Starting phenix.refine on Sat Dec 28 21:06:31 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9049096.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9049096.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9049096.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.15, 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: 0.65 Conformation dependent library (CDL) restraints added in 182.9 milliseconds Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 396 0.89 - 1.15: 1225 1.15 - 1.41: 621 1.41 - 1.67: 874 1.67 - 1.93: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.236 1.432 -0.195 9.70e-03 1.06e+04 4.05e+02 bond pdb=" C LYS A 122 " pdb=" O LYS A 122 " ideal model delta sigma weight residual 1.235 1.015 0.221 1.21e-02 6.83e+03 3.32e+02 bond pdb=" C LEU A 172 " pdb=" N ASN A 173 " ideal model delta sigma weight residual 1.332 1.581 -0.249 1.39e-02 5.18e+03 3.22e+02 bond pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta sigma weight residual 1.457 1.659 -0.202 1.14e-02 7.69e+03 3.13e+02 bond pdb=" CA VAL A 51 " pdb=" CB VAL A 51 " ideal model delta sigma weight residual 1.537 1.331 0.206 1.17e-02 7.31e+03 3.10e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 2954 4.32 - 8.63: 1867 8.63 - 12.95: 762 12.95 - 17.26: 172 17.26 - 21.58: 22 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 108.55 10.74 6.50e-01 2.37e+00 2.73e+02 angle pdb=" N ILE A 168 " pdb=" CA ILE A 168 " pdb=" C ILE A 168 " ideal model delta sigma weight residual 110.74 95.89 14.85 9.10e-01 1.21e+00 2.66e+02 angle pdb=" C ALA A 107 " pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta sigma weight residual 121.13 132.71 -11.58 7.30e-01 1.88e+00 2.52e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH1 ARG A 5 " ideal model delta sigma weight residual 121.50 135.02 -13.52 1.00e+00 1.00e+00 1.83e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.75 -10.52 8.10e-01 1.52e+00 1.69e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.49: 924 16.49 - 32.96: 120 32.96 - 49.44: 51 49.44 - 65.91: 14 65.91 - 82.39: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 57 " pdb=" C SER A 57 " pdb=" N LEU A 58 " pdb=" CA LEU A 58 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ALA A 11 " pdb=" C ALA A 11 " pdb=" N LYS A 12 " pdb=" CA LYS A 12 " ideal model delta harmonic sigma weight residual 180.00 161.39 18.61 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.229: 92 0.229 - 0.454: 87 0.454 - 0.679: 45 0.679 - 0.904: 16 0.904 - 1.129: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.46 -1.13 2.00e-01 2.50e+01 3.19e+01 chirality pdb=" CB THR A 124 " pdb=" CA THR A 124 " pdb=" OG1 THR A 124 " pdb=" CG2 THR A 124 " both_signs ideal model delta sigma weight residual False 2.55 1.42 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA ILE A 168 " pdb=" N ILE A 168 " pdb=" C ILE A 168 " pdb=" CB ILE A 168 " both_signs ideal model delta sigma weight residual False 2.43 3.36 -0.92 2.00e-01 2.50e+01 2.13e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.186 9.50e-02 1.11e+02 9.10e-02 1.03e+02 pdb=" NE ARG A 156 " -0.093 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " 0.109 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " -0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " 0.055 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " 0.074 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " -0.030 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " 0.026 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.046 9.50e-02 1.11e+02 6.85e-02 1.01e+02 pdb=" NE ARG A 48 " 0.093 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " 0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.011 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.122 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.041 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.078 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.009 2.00e-02 2.50e+03 5.53e-02 9.18e+01 pdb=" CG TYR A 141 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.142 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.053 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.015 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 1220 2.35 - 2.91: 8224 2.91 - 3.47: 10514 3.47 - 4.04: 15150 4.04 - 4.60: 21582 Nonbonded interactions: 56690 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.783 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.840 2.270 nonbonded pdb=" H ASP A 49 " pdb=" HA ASP A 49 " model vdw 1.852 1.816 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.852 2.450 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.852 2.100 ... (remaining 