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_5239121.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5239121.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5239121.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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 2.29, per 1000 atoms: 0.68 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: 0.86 Conformation dependent library (CDL) restraints added in 313.0 milliseconds Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.89: 412 0.89 - 1.14: 1190 1.14 - 1.40: 598 1.40 - 1.65: 883 1.65 - 1.90: 70 Bond restraints: 3153 Sorted by residual: bond pdb=" N ILE A 31 " pdb=" CA ILE A 31 " ideal model delta sigma weight residual 1.459 1.193 0.266 1.24e-02 6.50e+03 4.60e+02 bond pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta sigma weight residual 1.458 1.223 0.235 1.19e-02 7.06e+03 3.89e+02 bond pdb=" C GLU A 16 " pdb=" O GLU A 16 " ideal model delta sigma weight residual 1.236 1.000 0.236 1.25e-02 6.40e+03 3.58e+02 bond pdb=" C AGLU A 96 " pdb=" O AGLU A 96 " ideal model delta sigma weight residual 1.237 1.443 -0.206 1.17e-02 7.31e+03 3.10e+02 bond pdb=" N VAL A 44 " pdb=" CA VAL A 44 " ideal model delta sigma weight residual 1.458 1.253 0.205 1.17e-02 7.31e+03 3.07e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 2745 4.15 - 8.30: 1953 8.30 - 12.44: 831 12.44 - 16.59: 224 16.59 - 20.74: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BGLY A 65 " pdb=" C BGLY A 65 " pdb=" N BPRO A 66 " ideal model delta sigma weight residual 121.77 137.73 -15.96 1.00e+00 1.00e+00 2.55e+02 angle pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" O LYS A 182 " ideal model delta sigma weight residual 121.07 137.12 -16.05 1.10e+00 8.26e-01 2.13e+02 angle pdb=" O ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 123.20 137.69 -14.49 1.06e+00 8.90e-01 1.87e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH2 ARG A 156 " ideal model delta sigma weight residual 119.20 131.37 -12.17 9.00e-01 1.23e+00 1.83e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.03 137.34 -14.31 1.11e+00 8.12e-01 1.66e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 928 15.32 - 30.63: 113 30.63 - 45.95: 45 45.95 - 61.27: 21 61.27 - 76.58: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -151.59 -28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " pdb=" CA GLY A 118 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta harmonic sigma weight residual -180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.242: 102 0.242 - 0.482: 75 0.482 - 0.721: 44 0.721 - 0.960: 18 0.960 - 1.199: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 1.24 1.20 2.00e-01 2.50e+01 3.60e+01 chirality pdb=" CA LYS A 182 " pdb=" N LYS A 182 " pdb=" C LYS A 182 " pdb=" CB LYS A 182 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.12e+01 chirality pdb=" CA ALA A 6 " pdb=" N ALA A 6 " pdb=" C ALA A 6 " pdb=" CB ALA A 6 " both_signs ideal model delta sigma weight residual False 2.48 3.47 -0.98 2.00e-01 2.50e+01 2.40e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.002 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG BTYR A 67 " 0.103 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.081 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.056 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.070 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.077 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.094 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.005 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.067 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.088 2.00e-02 2.50e+03 6.13e-02 1.13e+02 pdb=" CG TYR A 141 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.069 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.091 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.087 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.075 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 68 " -0.042 2.00e-02 2.50e+03 8.69e-02 7.54e+01 pdb=" CG ASP A 68 " 0.150 2.00e-02 2.50e+03 pdb=" OD1 ASP A 68 " -0.051 2.00e-02 2.50e+03 pdb=" OD2 ASP A 68 " -0.057 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 851 2.29 - 2.87: 7855 2.87 - 3.44: 10617 3.44 - 4.02: 15259 4.02 - 4.60: 22059 Nonbonded interactions: 56641 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.711 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.771 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.808 2.450 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.812 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.812 2.100 ... (remaining 56636 