 3.650 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1209 r_free = 0.1390 target_work(ml) = 3.648 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1209 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.647695 | | target function (ml) not normalized (work): 303831.142410 | | target function (ml) not normalized (free): 16042.352328 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1209 0.1390 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1540 0.1540 0.1569 n_refl.: 87590 remove outliers: r(all,work,free)=0.1540 0.1540 0.1569 n_refl.: 87590 overall B=-0.02 to atoms: r(all,work,free)=0.1537 0.1537 0.1568 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1198 0.1357 n_refl.: 87590 remove outliers: r(all,work,free)=0.1201 0.1193 0.1357 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 0.3887 286.818 263.122 0.464 0.999 0.293 11.894-9.307 95.10 93 4 0.2443 468.264 453.814 0.839 1.001 0.273 9.237-7.194 97.73 208 7 0.2396 384.025 382.844 0.930 1.001 0.198 7.162-5.571 100.00 427 22 0.2125 293.725 282.859 0.914 1.002 0.170 5.546-4.326 100.00 867 58 0.1102 403.212 399.117 0.952 1.002 0.155 4.315-3.360 100.00 1859 96 0.0920 383.457 380.649 0.993 1.002 0.134 3.356-2.611 100.00 3867 181 0.1143 251.911 250.096 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1042 166.994 166.003 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.1009 81.551 81.688 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1286 36.163 35.736 1.020 1.000 0.000 1.221-1.150 99.97 13689 708 0.2125 22.785 21.405 0.978 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0050 b_overall=-0.0400 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1357 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=0.1193 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1357 | n_water=459 | time (s): 2.210 (total time: 2.210) Filter (dist) r_work=0.1193 r_free=0.1357 | n_water=459 | time (s): 39.140 (total time: 41.350) Filter (q & B) r_work=0.1194 r_free=0.1357 | n_water=458 | time (s): 2.960 (total time: 44.310) Compute maps r_work=0.1194 r_free=0.1357 | n_water=458 | time (s): 1.650 (total time: 45.960) Filter (map) r_work=0.1217 r_free=0.1373 | n_water=314 | time (s): 3.430 (total time: 49.390) Find peaks r_work=0.1217 r_free=0.1373 | n_water=314 | time (s): 0.660 (total time: 50.050) Add new water r_work=0.1281 r_free=0.1432 | n_water=488 | time (s): 3.180 (total time: 53.230) Refine new water occ: r_work=0.1208 r_free=0.1358 adp: r_work=0.1208 r_free=0.1362 occ: r_work=0.1193 r_free=0.1344 adp: r_work=0.1191 r_free=0.1347 occ: r_work=0.1182 r_free=0.1337 adp: r_work=0.1178 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1178 r_free=0.1336 r_work=0.1178 r_free=0.1336 | n_water=488 | time (s): 230.880 (total time: 284.110) Filter (q & B) r_work=0.1187 r_free=0.1342 | n_water=447 | time (s): 2.680 (total time: 286.790) Filter (dist only) r_work=0.1187 r_free=0.1342 | n_water=447 | time (s): 36.270 (total time: 323.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.975506 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.072316 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 0.1361 0.0167 0.006 0.9 1.9 0.5 0.0 0 0.988 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.61 1.67 3.447 21.618 48.072 3.633 11.84 13.58 1.74 3.976 21.455 48.072 3.622 Individual atomic B min max mean iso aniso Overall: 9.28 104.92 21.32 2.16 218 1756 Protein: 9.28 104.92 16.89 2.16 0 1519 Water: 11.56 69.62 36.36 N/A 218 229 Other: 17.77 27.15 22.28 N/A 0 8 Chain A: 9.28 104.92 19.46 N/A 0 1756 Chain S: 16.07 62.41 36.25 N/A 218 0 Histogram: Values Number of atoms 9.28 - 18.84 1230 18.84 - 28.41 271 28.41 - 37.97 214 37.97 - 47.53 135 47.53 - 57.10 84 57.10 - 66.66 27 66.66 - 76.22 8 76.22 - 85.79 2 85.79 - 95.35 1 95.35 - 104.