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_3495505.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3495505.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3495505.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 2.21, 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: 0.74 Conformation dependent library (CDL) restraints added in 261.2 milliseconds Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.93: 636 0.93 - 1.19: 1040 1.19 - 1.45: 691 1.45 - 1.71: 768 1.71 - 1.97: 18 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.461 1.271 0.191 9.20e-03 1.18e+04 4.29e+02 bond pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 1.330 1.574 -0.244 1.26e-02 6.30e+03 3.74e+02 bond pdb=" N BGLU A 64 " pdb=" CA BGLU A 64 " ideal model delta sigma weight residual 1.456 1.686 -0.230 1.22e-02 6.72e+03 3.55e+02 bond pdb=" C ILE A 117 " pdb=" O ILE A 117 " ideal model delta sigma weight residual 1.238 1.455 -0.217 1.17e-02 7.31e+03 3.46e+02 bond pdb=" C BGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 1.335 1.556 -0.221 1.26e-02 6.30e+03 3.08e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.07: 3311 5.07 - 10.15: 1882 10.15 - 15.22: 508 15.22 - 20.29: 73 20.29 - 25.36: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.27 141.39 -19.12 1.23e+00 6.61e-01 2.42e+02 angle pdb=" N ILE A 91 " pdb=" CA ILE A 91 " pdb=" C ILE A 91 " ideal model delta sigma weight residual 110.62 125.23 -14.61 1.02e+00 9.61e-01 2.05e+02 angle pdb=" N PRO A 43 " pdb=" CA PRO A 43 " pdb=" CB PRO A 43 " ideal model delta sigma weight residual 103.25 115.48 -12.23 8.80e-01 1.29e+00 1.93e+02 angle pdb=" C ILE A 21 " pdb=" N PRO A 22 " pdb=" CA PRO A 22 " ideal model delta sigma weight residual 119.19 104.58 14.61 1.06e+00 8.90e-01 1.90e+02 angle pdb=" O GLN A 95 " pdb=" C GLN A 95 " pdb=" N BGLU A 96 " ideal model delta sigma weight residual 122.27 105.71 16.56 1.23e+00 6.61e-01 1.81e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 944 17.07 - 34.14: 112 34.14 - 51.21: 37 51.21 - 68.28: 16 68.28 - 85.35: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 180.00 151.19 28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -156.69 -23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LEU A 172 " pdb=" C LEU A 172 " pdb=" N ASN A 173 " pdb=" CA ASN A 173 " ideal model delta harmonic sigma weight residual 180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.247: 116 0.247 - 0.494: 69 0.494 - 0.741: 43 0.741 - 0.988: 12 0.988 - 1.236: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 69 " pdb=" N VAL A 69 " pdb=" C VAL A 69 " pdb=" CB VAL A 69 " both_signs ideal model delta sigma weight residual False 2.44 3.68 -1.24 2.00e-01 2.50e+01 3.82e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.43 -1.16 2.00e-01 2.50e+01 3.36e+01 chirality pdb=" CA BGLU A 94 " pdb=" N BGLU A 94 " pdb=" C BGLU A 94 " pdb=" CB BGLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 3.54 -1.03 2.00e-01 2.50e+01 2.64e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.032 2.00e-02 2.50e+03 6.55e-02 1.29e+02 pdb=" CG TYR A 141 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.125 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.096 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.062 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.060 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 172 " -0.051 2.00e-02 2.50e+03 9.56e-02 9.14e+01 pdb=" C LEU A 172 " 0.165 2.00e-02 2.50e+03 pdb=" O LEU A 172 " -0.062 2.00e-02 2.50e+03 pdb=" N ASN A 173 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.067 2.00e-02 2.50e+03 5.22e-02 8.16e+01 pdb=" CG BTYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.076 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.040 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.050 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.002 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.079 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.077 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.042 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 1268 2.35 - 2.91: 8252 2.91 - 3.47: 10473 3.47 - 4.04: 15152 4.04 - 4.60: 21487 Nonbonded interactions: 56632 Sorted by model distance: nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.785 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.791 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.808 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.835 2.270 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.836 2.450 ... (remaining 56627 