56685 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_9049096_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= 0.2601 r_free= 0.1962 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787510 | | target function (ml) not normalized (work): 232216.321120 | | target function (ml) not normalized (free): 11854.817596 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3018 0.2154 7.0133 4.9671| | 2: 3.57 - 2.84 1.00 2876 122 0.2416 0.1759 4.3516 4.3489| | 3: 2.84 - 2.48 1.00 2833 165 0.2372 0.1755 4.1359 4.1567| | 4: 2.47 - 2.25 1.00 2825 136 0.2339 0.1493 3.8387 3.8487| | 5: 2.25 - 2.09 1.00 2756 127 0.2472 0.1521 3.7969 3.8133| | 6: 2.09 - 1.97 1.00 2846 113 0.2559 0.1686 3.4687 3.579| | 7: 1.97 - 1.87 1.00 2787 165 0.2542 0.1855 3.1207 3.1802| | 8: 1.87 - 1.79 1.00 2789 144 0.2426 0.1921 3.0457 3.1565| | 9: 1.79 - 1.72 1.00 2745 138 0.2411 0.1796 2.8932 2.9474| | 10: 1.72 - 1.66 1.00 2789 158 0.2402 0.2131 2.8045 2.9472| | 11: 1.66 - 1.61 1.00 2740 147 0.2496 0.1903 2.7418 2.7911| | 12: 1.61 - 1.56 1.00 2787 146 0.2511 0.1934 2.61 2.6493| | 13: 1.56 - 1.52 1.00 2745 130 0.2513 0.1930 2.577 2.6045| | 14: 1.52 - 1.48 1.00 2803 134 0.2643 0.2115 2.5229 2.6081| | 15: 1.48 - 1.45 1.00 2738 128 0.2587 0.1863 2.4246 2.4065| | 16: 1.45 - 1.42 1.00 2756 161 0.2576 0.2072 2.3743 2.4041| | 17: 1.42 - 1.39 1.00 2785 139 0.2651 0.2171 2.3203 2.3813| | 18: 1.39 - 1.36 1.00 2741 179 0.2647 0.2149 2.2646 2.393| | 19: 1.36 - 1.34 1.00 2807 134 0.2686 0.2480 2.2474 2.3359| | 20: 1.34 - 1.32 1.00 2696 147 0.2682 0.2141 2.1968 2.1731| | 21: 1.32 - 1.30 1.00 2785 112 0.2724 0.2384 2.1529 2.1918| | 22: 1.29 - 1.27 1.00 2704 152 0.2759 0.2702 2.1425 2.2289| | 23: 1.27 - 1.26 1.00 2802 156 0.2776 0.2643 2.1085 2.2517| | 24: 1.26 - 1.24 1.00 2744 132 0.2772 0.2503 2.0875 2.1512| | 25: 1.24 - 1.22 1.00 2734 148 0.2856 0.2403 2.0626 2.06| | 26: 1.22 - 1.21 1.00 2727 135 0.2857 0.2614 2.0134 2.1611| | 27: 1.21 - 1.19 1.00 2814 148 0.2939 0.2359 2.0062 1.9232| | 28: 1.19 - 1.18 1.00 2671 147 0.2959 0.2679 1.9744 1.9866| | 29: 1.18 - 1.16 1.00 2800 134 0.2968 0.2647 1.9572 2.0055| | 30: 1.16 - 1.15 1.00 2740 148 0.3019 0.2790 1.9173 1.9701| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.01 0.76 0.23 1505.45| | 2: 3.57 - 2.84 2876 122 0.80 26.28 1.27 0.23 1505.45| | 3: 2.84 - 2.48 2833 165 0.74 32.15 1.25 0.24 1247.47| | 4: 2.47 - 2.25 2825 136 0.81 25.66 1.25 0.25 577.95| | 5: 2.25 - 2.09 2756 127 0.77 29.51 1.28 0.25 577.95| | 6: 2.09 - 1.97 2846 113 0.83 22.60 1.30 0.25 314.72| | 7: 1.97 - 1.87 2787 165 0.90 16.61 1.28 0.26 90.22| | 8: 1.87 - 1.79 2789 144 0.86 21.12 1.24 0.26 90.22| | 9: 1.79 - 1.72 2745 138 0.88 18.77 1.23 0.25 56.18| | 10: 1.72 - 1.66 2789 158 0.86 20.44 1.22 0.25 49.37| | 11: 1.66 - 1.61 2740 147 0.85 21.56 1.24 0.25 47.63| | 12: 1.61 - 1.56 2787 146 0.88 18.88 1.24 0.25 30.06| | 13: 1.56 - 1.52 2745 130 0.86 20.68 1.23 0.25 30.06| | 14: 1.52 - 1.48 2803 134 0.86 21.11 1.24 0.25 26.89| | 15: 1.48 - 1.45 2738 128 0.87 20.32 1.23 0.25 21.08| | 16: 1.45 - 1.42 2756 161 0.85 21.75 1.23 0.25 21.08| | 17: 1.42 - 1.39 2785 139 0.86 21.29 1.23 0.25 18.10| | 18: 1.39 - 1.36 2741 179 0.86 21.85 1.22 0.25 16.37| | 19: 1.36 - 1.34 2807 134 0.85 22.59 1.22 0.25 16.37| | 20: 1.34 - 1.32 2696 147 0.86 21.37 1.21 0.24 13.66| | 21: 1.32 - 1.30 2785 112 0.85 22.60 1.21 0.24 13.47| | 22: 1.29 - 1.27 2704 152 0.85 23.06 1.21 0.24 13.17| | 23: 1.27 - 1.26 2802 156 0.85 22.87 1.20 0.24 11.67| | 24: 1.26 - 1.24 2744 132 0.85 23.25 1.20 0.24 11.67| | 25: 1.24 - 1.22 2734 148 0.84 23.87 1.20 0.24 10.89| | 26: 1.22 - 1.21 2727 135 0.84 23.76 1.20 0.23 10.02| | 27: 1.21 - 1.19 2814 148 0.83 24.90 1.20 0.23 10.02| | 28: 1.19 - 1.18 2671 147 0.83 24.62 1.19 0.23 9.04| | 29: 1.18 - 1.16 2800 134 0.83 24.78 1.17 0.23 8.67| | 30: 1.16 - 1.15 2740 148 0.82 26.25 1.16 0.23 8.67| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.67 max = 1505.45 mean = 218.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 22.79| |phase err.