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_5239121_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1962 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793278 | | target function (ml) not normalized (work): 232696.817095 | | target function (ml) not normalized (free): 11852.780319 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3037 0.2100 7.0553 4.9421| | 2: 3.57 - 2.84 1.00 2876 122 0.2459 0.1799 4.3528 4.3568| | 3: 2.84 - 2.48 1.00 2833 165 0.2314 0.1704 4.1283 4.161| | 4: 2.47 - 2.25 1.00 2825 136 0.2377 0.1469 3.8378 3.8301| | 5: 2.25 - 2.09 1.00 2756 127 0.2460 0.1542 3.8 3.8142| | 6: 2.09 - 1.97 1.00 2846 113 0.2512 0.1716 3.4717 3.5244| | 7: 1.97 - 1.87 1.00 2787 165 0.2604 0.1992 3.1566 3.2302| | 8: 1.87 - 1.79 1.00 2789 144 0.2508 0.1887 3.0732 3.1316| | 9: 1.79 - 1.72 1.00 2745 138 0.2408 0.1941 2.9019 2.9936| | 10: 1.72 - 1.66 1.00 2789 158 0.2425 0.1941 2.8117 2.8981| | 11: 1.66 - 1.61 1.00 2740 147 0.2473 0.1745 2.7368 2.7794| | 12: 1.61 - 1.56 1.00 2787 146 0.2546 0.1965 2.6422 2.6186| | 13: 1.56 - 1.52 1.00 2745 130 0.2536 0.1887 2.5791 2.5885| | 14: 1.52 - 1.48 1.00 2803 134 0.2549 0.2204 2.51 2.6211| | 15: 1.48 - 1.45 1.00 2738 128 0.2625 0.2114 2.4329 2.5215| | 16: 1.45 - 1.42 1.00 2756 161 0.2637 0.2314 2.3797 2.4761| | 17: 1.42 - 1.39 1.00 2785 139 0.2654 0.2190 2.3217 2.4275| | 18: 1.39 - 1.36 1.00 2741 179 0.2674 0.2202 2.2717 2.3363| | 19: 1.36 - 1.34 1.00 2807 134 0.2636 0.2461 2.2416 2.3365| | 20: 1.34 - 1.32 1.00 2696 147 0.2665 0.1984 2.2046 2.1226| | 21: 1.32 - 1.30 1.00 2785 112 0.2664 0.2487 2.1659 2.2516| | 22: 1.29 - 1.27 1.00 2704 152 0.2722 0.2674 2.1398 2.1889| | 23: 1.27 - 1.26 1.00 2802 156 0.2788 0.2353 2.1115 2.1513| | 24: 1.26 - 1.24 1.00 2744 132 0.2823 0.2470 2.0879 2.1742| | 25: 1.24 - 1.22 1.00 2734 148 0.2845 0.2537 2.0562 2.0834| | 26: 1.22 - 1.21 1.00 2727 135 0.2837 0.2520 1.9959 2.1479| | 27: 1.21 - 1.19 1.00 2814 148 0.2957 0.2575 2.0027 1.9854| | 28: 1.19 - 1.18 1.00 2671 147 0.2954 0.2860 1.9825 1.9973| | 29: 1.18 - 1.16 1.00 2800 134 0.2968 0.2598 1.9563 1.9853| | 30: 1.16 - 1.15 1.00 2740 148 0.3048 0.2878 1.9341 1.9666| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.92 0.76 0.23 1492.87| | 2: 3.57 - 2.84 2876 122 0.80 26.13 1.27 0.23 1492.87| | 3: 2.84 - 2.48 2833 165 0.74 32.00 1.24 0.24 1238.65| | 4: 2.47 - 2.25 2825 136 0.81 25.82 1.26 0.25 578.90| | 5: 2.25 - 2.09 2756 127 0.77 29.52 1.28 0.25 578.90| | 6: 2.09 - 1.97 2846 113 0.83 22.87 1.29 0.25 317.99| | 7: 1.97 - 1.87 2787 165 0.90 17.05 1.29 0.26 95.47| | 8: 1.87 - 1.79 2789 144 0.85 21.61 1.25 0.26 95.47| | 9: 1.79 - 1.72 2745 138 0.88 18.83 1.23 0.26 57.21| | 10: 1.72 - 1.66 2789 158 0.86 20.45 1.22 0.25 49.55| | 11: 1.66 - 1.61 2740 147 0.85 21.69 1.24 0.25 47.83| | 12: 1.61 - 1.56 2787 146 0.88 18.77 1.24 0.25 30.46| | 13: 1.56 - 1.52 2745 130 0.86 20.83 1.23 0.25 30.46| | 14: 1.52 - 1.48 2803 134 0.86 21.16 1.23 0.25 27.36| | 15: 1.48 - 1.45 2738 128 0.87 20.67 1.23 0.25 21.69| | 16: 1.45 - 1.42 2756 161 0.85 22.17 1.24 0.25 21.69| | 17: 1.42 - 1.39 2785 139 0.86 21.49 1.23 0.25 18.56| | 18: 1.39 - 1.36 2741 179 0.85 22.01 1.23 0.25 16.75| | 19: 1.36 - 1.34 2807 134 0.85 22.85 1.22 0.25 16.75| | 20: 1.34 - 1.32 2696 147 0.86 21.42 1.21 0.25 13.71| | 21: 1.32 - 1.30 2785 112 0.85 22.29 1.20 0.25 13.50| | 22: 1.29 - 1.27 2704 152 0.85 22.79 1.21 0.25 13.15| | 23: 1.27 - 1.26 2802 156 0.85 22.52 1.21 0.24 11.39| | 24: 1.26 - 1.24 2744 132 0.84 23.26 1.21 0.24 11.39| | 25: 1.24 - 1.22 2734 148 0.84 23.70 1.20 0.24 10.76| | 26: 1.22 - 1.21 2727 135 0.84 24.19 1.21 0.23 10.05| | 27: 1.21 - 1.19 2814 148 0.83 24.98 1.20 0.23 10.05| | 28: 1.19 - 1.18 2671 147 0.83 25.05 1.18 0.23 9.29| | 29: 1.18 - 1.16 2800 134 0.82 25.61 1.16 0.23 9.01| | 30: 1.16 - 1.15 2740 148 0.81 26.92 1.15 0.23 9.01| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.01 max = 1492.87 mean = 217.63| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.92| |phase err.