Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5638674.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_5638674.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5638674.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 =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.19, per 1000 atoms: 0.65 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: 0.85 Conformation dependent library (CDL) restraints added in 219.4 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: 0.67 - 0.91: 493 0.91 - 1.15: 1126 1.15 - 1.39: 584 1.39 - 1.64: 870 1.64 - 1.88: 80 Bond restraints: 3153 Sorted by residual: bond pdb=" N PHE A 162 " pdb=" CA PHE A 162 " ideal model delta sigma weight residual 1.459 1.699 -0.240 1.20e-02 6.94e+03 4.00e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.133 0.188 1.00e-02 1.00e+04 3.53e+02 bond pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 1.331 1.497 -0.167 8.90e-03 1.26e+04 3.50e+02 bond pdb=" C HIS A 138 " pdb=" O HIS A 138 " ideal model delta sigma weight residual 1.236 1.473 -0.237 1.32e-02 5.74e+03 3.24e+02 bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.496 -0.175 1.00e-02 1.00e+04 3.07e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.87: 3176 4.87 - 9.74: 1921 9.74 - 14.61: 576 14.61 - 19.48: 98 19.48 - 24.34: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 132.45 -13.25 9.00e-01 1.23e+00 2.17e+02 angle pdb=" O MET A 17 " pdb=" C MET A 17 " pdb=" N GLU A 18 " ideal model delta sigma weight residual 122.09 137.38 -15.29 1.04e+00 9.25e-01 2.16e+02 angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" O ILE A 21 " ideal model delta sigma weight residual 118.69 128.17 -9.48 6.70e-01 2.23e+00 2.00e+02 angle pdb=" CA MET A 17 " pdb=" C MET A 17 " pdb=" N GLU A 18 " ideal model delta sigma weight residual 116.97 100.54 16.43 1.20e+00 6.94e-01 1.88e+02 angle pdb=" N AASN A 76 " pdb=" CA AASN A 76 " pdb=" C AASN A 76 " ideal model delta sigma weight residual 111.33 127.20 -15.87 1.21e+00 6.83e-01 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.17: 923 17.17 - 34.33: 129 34.33 - 51.49: 44 51.49 - 68.65: 12 68.65 - 85.81: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ARG A 145 " pdb=" C ARG A 145 " pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA CYS A 46 " pdb=" C CYS A 46 " pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.220: 92 0.220 - 0.439: 82 0.439 - 0.658: 43 0.658 - 0.877: 22 0.877 - 1.095: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA GLU A 16 " pdb=" N GLU A 16 " pdb=" C GLU A 16 " pdb=" CB GLU A 16 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.10 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 3.41 -0.90 2.00e-01 2.50e+01 2.02e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 173 " 0.011 2.00e-02 2.50e+03 8.15e-02 9.95e+01 pdb=" CG ASN A 173 " -0.120 2.00e-02 2.50e+03 pdb=" OD1 ASN A 173 " 0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN A 173 " -0.077 2.00e-02 2.50e+03 pdb="HD21 ASN A 173 " -0.010 2.00e-02 2.50e+03 pdb="HD22 ASN A 173 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.120 9.50e-02 1.11e+02 7.64e-02 9.66e+01 pdb=" NE ARG A 48 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " 0.120 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.084 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.111 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.026 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " 0.025 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.050 2.00e-02 2.50e+03 5.39e-02 8.71e+01 pdb=" CG PHE A 162 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.068 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.039 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.103 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.014 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1076 2.33 - 2.89: 8139 2.89 - 3.46: 10488 3.46 - 4.03: 15238 4.03 - 4.60: 21760 Nonbonded interactions: 56701 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.757 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.803 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.815 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.816 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.844 2.450 x-y,-y,-z-4/3 ... (remaining 56696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_5638674_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1951 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789734 | | target function (ml) not normalized (work): 232401.610695 | | target function (ml) not normalized (free): 11828.354149 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3039 0.2122 6.9924 4.9504| | 2: 3.57 - 2.84 1.00 2876 122 0.2417 0.1811 4.3527 4.3609| | 3: 2.84 - 2.48 1.00 2833 165 0.2359 0.1706 4.1339 4.1744| | 4: 2.47 - 2.25 1.00 2825 136 0.2347 0.1415 3.8372 3.8307| | 5: 2.25 - 2.09 1.00 2756 127 0.2479 0.1612 3.8017 3.8297| | 6: 2.09 - 1.97 1.00 2846 113 0.2547 0.1669 3.4572 3.5421| | 7: 1.97 - 1.87 1.00 2787 165 0.2564 0.1701 3.1371 3.1317| | 8: 1.87 - 1.79 1.00 2789 144 0.2397 0.1991 3.0418 3.2021| | 9: 1.79 - 1.72 1.00 2745 138 0.2436 0.2089 2.897 3.0124| | 10: 1.72 - 1.66 1.00 2789 158 0.2436 0.1883 2.802 2.8442| | 11: 1.66 - 1.61 1.00 2740 147 0.2508 0.1851 2.7581 2.7709| | 12: 1.61 - 1.56 1.00 2787 146 0.2519 0.2046 2.6266 2.6512| | 13: 1.56 - 1.52 1.00 2745 130 0.2505 0.1881 2.5697 2.6097| | 14: 1.52 - 1.48 1.00 2803 134 0.2564 0.1875 2.4931 2.5134| | 15: 1.48 - 1.45 1.00 2738 128 0.2695 0.2197 2.4478 2.4767| | 16: 1.45 - 1.42 1.00 2756 161 0.2620 0.2169 2.3887 2.4483| | 17: 1.42 - 1.39 1.00 2785 139 0.2695 0.1934 2.3353 2.3264| | 18: 1.39 - 1.36 1.00 2741 179 0.2697 0.2313 2.2824 2.4053| | 19: 1.36 - 1.34 1.00 2807 134 0.2635 0.2225 2.2444 2.2789| | 20: 1.34 - 1.32 1.00 2696 147 0.2682 0.2197 2.2092 2.2036| | 21: 1.32 - 1.30 1.00 2785 112 0.2716 0.2454 2.1577 2.2358| | 22: 1.29 - 1.27 1.00 2704 152 0.2721 0.2719 2.1358 2.2204| | 23: 1.27 - 1.26 1.00 2802 156 0.2768 0.2403 2.1045 2.1796| | 24: 1.26 - 1.24 1.00 2744 132 0.2720 0.2516 2.0651 2.1711| | 25: 1.24 - 1.22 1.00 2734 148 0.2862 0.2476 2.0496 2.0478| | 26: 1.22 - 1.21 1.00 2727 135 0.2850 0.2429 2.0078 2.1158| | 27: 1.21 - 1.19 1.00 2814 148 0.3003 0.2562 2.0137 1.9795| | 28: 1.19 - 1.18 1.00 2671 147 0.3026 0.2673 1.9973 1.9648| | 29: 1.18 - 1.16 1.00 2800 134 0.3013 0.2936 1.9663 2.0293| | 30: 1.16 - 1.15 1.00 2740 148 0.3071 0.2561 1.9351 1.9506| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.16 0.76 0.23 1523.23| | 2: 3.57 - 2.84 2876 122 0.80 26.43 1.27 0.23 1523.23| | 3: 2.84 - 2.48 2833 165 0.73 32.46 1.24 0.24 1261.56| | 4: 2.47 - 2.25 2825 136 0.81 25.73 1.26 0.25 582.50| | 5: 2.25 - 2.09 2756 127 0.77 29.54 1.28 0.25 582.50| | 6: 2.09 - 1.97 2846 113 0.84 22.53 1.29 0.25 316.11| | 7: 1.97 - 1.87 2787 165 0.90 16.26 1.29 0.26 88.91| | 8: 1.87 - 1.79 2789 144 0.86 20.84 1.24 0.26 88.91| | 9: 1.79 - 1.72 2745 138 0.88 18.78 1.24 0.25 56.34| | 10: 1.72 - 1.66 2789 158 0.86 20.60 1.23 0.25 49.82| | 11: 1.66 - 1.61 2740 147 0.86 21.49 1.24 0.25 48.04| | 12: 1.61 - 1.56 2787 146 0.88 18.62 1.23 0.25 30.04| | 13: 1.56 - 1.52 2745 130 0.87 20.45 1.23 0.25 30.04| | 14: 1.52 - 1.48 2803 134 0.86 20.79 1.24 0.25 26.86| | 15: 1.48 - 1.45 2738 128 0.87 20.59 1.25 0.25 21.04| | 16: 1.45 - 1.42 2756 161 0.86 21.40 1.23 0.25 21.04| | 17: 1.42 - 1.39 2785 139 0.86 21.02 1.23 0.25 17.91| | 18: 1.39 - 1.36 2741 179 0.86 21.55 1.23 0.25 16.10| | 19: 1.36 - 1.34 2807 134 0.85 22.17 1.22 0.25 16.10| | 20: 1.34 - 1.32 2696 147 0.86 21.42 1.21 0.24 13.46| | 21: 1.32 - 1.30 2785 112 0.85 22.48 1.21 0.24 13.27| | 22: 1.29 - 1.27 2704 152 0.85 22.91 1.21 0.24 12.97| | 23: 1.27 - 1.26 2802 156 0.85 22.61 1.21 0.24 11.43| | 24: 1.26 - 1.24 2744 132 0.84 23.31 1.20 0.24 11.43| | 25: 1.24 - 1.22 2734 148 0.84 24.02 1.20 0.24 10.74| | 26: 1.22 - 1.21 2727 135 0.84 23.86 1.20 0.23 9.97| | 27: 1.21 - 1.19 2814 148 0.83 24.88 1.20 0.23 9.97| | 28: 1.19 - 1.18 2671 147 0.83 24.85 1.19 0.23 8.99| | 29: 1.18 - 1.16 2800 134 0.83 24.83 1.16 0.23 8.63| | 30: 1.16 - 1.15 2740 148 0.82 26.28 1.15 0.23 8.63| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.63 max = 1523.23 mean = 220.04| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 22.73| |phase err.(test): min = 0.00 max = 89.78 mean = 22.68| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.260 1557 Z= 5.315 Angle : 5.304 19.146 2118 Z= 3.778 Chirality : 0.398 1.095 243 Planarity : 0.032 0.113 284 Dihedral : 14.211 85.809 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % 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: -2.93 (0.45), residues: 224 helix: -2.98 (0.34), residues: 109 sheet: -0.98 (0.93), residues: 28 loop : -0.45 (0.55), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.139 0.024 ARG A 28 TYR 0.070 0.028 TYR A 139 PHE 0.074 0.039 PHE A 164 HIS 0.068 0.027 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= 0.2608 r_free= 0.1951 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789734 | | target function (ml) not normalized (work): 232401.610695 | | target function (ml) not