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_5382129.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5382129.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5382129.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.26, per 1000 atoms: 0.67 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: 0.88 Conformation dependent library (CDL) restraints added in 283.1 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: 0.65 - 0.90: 485 0.90 - 1.16: 1157 1.16 - 1.41: 569 1.41 - 1.66: 886 1.66 - 1.91: 56 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 20 " pdb=" O VAL A 20 " ideal model delta sigma weight residual 1.237 0.986 0.251 1.19e-02 7.06e+03 4.45e+02 bond pdb=" C THR A 34 " pdb=" N VAL A 35 " ideal model delta sigma weight residual 1.329 1.538 -0.209 1.15e-02 7.56e+03 3.30e+02 bond pdb=" CE1 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 1.321 1.501 -0.180 1.00e-02 1.00e+04 3.23e+02 bond pdb=" C THR A 34 " pdb=" O THR A 34 " ideal model delta sigma weight residual 1.236 1.029 0.207 1.17e-02 7.31e+03 3.12e+02 bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.520 1.732 -0.212 1.23e-02 6.61e+03 2.96e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 3268 4.88 - 9.75: 1836 9.75 - 14.62: 581 14.62 - 19.49: 83 19.49 - 24.37: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 105.62 13.58 9.00e-01 1.23e+00 2.28e+02 angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.12 137.98 -15.86 1.06e+00 8.90e-01 2.24e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 121.76 134.45 -12.69 8.70e-01 1.32e+00 2.13e+02 angle pdb=" CA BGLU A 96 " pdb=" C BGLU A 96 " pdb=" O BGLU A 96 " ideal model delta sigma weight residual 120.82 107.13 13.69 1.05e+00 9.07e-01 1.70e+02 angle pdb=" O ALA A 36 " pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 123.22 137.81 -14.59 1.14e+00 7.69e-01 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.64: 989 20.64 - 41.28: 86 41.28 - 61.92: 31 61.92 - 82.55: 3 82.55 - 103.19: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CD2 PHE A 164 " pdb=" CG PHE A 164 " pdb=" CD1 PHE A 164 " pdb=" HD1 PHE A 164 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA THR A 110 " pdb=" C THR A 110 " pdb=" N ALA A 111 " pdb=" CA ALA A 111 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.228: 111 0.228 - 0.449: 71 0.449 - 0.670: 44 0.670 - 0.892: 13 0.892 - 1.113: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.40 1.11 2.00e-01 2.50e+01 3.10e+01 chirality pdb=" CA ILE A 102 " pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CB ILE A 102 " both_signs ideal model delta sigma weight residual False 2.43 3.52 -1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.63e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.007 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG PHE A 164 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.112 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.032 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.112 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.025 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.043 2.00e-02 2.50e+03 5.35e-02 8.59e+01 pdb=" CG BTYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.025 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.086 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.093 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.028 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.019 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.075 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 49 " -0.052 2.00e-02 2.50e+03 9.22e-02 8.51e+01 pdb=" C ASP A 49 " 0.160 2.00e-02 2.50e+03 pdb=" O ASP A 49 " -0.053 2.00e-02 2.50e+03 pdb=" N VAL A 50 " -0.055 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1282 2.35 - 2.91: 8208 2.91 - 3.48: 10502 3.48 - 4.04: 15144 4.04 - 4.60: 21424 Nonbonded interactions: 56560 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.788 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.795 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.820 2.100 nonbonded pdb=" H LEU A 72 " pdb=" O ALA A 103 " model vdw 1.837 2.450 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.839 2.100 ... (remaining 56555 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_5382129_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= 0.2598 r_free= 0.1945 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789863 | | target function (ml) not normalized (work): 232412.339265 | | target function (ml) not normalized (free): 11799.002663 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3022 