(test): min = 0.00 max = 89.79 mean = 22.94| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.266 1557 Z= 5.538 Angle : 5.610 17.491 2118 Z= 3.877 Chirality : 0.426 1.199 243 Planarity : 0.033 0.128 284 Dihedral : 13.512 76.582 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % 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: -2.34 (0.51), residues: 224 helix: -3.09 (0.35), residues: 102 sheet: -0.83 (0.90), residues: 30 loop : 0.48 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.013 ARG A 156 TYR 0.100 0.040 TYR A 141 PHE 0.087 0.036 PHE A 164 HIS 0.054 0.018 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1962 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793278 | | target function (ml) not normalized (work): 232696.817095 | | target function (ml) not normalized (free): 11852.780319 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2569 0.2610 0.1962 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2569 0.2610 0.1962 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1984 0.1962 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2006 0.2010 0.1976 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1642 0.1635 0.1784 n_refl.: 87594 remove outliers: r(all,work,free)=0.1642 0.1634 0.1784 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 0.3837 386.166 358.071 0.663 1.003 0.401 11.894-9.307 99.02 97 4 0.1786 613.406 596.063 0.923 1.004 0.380 9.237-7.194 100.00 213 7 0.2132 501.690 491.186 0.956 1.004 0.349 7.162-5.571 100.00 427 22 0.2233 376.491 364.699 0.931 1.004 0.282 5.546-4.326 100.00 867 58 0.1267 516.829 511.417 0.964 1.004 0.235 4.315-3.360 100.00 1859 96 0.1146 491.508 487.478 1.005 1.003 0.231 3.356-2.611 100.00 3867 181 0.1424 322.895 319.924 0.996 1.003 0.067 2.608-2.026 99.99 8198 413 0.1358 214.050 211.658 1.005 1.001 0.000 2.025-1.573 100.00 17313 902 0.1649 104.531 103.826 1.014 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2061 46.353 44.991 1.003 0.996 0.000 1.221-1.150 99.97 13689 708 0.2568 29.206 26.903 0.977 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0488 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1634 r_free=0.1784 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=0.1634 r_free=0.1784 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.844941 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2002.648625 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 0.1462 0.0249 0.007 1.0 1.0 0.5 0.0 0 12.922 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 14.62 2.49 3.013 19.072 2002.649 0.017 12.39 15.32 2.93 3.094 19.478 2002.649 0.016 Individual atomic B min max mean iso aniso Overall: 8.51 118.53 20.87 2.87 0 1785 Protein: 8.51 118.53 17.80 2.87 0 1519 Water: 11.12 114.90 38.73 N/A 0 258 Other: 22.33 35.27 28.34 N/A 0 8 Chain A: 8.51 118.53 20.87 N/A 0 1785 Histogram: Values Number of atoms 8.51 - 19.51 1210 19.51 - 30.51 236 30.51 - 41.51 160 41.51 - 52.51 101 52.51 - 63.52 49 63.52 - 74.52 17 74.52 - 85.52 5 85.52 - 96.52 3 96.52 - 107.52 1 107.52 - 118.53 3 =========================== Idealize ADP of riding H ========================== r_work=0.1240 r_free=0.1532 r_work=0.1244 r_free=0.1536 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1244 r_free = 0.1536 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 = 0.1242 r_free = 0.1539 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 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= 0.1242 r_free= 0.1539 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015379 | | target function (ls_wunit_k1) not normalized (work): 1281.051101 | | target function (ls_wunit_k1) not normalized (free): 112.362248 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1257 0.1242 0.1539 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1699 0.1698 0.1771 n_refl.: 87593 remove outliers: r(all,work,free)=0.1699 0.1698 0.1771 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1719 0.1718 0.1785 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1255 0.1241 0.1535 n_refl.: 87593 remove outliers: r(all,work,free)=0.1255 0.1240 0.1535 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 0.3603 299.036 278.275 0.637 1.002 0.380 11.894-9.307 99.02 97 4 0.1620 479.039 467.419 0.910 1.003 0.380 9.237-7.194 100.00 213 7 0.1836 391.795 386.380 0.950 1.003 0.340 7.162-5.571 100.00 427 22 0.1725 294.020 288.796 0.925 1.003 0.254 5.546-4.326 100.00 867 58 0.0920 403.617 401.176 0.952 1.003 0.219 4.315-3.360 100.00 1859 96 0.0779 383.843 382.842 0.996 1.003 0.210 3.356-2.611 100.00 3867 181 0.1021 252.165 251.443 0.998 1.002 0.057 2.608-2.026 99.99 8198 413 0.0973 167.162 166.602 1.009 1.002 0.000 2.025-1.573 100.00 17313 902 0.1205 81.633 81.839 1.018 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1642 36.200 35.654 1.005 0.999 0.000 1.221-1.150 99.97 13689 708 0.2358 22.808 21.320 0.970 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0471 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1240 r_free=0.1535 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=0.1242 r_free=0.1536 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1242 r_free=0.1536 | n_water=258 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1251 r_free=0.1531 | n_water=252 | time (s): 26.510 (total time: 28.890) Filter (q & B) r_work=0.1254 r_free=0.1530 | n_water=249 | time (s): 4.060 (total time: 32.950) Compute maps r_work=0.1254 r_free=0.1530 | n_water=249 | time (s): 1.860 (total time: 34.810) Filter (map) r_work=0.1269 r_free=0.1538 | n_water=237 | time (s): 3.920 (total time: 38.730) Find peaks r_work=0.1269 r_free=0.1538 | n_water=237 | time (s): 0.710 (total time: 39.440) Add new water r_work=0.1427 r_free=0.1701 | n_water=457 | time (s): 3.940 (total time: 43.380) Refine new water occ: r_work=0.1332 r_free=0.1560 adp: r_work=0.1252 r_free=0.1515 occ: r_work=0.1262 r_free=0.1501 adp: r_work=0.1228 r_free=0.1492 occ: r_work=0.1231 r_free=0.1478 adp: r_work=0.1221 r_free=0.1480 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1480 r_work=0.1221 r_free=0.1480 | n_water=457 | time (s): 88.740 (total time: 132.120) Filter (q & B) r_work=0.1226 r_free=0.1485 | n_water=433 | time (s): 3.970 (total time: 136.090) Filter (dist only) r_work=0.1226 r_free=0.1485 | n_water=433 | time (s): 42.080 (total time: 178.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.985034 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1411.179835 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 0.1222 0.1514 0.0292 0.007 0.9 2.6 0.5 0.0 0 12.493 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.22 15.14 2.92 3.772 23.091 1411.180 0.015 11.97 14.83 2.86 4.097 22.950 1411.180 0.014 Individual atomic B min max mean iso aniso Overall: 8.92 114.27 23.19 2.56 196 1764 Protein: 8.92 114.27 17.63 2.57 0 1519 Water: 11.09 73.15 42.55 N/A 196 237 Other: 26.00 37.57 31.41 N/A 0 8 Chain A: 8.92 114.27 20.34 N/A 0 1764 Chain S: 18.13 70.22 48.87 N/A 196 0 Histogram: Values Number of atoms 8.92 - 19.46 1212 19.46 - 29.99 250 29.99 - 40.53 180 40.53 - 51.06 155 51.06 - 61.59 106 61.59 - 72.13 46 72.13 - 82.66 5 82.66 - 93.20 3 93.20 - 103.73 1 103.73 - 114.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1483 r_work=0.1197 r_free=0.1483 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1483 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1475 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.22 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= 0.1197 r_free= 0.1475 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013819 | | target function (ls_wunit_k1) not normalized (work): 1151.040600 | | target function (ls_wunit_k1) not normalized (free): 101.831345 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1197 0.1475 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1606 0.1602 0.1717 n_refl.: 87592 remove outliers: r(all,work,free)=0.1606 0.1602 0.1717 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1612 0.1608 0.1720 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1194 0.1472 n_refl.: 87592 remove outliers: r(all,work,free)=0.1207 0.1193 0.1472 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3433 294.973 271.150 0.603 1.002 0.380 11.894-9.307 99.02 97 4 0.1476 479.039 478.882 0.928 1.003 0.370 9.237-7.194 100.00 213 7 0.1642 391.795 392.343 0.978 1.003 0.280 7.162-5.571 100.00 427 22 0.1443 294.020 290.986 0.945 1.003 0.234 5.546-4.326 100.00 867 58 0.0823 403.617 400.856 0.958 1.003 0.219 4.315-3.360 100.00 1859 96 0.0723 383.843 382.794 1.001 1.003 0.217 3.356-2.611 100.00 3867 181 0.0960 252.165 251.470 1.008 1.002 0.067 2.608-2.026 99.99 8198 413 0.0958 167.162 166.797 1.017 1.002 0.000 2.025-1.573 100.00 17313 902 0.1175 81.633 81.847 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1605 36.200 35.703 1.016 0.999 0.000 1.221-1.150 99.97 13689 708 0.2333 22.808 21.327 0.977 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0559 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1472 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1193 r_free=0.1472 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1472 | n_water=433 | time (s): 2.000 (total time: 2.000) Filter (dist) r_work=0.1195 r_free=0.1471 | n_water=430 | time (s): 41.450 (total time: 43.450) Filter (q & B) r_work=0.1195 r_free=0.1471 | n_water=430 | time (s): 1.310 (total time: 44.760) Compute maps r_work=0.1195 r_free=0.1471 | n_water=430 | time (s): 1.360 (total time: 46.120) Filter (map) r_work=0.1236 r_free=0.1464 | n_water=294 | time (s): 3.550 (total time: 49.670) Find peaks r_work=0.1236 r_free=0.1464 | n_water=294 | time (s): 0.640 (total time: 50.310) Add new water r_work=0.1366 r_free=0.1588 | n_water=487 | time (s): 3.410 (total time: 53.720) Refine new water occ: r_work=0.1265 r_free=0.1507 adp: r_work=0.1265 r_free=0.1507 occ: r_work=0.1242 r_free=0.1492 adp: r_work=0.1239 r_free=0.1489 occ: r_work=0.1226 r_free=0.1482 adp: r_work=0.1219 r_free=0.1476 ADP+occupancy (water only), MIN, final r_work=0.1219 r_free=0.1476 r_work=0.1219 r_free=0.1476 | n_water=487 | time (s): 180.570 (total time: 234.290) Filter (q & B) r_work=0.1223 r_free=0.1473 | n_water=449 | time (s): 2.780 (total time: 237.070) Filter (dist only) r_work=0.1223 r_free=0.1473 | n_water=449 | time (s): 37.730 (total time: 274.