normalized (free): 11828.354149 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2609 0.1952 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2609 0.1952 n_refl.: 87602 remove outliers: r(all,work,free)=0.1978 0.1982 0.1952 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2004 0.2008 0.1965 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1636 0.1629 0.1770 n_refl.: 87594 remove outliers: r(all,work,free)=0.1636 0.1629 0.1770 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 0.3797 386.381 356.871 0.727 0.916 0.401 11.894-9.307 99.02 97 4 0.1785 613.748 595.966 1.010 0.916 0.380 9.237-7.194 100.00 213 7 0.2119 501.970 490.913 1.048 0.917 0.358 7.162-5.571 100.00 427 22 0.2217 376.701 364.377 1.015 0.917 0.290 5.546-4.326 100.00 867 58 0.1267 517.117 512.140 1.051 0.918 0.217 4.315-3.360 100.00 1859 96 0.1163 491.782 486.963 1.093 0.919 0.189 3.356-2.611 100.00 3867 181 0.1427 323.075 319.496 1.084 0.920 0.119 2.608-2.026 99.99 8198 413 0.1335 214.169 211.835 1.093 0.923 0.000 2.025-1.573 100.00 17313 902 0.1630 104.589 104.054 1.092 0.927 0.000 1.573-1.221 100.00 36679 1900 0.2058 46.379 45.121 1.071 0.934 0.000 1.221-1.150 99.97 13689 708 0.2614 29.222 26.951 1.033 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0465 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1629 r_free=0.1770 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1629 r_free=0.1770 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.821167 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2026.279919 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 0.1461 0.0253 0.008 0.9 1.0 0.5 0.0 0 13.411 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 14.61 2.53 3.013 19.062 2026.280 0.017 12.32 15.34 3.02 3.051 19.471 2026.280 0.015 Individual atomic B min max mean iso aniso Overall: 8.55 118.17 20.86 2.89 0 1785 Protein: 8.55 118.17 17.76 2.89 0 1519 Water: 11.11 114.79 38.89 N/A 0 258 Other: 22.48 34.84 28.13 N/A 0 8 Chain A: 8.55 118.17 20.86 N/A 0 1785 Histogram: Values Number of atoms 8.55 - 19.51 1210 19.51 - 30.47 232 30.47 - 41.43 163 41.43 - 52.40 99 52.40 - 63.36 52 63.36 - 74.32 18 74.32 - 85.28 4 85.28 - 96.24 4 96.24 - 107.21 0 107.21 - 118.17 3 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1534 r_work=0.1237 r_free=0.1539 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1539 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1236 r_free = 0.1540 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 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= 0.1236 r_free= 0.1540 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015291 | | target function (ls_wunit_k1) not normalized (work): 1273.677700 | | target function (ls_wunit_k1) not normalized (free): 112.926358 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1251 0.1236 0.1540 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1696 0.1695 0.1765 n_refl.: 87593 remove outliers: r(all,work,free)=0.1696 0.1695 0.1765 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1716 0.1715 0.1779 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1250 0.1236 0.1536 n_refl.: 87593 remove outliers: r(all,work,free)=0.1250 0.1236 0.1536 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 0.3602 298.567 279.035 0.635 1.003 0.380 11.894-9.307 99.02 97 4 0.1576 478.287 466.017 0.909 1.003 0.380 9.237-7.194 100.00 213 7 0.1835 391.180 385.571 0.948 1.003 0.340 7.162-5.571 100.00 427 22 0.1745 293.559 288.049 0.923 1.003 0.253 5.546-4.326 100.00 867 58 0.0927 402.984 400.312 0.950 1.003 0.204 4.315-3.360 100.00 1859 96 0.0775 383.241 382.270 0.995 1.002 0.190 3.356-2.611 100.00 3867 181 0.1019 251.769 251.131 0.999 1.002 0.120 2.608-2.026 99.99 8198 413 0.0968 166.900 166.363 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1194 81.505 81.704 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1636 36.143 35.603 1.006 0.999 0.000 1.221-1.150 99.97 13689 708 0.2353 22.772 21.286 0.970 0.997 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=0.1236 r_free=0.1536 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=0.1237 r_free=0.1538 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1237 r_free=0.1538 | n_water=258 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1246 r_free=0.1535 | n_water=252 | time (s): 26.050 (total time: 28.450) Filter (q & B) r_work=0.1250 r_free=0.1534 | n_water=249 | time (s): 3.810 (total time: 32.260) Compute maps r_work=0.1250 r_free=0.1534 | n_water=249 | time (s): 1.910 (total time: 34.170) Filter (map) r_work=0.1263 