(test): min = 0.00 max = 89.92 mean = 22.72| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.250 1557 Z= 5.564 Angle : 5.272 17.218 2118 Z= 3.760 Chirality : 0.389 1.129 243 Planarity : 0.032 0.084 284 Dihedral : 13.915 82.386 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 31.89 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.44), residues: 224 helix: -2.86 (0.37), residues: 109 sheet: -0.74 (0.76), residues: 28 loop : -0.74 (0.51), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.103 0.025 ARG A 156 TYR 0.115 0.046 TYR A 141 PHE 0.110 0.045 PHE A 164 HIS 0.058 0.032 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= 0.2601 r_free= 0.1962 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787510 | | target function (ml) not normalized (work): 232216.321120 | | target function (ml) not normalized (free): 11854.817596 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2560 0.2601 0.1962 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2560 0.2601 0.1962 n_refl.: 87602 remove outliers: r(all,work,free)=0.1972 0.1974 0.1962 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.1995 0.1998 0.1973 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1634 0.1626 0.1782 n_refl.: 87594 remove outliers: r(all,work,free)=0.1633 0.1625 0.1782 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 0.3806 386.325 357.869 0.677 1.002 0.407 11.894-9.307 99.02 97 4 0.1825 613.659 594.412 0.932 1.003 0.390 9.237-7.194 100.00 213 7 0.2155 501.897 490.959 0.958 1.003 0.349 7.162-5.571 100.00 427 22 0.2194 376.646 365.226 0.933 1.003 0.283 5.546-4.326 100.00 867 58 0.1265 517.042 511.767 0.962 1.003 0.234 4.315-3.360 100.00 1859 96 0.1137 491.711 487.780 1.007 1.003 0.219 3.356-2.611 100.00 3867 181 0.1436 323.028 319.521 0.995 1.002 0.089 2.608-2.026 99.99 8198 413 0.1338 214.138 212.008 1.007 1.002 0.000 2.025-1.573 100.00 17313 902 0.1622 104.574 103.958 1.013 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2063 46.372 45.140 1.002 0.998 0.000 1.221-1.150 99.97 13689 708 0.2569 29.218 27.055 0.976 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0433 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1625 r_free=0.1782 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A A 80 GLN B Total number of N/Q/H flips: 3 r_work=0.1636 r_free=0.1797 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.452219 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2018.800405 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 0.1211 0.1464 0.0253 0.008 1.0 1.0 0.5 0.0 0 13.226 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.64 2.53 3.013 19.048 2018.800 0.017 12.47 15.43 2.96 3.428 19.672 2018.800 0.016 Individual atomic B min max mean iso aniso Overall: 8.72 118.82 21.26 2.91 0 1785 Protein: 8.72 118.82 18.10 2.91 0 1519 Water: 11.16 114.49 39.57 N/A 0 258 Other: 23.86 38.58 30.48 N/A 0 8 Chain A: 8.72 118.82 21.26 N/A 0 1785 Histogram: Values Number of atoms 8.72 - 19.73 1210 19.73 - 30.74 225 30.74 - 41.75 156 41.75 - 52.76 109 52.76 - 63.77 50 63.77 - 74.78 19 74.78 - 85.79 9 85.79 - 96.80 2 96.80 - 107.81 2 107.81 - 118.82 3 =========================== Idealize ADP of riding H ========================== r_work=0.1247 r_free=0.1543 r_work=0.1251 r_free=0.1548 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1251 r_free = 0.1548 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1250 r_free = 0.1548 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1250 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015389 | | target function (ls_wunit_k1) not normalized (work): 1281.898539 | | target function (ls_wunit_k1) not normalized (free): 114.547398 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1264 0.1250 0.1548 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1716 0.1715 0.1780 n_refl.: 87593 remove outliers: r(all,work,free)=0.1716 0.1715 0.1780 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1736 0.1735 0.1794 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1263 0.1248 0.1541 n_refl.: 87593 remove outliers: r(all,work,free)=0.1262 0.1248 0.1541 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3626 297.892 276.885 0.633 1.001 0.380 11.894-9.307 99.02 97 4 0.1585 477.207 465.158 0.906 1.001 0.380 9.237-7.194 100.00 213 7 0.1820 390.297 384.460 0.947 1.001 0.340 7.162-5.571 100.00 427 22 0.1700 292.896 287.978 0.923 1.002 0.258 5.546-4.326 100.00 867 58 0.0907 402.074 399.721 0.949 1.002 0.214 4.315-3.360 100.00 1859 96 0.0762 382.375 381.142 0.995 1.002 0.200 3.356-2.611 100.00 3867 181 0.1014 251.201 250.523 0.997 1.002 0.052 2.608-2.026 99.99 8198 413 0.0984 166.523 165.941 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1225 81.321 81.523 1.016 1.003 0.000 1.573-1.221 100.00 36679 1900 0.1667 36.061 35.501 1.002 1.003 0.000 1.221-1.150 99.97 13689 708 0.2367 22.721 21.135 0.961 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0465 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1248 r_free=0.1541 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** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1250 r_free=0.1542 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1250 r_free=0.1542 | n_water=258 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1259 r_free=0.1540 | n_water=252 | time (s): 27.160 (total time: 