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.041993 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.639365 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 0.1225 0.1434 0.0209 0.006 0.9 2.2 0.5 0.0 0 1.021 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 14.34 2.09 3.601 22.126 49.639 3.722 12.13 13.95 1.83 4.201 21.894 49.639 3.652 Individual atomic B min max mean iso aniso Overall: 9.26 109.66 21.64 2.31 215 1761 Protein: 9.26 109.66 17.11 2.31 0 1519 Water: 11.58 71.94 36.84 N/A 215 234 Other: 21.71 33.52 27.78 N/A 0 8 Chain A: 9.26 109.66 19.77 N/A 0 1761 Chain S: 15.05 66.15 36.93 N/A 215 0 Histogram: Values Number of atoms 9.26 - 19.30 1241 19.30 - 29.34 275 29.34 - 39.38 219 39.38 - 49.42 126 49.42 - 59.46 80 59.46 - 69.50 24 69.50 - 79.54 5 79.54 - 89.58 3 89.58 - 99.62 1 99.62 - 109.66 2 =========================== Idealize ADP of riding H ========================== r_work=0.1213 r_free=0.1395 r_work=0.1214 r_free=0.1396 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1214 r_free = 0.1396 target_work(ml) = 3.653 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1392 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.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1207 r_free= 0.1392 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.650220 | | target function (ml) not normalized (work): 304037.805097 | | target function (ml) not normalized (free): 16053.366441 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1207 0.1392 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1532 0.1532 0.1571 n_refl.: 87589 remove outliers: r(all,work,free)=0.1532 0.1532 0.1571 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1530 0.1529 0.1570 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1196 0.1350 n_refl.: 87589 remove outliers: r(all,work,free)=0.1198 0.1191 0.1350 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 0.3892 289.699 255.730 0.465 1.000 0.297 11.894-9.307 94.12 92 4 0.2388 474.302 465.174 0.852 1.001 0.280 9.237-7.194 98.18 209 7 0.2374 383.336 386.622 0.945 1.001 0.175 7.162-5.571 100.00 427 22 0.2047 294.020 284.440 0.914 1.002 0.167 5.546-4.326 100.00 867 58 0.1099 403.617 399.159 0.953 1.002 0.154 4.315-3.360 100.00 1859 96 0.0933 383.843 381.114 0.993 1.002 0.144 3.356-2.611 100.00 3867 181 0.1144 252.165 250.154 1.000 1.002 0.053 2.608-2.026 99.99 8198 413 0.1038 167.162 166.221 1.012 1.002 0.000 2.025-1.573 100.00 17313 902 0.1001 81.633 81.777 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1287 36.200 35.774 1.019 1.000 0.000 1.221-1.150 99.97 13689 708 0.2130 22.808 21.427 0.977 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0050 b_overall=-0.0354 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1350 | n_water=449 | time (s): 2.070 (total time: 2.070) Filter (dist) r_work=0.1190 r_free=0.1350 | n_water=448 | time (s): 36.000 (total time: 38.070) Filter (q & B) r_work=0.1191 r_free=0.1352 | n_water=447 | time (s): 3.380 (total time: 41.450) Compute maps r_work=0.1191 r_free=0.1352 | n_water=447 | time (s): 1.430 (total time: 42.880) Filter (map) r_work=0.1217 r_free=0.1369 | n_water=312 | time (s): 2.540 (total time: 45.420) Find peaks r_work=0.1217 r_free=0.1369 | n_water=312 | time (s): 0.640 (total time: 46.060) Add new water r_work=0.1279 r_free=0.1418 | n_water=480 | time (s): 2.520 (total time: 48.580) Refine new water occ: r_work=0.1207 r_free=0.1367 adp: r_work=0.1207 r_free=0.1367 occ: r_work=0.1192 r_free=0.1360 adp: r_work=0.1191 r_free=0.1357 occ: r_work=0.1182 r_free=0.1352 adp: r_work=0.1178 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1178 r_free=0.1349 r_work=0.1178 r_free=0.1349 | n_water=480 | time (s): 180.220 (total time: 228.800) Filter (q & B) r_work=0.1185 r_free=0.1350 | n_water=446 | time (s): 2.980 (total time: 231.780) Filter (dist only) r_work=0.1185 r_free=0.1350 | n_water=445 | time (s): 41.220 (total time: 273.