0.2063 7.1061 4.9407| | 2: 3.57 - 2.84 1.00 2876 122 0.2420 0.1737 4.3443 4.3257| | 3: 2.84 - 2.48 1.00 2833 165 0.2330 0.1662 4.1217 4.1471| | 4: 2.47 - 2.25 1.00 2825 136 0.2330 0.1545 3.8284 3.8323| | 5: 2.25 - 2.09 1.00 2756 127 0.2442 0.1595 3.7903 3.8191| | 6: 2.09 - 1.97 1.00 2846 113 0.2531 0.1959 3.4633 3.6031| | 7: 1.97 - 1.87 1.00 2787 165 0.2550 0.1820 3.1305 3.181| | 8: 1.87 - 1.79 1.00 2789 144 0.2483 0.1899 3.05 3.1359| | 9: 1.79 - 1.72 1.00 2745 138 0.2409 0.1861 2.9159 2.9822| | 10: 1.72 - 1.66 1.00 2789 158 0.2434 0.2057 2.8101 2.8696| | 11: 1.66 - 1.61 1.00 2740 147 0.2503 0.1793 2.7469 2.7572| | 12: 1.61 - 1.56 1.00 2787 146 0.2472 0.1940 2.6208 2.6172| | 13: 1.56 - 1.52 1.00 2745 130 0.2547 0.1768 2.5614 2.572| | 14: 1.52 - 1.48 1.00 2803 134 0.2635 0.1893 2.509 2.5424| | 15: 1.48 - 1.45 1.00 2738 128 0.2608 0.2168 2.4345 2.493| | 16: 1.45 - 1.42 1.00 2756 161 0.2627 0.2069 2.3706 2.3903| | 17: 1.42 - 1.39 1.00 2785 139 0.2617 0.2028 2.3309 2.3292| | 18: 1.39 - 1.36 1.00 2741 179 0.2731 0.2349 2.2794 2.3587| | 19: 1.36 - 1.34 1.00 2807 134 0.2681 0.2257 2.2512 2.2714| | 20: 1.34 - 1.32 1.00 2696 147 0.2654 0.2327 2.1949 2.23| | 21: 1.32 - 1.30 1.00 2785 112 0.2671 0.2631 2.1559 2.2673| | 22: 1.29 - 1.27 1.00 2704 152 0.2744 0.2531 2.1383 2.2001| | 23: 1.27 - 1.26 1.00 2802 156 0.2729 0.2414 2.0988 2.1773| | 24: 1.26 - 1.24 1.00 2744 132 0.2781 0.2437 2.0692 2.1541| | 25: 1.24 - 1.22 1.00 2734 148 0.2863 0.2558 2.0572 2.0823| | 26: 1.22 - 1.21 1.00 2727 135 0.2889 0.2351 2.0137 2.094| | 27: 1.21 - 1.19 1.00 2814 148 0.2982 0.2503 2.0085 1.9638| | 28: 1.19 - 1.18 1.00 2671 147 0.2935 0.2780 1.9706 1.9949| | 29: 1.18 - 1.16 1.00 2800 134 0.2905 0.2631 1.9419 1.9842| | 30: 1.16 - 1.15 1.00 2740 148 0.3048 0.2908 1.923 1.9584| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.68 0.76 0.23 1451.38| | 2: 3.57 - 2.84 2876 122 0.81 25.78 1.27 0.23 1451.38| | 3: 2.84 - 2.48 2833 165 0.74 31.68 1.24 0.24 1204.73| | 4: 2.47 - 2.25 2825 136 0.81 25.45 1.26 0.25 564.63| | 5: 2.25 - 2.09 2756 127 0.77 29.10 1.28 0.25 564.63| | 6: 2.09 - 1.97 2846 113 0.83 22.77 1.29 0.25 310.81| | 7: 1.97 - 1.87 2787 165 0.90 16.93 1.29 0.25 94.35| | 8: 1.87 - 1.79 2789 144 0.85 21.67 1.26 0.25 94.35| | 9: 1.79 - 1.72 2745 138 0.88 18.64 1.23 0.25 56.41| | 10: 1.72 - 1.66 2789 158 0.87 20.03 1.22 0.25 48.81| | 11: 1.66 - 1.61 2740 147 0.85 21.49 1.24 0.25 47.02| | 12: 1.61 - 1.56 2787 146 0.89 18.13 1.22 0.25 28.80| | 13: 1.56 - 1.52 2745 130 0.87 20.04 1.24 0.25 28.80| | 14: 1.52 - 1.48 2803 134 0.86 20.66 1.24 0.25 25.90| | 15: 1.48 - 1.45 2738 128 0.87 20.15 1.23 0.25 20.60| | 16: 1.45 - 1.42 2756 161 0.86 21.41 1.24 0.25 20.60| | 17: 1.42 - 1.39 2785 139 0.87 20.55 1.22 0.25 17.73| | 18: 1.39 - 1.36 2741 179 0.86 21.75 1.24 0.25 16.07| | 19: 1.36 - 1.34 2807 134 0.85 22.35 1.22 0.25 16.07| | 20: 1.34 - 1.32 2696 147 0.86 21.38 1.21 0.25 13.59| | 21: 1.32 - 1.30 2785 112 0.85 22.38 1.20 0.25 13.42| | 22: 1.29 - 1.27 2704 152 0.85 22.78 1.21 0.24 13.07| | 23: 1.27 - 1.26 2802 156 0.86 22.24 1.21 0.24 11.31| | 24: 1.26 - 1.24 2744 132 0.85 23.10 1.21 0.24 11.31| | 25: 1.24 - 1.22 2734 148 0.84 23.67 1.20 0.24 10.65| | 26: 1.22 - 1.21 2727 135 0.84 23.80 1.20 0.23 9.91| | 27: 1.21 - 1.19 2814 148 0.83 24.69 1.21 0.23 9.91| | 28: 1.19 - 1.18 2671 147 0.83 25.08 1.18 0.23 9.12| | 29: 1.18 - 1.16 2800 134 0.83 25.13 1.16 0.22 8.83| | 30: 1.16 - 1.15 2740 148 0.81 26.94 1.15 0.22 8.83| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 8.83 max = 1451.38 mean = 211.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.62| |phase err.(test): min = 0.00 max = 89.90 mean = 22.67| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.258 1557 Z= 5.355 Angle : 5.248 15.864 2118 Z= 3.666 Chirality : 0.382 1.113 243 Planarity : 0.031 0.092 284 Dihedral : 14.092 103.191 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.16 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 32.43 % 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: -1.73 (0.51), residues: 224 helix: -1.88 (0.44), residues: 102 sheet: -2.14 (0.85), residues: 28 loop : 0.45 (0.60), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.121 0.024 ARG A 48 TYR 0.089 0.028 TYR A 141 PHE 0.078 0.032 PHE A 119 HIS 0.069 0.031 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= 0.2598 r_free= 0.1945 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789863 | | target function (ml) not normalized (work): 232412.339265 | | target function (ml) not normalized (free): 11799.002663 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2556 