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1358 r_work=0.1185 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1185 r_free = 0.1358 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1182 r_free = 0.1356 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1182 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.620692 | | target function (ml) not normalized (work): 301534.870091 | | target function (ml) not normalized (free): 15928.895268 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1190 0.1182 0.1356 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1509 0.1507 0.1574 n_refl.: 87577 remove outliers: r(all,work,free)=0.1509 0.1507 0.1574 n_refl.: 87577 overall B=-0.02 to atoms: r(all,work,free)=0.1506 0.1504 0.1572 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1181 0.1360 n_refl.: 87577 remove outliers: r(all,work,free)=0.1189 0.1180 0.1360 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3967 283.373 255.985 0.430 0.999 0.274 11.894-9.307 93.14 91 4 0.2554 458.099 447.190 0.827 1.000 0.200 9.237-7.194 97.73 208 7 0.2510 384.025 376.510 0.912 1.001 0.150 7.162-5.571 100.00 427 22 0.2266 293.725 282.641 0.908 1.002 0.144 5.546-4.326 100.00 867 58 0.1139 403.212 398.569 0.952 1.002 0.122 4.315-3.360 100.00 1859 96 0.0942 383.457 380.981 0.994 1.002 0.117 3.356-2.611 100.00 3867 181 0.1146 251.911 250.090 1.001 1.001 0.053 2.608-2.026 99.99 8198 413 0.1023 166.994 166.071 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0960 81.551 81.807 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1243 36.163 35.789 1.023 0.998 0.000 1.221-1.150 99.97 13689 708 0.2130 22.785 21.409 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0417 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1180 r_free=0.1360 After: r_work=0.1181 r_free=0.1360 ================================== NQH flips ================================== r_work=0.1181 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1181 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1181 r_free=0.1360 | n_water=447 | time (s): 1.710 (total time: 1.710) Filter (dist) r_work=0.1180 r_free=0.1359 | n_water=446 | time (s): 37.050 (total time: 38.760) Filter (q & B) r_work=0.1181 r_free=0.1361 | n_water=444 | time (s): 3.550 (total time: 42.310) Compute maps r_work=0.1181 r_free=0.1361 | n_water=444 | time (s): 1.780 (total time: 44.090) Filter (map) r_work=0.1202 r_free=0.1368 | n_water=329 | time (s): 3.680 (total time: 47.770) Find peaks r_work=0.1202 r_free=0.1368 | n_water=329 | time (s): 0.670 (total time: 48.440) Add new water r_work=0.1246 r_free=0.1409 | n_water=493 | time (s): 3.230 (total time: 51.670) Refine new water occ: r_work=0.1185 r_free=0.1352 adp: r_work=0.1185 r_free=0.1355 occ: r_work=0.1174 r_free=0.1345 adp: r_work=0.1173 r_free=0.1345 occ: r_work=0.1167 r_free=0.1343 adp: r_work=0.1164 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1164 r_free=0.1341 r_work=0.1164 r_free=0.1341 | n_water=493 | time (s): 162.300 (total time: 213.970) Filter (q & B) r_work=0.1173 r_free=0.1349 | n_water=442 | time (s): 3.100 (total time: 217.070) Filter (dist only) r_work=0.1173 r_free=0.1346 | n_water=440 | time (s): 37.450 (total time: 254.