29.530) Filter (q & B) r_work=0.1262 r_free=0.1539 | n_water=249 | time (s): 3.770 (total time: 33.300) Compute maps r_work=0.1262 r_free=0.1539 | n_water=249 | time (s): 1.850 (total time: 35.150) Filter (map) r_work=0.1274 r_free=0.1552 | n_water=236 | time (s): 3.830 (total time: 38.980) Find peaks r_work=0.1274 r_free=0.1552 | n_water=236 | time (s): 0.720 (total time: 39.700) Add new water r_work=0.1433 r_free=0.1712 | n_water=454 | time (s): 3.770 (total time: 43.470) Refine new water occ: r_work=0.1343 r_free=0.1567 adp: r_work=0.1264 r_free=0.1519 occ: r_work=0.1277 r_free=0.1515 adp: r_work=0.1241 r_free=0.1497 occ: r_work=0.1244 r_free=0.1488 adp: r_work=0.1234 r_free=0.1488 ADP+occupancy (water only), MIN, final r_work=0.1234 r_free=0.1488 r_work=0.1234 r_free=0.1488 | n_water=454 | time (s): 81.450 (total time: 124.920) Filter (q & B) r_work=0.1239 r_free=0.1496 | n_water=435 | time (s): 3.900 (total time: 128.820) Filter (dist only) r_work=0.1239 r_free=0.1496 | n_water=435 | time (s): 40.790 (total time: 169.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.386820 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1598.315221 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 0.1238 0.1516 0.0279 0.007 0.9 2.2 0.5 0.0 0 12.193 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 15.16 2.79 3.840 23.444 1598.315 0.015 12.05 14.90 2.85 4.364 23.230 1598.315 0.015 Individual atomic B min max mean iso aniso Overall: 8.71 113.94 23.41 2.64 199 1763 Protein: 8.71 113.94 17.77 2.64 0 1519 Water: 11.07 75.15 42.99 N/A 199 236 Other: 23.94 35.45 28.37 N/A 0 8 Chain A: 8.71 113.94 20.53 N/A 0 1763 Chain S: 13.80 75.15 48.91 N/A 199 0 Histogram: Values Number of atoms 8.71 - 19.23 1205 19.23 - 29.76 247 29.76 - 40.28 183 40.28 - 50.80 144 50.80 - 61.33 115 61.33 - 71.85 49 71.85 - 82.37 12 82.37 - 92.90 3 92.90 - 103.42 2 103.42 - 113.94 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1490 r_work=0.1205 r_free=0.1490 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1490 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 = 0.1205 r_free = 0.1484 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1205 r_free= 0.1484 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013963 | | target function (ls_wunit_k1) not normalized (work): 1163.049693 | | target function (ls_wunit_k1) not normalized (free): 100.398911 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1205 0.1484 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1613 0.1609 0.1735 n_refl.: 87592 remove outliers: r(all,work,free)=0.1613 0.1609 0.1735 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1617 0.1613 0.1737 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1202 0.1481 n_refl.: 87592 remove outliers: r(all,work,free)=0.1214 0.1201 0.1481 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3443 296.458 271.076 0.592 1.002 0.370 11.894-9.307 99.02 97 4 0.1465 477.207 475.903 0.916 1.003 0.370 9.237-7.194 100.00 213 7 0.1668 390.297 390.259 0.982 1.003 0.270 7.162-5.571 100.00 427 22 0.1497 292.896 288.807 0.941 1.003 0.229 5.546-4.326 100.00 867 58 0.0823 402.074 399.205 0.958 1.003 0.213 4.315-3.360 100.00 1859 96 0.0709 382.375 381.439 1.002 1.002 0.207 3.356-2.611 100.00 3867 181 0.0953 251.201 250.572 1.009 1.002 0.067 2.608-2.026 99.99 8198 413 0.0966 166.523 166.043 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1192 81.321 81.498 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1620 36.061 35.555 1.019 0.998 0.000 1.221-1.150 99.97 13689 708 0.2343 22.721 21.272 0.980 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0397 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1481 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1481 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1481 | n_water=435 | time (s): 2.210 (total time: 2.210) Filter (dist) r_work=0.1202 r_free=0.1481 | n_water=432 | time (s): 38.660 (total time: 40.870) Filter (q & B) r_work=0.1202 r_free=0.1481 | n_water=432 | time (s): 1.370 (total time: 42.240) Compute maps r_work=0.1202 r_free=0.1481 | n_water=432 | time (s): 1.620 (total time: 43.860) Filter (map) r_work=0.1240 r_free=0.1481 | n_water=291 | time (s): 2.600 (total time: 46.460) Find peaks r_work=0.1240 r_free=0.1481 | n_water=291 | time (s): 0.450 (total time: 46.910) Add new water r_work=0.1373 r_free=0.1620 | n_water=482 | time (s): 3.190 (total time: 50.100) Refine new water occ: r_work=0.1272 r_free=0.1531 adp: r_work=0.1273 r_free=0.1533 occ: r_work=0.1250 r_free=0.1509 adp: r_work=0.1248 r_free=0.1509 occ: r_work=0.1235 r_free=0.1495 adp: r_work=0.1227 r_free=0.1491 ADP+occupancy (water only), MIN, final r_work=0.1227 r_free=0.1491 r_work=0.1227 r_free=0.1491 | n_water=482 | time (s): 200.470 (total time: 250.570) Filter (q & B) r_work=0.1230 r_free=0.1493 | n_water=452 | time (s): 2.620 (total time: 253.190) Filter (dist only) r_work=0.1230 r_free=0.1492 | n_water=451 | time (s): 37.230 (total time: 290.