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_3495505_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= 0.2607 r_free= 0.1954 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794696 | | target function (ml) not normalized (work): 232814.910905 | | target function (ml) not normalized (free): 11852.326817 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3020 0.2200 6.9991 4.9684| | 2: 3.57 - 2.84 1.00 2876 122 0.2429 0.1766 4.3572 4.3533| | 3: 2.84 - 2.48 1.00 2833 165 0.2346 0.1643 4.1372 4.1688| | 4: 2.47 - 2.25 1.00 2825 136 0.2309 0.1444 3.8415 3.853| | 5: 2.25 - 2.09 1.00 2756 127 0.2486 0.1590 3.8093 3.8327| | 6: 2.09 - 1.97 1.00 2846 113 0.2550 0.1685 3.4774 3.5372| | 7: 1.97 - 1.87 1.00 2787 165 0.2589 0.1825 3.1464 3.2101| | 8: 1.87 - 1.79 1.00 2789 144 0.2502 0.1752 3.0746 3.0975| | 9: 1.79 - 1.72 1.00 2745 138 0.2387 0.1926 2.9097 2.9668| | 10: 1.72 - 1.66 1.00 2789 158 0.2415 0.1763 2.8208 2.857| | 11: 1.66 - 1.61 1.00 2740 147 0.2506 0.1869 2.7681 2.7695| | 12: 1.61 - 1.56 1.00 2787 146 0.2495 0.2161 2.614 2.706| | 13: 1.56 - 1.52 1.00 2745 130 0.2574 0.2017 2.5759 2.6583| | 14: 1.52 - 1.48 1.00 2803 134 0.2626 0.1987 2.5215 2.5117| | 15: 1.48 - 1.45 1.00 2738 128 0.2589 0.1963 2.4385 2.4334| | 16: 1.45 - 1.42 1.00 2756 161 0.2661 0.2118 2.3771 2.3786| | 17: 1.42 - 1.39 1.00 2785 139 0.2680 0.2065 2.3329 2.3852| | 18: 1.39 - 1.36 1.00 2741 179 0.2668 0.2401 2.2775 2.4032| | 19: 1.36 - 1.34 1.00 2807 134 0.2639 0.2372 2.2462 2.3548| | 20: 1.34 - 1.32 1.00 2696 147 0.2686 0.1990 2.1814 2.1427| | 21: 1.32 - 1.30 1.00 2785 112 0.2707 0.2247 2.1722 2.212| | 22: 1.29 - 1.27 1.00 2704 152 0.2801 0.2421 2.1492 2.2188| | 23: 1.27 - 1.26 1.00 2802 156 0.2777 0.2548 2.1012 2.19| | 24: 1.26 - 1.24 1.00 2744 132 0.2775 0.2291 2.0752 2.1007| | 25: 1.24 - 1.22 1.00 2734 148 0.2879 0.2618 2.0563 2.0802| | 26: 1.22 - 1.21 1.00 2727 135 0.2843 0.2553 2.0159 2.1759| | 27: 1.21 - 1.19 1.00 2814 148 0.3002 0.2588 2.0246 1.9784| | 28: 1.19 - 1.18 1.00 2671 147 0.3025 0.2904 1.9951 2.0199| | 29: 1.18 - 1.16 1.00 2800 134 0.3003 0.2732 1.9683 2.0713| | 30: 1.16 - 1.15 1.00 2740 148 0.3014 0.3055 1.9236 1.9798| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.11 0.76 0.23 1534.22| | 2: 3.57 - 2.84 2876 122 0.80 26.46 1.27 0.23 1534.22| | 3: 2.84 - 2.48 2833 165 0.73 32.45 1.24 0.24 1271.60| | 4: 2.47 - 2.25 2825 136 0.81 25.88 1.26 0.25 590.07| | 5: 2.25 - 2.09 2756 127 0.77 29.83 1.28 0.25 590.07| | 6: 2.09 - 1.97 2846 113 0.83 23.02 1.29 0.25 321.81| | 7: 1.97 - 1.87 2787 165 0.90 16.90 1.29 0.26 93.02| | 8: 1.87 - 1.79 2789 144 0.85 21.45 1.25 0.26 93.02| | 9: 1.79 - 1.72 2745 138 0.88 18.53 1.22 0.25 56.16| | 10: 1.72 - 1.66 2789 158 0.87 20.25 1.22 0.25 48.78| | 11: 1.66 - 1.61 2740 147 0.86 21.35 1.23 0.25 47.09| | 12: 1.61 - 1.56 2787 146 0.88 18.49 1.23 0.25 29.97| | 13: 1.56 - 1.52 2745 130 0.86 20.67 1.25 0.25 29.97| | 14: 1.52 - 1.48 2803 134 0.86 21.00 1.25 0.25 26.67| | 15: 1.48 - 1.45 2738 128 0.87 20.01 1.22 0.25 20.63| | 16: 1.45 - 1.42 2756 161 0.86 21.65 1.24 0.25 20.63| | 17: 1.42 - 1.39 2785 139 0.87 20.77 1.23 0.25 17.56| | 18: 1.39 - 1.36 2741 179 0.86 21.36 1.23 0.25 15.78| | 19: 1.36 - 1.34 2807 134 0.86 21.99 1.22 0.25 15.78| | 20: 1.34 - 1.32 2696 147 0.87 20.95 1.21 0.25 13.05| | 21: 1.32 - 1.30 2785 112 0.86 21.63 1.20 0.25 12.86| | 22: 1.29 - 1.27 2704 152 0.85 22.52 1.21 0.24 12.60| | 23: 1.27 - 1.26 2802 156 0.85 22.43 1.22 0.24 11.28| | 24: 1.26 - 1.24 2744 132 0.85 22.91 1.20 0.24 11.28| | 25: 1.24 - 1.22 2734 148 0.84 24.24 1.21 0.24 10.88| | 26: 1.22 - 1.21 2727 135 0.83 24.55 1.21 0.23 10.45| | 27: 1.21 - 1.19 2814 148 0.82 25.50 1.20 0.23 10.45| | 28: 1.19 - 1.18 2671 147 0.81 26.68 1.18 0.23 10.07| | 29: 1.18 - 1.16 2800 134 0.81 27.26 1.18 0.22 9.93| | 30: 1.16 - 1.15 2740 148 0.79 28.67 1.16 0.22 9.93| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.93 max = 1534.22 mean = 222.09| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 22.95| |phase err.