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.857479 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.893745 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1379 0.0176 0.007 1.1 3.5 0.5 0.0 0 0.929 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.79 1.76 3.274 21.094 45.894 3.630 12.03 13.74 1.71 3.433 21.041 45.894 3.621 Individual atomic B min max mean iso aniso Overall: 9.28 101.09 21.05 2.03 211 1756 Protein: 9.28 101.09 16.74 2.03 0 1519 Water: 11.52 68.90 35.90 N/A 211 229 Other: 18.22 25.89 22.29 N/A 0 8 Chain A: 9.28 101.09 19.31 N/A 0 1756 Chain S: 15.10 62.88 35.48 N/A 211 0 Histogram: Values Number of atoms 9.28 - 18.46 1219 18.46 - 27.64 277 27.64 - 36.83 201 36.83 - 46.01 146 46.01 - 55.19 79 55.19 - 64.37 28 64.37 - 73.55 12 73.55 - 82.73 2 82.73 - 91.91 1 91.91 - 101.09 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1374 r_work=0.1203 r_free=0.1374 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1374 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1369 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1198 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.619355 | | target function (ml) not normalized (work): 301412.679839 | | target function (ml) not normalized (free): 15930.430197 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1429 0.1400 5.6847 5.6246| | 2: 3.57 - 2.84 1.00 2888 124 0.1119 0.1482 5.1968 5.2753| | 3: 2.83 - 2.48 1.00 2820 163 0.1226 0.1303 5.0047 5.0317| | 4: 2.47 - 2.25 1.00 2825 136 0.1018 0.1201 4.7031 4.773| | 5: 2.25 - 2.09 1.00 2756 127 0.0992 0.1138 4.6447 4.7165| | 6: 2.09 - 1.97 1.00 2846 113 0.0974 0.1158 4.3519 4.4561| | 7: 1.97 - 1.87 1.00 2787 165 0.0998 0.1185 4.0759 4.1715| | 8: 1.87 - 1.79 1.00 2789 144 0.1016 0.1207 3.9853 4.0609| | 9: 1.79 - 1.72 1.00 2745 138 0.0962 0.1297 3.7158 3.8962| | 10: 1.72 - 1.66 1.00 2831 160 0.0996 0.1270 3.6272 3.7692| | 11: 1.66 - 1.61 1.00 2712 147 0.0967 0.1047 3.5626 3.5847| | 12: 1.61 - 1.56 1.00 2773 144 0.0914 0.1151 3.3392 3.4851| | 13: 1.56 - 1.52 1.00 2745 130 0.0976 0.1047 3.333 3.4157| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1091 3.2551 3.3256| | 15: 1.48 - 1.45 1.00 2738 128 0.1006 0.1335 3.1634 3.3334| | 16: 1.45 - 1.42 1.00 2756 161 0.1070 0.1236 3.1462 3.2423| | 17: 1.42 - 1.39 1.00 2785 139 0.1119 0.1309 3.1144 3.248| | 18: 1.39 - 1.36 1.00 2741 179 0.1146 0.1369 3.084 3.2713| | 19: 1.36 - 1.34 1.00 2807 134 0.1218 0.1616 3.0932 3.2857| | 20: 1.34 - 1.32 1.00 2696 147 0.1317 0.1499 3.0838 3.1367| | 21: 1.32 - 1.30 1.00 2785 112 0.1413 0.1571 3.0874 3.1391| | 22: 1.29 - 1.27 1.00 2704 152 0.1478 0.1949 3.0847 3.2945| | 23: 1.27 - 1.26 1.00 2802 156 0.1575 0.1864 3.1019 3.21| | 24: 1.26 - 1.24 1.00 2744 132 0.1632 0.1726 3.0947 3.1814| | 25: 1.24 - 1.22 1.00 2733 148 0.1789 0.2298 3.1076 3.2839| | 26: 1.22 - 1.21 1.00 2727 135 0.1860 0.1796 3.1228 3.2055| | 27: 1.21 - 1.19 1.00 2814 148 0.2015 0.2072 3.1419 3.1493| | 28: 1.19 - 1.18 1.00 2671 147 0.2151 0.2335 3.1402 3.1692| | 29: 1.18 - 1.16 1.00 2800 134 0.2213 0.2368 3.1258 3.2194| | 30: 1.16 - 1.15 1.00 2739 148 0.2384 0.2488 3.1163 3.1627| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2916 171 0.95 9.08 