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.008213 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.353566 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 0.1236 0.1464 0.0228 0.006 0.9 1.6 0.5 0.0 0 1.004 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.36 14.64 2.28 3.652 22.256 39.354 3.731 12.31 14.21 1.90 4.143 22.070 39.354 3.665 Individual atomic B min max mean iso aniso Overall: 9.17 108.97 21.86 2.30 217 1761 Protein: 9.17 108.97 17.33 2.30 0 1519 Water: 11.53 70.94 37.03 N/A 217 234 Other: 19.74 31.62 25.94 N/A 0 8 Chain A: 9.17 108.97 20.06 N/A 0 1761 Chain S: 16.23 59.97 36.44 N/A 217 0 Histogram: Values Number of atoms 9.17 - 19.15 1231 19.15 - 29.13 272 29.13 - 39.11 213 39.11 - 49.09 140 49.09 - 59.07 86 59.07 - 69.05 22 69.05 - 79.03 8 79.03 - 89.01 2 89.01 - 98.99 2 98.99 - 108.97 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1421 r_work=0.1232 r_free=0.1422 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1422 target_work(ml) = 3.665 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1423 target_work(ml) = 3.663 | | 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.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1227 r_free= 0.1423 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.662655 | | target function (ml) not normalized (work): 305077.216987 | | target function (ml) not normalized (free): 16101.201875 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1236 0.1227 0.1423 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1553 0.1552 0.1604 n_refl.: 87590 remove outliers: r(all,work,free)=0.1553 0.1552 0.1604 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1551 0.1550 0.1603 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1226 0.1217 0.1394 n_refl.: 87590 remove outliers: r(all,work,free)=0.1223 0.1214 0.1394 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3893 290.606 258.011 0.482 1.001 0.329 11.894-9.307 99.02 97 4 0.2420 477.207 466.591 0.848 1.002 0.329 9.237-7.194 98.18 209 7 0.2368 381.870 380.544 0.945 1.002 0.198 7.162-5.571 100.00 427 22 0.2066 292.896 282.892 0.910 1.002 0.167 5.546-4.326 100.00 867 58 0.1093 402.074 397.954 0.952 1.002 0.162 4.315-3.360 100.00 1859 96 0.0934 382.375 379.629 0.993 1.002 0.160 3.356-2.611 100.00 3867 181 0.1158 251.201 249.204 0.999 1.002 0.077 2.608-2.026 99.99 8198 413 0.1066 166.523 165.475 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1045 81.321 81.428 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1311 36.061 35.614 1.021 0.999 0.000 1.221-1.150 99.97 13689 708 0.2142 22.721 21.318 0.978 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0353 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1214 r_free=0.1394 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1214 r_free=0.1394 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1214 r_free=0.1394 | n_water=451 | time (s): 1.660 (total time: 1.660) Filter (dist) r_work=0.1214 r_free=0.1394 | n_water=451 | time (s): 38.650 (total time: 40.310) Filter (q & B) r_work=0.1214 r_free=0.1393 | n_water=450 | time (s): 2.560 (total time: 42.870) Compute maps r_work=0.1214 r_free=0.1393 | n_water=450 | time (s): 1.360 (total time: 44.230) Filter (map) r_work=0.1240 r_free=0.1400 | n_water=306 | time (s): 2.830 (total time: 47.060) Find peaks r_work=0.1240 r_free=0.1400 | n_water=306 | time (s): 0.570 (total time: 47.630) Add new water r_work=0.1309 r_free=0.1469 | n_water=467 | time (s): 2.590 (total time: 50.220) Refine new water occ: r_work=0.1232 r_free=0.1395 adp: r_work=0.1233 r_free=0.1397 occ: r_work=0.1217 r_free=0.1387 adp: r_work=0.1215 r_free=0.1387 occ: r_work=0.1206 r_free=0.1385 adp: r_work=0.1202 r_free=0.1382 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1382 r_work=0.1202 r_free=0.1382 | n_water=467 | time (s): 218.830 (total time: 269.050) Filter (q & B) r_work=0.1208 r_free=0.1375 | n_water=434 | time (s): 3.350 (total time: 272.400) Filter (dist only) r_work=0.1208 r_free=0.1374 | n_water=433 | time (s): 35.760 (total time: 308.