(test): min = 0.00 max = 89.87 mean = 22.92| |-----------------------------------------------------------------------------| ----------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 0.278 1557 Z= 5.407 Angle : 5.466 19.351 2118 Z= 3.832 Chirality : 0.408 1.236 243 Planarity : 0.032 0.129 284 Dihedral : 13.528 85.348 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 33.51 % 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: -2.76 (0.48), residues: 224 helix: -2.98 (0.36), residues: 109 sheet: -0.21 (0.80), residues: 28 loop : -0.43 (0.61), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.077 0.022 ARG A 156 TYR 0.131 0.041 TYR A 141 PHE 0.124 0.029 PHE A 119 HIS 0.086 0.034 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= 0.2607 r_free= 0.1954 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794696 | | target function (ml) not normalized (work): 232814.910905 | | target function (ml) not normalized (free): 11852.326817 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2608 0.1954 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2608 0.1954 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1984 0.1954 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.2001 0.2006 0.1964 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1645 0.1639 0.1770 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1639 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 0.3833 386.386 354.302 0.669 1.003 0.397 11.894-9.307 99.02 97 4 0.1798 613.756 594.557 0.928 1.004 0.380 9.237-7.194 100.00 213 7 0.2135 501.977 490.021 0.956 1.004 0.362 7.162-5.571 100.00 427 22 0.2213 376.706 364.462 0.930 1.004 0.295 5.546-4.326 100.00 867 58 0.1275 517.124 512.006 0.968 1.004 0.250 4.315-3.360 100.00 1859 96 0.1146 491.788 488.188 1.005 1.003 0.179 3.356-2.611 100.00 3867 181 0.1424 323.080 319.749 0.998 1.003 0.057 2.608-2.026 99.99 8198 413 0.1338 214.172 212.067 1.009 1.001 0.000 2.025-1.573 100.00 17313 902 0.1671 104.591 103.821 1.010 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2073 46.380 45.049 1.005 0.995 0.000 1.221-1.150 99.97 13689 708 0.2590 29.222 26.993 0.979 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0408 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1639 r_free=0.1770 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1640 r_free=0.1772 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.089285 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2005.166880 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1211 0.1462 0.0251 0.007 0.9 1.0 0.5 0.0 0 12.045 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.62 2.51 3.013 19.036 2005.167 0.017 12.42 15.43 3.01 3.113 19.469 2005.167 0.016 Individual atomic B min max mean iso aniso Overall: 8.43 118.53 20.88 2.86 0 1785 Protein: 8.43 118.53 17.78 2.86 0 1519 Water: 10.88 114.71 38.92 N/A 0 258 Other: 22.79 35.61 28.56 N/A 0 8 Chain A: 8.43 118.53 20.88 N/A 0 1785 Histogram: Values Number of atoms 8.43 - 19.44 1207 19.44 - 30.45 232 30.45 - 41.46 167 41.46 - 52.47 98 52.47 - 63.48 52 63.48 - 74.49 18 74.49 - 85.50 4 85.50 - 96.51 4 96.51 - 107.52 0 107.52 - 118.53 3 =========================== Idealize ADP of riding H ========================== r_work=0.1242 r_free=0.1543 r_work=0.1247 r_free=0.1548 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1247 r_free = 0.1548 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1247 r_free = 0.1553 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1247 r_free= 0.1553 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015453 | | target function (ls_wunit_k1) not normalized (work): 1287.149514 | | target function (ls_wunit_k1) not normalized (free): 114.763873 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1262 0.1247 0.1553 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1696 0.1694 0.1772 n_refl.: 87593 remove outliers: r(all,work,free)=0.1696 0.1694 0.1772 n_refl.: 87593 overall B=0.16 to atoms: r(all,work,free)=0.1721 0.1720 0.1789 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1261 0.1246 0.1547 n_refl.: 87593 remove outliers: r(all,work,free)=0.1260 0.1245 0.1547 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3511 301.865 276.532 0.624 1.002 0.370 11.894-9.307 99.02 97 4 0.1649 480.376 469.120 0.907 1.003 0.363 9.237-7.194 100.00 213 7 0.1813 392.889 388.101 0.950 1.003 0.340 7.162-5.571 100.00 427 22 0.1744 294.841 289.385 0.920 1.003 0.253 5.546-4.326 100.00 867 58 0.0925 404.744 402.078 0.952 1.003 0.220 4.315-3.360 100.00 1859 96 0.0782 384.915 384.026 0.995 1.002 0.189 3.356-2.611 100.00 3867 181 0.1018 252.869 252.261 0.999 1.002 0.119 2.608-2.026 99.99 8198 413 0.0971 167.629 167.090 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1210 81.861 82.061 1.016 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1659 36.301 35.762 1.004 0.999 0.000 1.221-1.150 99.97 13689 708 0.2366 22.872 21.381 0.968 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=0.0605 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1245 r_free=0.1547 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1247 r_free=0.1549 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1247 r_free=0.1549 | n_water=258 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1256 