r_free=0.1545 | n_water=236 | time (s): 4.020 (total time: 38.190) Find peaks r_work=0.1263 r_free=0.1545 | n_water=236 | time (s): 0.710 (total time: 38.900) Add new water r_work=0.1418 r_free=0.1696 | n_water=450 | time (s): 3.830 (total time: 42.730) Refine new water occ: r_work=0.1328 r_free=0.1570 adp: r_work=0.1248 r_free=0.1519 occ: r_work=0.1262 r_free=0.1512 adp: r_work=0.1226 r_free=0.1500 occ: r_work=0.1230 r_free=0.1484 adp: r_work=0.1220 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1489 r_work=0.1220 r_free=0.1489 | n_water=450 | time (s): 89.850 (total time: 132.580) Filter (q & B) r_work=0.1225 r_free=0.1492 | n_water=430 | time (s): 3.820 (total time: 136.400) Filter (dist only) r_work=0.1225 r_free=0.1492 | n_water=430 | time (s): 40.520 (total time: 176.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.891204 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1500.798090 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1226 0.1509 0.0284 0.007 0.9 2.2 0.5 0.0 0 12.446 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 15.09 2.84 3.768 23.024 1500.798 0.016 12.01 14.87 2.86 4.071 22.866 1500.798 0.015 Individual atomic B min max mean iso aniso Overall: 8.73 114.40 23.07 2.58 194 1763 Protein: 8.73 114.40 17.61 2.59 0 1519 Water: 11.06 73.31 42.31 N/A 194 236 Other: 21.66 32.82 26.32 N/A 0 8 Chain A: 8.73 114.40 20.25 N/A 0 1763 Chain S: 15.61 69.11 48.72 N/A 194 0 Histogram: Values Number of atoms 8.73 - 19.30 1206 19.30 - 29.87 253 29.87 - 40.43 189 40.43 - 51.00 143 51.00 - 61.57 103 61.57 - 72.13 52 72.13 - 82.70 5 82.70 - 93.27 3 93.27 - 103.83 1 103.83 - 114.40 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1487 r_work=0.1201 r_free=0.1487 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1487 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1481 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1203 r_free= 0.1481 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014159 | | target function (ls_wunit_k1) not normalized (work): 1179.415777 | | target function (ls_wunit_k1) not normalized (free): 105.231279 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1203 0.1481 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1603 0.1600 0.1695 n_refl.: 87592 remove outliers: r(all,work,free)=0.1603 0.1600 0.1695 n_refl.: 87592 overall B=0.09 to atoms: r(all,work,free)=0.1617 0.1615 0.1704 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1201 0.1478 n_refl.: 87592 remove outliers: r(all,work,free)=0.1213 0.1200 0.1478 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 0.3407 297.129 270.879 0.586 1.001 0.370 11.894-9.307 99.02 97 4 0.1553 478.287 475.012 0.904 1.002 0.370 9.237-7.194 100.00 213 7 0.1674 391.180 391.090 0.968 1.002 0.270 7.162-5.571 100.00 427 22 0.1537 293.559 289.267 0.928 1.002 0.240 5.546-4.326 100.00 867 58 0.0835 402.984 400.200 0.947 1.002 0.210 4.315-3.360 100.00 1859 96 0.0721 383.241 382.196 0.991 1.002 0.210 3.356-2.611 100.00 3867 181 0.0969 251.769 251.142 0.999 1.002 0.072 2.608-2.026 99.99 8198 413 0.0958 166.900 166.628 1.007 1.002 0.000 2.025-1.573 100.00 17313 902 0.1180 81.505 81.760 1.018 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1608 36.143 35.617 1.007 1.002 0.000 1.221-1.150 99.97 13689 708 0.2342 22.772 21.177 0.962 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=0.0360 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1478 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=0.1200 r_free=0.1478 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1478 | n_water=430 | time (s): 2.090 (total time: 2.090) Filter (dist) r_work=0.1199 r_free=0.1479 | n_water=428 | time (s): 37.680 (total time: 39.770) Filter (q & B) r_work=0.1200 r_free=0.1480 | n_water=427 | time (s): 3.160 (total time: 42.930) Compute maps r_work=0.1200 r_free=0.1480 | n_water=427 | time (s): 1.490 (total time: 44.420) Filter (map) r_work=0.1235 r_free=0.1487 | n_water=296 | time (s): 2.990 (total time: 47.410) Find peaks r_work=0.1235 r_free=0.1487 | n_water=296 | time (s): 0.500 (total time: 47.910) Add new water r_work=0.1361 r_free=0.1626 | n_water=490 | time (s): 2.860 (total time: 50.770) Refine new water occ: r_work=0.1263 r_free=0.1534 adp: r_work=0.1264 r_free=0.1536 occ: r_work=0.1242 r_free=0.1509 adp: r_work=0.1240 r_free=0.1510 occ: r_work=0.1227 r_free=0.1488 adp: r_work=0.1221 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1487 r_work=0.1221 r_free=0.1487 | n_water=490 | time (s): 214.630 (total time: 265.400) Filter (q & B) r_work=0.1225 r_free=0.1493 | n_water=457 | time (s): 3.460 (total time: 268.860) Filter (dist only) r_work=0.1225 r_free=0.1493 | n_water=457 | time (s): 35.870 (total time: 304.