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.380127 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.837685 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 0.1186 0.1353 0.0167 0.006 1.0 3.8 0.5 0.0 0 1.190 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.86 13.53 1.67 3.400 21.385 38.838 3.630 11.83 13.54 1.71 3.603 21.320 38.838 3.623 Individual atomic B min max mean iso aniso Overall: 9.27 105.71 21.24 2.14 215 1757 Protein: 9.27 105.71 16.96 2.14 0 1519 Water: 11.61 71.33 35.78 N/A 215 230 Other: 20.95 30.82 26.66 N/A 0 8 Chain A: 9.27 105.71 19.52 N/A 0 1757 Chain S: 15.39 66.28 35.35 N/A 215 0 Histogram: Values Number of atoms 9.27 - 18.92 1230 18.92 - 28.56 279 28.56 - 38.20 216 38.20 - 47.85 142 47.85 - 57.49 68 57.49 - 67.14 23 67.14 - 76.78 9 76.78 - 86.42 2 86.42 - 96.07 1 96.07 - 105.71 2 =========================== Idealize ADP of riding H ========================== r_work=0.1183 r_free=0.1354 r_work=0.1184 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1184 r_free = 0.1355 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1180 r_free = 0.1353 target_work(ml) = 3.622 | | 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= 0.1180 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621607 | | target function (ml) not normalized (work): 301607.457851 | | target function (ml) not normalized (free): 15937.227109 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1188 0.1180 0.1353 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1506 0.1504 0.1576 n_refl.: 87576 remove outliers: r(all,work,free)=0.1506 0.1504 0.1576 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1504 0.1502 0.1574 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1187 0.1179 0.1356 n_refl.: 87576 remove outliers: r(all,work,free)=0.1187 0.1179 0.1356 n_refl.: 87575 ======================== 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 0.3981 289.699 256.530 0.449 1.000 0.289 11.894-9.307 93.14 91 4 0.2325 474.353 455.683 0.836 1.001 0.267 9.237-7.194 98.18 209 7 0.2455 383.336 377.677 0.911 1.001 0.140 7.162-5.571 100.00 427 22 0.2173 294.020 283.104 0.906 1.002 0.130 5.546-4.326 100.00 867 58 0.1124 403.617 399.756 0.954 1.002 0.127 4.315-3.360 100.00 1859 96 0.0940 383.843 381.569 0.993 1.002 0.113 3.356-2.611 100.00 3867 181 0.1148 252.165 250.357 1.002 1.001 0.043 2.608-2.026 99.99 8198 413 0.1023 167.162 166.328 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0976 81.633 81.907 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1242 36.200 35.831 1.020 0.999 0.000 1.221-1.150 99.97 13689 708 0.2118 22.808 21.441 0.978 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0343 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1179 r_free=0.1356 After: r_work=0.1179 r_free=0.1356 ================================== NQH flips ================================== r_work=0.1179 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1179 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1179 r_free=0.1356 | n_water=445 | time (s): 1.760 (total time: 1.760) Filter (dist) r_work=0.1179 r_free=0.1356 | n_water=445 | time (s): 35.290 (total time: 37.050) Filter (q & B) r_work=0.1179 r_free=0.1356 | n_water=441 | time (s): 2.810 (total time: 39.860) Compute maps r_work=0.1179 r_free=0.1356 | n_water=441 | time (s): 1.390 (total time: 41.250) Filter (map) r_work=0.1201 r_free=0.1357 | n_water=340 | time (s): 3.390 (total time: 44.640) Find peaks r_work=0.1201 r_free=0.1357 | n_water=340 | time (s): 0.500 (total time: 45.140) Add new water r_work=0.1250 r_free=0.1389 | n_water=493 | time (s): 2.320 (total time: 47.460) Refine new water occ: r_work=0.1189 r_free=0.1348 adp: r_work=0.1188 r_free=0.1347 occ: r_work=0.1178 r_free=0.1343 adp: r_work=0.1176 r_free=0.1341 occ: r_work=0.1170 r_free=0.1340 adp: r_work=0.1167 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1167 r_free=0.1337 r_work=0.1167 r_free=0.1337 | n_water=493 | time (s): 128.640 (total time: 176.100) Filter (q & B) r_work=0.1175 r_free=0.1346 | n_water=454 | time (s): 2.960 (total time: 179.060) Filter (dist only) r_work=0.1175 r_free=0.1344 | n_water=453 | time (s): 40.920 (total time: 219.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.167767 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.996282 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 0.1198 0.1370 0.0172 0.007 1.1 4.8 0.5 0.0 0 1.084 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.70 1.72 3.297 21.242 43.996 3.631 11.98 13.72 1.74 3.729 21.108 43.996 3.622 Individual atomic B min max mean iso aniso Overall: 9.30 100.70 21.04 2.00 223 1757 Protein: 9.30 100.70 16.64 2.00 0 1519 Water: 11.58 69.82 35.74 N/A 223 230 Other: 20.56 28.66 24.83 N/A 0 8 Chain A: 9.30 100.70 19.18 N/A 0 1757 Chain S: 14.03 66.76 35.74 N/A 223 0 Histogram: Values Number of atoms 9.30 - 18.44 1219 18.44 - 27.58 282 27.58 - 36.72 212 36.72 - 45.86 139 45.86 - 