r_free=0.1548 | n_water=252 | time (s): 27.990 (total time: 30.350) Filter (q & B) r_work=0.1259 r_free=0.1547 | n_water=249 | time (s): 3.680 (total time: 34.030) Compute maps r_work=0.1259 r_free=0.1547 | n_water=249 | time (s): 1.870 (total time: 35.900) Filter (map) r_work=0.1272 r_free=0.1556 | n_water=236 | time (s): 3.870 (total time: 39.770) Find peaks r_work=0.1272 r_free=0.1556 | n_water=236 | time (s): 0.740 (total time: 40.510) Add new water r_work=0.1429 r_free=0.1718 | n_water=455 | time (s): 3.710 (total time: 44.220) Refine new water occ: r_work=0.1342 r_free=0.1585 adp: r_work=0.1259 r_free=0.1541 occ: r_work=0.1273 r_free=0.1523 adp: r_work=0.1238 r_free=0.1515 occ: r_work=0.1241 r_free=0.1496 adp: r_work=0.1230 r_free=0.1500 ADP+occupancy (water only), MIN, final r_work=0.1230 r_free=0.1500 r_work=0.1230 r_free=0.1500 | n_water=455 | time (s): 78.930 (total time: 123.150) Filter (q & B) r_work=0.1237 r_free=0.1504 | n_water=434 | time (s): 4.040 (total time: 127.190) Filter (dist only) r_work=0.1237 r_free=0.1503 | n_water=433 | time (s): 45.140 (total time: 172.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.077434 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1374.504184 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1519 0.0290 0.007 0.9 1.9 0.5 0.0 0 12.539 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 15.19 2.90 3.768 23.080 1374.504 0.015 12.03 14.88 2.85 4.106 22.925 1374.504 0.015 Individual atomic B min max mean iso aniso Overall: 8.89 114.45 23.13 2.56 197 1763 Protein: 8.89 114.45 17.64 2.56 0 1519 Water: 11.07 72.80 42.28 N/A 197 236 Other: 24.65 35.98 29.51 N/A 0 8 Chain A: 8.89 114.45 20.32 N/A 0 1763 Chain S: 16.55 71.28 48.34 N/A 197 0 Histogram: Values Number of atoms 8.89 - 19.45 1214 19.45 - 30.01 247 30.01 - 40.56 196 40.56 - 51.12 135 51.12 - 61.67 105 61.67 - 72.23 52 72.23 - 82.79 5 82.79 - 93.34 3 93.34 - 103.90 1 103.90 - 114.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1489 r_work=0.1204 r_free=0.1488 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1488 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1476 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1203 r_free= 0.1476 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013924 | | target function (ls_wunit_k1) not normalized (work): 1159.808306 | | target function (ls_wunit_k1) not normalized (free): 103.290710 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1203 0.1476 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1561 0.1554 0.1706 n_refl.: 87591 remove outliers: r(all,work,free)=0.1561 0.1554 0.1706 n_refl.: 87591 overall B=0.04 to atoms: r(all,work,free)=0.1567 0.1560 0.1710 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1199 0.1470 n_refl.: 87591 remove outliers: r(all,work,free)=0.1212 0.1199 0.1470 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 0.3449 298.426 278.781 0.622 0.947 0.350 11.894-9.307 99.02 97 4 0.1639 480.376 477.548 0.961 0.948 0.330 9.237-7.194 100.00 213 7 0.1644 392.889 395.077 1.035 0.948 0.280 7.162-5.571 100.00 427 22 0.1541 294.841 289.747 0.989 0.948 0.219 5.546-4.326 100.00 867 58 0.0830 404.744 402.056 1.012 0.949 0.206 4.315-3.360 100.00 1859 96 0.0713 384.915 383.726 1.059 0.949 0.203 3.356-2.611 100.00 3867 181 0.0956 252.869 251.982 1.065 0.949 0.072 2.608-2.026 99.99 8198 413 0.0957 167.629 167.137 1.073 0.949 0.000 2.025-1.573 100.00 17313 902 0.1183 81.861 82.036 1.080 0.950 0.000 1.573-1.221 100.00 36679 1900 0.1614 36.301 35.799 1.066 0.951 0.000 1.221-1.150 99.97 13689 708 0.2343 22.872 21.411 1.024 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0636 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1470 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1470 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1470 | n_water=433 | time (s): 1.590 (total time: 1.590) Filter (dist) r_work=0.1198 r_free=0.1470 | n_water=431 | time (s): 39.260 (total time: 40.850) Filter (q & B) r_work=0.1198 r_free=0.1470 | n_water=431 | time (s): 1.130 (total time: 41.980) Compute maps r_work=0.1198 r_free=0.1470 | n_water=431 | time (s): 1.530 (total time: 43.510) Filter (map) r_work=0.1249 r_free=0.1485 | n_water=295 | time (s): 3.340 (total time: 46.850) Find peaks r_work=0.1249 r_free=0.1485 | n_water=295 | time (s): 0.570 (total time: 47.420) Add new water r_work=0.1368 r_free=0.1583 | n_water=482 | time (s): 2.620 (total time: 50.040) Refine new water occ: r_work=0.1263 r_free=0.1506 adp: r_work=0.1264 r_free=0.1505 occ: r_work=0.1241 r_free=0.1493 adp: r_work=0.1238 r_free=0.1489 occ: r_work=0.1227 r_free=0.1488 adp: r_work=0.1219 r_free=0.1481 ADP+occupancy (water only), MIN, final r_work=0.1219 r_free=0.1481 r_work=0.1219 r_free=0.1481 | n_water=482 | time (s): 191.810 (total time: 241.850) Filter (q & B) r_work=0.1224 r_free=0.1483 | n_water=445 | time (s): 2.940 (total time: 244.790) Filter (dist only) r_work=0.1224 r_free=0.1483 | n_water=445 | time (s): 36.250 (total time: 281.