1.00 0.98 6192.81| | 2: 3.57 - 2.84 2888 124 0.92 13.15 1.01 0.98 6192.81| | 3: 2.83 - 2.48 2820 163 0.89 17.32 0.99 0.98 5192.12| | 4: 2.47 - 2.25 2825 136 0.91 14.44 1.00 0.98 2611.64| | 5: 2.25 - 2.09 2756 127 0.89 16.73 1.01 0.98 2611.64| | 6: 2.09 - 1.97 2846 113 0.92 13.47 1.02 0.98 1535.64| | 7: 1.97 - 1.87 2787 165 0.94 10.70 1.02 0.97 617.96| | 8: 1.87 - 1.79 2789 144 0.91 14.27 0.99 0.97 617.96| | 9: 1.79 - 1.72 2745 138 0.93 11.31 0.98 0.97 334.05| | 10: 1.72 - 1.66 2831 160 0.93 12.16 0.98 0.97 277.19| | 11: 1.66 - 1.61 2712 147 0.93 12.80 0.98 0.97 264.51| | 12: 1.61 - 1.56 2773 144 0.95 9.42 0.99 0.97 144.94| | 13: 1.56 - 1.52 2745 130 0.94 10.98 1.02 0.97 144.94| | 14: 1.52 - 1.48 2803 134 0.94 11.15 1.02 0.98 129.86| | 15: 1.48 - 1.45 2738 128 0.95 10.33 1.01 0.98 102.25| | 16: 1.45 - 1.42 2756 161 0.94 11.51 1.02 0.98 102.25| | 17: 1.42 - 1.39 2785 139 0.94 11.41 1.01 0.98 92.75| | 18: 1.39 - 1.36 2741 179 0.94 11.70 1.01 0.98 87.24| | 19: 1.36 - 1.34 2807 134 0.94 12.25 1.00 0.98 87.24| | 20: 1.34 - 1.32 2696 147 0.94 12.41 0.99 0.97 82.11| | 21: 1.32 - 1.30 2785 112 0.94 13.36 0.98 0.96 81.75| | 22: 1.29 - 1.27 2704 152 0.93 13.93 0.98 0.96 81.88| | 23: 1.27 - 1.26 2802 156 0.92 14.80 0.98 0.95 82.52| | 24: 1.26 - 1.24 2744 132 0.93 14.90 0.97 0.95 82.52| | 25: 1.24 - 1.22 2733 148 0.91 16.29 0.96 0.94 84.06| | 26: 1.22 - 1.21 2727 135 0.90 18.04 1.02 0.93 85.78| | 27: 1.21 - 1.19 2814 148 0.89 18.69 1.02 0.93 85.78| | 28: 1.19 - 1.18 2671 147 0.88 20.23 1.01 0.93 89.39| | 29: 1.18 - 1.16 2800 134 0.88 20.51 0.99 0.93 90.75| | 30: 1.16 - 1.15 2739 148 0.86 21.97 0.98 0.93 90.75| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 81.75 max = 6192.81 mean = 965.90| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 13.96| |phase err.(test): min = 0.00 max = 89.74 mean = 14.03| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1198 0.1369 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1521 0.1520 0.1571 n_refl.: 87574 remove outliers: r(all,work,free)=0.1521 0.1520 0.1571 n_refl.: 87574 overall B=-0.01 to atoms: r(all,work,free)=0.1519 0.1518 0.1570 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1198 0.1372 n_refl.: 87574 remove outliers: r(all,work,free)=0.1207 0.1198 0.1372 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3994 283.373 263.512 0.435 0.998 0.257 11.894-9.307 93.14 91 4 0.2601 458.099 441.314 0.813 1.000 0.187 9.237-7.194 97.27 207 7 0.2554 383.552 374.944 0.900 1.000 0.145 7.162-5.571 100.00 427 22 0.2286 293.725 282.057 0.905 1.001 0.134 5.546-4.326 100.00 867 58 0.1209 403.212 398.034 0.951 1.001 0.121 4.315-3.360 100.00 1859 96 0.0986 383.457 381.027 0.996 1.001 0.117 3.356-2.611 100.00 3867 181 0.1185 251.911 250.163 1.001 1.001 0.110 2.608-2.026 99.99 8198 413 0.1039 166.994 166.055 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0978 81.551 81.852 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1226 36.163 35.806 1.019 1.000 0.000 1.221-1.150 99.97 13689 708 0.2119 22.785 21.386 0.974 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0326 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2609 0.1983 0.083 5.240 8.8 119.3 19.9 258 0.000 1_bss: 0.1643 0.1788 0.083 5.240 9.1 119.5 20.1 258 0.000 1_settarget: 0.1643 0.1788 0.083 5.240 9.1 119.5 20.1 258 0.000 1_nqh: 0.1647 0.1791 0.083 5.240 9.1 119.5 20.1 258 0.003 1_weight: 0.1647 0.1791 0.083 5.240 