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.111026 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.136906 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 0.1230 0.1456 0.0226 0.006 0.9 1.9 0.5 0.0 0 1.056 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 14.56 2.26 3.601 22.144 47.137 3.722 12.16 14.14 1.98 4.166 21.944 47.137 3.651 Individual atomic B min max mean iso aniso Overall: 9.23 109.77 21.72 2.31 223 1761 Protein: 9.23 109.77 17.18 2.31 0 1519 Water: 11.54 72.23 36.77 N/A 223 234 Other: 18.62 28.88 23.60 N/A 0 8 Chain A: 9.23 109.77 19.81 N/A 0 1761 Chain S: 15.67 67.59 36.81 N/A 223 0 Histogram: Values Number of atoms 9.23 - 19.29 1241 19.29 - 29.34 281 29.34 - 39.40 214 39.40 - 49.45 135 49.45 - 59.50 77 59.50 - 69.56 24 69.56 - 79.61 6 79.61 - 89.67 3 89.67 - 99.72 1 99.72 - 109.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.1216 r_free=0.1414 r_work=0.1217 r_free=0.1414 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1217 r_free = 0.1414 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1411 target_work(ml) = 3.648 | | 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= 0.1210 r_free= 0.1411 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.648228 | | target function (ml) not normalized (work): 303875.484141 | | target function (ml) not normalized (free): 16047.322695 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1210 0.1411 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1543 0.1543 0.1582 n_refl.: 87590 remove outliers: r(all,work,free)=0.1543 0.1543 0.1582 n_refl.: 87590 overall B=-0.02 to atoms: r(all,work,free)=0.1538 0.1538 0.1579 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1197 0.1375 n_refl.: 87590 remove outliers: r(all,work,free)=0.1201 0.1193 0.1375 n_refl.: 87580 ======================== 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 0.3682 293.876 262.642 0.490 1.000 0.350 11.894-9.307 98.04 96 4 0.2351 478.411 459.495 0.844 1.001 0.323 9.237-7.194 97.73 208 7 0.2315 383.808 384.899 0.939 1.002 0.175 7.162-5.571 100.00 427 22 0.2092 293.559 283.235 0.906 1.002 0.165 5.546-4.326 100.00 867 58 0.1105 402.984 398.866 0.953 1.002 0.155 4.315-3.360 100.00 1859 96 0.0924 383.241 380.681 0.995 1.002 0.150 3.356-2.611 100.00 3867 181 0.1161 251.769 249.750 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1041 166.900 165.950 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.1008 81.505 81.677 1.029 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1280 36.143 35.718 1.024 0.999 0.000 1.221-1.150 99.97 13689 708 0.2126 22.772 21.398 0.985 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0660 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1375 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1375 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1375 | n_water=457 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1193 r_free=0.1375 | n_water=457 | time (s): 37.560 (total time: 39.950) Filter (q & B) r_work=0.1193 r_free=0.1374 | n_water=456 | time (s): 3.570 (total time: 43.520) Compute maps r_work=0.1193 r_free=0.1374 | n_water=456 | time (s): 1.630 (total time: 45.150) Filter (map) r_work=0.1216 r_free=0.1386 | n_water=312 | time (s): 3.040 (total time: 48.190) Find peaks r_work=0.1216 r_free=0.1386 | n_water=312 | time (s): 0.460 (total time: 48.650) Add new water r_work=0.1280 r_free=0.1462 | n_water=466 | time (s): 3.000 (total time: 51.650) Refine new water occ: r_work=0.1211 r_free=0.1385 adp: r_work=0.1212 r_free=0.1388 occ: r_work=0.1197 r_free=0.1370 adp: r_work=0.1196 r_free=0.1372 occ: r_work=0.1186 r_free=0.1356 adp: r_work=0.1183 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1357 r_work=0.1183 r_free=0.1357 | n_water=466 | time (s): 197.360 (total time: 249.010) Filter (q & B) r_work=0.1190 r_free=0.1360 | n_water=434 | time (s): 3.290 (total time: 252.300) Filter (dist only) r_work=0.1190 r_free=0.1359 | n_water=432 | time (s): 35.300 (total time: 287.