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.096283 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.807870 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 0.1444 0.0219 0.006 0.9 1.6 0.5 0.0 0 1.048 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.44 2.19 3.600 22.131 47.808 3.725 12.02 13.92 1.91 4.131 21.923 47.808 3.651 Individual atomic B min max mean iso aniso Overall: 9.22 109.85 21.69 2.32 213 1759 Protein: 9.22 109.85 17.19 2.32 0 1519 Water: 11.54 71.80 36.96 N/A 213 232 Other: 19.69 31.36 25.70 N/A 0 8 Chain A: 9.22 109.85 19.83 N/A 0 1759 Chain S: 15.10 64.20 37.03 N/A 213 0 Histogram: Values Number of atoms 9.22 - 19.28 1237 19.28 - 29.34 272 29.34 - 39.41 217 39.41 - 49.47 130 49.47 - 59.53 81 59.53 - 69.60 23 69.60 - 79.66 6 79.66 - 89.72 3 89.72 - 99.79 1 99.79 - 109.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1392 r_work=0.1203 r_free=0.1393 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1393 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1390 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.21 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= 0.1198 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.648888 | | target function (ml) not normalized (work): 303930.450429 | | target function (ml) not normalized (free): 16042.678812 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1198 0.1390 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1524 0.1523 0.1582 n_refl.: 87590 remove outliers: r(all,work,free)=0.1524 0.1523 0.1582 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1523 0.1521 0.1581 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1192 0.1371 n_refl.: 87590 remove outliers: r(all,work,free)=0.1197 0.1188 0.1371 n_refl.: 87581 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3797 295.160 261.853 0.481 0.999 0.324 11.894-9.307 98.04 96 4 0.2418 480.501 466.449 0.853 1.001 0.320 9.237-7.194 98.18 209 7 0.2194 384.406 389.549 0.954 1.001 0.183 7.162-5.571 100.00 427 22 0.1988 294.841 284.986 0.908 1.002 0.175 5.546-4.326 100.00 867 58 0.1110 404.744 399.900 0.952 1.002 0.166 4.315-3.360 100.00 1859 96 0.0917 384.915 382.414 0.994 1.002 0.159 3.356-2.611 100.00 3867 181 0.1139 252.869 251.058 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1038 167.629 166.679 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1010 81.861 82.026 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1289 36.301 35.883 1.019 0.999 0.000 1.221-1.150 99.97 13689 708 0.2130 22.872 21.479 0.976 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0234 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1371 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=0.1188 r_free=0.1371 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1371 | n_water=445 | time (s): 1.830 (total time: 1.830) Filter (dist) r_work=0.1188 r_free=0.1371 | n_water=443 | time (s): 38.520 (total time: 40.350) Filter (q & B) r_work=0.1188 r_free=0.1371 | n_water=443 | time (s): 0.760 (total time: 41.110) Compute maps r_work=0.1188 r_free=0.1371 | n_water=443 | time (s): 1.480 (total time: 42.590) Filter (map) r_work=0.1215 r_free=0.1379 | n_water=314 | time (s): 3.350 (total time: 45.940) Find peaks r_work=0.1215 r_free=0.1379 | n_water=314 | time (s): 0.670 (total time: 46.610) Add new water r_work=0.1286 r_free=0.1461 | n_water=479 | time (s): 2.410 (total time: 49.020) Refine new water occ: r_work=0.1209 r_free=0.1384 adp: r_work=0.1209 r_free=0.1386 occ: r_work=0.1194 r_free=0.1370 adp: r_work=0.1192 r_free=0.1371 occ: r_work=0.1183 r_free=0.1361 adp: r_work=0.1179 r_free=0.1360 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1360 r_work=0.1179 r_free=0.1360 | n_water=479 | time (s): 215.980 (total time: 265.000) Filter (q & B) r_work=0.1186 r_free=0.1364 | n_water=445 | time (s): 3.100 (total time: 268.100) Filter (dist only) r_work=0.1186 r_free=0.1363 | n_water=444 | time (s): 37.530 (total time: 305.