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.346713 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.359933 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 0.1387 0.0179 0.006 1.0 3.5 0.5 0.0 0 1.173 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.87 1.79 3.436 21.558 43.360 3.647 11.84 13.74 1.90 3.885 21.412 43.360 3.626 Individual atomic B min max mean iso aniso Overall: 9.30 104.39 21.21 2.16 203 1757 Protein: 9.30 104.39 17.00 2.17 0 1519 Water: 11.48 69.63 35.91 N/A 203 230 Other: 20.43 28.89 24.47 N/A 0 8 Chain A: 9.30 104.39 19.62 N/A 0 1757 Chain S: 15.70 59.99 35.02 N/A 203 0 Histogram: Values Number of atoms 9.30 - 18.81 1226 18.81 - 28.32 279 28.32 - 37.83 210 37.83 - 47.34 126 47.34 - 56.85 77 56.85 - 66.35 28 66.35 - 75.86 9 75.86 - 85.37 2 85.37 - 94.88 1 94.88 - 104.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1374 r_work=0.1185 r_free=0.1374 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1185 r_free = 0.1374 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1182 r_free = 0.1373 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1182 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.625462 | | target function (ml) not normalized (work): 301953.849302 | | target function (ml) not normalized (free): 15951.205121 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1182 0.1373 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1513 0.1512 0.1571 n_refl.: 87583 remove outliers: r(all,work,free)=0.1513 0.1512 0.1571 n_refl.: 87583 overall B=-0.02 to atoms: r(all,work,free)=0.1509 0.1508 0.1569 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1181 0.1370 n_refl.: 87583 remove outliers: r(all,work,free)=0.1189 0.1180 0.1370 n_refl.: 87581 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3858 286.008 257.489 0.458 1.000 0.287 11.894-9.307 98.04 96 4 0.2437 481.020 462.257 0.844 1.002 0.263 9.237-7.194 98.18 209 7 0.2477 381.870 375.255 0.913 1.002 0.178 7.162-5.571 100.00 427 22 0.2184 292.896 283.149 0.904 1.002 0.147 5.546-4.326 100.00 867 58 0.1138 402.074 397.931 0.953 1.002 0.130 4.315-3.360 100.00 1859 96 0.0943 382.375 379.606 0.994 1.002 0.120 3.356-2.611 100.00 3867 181 0.1143 251.201 249.442 1.002 1.002 0.053 2.608-2.026 99.99 8198 413 0.1018 166.523 165.612 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0974 81.321 81.569 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.061 35.686 1.024 0.998 0.000 1.221-1.150 99.97 13689 708 0.2124 22.721 21.366 0.983 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0567 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1180 r_free=0.1370 After: r_work=0.1181 r_free=0.1370 ================================== NQH flips ================================== r_work=0.1181 r_free=0.1370 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=0.1181 r_free=0.1370 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1181 r_free=0.1370 | n_water=433 | time (s): 1.840 (total time: 1.840) Filter (dist) r_work=0.1181 r_free=0.1370 | n_water=433 | time (s): 37.120 (total time: 38.960) Filter (q & B) r_work=0.1181 r_free=0.1372 | n_water=432 | time (s): 3.620 (total time: 42.580) Compute maps r_work=0.1181 r_free=0.1372 | n_water=432 | time (s): 1.580 (total time: 44.160) Filter (map) r_work=0.1202 r_free=0.1380 | n_water=329 | time (s): 2.810 (total time: 46.970) Find peaks r_work=0.1202 r_free=0.1380 | n_water=329 | time (s): 0.480 (total time: 47.450) Add new water r_work=0.1254 r_free=0.1421 | n_water=492 | time (s): 2.980 (total time: 50.430) Refine new water occ: r_work=0.1189 r_free=0.1364 adp: r_work=0.1189 r_free=0.1366 occ: r_work=0.1176 r_free=0.1355 adp: r_work=0.1175 r_free=0.1355 occ: r_work=0.1167 r_free=0.1352 adp: r_work=0.1164 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1164 r_free=0.1350 r_work=0.1164 r_free=0.1350 | n_water=492 | time (s): 244.580 (total time: 295.010) Filter (q & B) r_work=0.1172 r_free=0.1353 | n_water=452 | time (s): 2.970 (total time: 297.980) Filter (dist only) r_work=0.1172 r_free=0.1353 | n_water=451 | time (s): 41.000 (total time: 338.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.931926 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 53.485891 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1213 0.1402 0.0189 0.006 1.0 5.8 0.5 0.0 0 0.966 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 14.02 1.89 3.303 21.257 53.486 3.639 12.12 14.01 1.88 3.817 21.147 53.486 3.626 Individual atomic B min max mean iso aniso Overall: 9.21 99.37 21.12 2.02 221 1757 Protein: 9.21 99.37 16.62 2.02 0 1519 Water: 11.45 66.83 36.24 N/A 221 230 Other: 20.21 27.16 23.63 N/A 0 8 Chain A: 9.21 99.37 19.23 N/A 0 1757 Chain S: 14.71 56.58 36.22 N/A 221 0 Histogram: Values Number of atoms 9.21 - 18.22 1211 18.22 - 27.24 275 27.24 - 36.26 204 36.26 - 45.27 160 45.27 - 54.29 76 54.29 - 63.30 34 63.30 - 72.32 13 72.32 - 81.34 2 81.34 - 90.35 1 90.35 - 99.37 2 =========================== Idealize