55.00 83 55.00 - 64.14 29 64.14 - 73.28 11 73.28 - 82.42 2 82.42 - 91.56 1 91.56 - 100.70 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1372 r_work=0.1198 r_free=0.1372 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1372 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1369 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1195 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621380 | | target function (ml) not normalized (work): 301584.873898 | | target function (ml) not normalized (free): 15952.328803 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1431 0.1386 5.7107 5.6081| | 2: 3.57 - 2.84 1.00 2888 124 0.1104 0.1453 5.1828 5.2655| | 3: 2.83 - 2.48 1.00 2820 163 0.1231 0.1283 4.9983 5.0162| | 4: 2.47 - 2.25 1.00 2825 136 0.1020 0.1123 4.6983 4.7517| | 5: 2.25 - 2.09 1.00 2756 127 0.0987 0.1142 4.6377 4.7217| | 6: 2.09 - 1.97 1.00 2846 113 0.0980 0.1236 4.3535 4.4726| | 7: 1.97 - 1.87 1.00 2787 165 0.0985 0.1243 4.0797 4.2002| | 8: 1.87 - 1.79 1.00 2789 144 0.1020 0.1272 3.999 4.0874| | 9: 1.79 - 1.72 1.00 2745 138 0.0948 0.1255 3.7184 3.8925| | 10: 1.72 - 1.66 1.00 2831 160 0.1003 0.1281 3.6389 3.7872| | 11: 1.66 - 1.61 1.00 2712 147 0.0962 0.1098 3.5702 3.6069| | 12: 1.61 - 1.56 1.00 2773 144 0.0909 0.1141 3.3471 3.4721| | 13: 1.56 - 1.52 1.00 2745 130 0.0975 0.1093 3.3377 3.4569| | 14: 1.52 - 1.48 1.00 2803 134 0.0983 0.1128 3.2574 3.3504| | 15: 1.48 - 1.45 1.00 2738 128 0.1012 0.1313 3.1672 3.3037| | 16: 1.45 - 1.42 1.00 2756 161 0.1064 0.1260 3.1477 3.2499| | 17: 1.42 - 1.39 1.00 2785 139 0.1113 0.1304 3.1132 3.2316| | 18: 1.39 - 1.36 1.00 2741 179 0.1144 0.1395 3.0843 3.2835| | 19: 1.36 - 1.34 1.00 2807 134 0.1203 0.1629 3.0924 3.2779| | 20: 1.34 - 1.32 1.00 2696 147 0.1321 0.1464 3.0897 3.1402| | 21: 1.32 - 1.30 1.00 2785 112 0.1411 0.1615 3.0869 3.1645| | 22: 1.29 - 1.27 1.00 2704 152 0.1464 0.1927 3.0812 3.2901| | 23: 1.27 - 1.26 1.00 2802 156 0.1563 0.1866 3.1006 3.219| | 24: 1.26 - 1.24 1.00 2744 132 0.1630 0.1787 3.097 3.1967| | 25: 1.24 - 1.22 1.00 2733 148 0.1792 0.2322 3.1082 3.2912| | 26: 1.22 - 1.21 1.00 2727 135 0.1860 0.1796 3.1245 3.2128| | 27: 1.21 - 1.19 1.00 2814 148 0.2004 0.2118 3.1396 3.1538| | 28: 1.19 - 1.18 1.00 2671 147 0.2142 0.2355 3.1411 3.1759| | 29: 1.18 - 1.16 1.00 2800 134 0.2215 0.2362 3.1289 3.226| | 30: 1.16 - 1.15 1.00 2739 148 0.2370 0.2511 3.1159 3.1685| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2917 171 0.95 8.78 1.00 0.97 6018.30| | 2: 3.57 - 2.84 2888 124 0.92 12.97 1.01 0.97 6018.30| | 3: 2.83 - 2.48 2820 163 0.89 17.11 0.99 0.97 5055.92| | 4: 2.47 - 2.25 2825 136 0.91 14.36 1.00 0.98 2574.24| | 5: 2.25 - 2.09 2756 127 0.90 16.61 1.01 0.98 2574.24| | 6: 2.09 - 1.97 2846 113 0.92 13.60 1.02 0.97 1531.38| | 7: 1.97 - 1.87 2787 165 0.94 11.00 1.02 0.97 641.96| | 8: 1.87 - 1.79 2789 144 0.91 14.60 0.99 0.97 641.96| | 9: 1.79 - 1.72 2745 138 0.93 11.53 0.98 0.97 345.77| | 10: 1.72 - 1.66 2831 160 0.93 12.35 0.98 0.97 286.45| | 11: 1.66 - 1.61 2712 147 0.93 13.03 0.98 0.97 273.32| | 12: 1.61 - 1.56 2773 144 0.95 9.63 0.99 0.97 149.46| | 13: 1.56 - 1.52 2745 130 0.94 11.21 1.02 0.97 149.46| | 14: 1.52 - 1.48 2803 134 0.94 11.37 1.02 0.97 133.33| | 15: 1.48 - 1.45 2738 128 0.95 10.44 1.01 0.98 103.78| | 16: 1.45 - 1.42 2756 161 0.94 11.66 1.02 0.98 103.78| | 17: 1.42 - 1.39 2785 139 0.94 11.51 1.01 0.98 94.03| | 18: 1.39 - 1.36 2741 179 0.94 11.81 1.01 0.98 88.39| | 19: 1.36 - 1.34 2807 134 0.94 12.36 1.00 0.98 88.39| | 20: 1.34 - 1.32 2696 147 0.94 12.49 0.99 0.96 83.31| | 21: 1.32 - 1.30 2785 112 0.93 13.44 0.98 0.96 82.95| | 22: 1.29 - 1.27 2704 152 0.93 14.03 0.98 0.96 83.14| | 23: 1.27 - 1.26 2802 156 0.92 14.90 0.97 0.94 84.08| | 24: 1.26 - 1.24 2744 132 0.92 15.09 0.97 0.94 84.08| | 25: 1.24 - 1.22 2733 148 0.91 16.50 0.96 0.94 85.71| | 26: 1.22 - 1.21 2727 135 0.90 18.27 1.02 0.93 87.52| | 27: 1.21 - 1.19 2814 148 0.89 18.95 1.02 0.93 87.52| | 28: 1.19 - 1.18 2671 147 0.88 20.40 1.01 0.93 91.15| | 29: 1.18 - 1.16 2800 134 0.88 20.79 0.99 0.92 92.52| | 30: 1.16 - 1.15 2739 148 0.86 22.18 0.98 0.92 92.52| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 82.95 max = 6018.30 mean = 950.33| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.08| |phase err.