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.954508 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.309481 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 0.1371 0.0173 0.006 0.9 2.2 0.5 0.0 0 0.977 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.71 1.73 3.404 21.352 51.309 3.635 11.81 13.60 1.79 3.794 21.230 51.309 3.618 Individual atomic B min max mean iso aniso Overall: 9.31 104.93 21.05 2.16 199 1760 Protein: 9.31 104.93 16.89 2.16 0 1519 Water: 11.59 70.90 35.65 N/A 199 233 Other: 18.32 25.95 21.96 N/A 0 8 Chain A: 9.31 104.93 19.46 N/A 0 1760 Chain S: 15.76 63.44 35.08 N/A 199 0 Histogram: Values Number of atoms 9.31 - 18.87 1232 18.87 - 28.43 280 28.43 - 38.00 208 38.00 - 47.56 134 47.56 - 57.12 69 57.12 - 66.68 23 66.68 - 76.25 8 76.25 - 85.81 2 85.81 - 95.37 1 95.37 - 104.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.1182 r_free=0.1361 r_work=0.1182 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1182 r_free = 0.1361 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1178 r_free = 0.1356 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1178 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.615951 | | target function (ml) not normalized (work): 301150.888351 | | target function (ml) not normalized (free): 15916.692926 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1187 0.1178 0.1356 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1509 0.1509 0.1545 n_refl.: 87580 remove outliers: r(all,work,free)=0.1509 0.1509 0.1545 n_refl.: 87580 overall B=-0.02 to atoms: r(all,work,free)=0.1506 0.1505 0.1543 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1187 0.1178 0.1357 n_refl.: 87580 remove outliers: r(all,work,free)=0.1185 0.1177 0.1357 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3966 289.244 257.054 0.459 1.000 0.306 11.894-9.307 96.08 94 4 0.2362 475.516 461.873 0.858 1.002 0.252 9.237-7.194 97.73 208 7 0.2476 383.808 374.812 0.903 1.002 0.176 7.162-5.571 100.00 427 22 0.2200 293.559 281.885 0.899 1.002 0.150 5.546-4.326 100.00 867 58 0.1162 402.984 398.151 0.953 1.002 0.135 4.315-3.360 100.00 1859 96 0.0964 383.241 380.964 0.996 1.002 0.130 3.356-2.611 100.00 3867 181 0.1157 251.769 249.614 1.001 1.002 0.057 2.608-2.026 99.99 8198 413 0.1015 166.900 166.020 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0952 81.505 81.778 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1230 36.143 35.761 1.023 0.998 0.000 1.221-1.150 99.97 13689 708 0.2123 22.772 21.390 0.983 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0510 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1177 r_free=0.1357 After: r_work=0.1177 r_free=0.1357 ================================== NQH flips ================================== r_work=0.1177 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1177 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1177 r_free=0.1357 | n_water=432 | time (s): 2.100 (total time: 2.100) Filter (dist) r_work=0.1177 r_free=0.1356 | n_water=431 | time (s): 37.760 (total time: 39.860) Filter (q & B) r_work=0.1178 r_free=0.1357 | n_water=426 | time (s): 3.630 (total time: 43.490) Compute maps r_work=0.1178 r_free=0.1357 | n_water=426 | time (s): 1.650 (total time: 45.140) Filter (map) r_work=0.1196 r_free=0.1368 | n_water=327 | time (s): 2.840 (total time: 47.980) Find peaks r_work=0.1196 r_free=0.1368 | n_water=327 | time (s): 0.530 (total time: 48.510) Add new water r_work=0.1250 r_free=0.1411 | n_water=494 | time (s): 3.660 (total time: 52.170) Refine new water occ: r_work=0.1185 r_free=0.1344 adp: r_work=0.1185 r_free=0.1347 occ: r_work=0.1171 r_free=0.1329 adp: r_work=0.1170 r_free=0.1333 occ: r_work=0.1161 r_free=0.1323 adp: r_work=0.1158 r_free=0.1325 ADP+occupancy (water only), MIN, final r_work=0.1158 r_free=0.1325 r_work=0.1158 r_free=0.1325 | n_water=494 | time (s): 249.780 (total time: 301.950) Filter (q & B) r_work=0.1166 r_free=0.1336 | n_water=449 | time (s): 3.500 (total time: 305.450) Filter (dist only) r_work=0.1166 r_free=0.1335 | n_water=448 | time (s): 38.810 (total time: 344.260) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.930524 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.869428 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 4.2 0.5 0.0 0 0.965 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.70 1.72 3.274 21.113 35.869 3.624 12.00 13.69 1.69 3.295 21.099 35.869 3.622 Individual atomic B min max mean iso aniso Overall: 9.26 104.22 21.15 2.10 215 1760 Protein: 9.26 104.22 16.83 2.10 0 1519 Water: 11.46 70.80 35.76 N/A 215 233 Other: 18.41 25.74 21.95 N/A 0 8 Chain A: 9.26 104.22 19.41 N/A 0 1760 Chain S: 15.52 60.03 35.39 N/A 215 0 Histogram: Values Number of atoms 9.26 - 18.75 1229 18.75 - 28.25 294 28.25 - 37.75 202 37.75 - 47.24 134 47.24 - 56.74 78 56.74 - 66.24 23 66.24 - 75.73 11 75.73 - 85.23 1 85.23 - 94.73 1 94.73 - 104.