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.989098 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.340060 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 0.1191 0.1371 0.0181 0.006 1.0 1.6 0.5 0.0 0 0.995 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.71 1.81 3.415 21.461 47.340 3.639 11.83 13.69 1.86 3.766 21.347 47.340 3.626 Individual atomic B min max mean iso aniso Overall: 9.30 105.30 21.22 2.16 214 1757 Protein: 9.30 105.30 16.94 2.17 0 1519 Water: 11.44 70.61 35.80 N/A 214 230 Other: 18.95 28.46 23.75 N/A 0 8 Chain A: 9.30 105.30 19.51 N/A 0 1757 Chain S: 13.29 64.46 35.26 N/A 214 0 Histogram: Values Number of atoms 9.30 - 18.90 1236 18.90 - 28.50 276 28.50 - 38.10 211 38.10 - 47.70 140 47.70 - 57.30 67 57.30 - 66.90 28 66.90 - 76.50 8 76.50 - 86.10 2 86.10 - 95.70 1 95.70 - 105.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.1183 r_free=0.1369 r_work=0.1184 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1184 r_free = 0.1370 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1180 r_free = 0.1368 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1180 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.624551 | | target function (ml) not normalized (work): 301870.711332 | | target function (ml) not normalized (free): 15954.315799 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1189 0.1180 0.1368 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1505 0.1504 0.1552 n_refl.: 87581 remove outliers: r(all,work,free)=0.1505 0.1504 0.1552 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1502 0.1501 0.1550 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1188 0.1179 0.1366 n_refl.: 87581 remove outliers: r(all,work,free)=0.1186 0.1177 0.1366 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4095 295.160 255.735 0.456 0.999 0.330 11.894-9.307 95.10 93 4 0.2256 489.049 462.207 0.843 1.000 0.330 9.237-7.194 97.73 208 7 0.2403 385.485 379.329 0.921 1.001 0.150 7.162-5.571 100.00 427 22 0.2184 294.841 283.769 0.901 1.001 0.139 5.546-4.326 100.00 867 58 0.1146 404.744 399.953 0.953 1.001 0.139 4.315-3.360 100.00 1859 96 0.0934 384.915 382.423 0.994 1.001 0.129 3.356-2.611 100.00 3867 181 0.1149 252.869 251.216 1.002 1.001 0.110 2.608-2.026 99.99 8198 413 0.1021 167.629 166.852 1.011 1.002 0.000 2.025-1.573 100.00 17313 902 0.0970 81.861 82.193 1.026 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1238 36.301 35.937 1.018 1.002 0.000 1.221-1.150 99.97 13689 708 0.2120 22.872 21.444 0.973 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0370 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1177 r_free=0.1366 After: r_work=0.1178 r_free=0.1366 ================================== NQH flips ================================== r_work=0.1178 r_free=0.1366 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=0.1178 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1366 | n_water=444 | time (s): 1.610 (total time: 1.610) Filter (dist) r_work=0.1178 r_free=0.1366 | n_water=444 | time (s): 37.080 (total time: 38.690) Filter (q & B) r_work=0.1178 r_free=0.1365 | n_water=443 | time (s): 2.890 (total time: 41.580) Compute maps r_work=0.1178 r_free=0.1365 | n_water=443 | time (s): 1.190 (total time: 42.770) Filter (map) r_work=0.1204 r_free=0.1373 | n_water=331 | time (s): 3.180 (total time: 45.950) Find peaks r_work=0.1204 r_free=0.1373 | n_water=331 | time (s): 0.470 (total time: 46.420) Add new water r_work=0.1256 r_free=0.1420 | n_water=484 | time (s): 2.480 (total time: 48.900) Refine new water occ: r_work=0.1190 r_free=0.1356 adp: r_work=0.1190 r_free=0.1358 occ: r_work=0.1177 r_free=0.1344 adp: r_work=0.1176 r_free=0.1346 occ: r_work=0.1167 r_free=0.1337 adp: r_work=0.1164 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1164 r_free=0.1338 r_work=0.1164 r_free=0.1338 | n_water=484 | time (s): 246.680 (total time: 295.580) Filter (q & B) r_work=0.1173 r_free=0.1351 | n_water=446 | time (s): 3.470 (total time: 299.050) Filter (dist only) r_work=0.1173 r_free=0.1351 | n_water=445 | time (s): 39.470 (total time: 338.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.933030 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 52.888140 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 0.1202 0.1378 0.0176 0.007 1.1 2.2 0.5 0.0 0 0.967 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.78 1.76 3.293 21.128 52.888 3.634 12.03 13.77 1.74 3.633 21.034 52.888 3.625 Individual atomic B min max mean iso aniso Overall: 9.26 100.76 20.96 2.04 215 1757 Protein: 9.26 100.76 16.67 2.04 0 1519 Water: 11.52 69.15 35.56 N/A 215 230 Other: 18.69 25.76 22.66 N/A 0 8 Chain A: 9.26 100.76 19.23 N/A 0 1757 Chain S: 14.13 64.89 35.06 N/A 215 0 Histogram: Values Number of atoms 9.26 - 18.41 1216 18.41 - 27.56 275 27.56 - 36.71 225 36.71 - 45.86 143 45.86 - 55.01 66 55.01 - 64.16 30 64.16 - 73.31 12 73.31 - 82.46 2 82.46 - 91.61 1 91.61 - 100.