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1207 0.1458 0.008 0.972 9.1 119.5 20.1 258 0.120 1_adp: 0.1238 0.1534 0.008 0.972 8.6 118.7 21.0 258 0.120 1_regHadp: 0.1242 0.1539 0.008 0.972 8.6 118.7 21.0 258 0.120 1_occ: 0.1243 0.1544 0.008 0.972 8.6 118.7 21.0 258 0.120 2_bss: 0.1240 0.1537 0.008 0.972 8.7 118.8 21.1 258 0.120 2_settarget: 0.1240 0.1537 0.008 0.972 8.7 118.8 21.1 258 0.120 2_updatecdl: 0.1240 0.1537 0.008 0.979 8.7 118.8 21.1 258 0.120 2_nqh: 0.1242 0.1539 0.008 0.979 8.7 118.8 21.1 258 0.123 2_sol: 0.1226 0.1477 0.008 0.979 8.7 118.8 23.6 437 n/a 2_weight: 0.1226 0.1477 0.008 0.979 8.7 118.8 23.6 437 n/a 2_xyzrec: 0.1227 0.1518 0.007 0.872 8.7 118.8 23.6 437 n/a 2_adp: 0.1192 0.1484 0.007 0.872 8.6 114.5 23.3 437 n/a 2_regHadp: 0.1192 0.1484 0.007 0.872 8.6 114.5 23.3 437 n/a 2_occ: 0.1195 0.1472 0.007 0.872 8.6 114.5 23.3 437 n/a 3_bss: 0.1191 0.1474 0.007 0.872 8.7 114.5 23.3 437 n/a 3_settarget: 0.1191 0.1474 0.007 0.872 8.7 114.5 23.3 437 n/a 3_updatecdl: 0.1191 0.1474 0.007 0.873 8.7 114.5 23.3 437 n/a 3_nqh: 0.1191 0.1474 0.007 0.873 8.7 114.5 23.3 437 n/a 3_sol: 0.1219 0.1479 0.007 0.873 8.7 114.5 22.1 459 n/a 3_weight: 0.1219 0.1479 0.007 0.873 8.7 114.5 22.1 459 n/a 3_xyzrec: 0.1226 0.1436 0.006 0.928 8.7 114.5 22.1 459 n/a 3_adp: 0.1212 0.1392 0.006 0.928 9.2 109.9 21.8 459 n/a 3_regHadp: 0.1213 0.1392 0.006 0.928 9.2 109.9 21.8 459 n/a 3_occ: 0.1209 0.1390 0.006 0.928 9.2 109.9 21.8 459 n/a 4_bss: 0.1193 0.1357 0.006 0.928 9.1 109.9 21.8 459 n/a 4_settarget: 0.1193 0.1357 0.006 0.928 9.1 109.9 21.8 459 n/a 4_updatecdl: 0.1193 0.1357 0.006 0.926 9.1 109.9 21.8 459 n/a 4_nqh: 0.1193 0.1357 0.006 0.926 9.1 109.9 21.8 459 n/a 4_sol: 0.1187 0.1342 0.006 0.926 9.1 109.9 21.6 447 n/a 4_weight: 0.1187 0.1342 0.006 0.926 9.1 109.9 21.6 447 n/a 4_xyzrec: 0.1195 0.1361 0.006 0.949 9.1 109.9 21.6 447 n/a 4_adp: 0.1184 0.1358 0.006 0.949 9.3 104.9 21.3 447 n/a 4_regHadp: 0.1185 0.1358 0.006 0.949 9.3 104.9 21.3 447 n/a 4_occ: 0.1182 0.1356 0.006 0.949 9.3 104.9 21.3 447 n/a 5_bss: 0.1180 0.1360 0.006 0.949 9.3 104.9 21.3 447 n/a 5_settarget: 0.1180 0.1360 0.006 0.949 9.3 104.9 21.3 447 n/a 5_updatecdl: 0.1180 0.1360 0.006 0.953 9.3 104.9 21.3 447 n/a 5_setrh: 0.1181 0.1360 0.006 0.953 9.3 104.9 21.3 447 n/a 5_nqh: 0.1181 0.1360 0.006 0.953 9.3 104.9 21.3 447 n/a 5_sol: 0.1173 0.1346 0.006 0.953 9.3 104.9 21.1 440 n/a 5_weight: 0.1173 0.1346 0.006 0.953 9.3 104.9 21.1 440 n/a 5_xyzrec: 0.1203 0.1379 0.007 1.073 9.3 104.9 21.1 440 n/a 5_adp: 0.1203 0.1374 0.007 1.073 9.3 101.1 21.0 440 n/a 5_regHadp: 0.1203 0.1374 0.007 1.073 9.3 101.1 21.0 440 n/a 5_occ: 0.1198 0.1369 0.007 1.073 9.3 101.1 21.0 440 n/a end: 0.1198 0.1372 0.007 1.073 9.3 101.1 21.0 440 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2686906_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2686906_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7200 Refinement macro-cycles (run) : 3476.9700 Write final files (write_after_run_outputs) : 70.1600 Total : 3551.8500 Total CPU time: 59.81 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:34 PST -0800 (1735452694.53 s) Start R-work = 0.1643, R-free = 0.1788 Final R-work = 0.1198, R-free = 0.1372 =============================================================================== Job complete usr+sys time: 3687.55 seconds wall clock time: 66 minutes 46.13 seconds (4006.13 seconds total)