0.2598 0.1946 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2556 0.2598 0.1946 n_refl.: 87602 remove outliers: r(all,work,free)=0.1968 0.1971 0.1946 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.1993 0.1996 0.1961 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1632 0.1626 0.1760 n_refl.: 87594 remove outliers: r(all,work,free)=0.1631 0.1624 0.1760 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.87 87 5 0.3826 381.975 358.101 0.668 1.003 0.401 11.894-9.307 98.04 96 4 0.1737 616.052 589.255 0.928 1.003 0.380 9.237-7.194 100.00 213 7 0.2146 501.818 491.150 0.956 1.003 0.339 7.162-5.571 100.00 427 22 0.2177 376.587 363.853 0.929 1.003 0.320 5.546-4.326 100.00 867 58 0.1283 516.960 511.048 0.963 1.003 0.219 4.315-3.360 100.00 1859 96 0.1140 491.633 487.921 1.003 1.003 0.199 3.356-2.611 100.00 3867 181 0.1421 322.977 319.959 0.997 1.002 0.043 2.608-2.026 99.99 8198 413 0.1335 214.104 212.250 1.005 1.001 0.000 2.025-1.573 100.00 17313 902 0.1633 104.557 103.983 1.015 0.998 0.000 1.573-1.221 100.00 36679 1900 0.2061 46.365 45.072 1.005 0.995 0.000 1.221-1.150 99.97 13689 708 0.2560 29.213 26.984 0.977 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0467 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1624 r_free=0.1760 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1624 r_free=0.1760 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.257906 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2031.225959 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 0.1208 0.1460 0.0252 0.007 1.0 1.3 0.5 0.0 0 12.629 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 14.60 2.52 3.013 19.062 2031.226 0.017 12.41 15.36 2.95 3.268 19.603 2031.226 0.015 Individual atomic B min max mean iso aniso Overall: 8.53 118.54 21.11 2.88 0 1785 Protein: 8.53 118.54 17.96 2.88 0 1519 Water: 11.13 114.50 39.42 N/A 0 258 Other: 23.34 37.07 29.49 N/A 0 8 Chain A: 8.53 118.54 21.11 N/A 0 1785 Histogram: Values Number of atoms 8.53 - 19.53 1203 19.53 - 30.53 230 30.53 - 41.54 162 41.54 - 52.54 106 52.54 - 63.54 52 63.54 - 74.54 18 74.54 - 85.54 7 85.54 - 96.54 4 96.54 - 107.54 0 107.54 - 118.54 3 =========================== Idealize ADP of riding H ========================== r_work=0.1242 r_free=0.1536 r_work=0.1246 r_free=0.1542 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1246 r_free = 0.1542 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1245 r_free = 0.1545 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1245 r_free= 0.1545 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015208 | | target function (ls_wunit_k1) not normalized (work): 1266.773748 | | target function (ls_wunit_k1) not normalized (free): 112.566844 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1260 0.1245 0.1545 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1700 0.1699 0.1764 n_refl.: 87591 remove outliers: r(all,work,free)=0.1700 0.1699 0.1764 n_refl.: 87591 overall B=0.14 to atoms: r(all,work,free)=0.1722 0.1722 0.1780 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1257 0.1243 0.1539 n_refl.: 87591 remove outliers: r(all,work,free)=0.1257 0.1242 0.1539 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3586 294.773 275.615 0.616 1.003 0.372 11.894-9.307 98.04 96 4 0.1528 479.601 468.246 0.913 1.003 0.367 9.237-7.194 100.00 213 7 0.1806 390.669 385.372 0.949 1.003 0.340 7.162-5.571 100.00 427 22 0.1712 293.175 287.705 0.923 1.003 0.290 5.546-4.326 100.00 867 58 0.0920 402.457 399.868 0.949 1.003 0.199 4.315-3.360 100.00 1859 96 0.0770 382.740 381.823 0.995 1.003 0.190 3.356-2.611 100.00 3867 181 0.1017 251.440 250.726 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0977 166.682 166.105 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1214 81.399 81.578 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1653 36.096 35.560 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2363 22.743 21.251 0.970 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0531 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1242 r_free=0.1539 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1244 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1244 r_free=0.1540 | n_water=258 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1253 r_free=0.1538 | n_water=252 | time (s): 26.190 (total time: 28.680) Filter (q & B) r_work=0.1257 r_free=0.1538 | n_water=249 | time (s): 3.830 (total time: 32.510) Compute maps r_work=0.1257 r_free=0.1538 | n_water=249 | time (s): 1.880 (total time: 34.390) Filter (map) r_work=0.1272 r_free=0.1543 | n_water=236 | time (s): 3.550 (total time: 37.940) Find peaks r_work=0.1272 r_free=0.1543 | n_water=236 | time (s): 0.680 (total time: 38.620) Add new water r_work=0.1417 r_free=0.1687 | n_water=441 | time (s): 3.550 (total time: 42.170) Refine new water occ: r_work=0.1324 r_free=0.1571 adp: r_work=0.1252 r_free=0.1523 occ: r_work=0.1264 r_free=0.1513 adp: r_work=0.1231 r_free=0.1499 occ: r_work=0.1235 r_free=0.1490 adp: r_work=0.1225 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1225 r_free=0.1489 r_work=0.1225 r_free=0.1489 | n_water=441 | time (s): 82.660 (total time: 124.830) Filter (q & B) r_work=0.1230 r_free=0.1494 | n_water=418 | time (s): 3.940 (total time: 128.770) Filter (dist only) r_work=0.1230 r_free=0.1494 | n_water=418 | time (s): 39.050 (total time: 167.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.815472 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1434.355762 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 0.1516 0.0289 0.007 0.9 2.2 0.5 0.0 0 12.908 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 15.16 2.89 3.805 23.159 1434.356 0.015 12.01 14.90 2.89 4.251 22.951 1434.356 0.015 Individual atomic B min max mean iso aniso Overall: 8.77 113.68 23.01 2.59 182 1763 Protein: 8.77 113.68 17.73 2.59 0 1519 Water: 10.91 72.78 42.13 N/A 182 236 Other: 23.00 33.92 27.83 N/A 0 8 Chain A: 8.77 113.68 20.43 N/A 0 1763 Chain S: 18.22 70.38 48.03 N/A 182 0 Histogram: Values Number of atoms 8.77 - 19.26 1202 19.26 - 29.75 251 29.75 - 40.24 187 40.24 - 50.73 140 50.73 - 61.22 109 61.22 - 71.71 44 71.71 - 82.20 6 82.20 - 92.70 3 92.70 - 103.19 1 103.19 - 113.68 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1490 r_work=0.1201 r_free=0.1489 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1489 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 = 0.1201 r_free = 0.1486 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1201 r_free= 0.1486 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013915 | | target function (ls_wunit_k1) not normalized (work): 1159.062950 | | target function (ls_wunit_k1) not normalized (free): 103.588711 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1201 0.1486 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1618 0.1615 0.1714 n_refl.: 87590 remove outliers: r(all,work,free)=0.1618 0.1615 0.1714 n_refl.: 87590 overall B=0.03 to atoms: r(all,work,free)=0.1623 0.1620 0.1717 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1199 0.1480 n_refl.: 87590 remove outliers: r(all,work,free)=0.1211 0.1197 0.1480 n_refl.: 87587 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3350 290.893 270.852 0.564 1.003 0.340 11.894-9.307 98.04 96 4 0.1544 479.601 477.710 0.922 1.003 0.333 9.237-7.194 100.00 213 7 0.1732 390.669 391.101 0.978 1.003 0.269 7.162-5.571 100.00 427 22 0.1504 293.175 289.351 0.936 1.003 0.250 5.546-4.326 100.00 867 58 0.0822 402.457 399.898 0.957 1.003 0.215 4.315-3.360 100.00 1859 96 0.0706 382.740 381.907 1.002 1.002 0.210 3.356-2.611 100.00 3867 181 0.0949 251.440 250.862 1.010 1.002 0.067 2.608-2.026 99.99 8198 413 0.0956 166.682 166.286 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1186 81.399 81.604 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1621 36.096 35.586 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2339 22.743 21.268 0.979 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0499 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1480 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1480 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1480 | n_water=418 | time (s): 1.480 (total time: 1.480) Filter (dist) r_work=0.1197 r_free=0.1480 | n_water=418 | time (s): 32.050 (total time: 33.530) Filter (q & B) r_work=0.1197 r_free=0.1480 | n_water=418 | time (s): 0.960 (total time: 34.490) Compute maps r_work=0.1197 r_free=0.1480 | n_water=418 | time (s): 1.570 (total time: 36.060) Filter (map) r_work=0.1234 r_free=0.1478 | n_water=297 | time (s): 3.480 (total time: 39.540) Find peaks r_work=0.1234 r_free=0.1478 | n_water=297 | time (s): 0.610 (total time: 40.150) Add new water r_work=0.1364 r_free=0.1598 | n_water=495 | time (s): 3.270 (total time: 43.420) Refine new water occ: r_work=0.1263 r_free=0.1504 adp: r_work=0.1264 r_free=0.1505 occ: r_work=0.1242 r_free=0.1484 adp: r_work=0.1240 r_free=0.1485 occ: r_work=0.1227 r_free=0.1467 adp: r_work=0.1220 r_free=0.1465 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1465 r_work=0.1220 r_free=0.1465 | n_water=495 | time (s): 242.460 (total time: 285.880) Filter (q & B) r_work=0.1223 r_free=0.1472 | n_water=459 | time (s): 2.710 (total time: 288.590) Filter (dist only) r_work=0.1223 r_free=0.1472 | n_water=459 | time (s): 36.420 (total time: 325.