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1377 r_work=0.1203 r_free=0.1377 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1377 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1374 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1201 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.624464 | | target function (ml) not normalized (work): 301848.963919 | | target function (ml) not normalized (free): 15951.352698 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1429 0.1434 5.6915 5.6675| | 2: 3.57 - 2.84 1.00 2888 124 0.1137 0.1500 5.2249 5.2913| | 3: 2.83 - 2.48 1.00 2820 163 0.1230 0.1266 5.0278 5.0461| | 4: 2.47 - 2.25 1.00 2825 136 0.1054 0.1210 4.7331 4.7931| | 5: 2.25 - 2.09 1.00 2756 127 0.0995 0.1142 4.6694 4.7376| | 6: 2.09 - 1.97 1.00 2846 113 0.0968 0.1140 4.3651 4.4816| | 7: 1.97 - 1.87 1.00 2787 165 0.0994 0.1222 4.0889 4.1853| | 8: 1.87 - 1.79 1.00 2789 144 0.1031 0.1201 4.0024 4.0821| | 9: 1.79 - 1.72 1.00 2745 138 0.0961 0.1293 3.7224 3.8962| | 10: 1.72 - 1.66 1.00 2831 160 0.1002 0.1273 3.6355 3.7772| | 11: 1.66 - 1.61 1.00 2712 147 0.0958 0.1081 3.5665 3.6011| | 12: 1.61 - 1.56 1.00 2773 144 0.0916 0.1174 3.3417 3.4949| | 13: 1.56 - 1.52 1.00 2745 130 0.0965 0.1036 3.3348 3.4204| | 14: 1.52 - 1.48 1.00 2803 134 0.0975 0.1098 3.2553 3.3426| | 15: 1.48 - 1.45 1.00 2738 128 0.0995 0.1288 3.1566 3.3128| | 16: 1.45 - 1.42 1.00 2756 161 0.1053 0.1249 3.14 3.2394| | 17: 1.42 - 1.39 1.00 2785 139 0.1112 0.1259 3.1096 3.2142| | 18: 1.39 - 1.36 1.00 2741 179 0.1140 0.1355 3.0786 3.2462| | 19: 1.36 - 1.34 1.00 2807 134 0.1213 0.1577 3.0875 3.2515| | 20: 1.34 - 1.32 1.00 2696 147 0.1318 0.1491 3.0854 3.1326| | 21: 1.32 - 1.30 1.00 2785 112 0.1412 0.1592 3.0853 3.156| | 22: 1.29 - 1.27 1.00 2704 152 0.1466 0.1883 3.0814 3.2836| | 23: 1.27 - 1.26 1.00 2802 156 0.1569 0.1876 3.1015 3.2221| | 24: 1.26 - 1.24 1.00 2744 132 0.1618 0.1751 3.0936 3.1896| | 25: 1.24 - 1.22 1.00 2733 148 0.1781 0.2300 3.1062 3.2907| | 26: 1.22 - 1.21 1.00 2727 135 0.1859 0.1800 3.1235 3.2054| | 27: 1.21 - 1.19 1.00 2814 148 0.1998 0.2085 3.141 3.1513| | 28: 1.19 - 1.18 1.00 2671 147 0.2147 0.2324 3.1441 3.1721| | 29: 1.18 - 1.16 1.00 2800 134 0.2208 0.2357 3.1274 3.2187| | 30: 1.16 - 1.15 1.00 2739 148 0.2372 0.2457 3.1159 3.1647| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.94 9.44 1.00 0.97 6628.19| | 2: 3.57 - 2.84 2888 124 0.92 13.66 1.01 0.97 6628.19| | 3: 2.83 - 2.48 2820 163 0.88 17.91 0.99 0.98 5553.58| | 4: 2.47 - 2.25 2825 136 0.91 14.98 1.00 0.98 2782.50| | 5: 2.25 - 2.09 2756 127 0.89 17.26 1.01 0.98 2782.50| | 6: 2.09 - 1.97 2846 113 0.91 13.93 1.02 0.98 1629.28| | 7: 1.97 - 1.87 2787 165 0.94 10.91 1.02 0.97 645.73| | 8: 1.87 - 1.79 2789 144 0.91 14.63 1.00 0.97 645.73| | 9: 1.79 - 1.72 2745 138 0.93 11.50 0.98 0.97 344.97| | 10: 1.72 - 1.66 2831 160 0.93 12.30 0.98 0.97 284.74| | 11: 1.66 - 1.61 2712 147 0.93 12.95 0.98 0.97 271.49| | 12: 1.61 - 1.56 2773 144 0.95 9.47 0.99 0.97 146.57| | 13: 1.56 - 1.52 2745 130 0.94 10.97 1.02 0.97 146.57| | 14: 1.52 - 1.48 2803 134 0.94 11.15 1.02 0.98 130.54| | 15: 1.48 - 1.45 2738 128 0.95 10.17 1.01 0.98 101.19| | 16: 1.45 - 1.42 2756 161 0.94 11.40 1.01 0.98 101.19| | 17: 1.42 - 1.39 2785 139 0.95 11.19 1.01 0.99 91.20| | 18: 1.39 - 1.36 2741 179 0.95 11.49 1.01 0.99 85.41| | 19: 1.36 - 1.34 2807 134 0.94 12.04 1.00 0.99 85.41| | 20: 1.34 - 1.32 2696 147 0.94 12.24 0.99 0.97 81.02| | 21: 1.32 - 1.30 2785 112 0.94 13.14 0.98 0.97 80.72| | 22: 1.29 - 1.27 2704 152 0.93 13.75 0.98 0.96 80.98| | 23: 1.27 - 1.26 2802 156 0.93 14.71 0.97 0.95 82.33| | 24: 1.26 - 1.24 2744 132 0.93 14.82 0.97 0.95 82.33| | 25: 1.24 - 1.22 2733 148 0.92 16.20 0.96 0.94 84.08| | 26: 1.22 - 1.21 2727 135 0.90 18.02 1.02 0.94 86.02| | 27: 1.21 - 1.19 2814 148 0.89 18.58 1.02 0.94 86.02| | 28: 1.19 - 1.18 2671 147 0.88 20.13 1.01 0.93 89.32| | 29: 1.18 - 1.16 2800 134 0.88 20.41 0.99 0.93 90.56| | 30: 1.16 - 1.15 2739 148 0.86 21.83 0.98 0.93 90.56| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 80.72 max = 6628.19 mean = 1025.81| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 14.03| |phase err.