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1369 r_work=0.1200 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1369 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1367 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1197 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.620593 | | target function (ml) not normalized (work): 301526.646610 | | target function (ml) not normalized (free): 15927.170837 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1416 0.1442 5.6698 5.6449| | 2: 3.57 - 2.84 1.00 2888 124 0.1127 0.1429 5.2013 5.2637| | 3: 2.83 - 2.48 1.00 2820 163 0.1216 0.1289 5.0048 5.0283| | 4: 2.47 - 2.25 1.00 2825 136 0.1012 0.1163 4.7041 4.7609| | 5: 2.25 - 2.09 1.00 2756 127 0.0982 0.1101 4.6482 4.717| | 6: 2.09 - 1.97 1.00 2846 113 0.0977 0.1166 4.3537 4.4684| | 7: 1.97 - 1.87 1.00 2787 165 0.0997 0.1196 4.0747 4.1809| | 8: 1.87 - 1.79 1.00 2789 144 0.1022 0.1199 3.9878 4.0644| | 9: 1.79 - 1.72 1.00 2745 138 0.0967 0.1293 3.7167 3.9063| | 10: 1.72 - 1.66 1.00 2831 160 0.1005 0.1287 3.634 3.779| | 11: 1.66 - 1.61 1.00 2712 147 0.0965 0.1090 3.5654 3.6099| | 12: 1.61 - 1.56 1.00 2773 144 0.0927 0.1120 3.3488 3.4553| | 13: 1.56 - 1.52 1.00 2745 130 0.0980 0.1025 3.3365 3.408| | 14: 1.52 - 1.48 1.00 2803 134 0.0994 0.1121 3.2596 3.3431| | 15: 1.48 - 1.45 1.00 2738 128 0.1013 0.1308 3.1653 3.3161| | 16: 1.45 - 1.42 1.00 2756 161 0.1059 0.1255 3.1434 3.2429| | 17: 1.42 - 1.39 1.00 2785 139 0.1120 0.1274 3.1152 3.2255| | 18: 1.39 - 1.36 1.00 2741 179 0.1154 0.1387 3.0837 3.2581| | 19: 1.36 - 1.34 1.00 2807 134 0.1214 0.1574 3.0877 3.271| | 20: 1.34 - 1.32 1.00 2696 147 0.1322 0.1417 3.0854 3.1134| | 21: 1.32 - 1.30 1.00 2785 112 0.1414 0.1641 3.085 3.1695| | 22: 1.29 - 1.27 1.00 2704 152 0.1477 0.1919 3.0838 3.272| | 23: 1.27 - 1.26 1.00 2802 156 0.1586 0.1845 3.1053 3.2089| | 24: 1.26 - 1.24 1.00 2744 132 0.1635 0.1799 3.0975 3.2075| | 25: 1.24 - 1.22 1.00 2733 148 0.1801 0.2320 3.1103 3.2883| | 26: 1.22 - 1.21 1.00 2727 135 0.1871 0.1776 3.1254 3.1932| | 27: 1.21 - 1.19 1.00 2814 148 0.2019 0.2103 3.142 3.1471| | 28: 1.19 - 1.18 1.00 2671 147 0.2152 0.2300 3.1414 3.1602| | 29: 1.18 - 1.16 1.00 2800 134 0.2221 0.2373 3.129 3.2192| | 30: 1.16 - 1.15 1.00 2739 148 0.2384 0.2523 3.1182 3.177| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2919 171 0.95 9.19 1.00 0.97 6336.78| | 2: 3.57 - 2.84 2888 124 0.92 13.49 1.01 0.97 6336.78| | 3: 2.83 - 2.48 2820 163 0.89 17.59 0.99 0.97 5309.85| | 4: 2.47 - 2.25 2825 136 0.91 14.64 1.00 0.98 2661.71| | 5: 2.25 - 2.09 2756 127 0.89 16.98 1.01 0.98 2661.71| | 6: 2.09 - 1.97 2846 113 0.92 13.65 1.02 0.98 1560.46| | 7: 1.97 - 1.87 2787 165 0.94 10.77 1.02 0.97 621.24| | 8: 1.87 - 1.79 2789 144 0.91 14.35 1.00 0.97 621.24| | 9: 1.79 - 1.72 2745 138 0.93 11.38 0.98 0.97 336.46| | 10: 1.72 - 1.66 2831 160 0.93 12.20 0.98 0.97 279.42| | 11: 1.66 - 1.61 2712 147 0.93 12.80 0.98 0.97 266.62| | 12: 1.61 - 1.56 2773 144 0.95 9.43 0.99 0.97 145.86| | 13: 1.56 - 1.52 2745 130 0.94 11.01 1.02 0.97 145.86| | 14: 1.52 - 1.48 2803 134 0.94 11.15 1.02 0.97 130.17| | 15: 1.48 - 1.45 2738 128 0.95 10.24 1.01 0.98 101.42| | 16: 1.45 - 1.42 2756 161 0.94 11.43 1.02 0.98 101.42| | 17: 1.42 - 1.39 2785 139 0.95 11.27 1.01 0.98 91.58| | 18: 1.39 - 1.36 2741 179 0.94 11.63 1.01 0.98 85.89| | 19: 1.36 - 1.34 2807 134 0.94 12.18 1.00 0.98 85.89| | 20: 1.34 - 1.32 2696 147 0.94 12.34 0.99 0.97 81.15| | 21: 1.32 - 1.30 2785 112 0.94 13.21 0.99 0.96 80.82| | 22: 1.29 - 1.27 2704 152 0.93 13.77 0.99 0.96 81.06| | 23: 1.27 - 1.26 2802 156 0.92 14.80 0.98 0.95 82.28| | 24: 1.26 - 1.24 2744 132 0.92 14.93 0.97 0.95 82.28| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.94 84.03| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.02 0.93 85.98| | 27: 1.21 - 1.19 2814 148 0.89 18.73 1.02 0.93 85.98| | 28: 1.19 - 1.18 2671 147 0.88 20.26 1.01 0.93 89.50| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.93 90.82| | 30: 1.16 - 1.15 2739 148 0.86 21.98 0.98 0.93 90.82| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 80.82 max = 6336.78 mean = 984.56| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 14.00| |phase err.