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.100837 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.104308 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1450 0.0221 0.006 0.9 3.5 0.5 0.0 0 1.050 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.50 2.21 3.621 22.232 43.104 3.726 12.16 14.12 1.96 4.187 22.026 43.104 3.653 Individual atomic B min max mean iso aniso Overall: 9.30 108.71 21.83 2.30 225 1761 Protein: 9.30 108.71 17.23 2.30 0 1519 Water: 11.55 71.59 36.97 N/A 225 234 Other: 18.98 29.96 24.63 N/A 0 8 Chain A: 9.30 108.71 19.92 N/A 0 1761 Chain S: 16.08 68.13 36.77 N/A 225 0 Histogram: Values Number of atoms 9.30 - 19.24 1237 19.24 - 29.18 273 29.18 - 39.12 218 39.12 - 49.06 137 49.06 - 59.01 84 59.01 - 68.95 24 68.95 - 78.89 7 78.89 - 88.83 3 88.83 - 98.77 1 98.77 - 108.71 2 =========================== Idealize ADP of riding H ========================== r_work=0.1216 r_free=0.1412 r_work=0.1217 r_free=0.1413 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1217 r_free = 0.1413 target_work(ml) = 3.653 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1209 r_free = 0.1412 target_work(ml) = 3.650 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1209 r_free= 0.1412 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.649774 | | target function (ml) not normalized (work): 303993.326672 | | target function (ml) not normalized (free): 16052.928151 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1209 0.1412 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1545 0.1543 0.1609 n_refl.: 87587 remove outliers: r(all,work,free)=0.1545 0.1543 0.1609 n_refl.: 87587 overall B=-0.02 to atoms: r(all,work,free)=0.1541 0.1540 0.1607 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1200 0.1388 n_refl.: 87587 remove outliers: r(all,work,free)=0.1205 0.1196 0.1388 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3822 282.843 259.089 0.461 0.999 0.295 11.894-9.307 95.10 93 4 0.2335 473.029 454.262 0.861 1.001 0.254 9.237-7.194 97.73 208 7 0.2207 383.307 384.370 0.941 1.001 0.204 7.162-5.571 100.00 427 22 0.2034 293.175 283.450 0.915 1.002 0.177 5.546-4.326 100.00 867 58 0.1087 402.457 397.721 0.953 1.002 0.161 4.315-3.360 100.00 1859 96 0.0916 382.740 380.222 0.993 1.002 0.153 3.356-2.611 100.00 3867 181 0.1138 251.440 249.481 1.000 1.002 0.067 2.608-2.026 99.99 8198 413 0.1058 166.682 165.660 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.1024 81.399 81.503 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1297 36.096 35.660 1.023 0.999 0.000 1.221-1.150 99.97 13689 708 0.2138 22.743 21.348 0.982 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0532 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1388 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=0.1196 r_free=0.1390 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1390 | n_water=459 | time (s): 1.860 (total time: 1.860) Filter (dist) r_work=0.1196 r_free=0.1390 | n_water=458 | time (s): 41.810 (total time: 43.670) Filter (q & B) r_work=0.1196 r_free=0.1391 | n_water=457 | time (s): 2.750 (total time: 46.420) Compute maps r_work=0.1196 r_free=0.1391 | n_water=457 | time (s): 1.490 (total time: 47.910) Filter (map) r_work=0.1221 r_free=0.1398 | n_water=311 | time (s): 2.950 (total time: 50.860) Find peaks r_work=0.1221 r_free=0.1398 | n_water=311 | time (s): 0.670 (total time: 51.530) Add new water r_work=0.1292 r_free=0.1470 | n_water=480 | time (s): 3.170 (total time: 54.700) Refine new water occ: r_work=0.1219 r_free=0.1393 adp: r_work=0.1220 r_free=0.1396 occ: r_work=0.1204 r_free=0.1378 adp: r_work=0.1202 r_free=0.1379 occ: r_work=0.1193 r_free=0.1366 adp: r_work=0.1189 r_free=0.1366 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1366 r_work=0.1189 r_free=0.1366 | n_water=480 | time (s): 177.170 (total time: 231.870) Filter (q & B) r_work=0.1196 r_free=0.1374 | n_water=444 | time (s): 2.680 (total time: 234.550) Filter (dist only) r_work=0.1196 r_free=0.1373 | n_water=443 | time (s): 37.010 (total time: 271.