ADP of riding H ========================== r_work=0.1212 r_free=0.1401 r_work=0.1213 r_free=0.1401 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1213 r_free = 0.1401 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1399 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1210 r_free= 0.1399 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.625847 | | target function (ml) not normalized (work): 301978.693257 | | target function (ml) not normalized (free): 15977.384533 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2923 171 0.1449 0.1467 5.6961 5.6784| | 2: 3.57 - 2.84 1.00 2888 124 0.1140 0.1524 5.2322 5.3082| | 3: 2.83 - 2.48 1.00 2820 163 0.1256 0.1295 5.0425 5.0614| | 4: 2.47 - 2.25 1.00 2825 136 0.1047 0.1211 4.7383 4.8005| | 5: 2.25 - 2.09 1.00 2756 127 0.1010 0.1149 4.6811 4.7504| | 6: 2.09 - 1.97 1.00 2846 113 0.0995 0.1238 4.3745 4.4937| | 7: 1.97 - 1.87 1.00 2787 165 0.1005 0.1289 4.0847 4.2083| | 8: 1.87 - 1.79 1.00 2789 144 0.1034 0.1270 4.0054 4.0918| | 9: 1.79 - 1.72 1.00 2745 138 0.0952 0.1286 3.7149 3.8989| | 10: 1.72 - 1.66 1.00 2831 160 0.0992 0.1197 3.6317 3.7439| | 11: 1.66 - 1.61 1.00 2712 147 0.0952 0.1118 3.5665 3.6178| | 12: 1.61 - 1.56 1.00 2773 144 0.0911 0.1147 3.3464 3.4705| | 13: 1.56 - 1.52 1.00 2745 130 0.0981 0.1057 3.3374 3.4412| | 14: 1.52 - 1.48 1.00 2803 134 0.0986 0.1174 3.2565 3.371| | 15: 1.48 - 1.45 1.00 2738 128 0.1015 0.1344 3.1676 3.3323| | 16: 1.45 - 1.42 1.00 2756 161 0.1061 0.1246 3.1487 3.2345| | 17: 1.42 - 1.39 1.00 2785 139 0.1110 0.1296 3.1123 3.2313| | 18: 1.39 - 1.36 1.00 2741 179 0.1151 0.1400 3.084 3.2791| | 19: 1.36 - 1.34 1.00 2807 134 0.1208 0.1631 3.0907 3.2842| | 20: 1.34 - 1.32 1.00 2696 147 0.1321 0.1480 3.0849 3.1417| | 21: 1.32 - 1.30 1.00 2785 112 0.1408 0.1614 3.0827 3.1663| | 22: 1.29 - 1.27 1.00 2704 152 0.1466 0.1873 3.0795 3.2703| | 23: 1.27 - 1.26 1.00 2802 156 0.1569 0.1838 3.0982 3.205| | 24: 1.26 - 1.24 1.00 2744 132 0.1627 0.1788 3.093 3.1997| | 25: 1.24 - 1.22 1.00 2733 148 0.1784 0.2246 3.1031 3.2774| | 26: 1.22 - 1.21 1.00 2727 135 0.1855 0.1784 3.1166 3.1978| | 27: 1.21 - 1.19 1.00 2814 148 0.2004 0.2147 3.1345 3.1542| | 28: 1.19 - 1.18 1.00 2671 147 0.2143 0.2304 3.135 3.1621| | 29: 1.18 - 1.16 1.00 2800 134 0.2214 0.2405 3.1231 3.2255| | 30: 1.16 - 1.15 1.00 2739 148 0.2368 0.2479 3.1122 3.1615| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2923 171 0.94 9.74 1.00 0.96 6887.13| | 2: 3.57 - 2.84 2888 124 0.91 14.23 1.01 0.96 6887.13| | 3: 2.83 - 2.48 2820 163 0.88 18.36 0.98 0.96 5766.41| | 4: 2.47 - 2.25 2825 136 0.90 15.42 1.00 0.97 2876.45| | 5: 2.25 - 2.09 2756 127 0.89 17.74 1.01 0.97 2876.45| | 6: 2.09 - 1.97 2846 113 0.91 14.25 1.02 0.97 1677.07| | 7: 1.97 - 1.87 2787 165 0.94 11.18 1.02 0.97 654.15| | 8: 1.87 - 1.79 2789 144 0.91 14.85 1.00 0.97 654.15| | 9: 1.79 - 1.72 2745 138 0.93 11.62 0.99 0.97 345.95| | 10: 1.72 - 1.66 2831 160 0.93 12.37 0.98 0.97 284.23| | 11: 1.66 - 1.61 2712 147 0.93 12.97 0.99 0.97 271.34| | 12: 1.61 - 1.56 2773 144 0.95 9.66 0.99 0.97 149.74| | 13: 1.56 - 1.52 2745 130 0.94 11.27 1.02 0.97 149.74| | 14: 1.52 - 1.48 2803 134 0.94 11.37 1.02 0.97 133.84| | 15: 1.48 - 1.45 2738 128 0.95 10.60 1.02 0.98 104.73| | 16: 1.45 - 1.42 2756 161 0.94 11.78 1.02 0.98 104.73| | 17: 1.42 - 1.39 2785 139 0.94 11.56 1.01 0.98 94.61| | 18: 1.39 - 1.36 2741 179 0.94 11.91 1.01 0.98 88.76| | 19: 1.36 - 1.34 2807 134 0.94 12.51 1.00 0.98 88.76| | 20: 1.34 - 1.32 2696 147 0.94 12.63 0.99 0.96 83.13| | 21: 1.32 - 1.30 2785 112 0.93 13.48 0.99 0.96 82.73| | 22: 1.29 - 1.27 2704 152 0.93 14.05 0.99 0.96 82.78| | 23: 1.27 - 1.26 2802 156 0.92 14.92 0.98 0.94 83.03| | 24: 1.26 - 1.24 2744 132 0.92 15.07 0.97 0.94 83.03| | 25: 1.24 - 1.22 2733 148 0.91 16.43 0.97 0.94 84.44| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.02 0.93 86.01| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.02 0.93 86.01| | 28: 1.19 - 1.18 2671 147 0.88 20.29 1.01 0.92 89.41| | 29: 1.18 - 1.16 2800 134 0.88 20.62 0.99 0.92 90.69| | 30: 1.16 - 1.15 2739 148 0.86 22.02 0.98 0.92 90.69| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 82.73 max = 6887.13 mean = 1061.01| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.92 mean = 14.32| |phase err.(test): min = 0.00 max = 89.29 mean = 14.