(test): min = 0.00 max = 88.53 mean = 14.21| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1195 0.1369 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1505 0.1502 0.1584 n_refl.: 87575 remove outliers: r(all,work,free)=0.1505 0.1502 0.1584 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1503 0.1500 0.1583 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1195 0.1372 n_refl.: 87575 remove outliers: r(all,work,free)=0.1203 0.1194 0.1372 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 0.3965 289.699 255.492 0.434 0.998 0.280 11.894-9.307 91.18 89 4 0.2504 464.080 453.178 0.832 1.000 0.184 9.237-7.194 97.73 208 7 0.2536 382.860 377.304 0.900 1.001 0.130 7.162-5.571 100.00 427 22 0.2252 294.020 282.876 0.901 1.001 0.130 5.546-4.326 100.00 867 58 0.1204 403.617 399.076 0.954 1.002 0.113 4.315-3.360 100.00 1859 96 0.0992 383.843 381.279 0.994 1.001 0.107 3.356-2.611 100.00 3867 181 0.1179 252.165 250.132 1.000 1.001 0.043 2.608-2.026 99.99 8198 413 0.1037 167.162 166.251 1.014 1.000 0.000 2.025-1.573 100.00 17313 902 0.0973 81.633 81.853 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1223 36.200 35.813 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2116 22.808 21.418 0.977 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0226 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2609 0.1962 0.083 5.610 8.8 119.3 19.9 258 0.000 1_bss: 0.1634 0.1784 0.083 5.610 9.1 119.5 20.1 258 0.000 1_settarget: 0.1634 0.1784 0.083 5.610 9.1 119.5 20.1 258 0.000 1_nqh: 0.1634 0.1784 0.083 5.610 9.1 119.5 20.1 258 0.000 1_weight: 0.1634 0.1784 0.083 5.610 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1213 0.1462 0.007 0.956 9.1 119.5 20.1 258 0.122 1_adp: 0.1240 0.1532 0.007 0.956 8.5 118.5 20.9 258 0.122 1_regHadp: 0.1244 0.1536 0.007 0.956 8.5 118.5 20.9 258 0.122 1_occ: 0.1242 0.1539 0.007 0.956 8.5 118.5 20.9 258 0.122 2_bss: 0.1240 0.1535 0.007 0.956 8.6 118.6 21.0 258 0.122 2_settarget: 0.1240 0.1535 0.007 0.956 8.6 118.6 21.0 258 0.122 2_updatecdl: 0.1240 0.1535 0.008 0.966 8.6 118.6 21.0 258 0.122 2_nqh: 0.1242 0.1536 0.008 0.966 8.6 118.6 21.0 258 0.125 2_sol: 0.1226 0.1485 0.008 0.966 8.6 118.6 23.4 433 n/a 2_weight: 0.1226 0.1485 0.008 0.966 8.6 118.6 23.4 433 n/a 2_xyzrec: 0.1222 0.1514 0.007 0.877 8.6 118.6 23.4 433 n/a 2_adp: 0.1197 0.1483 0.007 0.877 8.9 114.3 23.2 433 n/a 2_regHadp: 0.1197 0.1483 0.007 0.877 8.9 114.3 23.2 433 n/a 2_occ: 0.1197 0.1475 0.007 0.877 8.9 114.3 23.2 433 n/a 3_bss: 0.1193 0.1472 0.007 0.877 9.0 114.3 23.2 433 n/a 3_settarget: 0.1193 0.1472 0.007 0.877 9.0 114.3 23.2 433 n/a 3_updatecdl: 0.1193 0.1472 0.007 0.879 9.0 114.3 23.2 433 n/a 3_nqh: 0.1193 0.1472 0.007 0.879 9.0 114.3 23.2 433 n/a 3_sol: 0.1223 0.1473 0.007 0.879 9.0 114.3 22.1 449 n/a 3_weight: 0.1223 0.1473 0.007 0.879 9.0 114.3 22.1 449 n/a 3_xyzrec: 0.1225 0.1434 0.006 0.923 9.0 114.3 22.1 449 n/a 3_adp: 0.1213 0.1395 0.006 0.923 9.3 109.7 21.6 449 n/a 3_regHadp: 0.1214 0.1396 0.006 0.923 9.3 109.7 21.6 449 n/a 3_occ: 0.1207 0.1392 0.006 0.923 9.3 109.7 21.6 449 n/a 4_bss: 0.1191 0.1350 0.006 0.923 9.3 109.6 21.6 449 n/a 4_settarget: 0.1191 0.1350 0.006 0.923 9.3 109.6 21.6 449 n/a 4_updatecdl: 0.1191 0.1350 0.006 0.921 9.3 109.6 21.6 449 n/a 4_nqh: 0.1191 0.1350 0.006 0.921 9.3 109.6 21.6 449 n/a 4_sol: 0.1185 0.1350 0.006 0.921 9.3 109.6 21.4 445 n/a 4_weight: 0.1185 0.1350 0.006 0.921 9.3 109.6 21.4 445 n/a 4_xyzrec: 0.1186 0.1353 0.006 0.991 9.3 109.6 21.4 445 n/a 4_adp: 0.1183 0.1354 0.006 0.991 9.3 105.7 21.2 445 n/a 4_regHadp: 0.1184 0.1355 0.006 0.991 9.3 105.7 21.2 445 n/a 4_occ: 0.1180 0.1353 0.006 0.991 9.3 105.7 21.2 445 n/a 5_bss: 0.1179 0.1356 0.006 0.991 9.3 105.7 21.2 445 n/a 5_settarget: 0.1179 0.1356 0.006 0.991 9.3 105.7 21.2 445 n/a 5_updatecdl: 0.1179 0.1356 0.006 0.993 9.3 105.7 21.2 445 n/a 5_setrh: 0.1179 0.1356 0.006 0.993 9.3 105.7 21.2 445 n/a 5_nqh: 0.1179 0.1356 0.006 0.993 9.3 105.7 21.2 445 n/a 5_sol: 0.1175 0.1344 0.006 0.993 9.3 105.7 21.3 453 n/a 5_weight: 0.1175 0.1344 0.006 0.993 9.3 105.7 21.3 453 n/a 5_xyzrec: 0.1198 0.1370 0.007 1.108 9.3 105.7 21.3 453 n/a 5_adp: 0.1198 0.1372 0.007 1.108 9.3 100.7 21.0 453 n/a 5_regHadp: 0.1198 0.1372 0.007 1.108 9.3 100.7 21.0 453 n/a 5_occ: 0.1195 0.1369 0.007 1.108 9.3 100.7 21.0 453 n/a end: 0.1194 0.1372 0.007 1.108 9.3 100.7 21.0 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5239121_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5239121_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.4800 Refinement macro-cycles (run) : 3424.8300 Write final files (write_after_run_outputs) : 67.8900 Total : 3498.2000 Total CPU time: 58.93 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:10:06 PST -0800 (1735452606.21 s) Start R-work = 0.1634, R-free = 0.1784 Final R-work = 0.1194, R-free = 0.1372 =============================================================================== Job complete usr+sys time: 3642.06 seconds wall clock time: 65 minutes 25.08 seconds (3925.08 seconds total)