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.061358 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.996234 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 0.1199 0.1380 0.0181 0.006 1.0 3.8 0.5 0.0 0 1.031 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.80 1.81 3.413 21.477 50.996 3.637 11.76 13.67 1.91 3.802 21.360 50.996 3.617 Individual atomic B min max mean iso aniso Overall: 9.27 105.07 21.23 2.19 212 1758 Protein: 9.27 105.07 16.96 2.19 0 1519 Water: 11.47 70.04 35.83 N/A 212 231 Other: 18.97 27.04 22.79 N/A 0 8 Chain A: 9.27 105.07 19.53 N/A 0 1758 Chain S: 15.12 59.88 35.31 N/A 212 0 Histogram: Values Number of atoms 9.27 - 18.85 1222 18.85 - 28.43 292 28.43 - 38.01 205 38.01 - 47.59 136 47.59 - 57.17 76 57.17 - 66.75 26 66.75 - 76.33 8 76.33 - 85.91 2 85.91 - 95.49 1 95.49 - 105.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.1176 r_free=0.1367 r_work=0.1176 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1176 r_free = 0.1368 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1169 r_free = 0.1362 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1169 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.614760 | | target function (ml) not normalized (work): 301037.181861 | | target function (ml) not normalized (free): 15920.336658 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1179 0.1169 0.1362 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1494 0.1491 0.1578 n_refl.: 87576 remove outliers: r(all,work,free)=0.1494 0.1491 0.1578 n_refl.: 87576 overall B=-0.02 to atoms: r(all,work,free)=0.1491 0.1488 0.1576 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1178 0.1169 0.1365 n_refl.: 87576 remove outliers: r(all,work,free)=0.1178 0.1169 0.1365 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4059 282.843 250.301 0.443 0.999 0.304 11.894-9.307 95.10 93 4 0.2277 473.029 456.885 0.857 1.001 0.300 9.237-7.194 97.73 208 7 0.2343 383.307 377.753 0.921 1.001 0.130 7.162-5.571 100.00 427 22 0.2083 293.175 283.357 0.911 1.001 0.130 5.546-4.326 100.00 867 58 0.1124 402.457 397.630 0.951 1.001 0.130 4.315-3.360 100.00 1859 96 0.0948 382.740 380.186 0.993 1.001 0.123 3.356-2.611 100.00 3867 181 0.1140 251.440 249.513 1.001 1.001 0.048 2.608-2.026 99.99 8198 413 0.1011 166.682 165.761 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0960 81.399 81.688 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1238 36.096 35.738 1.020 1.001 0.000 1.221-1.150 99.97 13689 708 0.2122 22.743 21.336 0.975 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0431 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1169 r_free=0.1365 After: r_work=0.1169 r_free=0.1365 ================================== NQH flips ================================== r_work=0.1169 r_free=0.1365 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=0.1169 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1169 r_free=0.1365 | n_water=443 | time (s): 1.770 (total time: 1.770) Filter (dist) r_work=0.1169 r_free=0.1365 | n_water=443 | time (s): 36.400 (total time: 38.170) Filter (q & B) r_work=0.1170 r_free=0.1366 | n_water=439 | time (s): 3.140 (total time: 41.310) Compute maps r_work=0.1170 r_free=0.1366 | n_water=439 | time (s): 1.730 (total time: 43.040) Filter (map) r_work=0.1189 r_free=0.1376 | n_water=334 | time (s): 2.830 (total time: 45.870) Find peaks r_work=0.1189 r_free=0.1376 | n_water=334 | time (s): 0.470 (total time: 46.340) Add new water r_work=0.1240 r_free=0.1426 | n_water=495 | time (s): 2.910 (total time: 49.250) Refine new water occ: r_work=0.1181 r_free=0.1352 adp: r_work=0.1181 r_free=0.1356 occ: r_work=0.1169 r_free=0.1336 adp: r_work=0.1167 r_free=0.1340 occ: r_work=0.1160 r_free=0.1325 adp: r_work=0.1157 r_free=0.1327 ADP+occupancy (water only), MIN, final r_work=0.1157 r_free=0.1327 r_work=0.1157 r_free=0.1327 | n_water=495 | time (s): 206.200 (total time: 255.450) Filter (q & B) r_work=0.1165 r_free=0.1336 | n_water=452 | time (s): 2.760 (total time: 258.210) Filter (dist only) r_work=0.1165 r_free=0.1335 | n_water=450 | time (s): 37.270 (total time: 295.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.972825 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 34.121226 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 0.1185 0.1355 0.0170 0.007 1.1 4.8 0.5 0.0 0 0.986 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.85 13.55 1.70 3.301 21.202 34.121 3.620 11.88 13.53 1.65 3.330 21.183 34.121 3.619 Individual atomic B min max mean iso aniso Overall: 9.30 103.90 21.23 2.11 219 1758 Protein: 9.30 103.90 16.90 2.11 0 1519 Water: 11.58 69.93 35.81 N/A 219 231 Other: 19.19 26.76 22.81 N/A 0 8 Chain A: 9.30 103.90 19.47 N/A 0 1758 Chain S: 15.06 59.91 35.35 N/A 219 0 Histogram: Values Number of atoms 9.30 - 18.76 1224 18.76 - 28.22 296 28.22 - 37.68 198 37.68 - 47.14 147 47.14 - 56.60 73 56.60 - 66.06 25 66.06 - 75.52 9 75.52 - 84.98 2 84.98 - 94.44 1 94.44 - 103.