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1210 0.1399 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1530 0.1527 0.1602 n_refl.: 87581 remove outliers: r(all,work,free)=0.1530 0.1527 0.1602 n_refl.: 87581 overall B=-0.02 to atoms: r(all,work,free)=0.1526 0.1524 0.1600 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1220 0.1211 0.1403 n_refl.: 87581 remove outliers: r(all,work,free)=0.1219 0.1209 0.1403 n_refl.: 87578 ======================== 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 0.3915 282.573 251.641 0.439 0.999 0.304 11.894-9.307 97.06 95 4 0.2485 481.184 460.269 0.848 1.001 0.212 9.237-7.194 97.73 208 7 0.2514 382.941 373.717 0.906 1.001 0.130 7.162-5.571 100.00 427 22 0.2251 292.896 282.992 0.897 1.001 0.130 5.546-4.326 100.00 867 58 0.1209 402.074 397.432 0.952 1.001 0.127 4.315-3.360 100.00 1859 96 0.1027 382.375 379.588 0.995 1.001 0.113 3.356-2.611 100.00 3867 181 0.1211 251.201 249.308 0.999 1.001 0.043 2.608-2.026 99.99 8198 413 0.1059 166.523 165.479 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0981 81.321 81.575 1.028 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1225 36.061 35.709 1.021 1.000 0.000 1.221-1.150 99.97 13689 708 0.2112 22.721 21.320 0.977 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0463 ================= 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 : 0.2601 0.1962 0.082 5.272 8.8 119.3 19.9 258 0.000 1_bss: 0.1625 0.1782 0.082 5.272 9.0 119.5 20.1 258 0.000 1_settarget: 0.1625 0.1782 0.082 5.272 9.0 119.5 20.1 258 0.000 1_nqh: 0.1636 0.1797 0.082 5.272 9.0 119.5 20.1 258 0.010 1_weight: 0.1636 0.1797 0.082 5.272 9.0 119.5 20.1 258 0.010 1_xyzrec: 0.1211 0.1464 0.008 0.958 9.0 119.5 20.1 258 0.129 1_adp: 0.1247 0.1543 0.008 0.958 8.7 118.8 21.3 258 0.129 1_regHadp: 0.1251 0.1548 0.008 0.958 8.7 118.8 21.3 258 0.129 1_occ: 0.1250 0.1548 0.008 0.958 8.7 118.8 21.3 258 0.129 2_bss: 0.1248 0.1541 0.008 0.958 8.8 118.9 21.4 258 0.129 2_settarget: 0.1248 0.1541 0.008 0.958 8.8 118.9 21.4 258 0.129 2_updatecdl: 0.1248 0.1541 0.008 0.977 8.8 118.9 21.4 258 0.129 2_nqh: 0.1250 0.1542 0.008 0.977 8.8 118.9 21.4 258 0.129 2_sol: 0.1239 0.1496 0.008 0.977 8.8 118.9 23.8 435 n/a 2_weight: 0.1239 0.1496 0.008 0.977 8.8 118.9 23.8 435 n/a 2_xyzrec: 0.1238 0.1516 0.007 0.870 8.8 118.9 23.8 435 n/a 2_adp: 0.1205 0.1490 0.007 0.870 8.7 113.9 23.4 435 n/a 2_regHadp: 0.1205 0.1490 0.007 0.870 8.7 113.9 23.4 435 n/a 2_occ: 0.1205 0.1484 0.007 0.870 8.7 113.9 23.4 435 n/a 3_bss: 0.1201 0.1481 0.007 0.870 8.7 114.0 23.4 435 n/a 3_settarget: 0.1201 0.1481 0.007 0.870 8.7 114.0 23.4 435 n/a 3_updatecdl: 0.1201 0.1481 0.007 0.871 8.7 114.0 23.4 435 n/a 3_nqh: 0.1201 0.1481 0.007 0.871 8.7 114.0 23.4 435 n/a 3_sol: 0.1230 0.1492 0.007 0.871 8.7 114.0 22.2 451 n/a 3_weight: 0.1230 0.1492 0.007 0.871 8.7 114.0 22.2 451 n/a 3_xyzrec: 0.1236 0.1464 0.006 0.918 8.7 114.0 22.2 451 n/a 3_adp: 0.1231 0.1421 0.006 0.918 9.2 109.0 21.9 451 n/a 3_regHadp: 0.1232 0.1422 0.006 0.918 9.2 109.0 21.9 451 n/a 3_occ: 0.1227 0.1423 0.006 0.918 9.2 109.0 21.9 451 n/a 4_bss: 0.1214 0.1394 0.006 0.918 9.2 109.0 21.8 451 n/a 4_settarget: 0.1214 0.1394 0.006 0.918 9.2 109.0 21.8 451 n/a 4_updatecdl: 0.1214 0.1394 0.006 0.915 9.2 109.0 21.8 451 n/a 4_nqh: 0.1214 0.1394 0.006 0.915 9.2 109.0 21.8 451 n/a 4_sol: 0.1208 0.1374 0.006 0.915 9.2 109.0 21.5 433 n/a 4_weight: 0.1208 0.1374 0.006 0.915 9.2 109.0 21.5 433 n/a 4_xyzrec: 0.1208 0.1387 0.006 0.978 9.2 109.0 21.5 433 n/a 4_adp: 0.1184 0.1374 0.006 0.978 9.3 104.4 21.2 433 n/a 4_regHadp: 0.1185 0.1374 0.006 0.978 9.3 104.4 21.2 433 n/a 4_occ: 0.1182 0.1373 0.006 0.978 9.3 104.4 21.2 433 n/a 5_bss: 0.1180 0.1370 0.006 0.978 9.3 104.4 21.2 433 n/a 5_settarget: 0.1180 0.1370 0.006 0.978 9.3 104.4 21.2 433 n/a 5_updatecdl: 0.1180 0.1370 0.006 0.981 9.3 104.4 21.2 433 n/a 5_setrh: 0.1181 0.1370 0.006 0.981 9.3 104.4 21.2 433 n/a 5_nqh: 0.1181 0.1370 0.006 0.981 9.3 104.4 21.2 433 n/a 5_sol: 0.1172 0.1353 0.006 0.981 9.3 104.4 21.3 451 n/a 5_weight: 0.1172 0.1353 0.006 0.981 9.3 104.4 21.3 451 n/a 5_xyzrec: 0.1213 0.1402 0.006 1.020 9.3 104.4 21.3 451 n/a 5_adp: 0.1212 0.1401 0.006 1.020 9.2 99.4 21.1 451 n/a 5_regHadp: 0.1213 0.1401 0.006 1.020 9.2 99.4 21.1 451 n/a 5_occ: 0.1210 0.1399 0.006 1.020 9.2 99.4 21.1 451 n/a end: 0.1209 0.1403 0.006 1.020 9.2 99.4 21.1 451 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_9049096_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_9049096_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7200 Refinement macro-cycles (run) : 3523.9000 Write final files (write_after_run_outputs) : 61.3400 Total : 3589.9600 Total CPU time: 60.43 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:07 PST -0800 (1735452727.50 s) Start R-work = 0.1625, R-free = 0.1782 Final R-work = 0.1209, R-free = 0.1403 =============================================================================== Job complete usr+sys time: 3726.54 seconds wall clock time: 67 minutes 21.37 seconds (4041.37 seconds total)