(test): min = 0.00 max = 89.84 mean = 14.07| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1197 0.1367 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1516 0.1514 0.1576 n_refl.: 87577 remove outliers: r(all,work,free)=0.1516 0.1514 0.1576 n_refl.: 87577 overall B=-0.02 to atoms: r(all,work,free)=0.1513 0.1511 0.1574 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1197 0.1369 n_refl.: 87577 remove outliers: r(all,work,free)=0.1205 0.1197 0.1369 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3928 289.244 256.848 0.442 0.999 0.285 11.894-9.307 96.08 94 4 0.2443 475.516 457.316 0.839 1.001 0.260 9.237-7.194 97.73 208 7 0.2479 383.808 376.461 0.904 1.002 0.138 7.162-5.571 100.00 427 22 0.2259 293.559 281.728 0.897 1.002 0.135 5.546-4.326 100.00 867 58 0.1187 402.984 398.245 0.953 1.002 0.124 4.315-3.360 100.00 1859 96 0.1003 383.241 380.797 0.997 1.002 0.122 3.356-2.611 100.00 3867 181 0.1190 251.769 249.660 1.000 1.001 0.120 2.608-2.026 99.99 8198 413 0.1027 166.900 165.992 1.015 1.000 0.000 2.025-1.573 100.00 17313 902 0.0981 81.505 81.771 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1230 36.143 35.778 1.023 0.996 0.000 1.221-1.150 99.97 13689 708 0.2125 22.772 21.398 0.983 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0417 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2608 0.1951 0.080 5.304 8.8 119.3 19.9 258 0.000 1_bss: 0.1629 0.1770 0.080 5.304 9.0 119.5 20.1 258 0.000 1_settarget: 0.1629 0.1770 0.080 5.304 9.0 119.5 20.1 258 0.000 1_nqh: 0.1629 0.1770 0.080 5.304 9.0 119.5 20.1 258 0.000 1_weight: 0.1629 0.1770 0.080 5.304 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1208 0.1461 0.008 0.947 9.0 119.5 20.1 258 0.124 1_adp: 0.1233 0.1534 0.008 0.947 8.5 118.2 20.9 258 0.124 1_regHadp: 0.1237 0.1539 0.008 0.947 8.5 118.2 20.9 258 0.124 1_occ: 0.1236 0.1540 0.008 0.947 8.5 118.2 20.9 258 0.124 2_bss: 0.1236 0.1536 0.008 0.947 8.7 118.3 21.0 258 0.124 2_settarget: 0.1236 0.1536 0.008 0.947 8.7 118.3 21.0 258 0.124 2_updatecdl: 0.1236 0.1536 0.008 0.967 8.7 118.3 21.0 258 0.124 2_nqh: 0.1237 0.1538 0.008 0.967 8.7 118.3 21.0 258 0.127 2_sol: 0.1225 0.1492 0.008 0.967 8.7 118.3 23.4 430 n/a 2_weight: 0.1225 0.1492 0.008 0.967 8.7 118.3 23.4 430 n/a 2_xyzrec: 0.1226 0.1509 0.007 0.870 8.7 118.3 23.4 430 n/a 2_adp: 0.1201 0.1487 0.007 0.870 8.7 114.4 23.1 430 n/a 2_regHadp: 0.1201 0.1487 0.007 0.870 8.7 114.4 23.1 430 n/a 2_occ: 0.1203 0.1481 0.007 0.870 8.7 114.4 23.1 430 n/a 3_bss: 0.1200 0.1478 0.007 0.870 8.8 114.5 23.2 430 n/a 3_settarget: 0.1200 0.1478 0.007 0.870 8.8 114.5 23.2 430 n/a 3_updatecdl: 0.1200 0.1478 0.007 0.870 8.8 114.5 23.2 430 n/a 3_nqh: 0.1200 0.1478 0.007 0.870 8.8 114.5 23.2 430 n/a 3_sol: 0.1225 0.1493 0.007 0.870 8.8 114.5 22.1 457 n/a 3_weight: 0.1225 0.1493 0.007 0.870 8.8 114.5 22.1 457 n/a 3_xyzrec: 0.1230 0.1456 0.006 0.926 8.8 114.5 22.1 457 n/a 3_adp: 0.1216 0.1414 0.006 0.926 9.2 109.8 21.7 457 n/a 3_regHadp: 0.1217 0.1414 0.006 0.926 9.2 109.8 21.7 457 n/a 3_occ: 0.1210 0.1411 0.006 0.926 9.2 109.8 21.7 457 n/a 4_bss: 0.1193 0.1375 0.006 0.926 9.2 109.8 21.7 457 n/a 4_settarget: 0.1193 0.1375 0.006 0.926 9.2 109.8 21.7 457 n/a 4_updatecdl: 0.1193 0.1375 0.006 0.925 9.2 109.8 21.7 457 n/a 4_nqh: 0.1193 0.1375 0.006 0.925 9.2 109.8 21.7 457 n/a 4_sol: 0.1190 0.1359 0.006 0.925 9.2 109.8 21.3 432 n/a 4_weight: 0.1190 0.1359 0.006 0.925 9.2 109.8 21.3 432 n/a 4_xyzrec: 0.1198 0.1371 0.006 0.949 9.2 109.8 21.3 432 n/a 4_adp: 0.1182 0.1361 0.006 0.949 9.3 104.9 21.0 432 n/a 4_regHadp: 0.1182 0.1361 0.006 0.949 9.3 104.9 21.0 432 n/a 4_occ: 0.1178 0.1356 0.006 0.949 9.3 104.9 21.0 432 n/a 5_bss: 0.1177 0.1357 0.006 0.949 9.3 104.9 21.0 432 n/a 5_settarget: 0.1177 0.1357 0.006 0.949 9.3 104.9 21.0 432 n/a 5_updatecdl: 0.1177 0.1357 0.006 0.950 9.3 104.9 21.0 432 n/a 5_setrh: 0.1177 0.1357 0.006 0.950 9.3 104.9 21.0 432 n/a 5_nqh: 0.1177 0.1357 0.006 0.950 9.3 104.9 21.0 432 n/a 5_sol: 0.1166 0.1335 0.006 0.950 9.3 104.9 21.2 448 n/a 5_weight: 0.1166 0.1335 0.006 0.950 9.3 104.9 21.2 448 n/a 5_xyzrec: 0.1198 0.1370 0.007 1.065 9.3 104.9 21.2 448 n/a 5_adp: 0.1200 0.1369 0.007 1.065 9.3 104.2 21.1 448 n/a 5_regHadp: 0.1200 0.1369 0.007 1.065 9.3 104.2 21.1 448 n/a 5_occ: 0.1197 0.1367 0.007 1.065 9.3 104.2 21.1 448 n/a end: 0.1197 0.1369 0.007 1.065 9.2 104.2 21.1 448 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5638674_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5638674_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.0700 Refinement macro-cycles (run) : 3690.5200 Write final files (write_after_run_outputs) : 60.6700 Total : 3756.2600 Total CPU time: 63.23 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:14:11 PST -0800 (1735452851.50 s) Start R-work = 0.1629, R-free = 0.1770 Final R-work = 0.1197, R-free = 0.1369 =============================================================================== Job complete usr+sys time: 3888.85 seconds wall clock time: 69 minutes 19.47 seconds (4159.47 seconds total)