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1188 r_free=0.1353 r_work=0.1188 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1353 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1185 r_free = 0.1353 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1185 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.617505 | | target function (ml) not normalized (work): 301265.781823 | | target function (ml) not normalized (free): 15912.176338 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1388 0.1408 5.6675 5.6179| | 2: 3.57 - 2.84 1.00 2888 124 0.1086 0.1379 5.1698 5.2258| | 3: 2.83 - 2.48 1.00 2820 163 0.1206 0.1235 4.9822 4.9893| | 4: 2.47 - 2.25 1.00 2825 136 0.1002 0.1167 4.682 4.7587| | 5: 2.25 - 2.09 1.00 2756 127 0.0975 0.1070 4.6258 4.6872| | 6: 2.09 - 1.97 1.00 2846 113 0.0965 0.1200 4.339 4.4829| | 7: 1.97 - 1.87 1.00 2787 165 0.0992 0.1204 4.0741 4.1779| | 8: 1.87 - 1.79 1.00 2789 144 0.1019 0.1246 3.9835 4.083| | 9: 1.79 - 1.72 1.00 2745 138 0.0970 0.1308 3.7166 3.9258| | 10: 1.72 - 1.66 1.00 2831 160 0.1002 0.1231 3.629 3.735| | 11: 1.66 - 1.61 1.00 2712 147 0.0974 0.1103 3.566 3.613| | 12: 1.61 - 1.56 1.00 2773 144 0.0930 0.1147 3.3504 3.4542| | 13: 1.56 - 1.52 1.00 2745 130 0.0981 0.1044 3.3356 3.4162| | 14: 1.52 - 1.48 1.00 2803 134 0.0997 0.1123 3.261 3.3499| | 15: 1.48 - 1.45 1.00 2738 128 0.1020 0.1316 3.1676 3.2894| | 16: 1.45 - 1.42 1.00 2756 161 0.1068 0.1246 3.1462 3.227| | 17: 1.42 - 1.39 1.00 2785 139 0.1125 0.1272 3.1164 3.2309| | 18: 1.39 - 1.36 1.00 2741 179 0.1167 0.1385 3.0891 3.2755| | 19: 1.36 - 1.34 1.00 2807 134 0.1223 0.1591 3.0946 3.2895| | 20: 1.34 - 1.32 1.00 2696 147 0.1327 0.1463 3.0892 3.1317| | 21: 1.32 - 1.30 1.00 2785 112 0.1431 0.1636 3.0928 3.1706| | 22: 1.29 - 1.27 1.00 2704 152 0.1481 0.1949 3.0878 3.2979| | 23: 1.27 - 1.26 1.00 2802 156 0.1594 0.1818 3.1084 3.2049| | 24: 1.26 - 1.24 1.00 2744 132 0.1638 0.1782 3.0991 3.1996| | 25: 1.24 - 1.22 1.00 2733 148 0.1809 0.2339 3.1134 3.2933| | 26: 1.22 - 1.21 1.00 2727 135 0.1874 0.1780 3.1257 3.1937| | 27: 1.21 - 1.19 1.00 2814 148 0.2019 0.2100 3.1422 3.1387| | 28: 1.19 - 1.18 1.00 2671 147 0.2143 0.2318 3.1371 3.1582| | 29: 1.18 - 1.16 1.00 2800 134 0.2225 0.2354 3.1273 3.2155| | 30: 1.16 - 1.15 1.00 2739 148 0.2376 0.2522 3.1153 3.169| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2918 171 0.95 8.85 1.00 0.97 5896.02| | 2: 3.57 - 2.84 2888 124 0.92 12.91 1.01 0.97 5896.02| | 3: 2.83 - 2.48 2820 163 0.89 17.08 0.99 0.97 4950.64| | 4: 2.47 - 2.25 2825 136 0.91 14.22 1.00 0.98 2512.82| | 5: 2.25 - 2.09 2756 127 0.90 16.47 1.01 0.98 2512.82| | 6: 2.09 - 1.97 2846 113 0.92 13.40 1.02 0.97 1490.89| | 7: 1.97 - 1.87 2787 165 0.94 10.75 1.02 0.97 619.32| | 8: 1.87 - 1.79 2789 144 0.91 14.35 0.99 0.97 619.32| | 9: 1.79 - 1.72 2745 138 0.93 11.36 0.98 0.97 334.37| | 10: 1.72 - 1.66 2831 160 0.93 12.18 0.98 0.97 277.31| | 11: 1.66 - 1.61 2712 147 0.93 12.86 0.98 0.97 264.68| | 12: 1.61 - 1.56 2773 144 0.95 9.45 0.99 0.97 145.59| | 13: 1.56 - 1.52 2745 130 0.94 11.01 1.02 0.97 145.59| | 14: 1.52 - 1.48 2803 134 0.94 11.12 1.02 0.97 130.02| | 15: 1.48 - 1.45 2738 128 0.95 10.33 1.01 0.98 101.50| | 16: 1.45 - 1.42 2756 161 0.94 11.45 1.02 0.98 101.50| | 17: 1.42 - 1.39 2785 139 0.95 11.34 1.01 0.98 92.38| | 18: 1.39 - 1.36 2741 179 0.94 11.82 1.01 0.98 87.09| | 19: 1.36 - 1.34 2807 134 0.94 12.29 1.00 0.98 87.09| | 20: 1.34 - 1.32 2696 147 0.94 12.51 0.99 0.96 82.63| | 21: 1.32 - 1.30 2785 112 0.93 13.45 0.98 0.96 82.32| | 22: 1.29 - 1.27 2704 152 0.93 13.89 0.98 0.96 82.50| | 23: 1.27 - 1.26 2802 156 0.92 14.96 0.97 0.95 83.40| | 24: 1.26 - 1.24 2744 132 0.92 15.05 0.97 0.95 83.40| | 25: 1.24 - 1.22 2733 148 0.91 16.44 0.96 0.94 84.74| | 26: 1.22 - 1.21 2727 135 0.90 18.17 1.03 0.93 86.22| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.02 0.93 86.22| | 28: 1.19 - 1.18 2671 147 0.88 20.21 1.01 0.93 89.07| | 29: 1.18 - 1.16 2800 134 0.88 20.51 0.99 0.93 90.14| | 30: 1.16 - 1.15 2739 148 0.86 21.90 0.98 0.93 90.14| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.32 max = 5896.02 mean = 929.21| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.96| |phase err.