(test): min = 0.00 max = 88.98 mean = 14.12| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1201 0.1374 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1517 0.1517 0.1557 n_refl.: 87577 remove outliers: r(all,work,free)=0.1517 0.1517 0.1557 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1515 0.1514 0.1555 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1202 0.1376 n_refl.: 87577 remove outliers: r(all,work,free)=0.1209 0.1201 0.1376 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4032 290.508 258.319 0.436 1.001 0.283 11.894-9.307 93.14 91 4 0.2313 482.291 465.766 0.861 1.002 0.257 9.237-7.194 97.73 208 7 0.2521 385.485 378.010 0.911 1.002 0.120 7.162-5.571 100.00 427 22 0.2294 294.841 283.068 0.893 1.002 0.107 5.546-4.326 100.00 867 58 0.1202 404.744 399.668 0.952 1.002 0.107 4.315-3.360 100.00 1859 96 0.1000 384.915 381.916 0.994 1.002 0.104 3.356-2.611 100.00 3867 181 0.1199 252.869 251.006 1.001 1.002 0.100 2.608-2.026 99.99 8198 413 0.1053 167.629 166.659 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0977 81.861 82.125 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1218 36.301 35.931 1.022 0.997 0.000 1.221-1.150 99.97 13689 708 0.2112 22.872 21.500 0.980 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0348 ================= 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 : 0.2607 0.1954 0.083 5.466 8.8 119.3 19.9 258 0.000 1_bss: 0.1639 0.1770 0.083 5.466 9.0 119.5 20.1 258 0.000 1_settarget: 0.1639 0.1770 0.083 5.466 9.0 119.5 20.1 258 0.000 1_nqh: 0.1640 0.1772 0.083 5.466 9.0 119.5 20.1 258 0.003 1_weight: 0.1640 0.1772 0.083 5.466 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1211 0.1462 0.007 0.940 9.0 119.5 20.1 258 0.127 1_adp: 0.1242 0.1543 0.007 0.940 8.4 118.5 20.9 258 0.127 1_regHadp: 0.1247 0.1548 0.007 0.940 8.4 118.5 20.9 258 0.127 1_occ: 0.1247 0.1553 0.007 0.940 8.4 118.5 20.9 258 0.127 2_bss: 0.1245 0.1547 0.007 0.940 8.6 118.7 21.0 258 0.127 2_settarget: 0.1245 0.1547 0.007 0.940 8.6 118.7 21.0 258 0.127 2_updatecdl: 0.1245 0.1547 0.007 0.946 8.6 118.7 21.0 258 0.127 2_nqh: 0.1247 0.1549 0.007 0.946 8.6 118.7 21.0 258 0.127 2_sol: 0.1237 0.1503 0.007 0.946 8.6 118.7 23.4 433 n/a 2_weight: 0.1237 0.1503 0.007 0.946 8.6 118.7 23.4 433 n/a 2_xyzrec: 0.1229 0.1519 0.007 0.875 8.6 118.7 23.4 433 n/a 2_adp: 0.1204 0.1489 0.007 0.875 8.9 114.5 23.1 433 n/a 2_regHadp: 0.1204 0.1488 0.007 0.875 8.9 114.5 23.1 433 n/a 2_occ: 0.1203 0.1476 0.007 0.875 8.9 114.5 23.1 433 n/a 3_bss: 0.1199 0.1470 0.007 0.875 8.9 114.5 23.2 433 n/a 3_settarget: 0.1199 0.1470 0.007 0.875 8.9 114.5 23.2 433 n/a 3_updatecdl: 0.1199 0.1470 0.007 0.878 8.9 114.5 23.2 433 n/a 3_nqh: 0.1199 0.1470 0.007 0.878 8.9 114.5 23.2 433 n/a 3_sol: 0.1224 0.1483 0.007 0.878 8.9 114.5 22.1 445 n/a 3_weight: 0.1224 0.1483 0.007 0.878 8.9 114.5 22.1 445 n/a 3_xyzrec: 0.1226 0.1444 0.006 0.926 8.9 114.5 22.1 445 n/a 3_adp: 0.1202 0.1392 0.006 0.926 9.2 109.8 21.7 445 n/a 3_regHadp: 0.1203 0.1393 0.006 0.926 9.2 109.8 21.7 445 n/a 3_occ: 0.1198 0.1390 0.006 0.926 9.2 109.8 21.7 445 n/a 4_bss: 0.1188 0.1371 0.006 0.926 9.2 109.8 21.7 445 n/a 4_settarget: 0.1188 0.1371 0.006 0.926 9.2 109.8 21.7 445 n/a 4_updatecdl: 0.1188 0.1371 0.006 0.923 9.2 109.8 21.7 445 n/a 4_nqh: 0.1188 0.1371 0.006 0.923 9.2 109.8 21.7 445 n/a 4_sol: 0.1186 0.1363 0.006 0.923 9.2 109.8 21.4 444 n/a 4_weight: 0.1186 0.1363 0.006 0.923 9.2 109.8 21.4 444 n/a 4_xyzrec: 0.1191 0.1371 0.006 0.958 9.2 109.8 21.4 444 n/a 4_adp: 0.1183 0.1369 0.006 0.958 9.3 105.3 21.2 444 n/a 4_regHadp: 0.1184 0.1370 0.006 0.958 9.3 105.3 21.2 444 n/a 4_occ: 0.1180 0.1368 0.006 0.958 9.3 105.3 21.2 444 n/a 5_bss: 0.1177 0.1366 0.006 0.958 9.3 105.3 21.2 444 n/a 5_settarget: 0.1177 0.1366 0.006 0.958 9.3 105.3 21.2 444 n/a 5_updatecdl: 0.1177 0.1366 0.006 0.958 9.3 105.3 21.2 444 n/a 5_setrh: 0.1178 0.1366 0.006 0.958 9.3 105.3 21.2 444 n/a 5_nqh: 0.1178 0.1366 0.006 0.958 9.3 105.3 21.2 444 n/a 5_sol: 0.1173 0.1351 0.006 0.958 9.3 105.3 21.1 445 n/a 5_weight: 0.1173 0.1351 0.006 0.958 9.3 105.3 21.1 445 n/a 5_xyzrec: 0.1202 0.1378 0.007 1.076 9.3 105.3 21.1 445 n/a 5_adp: 0.1203 0.1377 0.007 1.076 9.3 100.8 21.0 445 n/a 5_regHadp: 0.1203 0.1377 0.007 1.076 9.3 100.8 21.0 445 n/a 5_occ: 0.1201 0.1374 0.007 1.076 9.3 100.8 21.0 445 n/a end: 0.1201 0.1376 0.007 1.076 9.2 100.7 20.9 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3495505_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3495505_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8700 Refinement macro-cycles (run) : 3522.8000 Write final files (write_after_run_outputs) : 67.5100 Total : 3595.1800 Total CPU time: 60.55 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:45 PST -0800 (1735452705.76 s) Start R-work = 0.1639, R-free = 0.1770 Final R-work = 0.1201, R-free = 0.1376 =============================================================================== Job complete usr+sys time: 3731.58 seconds wall clock time: 66 minutes 57.78 seconds (4017.78 seconds total)