(test): min = 0.00 max = 88.30 mean = 14.06| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1185 0.1353 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1502 0.1501 0.1553 n_refl.: 87576 remove outliers: r(all,work,free)=0.1502 0.1501 0.1553 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1500 0.1499 0.1551 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1186 0.1353 n_refl.: 87576 remove outliers: r(all,work,free)=0.1193 0.1185 0.1353 n_refl.: 87572 ======================== 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 0.4131 282.843 251.824 0.422 1.000 0.277 11.894-9.307 93.14 91 4 0.2344 473.237 458.179 0.849 1.002 0.253 9.237-7.194 96.82 206 7 0.2404 385.137 374.462 0.909 1.002 0.130 7.162-5.571 100.00 427 22 0.2213 293.175 281.709 0.901 1.002 0.110 5.546-4.326 100.00 867 58 0.1160 402.457 397.992 0.952 1.002 0.110 4.315-3.360 100.00 1859 96 0.0967 382.740 379.979 0.995 1.002 0.107 3.356-2.611 100.00 3867 181 0.1156 251.440 249.563 1.001 1.001 0.090 2.608-2.026 99.99 8198 413 0.1021 166.682 165.766 1.014 1.000 0.000 2.025-1.573 100.00 17313 902 0.0979 81.399 81.666 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1237 36.096 35.735 1.023 0.996 0.000 1.221-1.150 99.97 13689 708 0.2125 22.743 21.368 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0400 ================= 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 : 0.2598 0.1945 0.081 5.248 8.8 119.3 19.9 258 0.000 1_bss: 0.1624 0.1760 0.081 5.248 9.0 119.5 20.1 258 0.000 1_settarget: 0.1624 0.1760 0.081 5.248 9.0 119.5 20.1 258 0.000 1_nqh: 0.1624 0.1760 0.081 5.248 9.0 119.5 20.1 258 0.000 1_weight: 0.1624 0.1760 0.081 5.248 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1208 0.1460 0.007 0.955 9.0 119.5 20.1 258 0.122 1_adp: 0.1242 0.1536 0.007 0.955 8.5 118.5 21.1 258 0.122 1_regHadp: 0.1246 0.1542 0.007 0.955 8.5 118.5 21.1 258 0.122 1_occ: 0.1245 0.1545 0.007 0.955 8.5 118.5 21.1 258 0.122 2_bss: 0.1242 0.1539 0.007 0.955 8.7 118.7 21.3 258 0.122 2_settarget: 0.1242 0.1539 0.007 0.955 8.7 118.7 21.3 258 0.122 2_updatecdl: 0.1242 0.1539 0.007 0.961 8.7 118.7 21.3 258 0.122 2_nqh: 0.1244 0.1540 0.007 0.961 8.7 118.7 21.3 258 0.125 2_sol: 0.1230 0.1494 0.007 0.961 8.7 118.7 23.4 418 n/a 2_weight: 0.1230 0.1494 0.007 0.961 8.7 118.7 23.4 418 n/a 2_xyzrec: 0.1227 0.1516 0.007 0.883 8.7 118.7 23.4 418 n/a 2_adp: 0.1201 0.1490 0.007 0.883 8.8 113.7 23.0 418 n/a 2_regHadp: 0.1201 0.1489 0.007 0.883 8.8 113.7 23.0 418 n/a 2_occ: 0.1201 0.1486 0.007 0.883 8.8 113.7 23.0 418 n/a 3_bss: 0.1197 0.1480 0.007 0.883 8.8 113.7 23.0 418 n/a 3_settarget: 0.1197 0.1480 0.007 0.883 8.8 113.7 23.0 418 n/a 3_updatecdl: 0.1197 0.1480 0.007 0.883 8.8 113.7 23.0 418 n/a 3_nqh: 0.1197 0.1480 0.007 0.883 8.8 113.7 23.0 418 n/a 3_sol: 0.1223 0.1472 0.007 0.883 8.8 113.7 22.2 459 n/a 3_weight: 0.1223 0.1472 0.007 0.883 8.8 113.7 22.2 459 n/a 3_xyzrec: 0.1229 0.1450 0.006 0.922 8.8 113.7 22.2 459 n/a 3_adp: 0.1216 0.1412 0.006 0.922 9.3 108.7 21.8 459 n/a 3_regHadp: 0.1217 0.1413 0.006 0.922 9.3 108.7 21.8 459 n/a 3_occ: 0.1209 0.1412 0.006 0.922 9.3 108.7 21.8 459 n/a 4_bss: 0.1196 0.1388 0.006 0.922 9.3 108.7 21.8 459 n/a 4_settarget: 0.1196 0.1388 0.006 0.922 9.3 108.7 21.8 459 n/a 4_updatecdl: 0.1196 0.1388 0.006 0.924 9.3 108.7 21.8 459 n/a 4_nqh: 0.1196 0.1390 0.006 0.924 9.3 108.7 21.8 459 n/a 4_sol: 0.1196 0.1373 0.006 0.924 9.3 108.7 21.4 443 n/a 4_weight: 0.1196 0.1373 0.006 0.924 9.3 108.7 21.4 443 n/a 4_xyzrec: 0.1199 0.1380 0.006 0.955 9.3 108.7 21.4 443 n/a 4_adp: 0.1176 0.1367 0.006 0.955 9.3 105.1 21.2 443 n/a 4_regHadp: 0.1176 0.1368 0.006 0.955 9.3 105.1 21.2 443 n/a 4_occ: 0.1169 0.1362 0.006 0.955 9.3 105.1 21.2 443 n/a 5_bss: 0.1169 0.1365 0.006 0.955 9.3 105.1 21.2 443 n/a 5_settarget: 0.1169 0.1365 0.006 0.955 9.3 105.1 21.2 443 n/a 5_updatecdl: 0.1169 0.1365 0.006 0.952 9.3 105.1 21.2 443 n/a 5_setrh: 0.1169 0.1365 0.006 0.952 9.3 105.1 21.2 443 n/a 5_nqh: 0.1169 0.1365 0.006 0.952 9.3 105.1 21.2 443 n/a 5_sol: 0.1165 0.1335 0.006 0.952 9.3 105.1 21.3 450 n/a 5_weight: 0.1165 0.1335 0.006 0.952 9.3 105.1 21.3 450 n/a 5_xyzrec: 0.1185 0.1355 0.007 1.052 9.3 105.1 21.3 450 n/a 5_adp: 0.1188 0.1353 0.007 1.052 9.3 103.9 21.2 450 n/a 5_regHadp: 0.1188 0.1353 0.007 1.052 9.3 103.9 21.2 450 n/a 5_occ: 0.1185 0.1353 0.007 1.052 9.3 103.9 21.2 450 n/a end: 0.1185 0.1353 0.007 1.052 9.3 103.9 21.2 450 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5382129_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5382129_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7300 Refinement macro-cycles (run) : 3455.5700 Write final files (write_after_run_outputs) : 70.5500 Total : 3530.8500 Total CPU time: 59.45 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:10:31 PST -0800 (1735452631.85 s) Start R-work = 0.1624, R-free = 0.1760 Final R-work = 0.1185, R-free = 0.1353 =============================================================================== Job complete usr+sys time: 3668.79 seconds wall clock time: 65 minutes 45.37 seconds (3945.37 seconds total)