Starting phenix.refine on Sat Dec 28 21:06:31 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6017437.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6017437.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6017437.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 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.17, per 1000 atoms: 0.64 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 277.5 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: 0.62 - 0.89: 392 0.89 - 1.16: 1231 1.16 - 1.43: 698 1.43 - 1.70: 807 1.70 - 1.97: 25 Bond restraints: 3153 Sorted by residual: bond pdb=" N MET A 17 " pdb=" CA MET A 17 " ideal model delta sigma weight residual 1.459 1.669 -0.210 1.19e-02 7.06e+03 3.11e+02 bond pdb=" CA ALA A 36 " pdb=" C ALA A 36 " ideal model delta sigma weight residual 1.525 1.309 0.216 1.28e-02 6.10e+03 2.85e+02 bond pdb=" C LYS A 122 " pdb=" N VAL A 123 " ideal model delta sigma weight residual 1.332 1.134 0.198 1.20e-02 6.94e+03 2.73e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.201 0.177 1.10e-02 8.26e+03 2.59e+02 bond pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 1.330 1.539 -0.209 1.30e-02 5.92e+03 2.58e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 2948 4.41 - 8.82: 1933 8.82 - 13.22: 713 13.22 - 17.63: 166 17.63 - 22.03: 17 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 181 " pdb=" C VAL A 181 " pdb=" N LYS A 182 " ideal model delta sigma weight residual 121.87 104.73 17.14 9.70e-01 1.06e+00 3.12e+02 angle pdb=" CA LEU A 58 " pdb=" C LEU A 58 " pdb=" O LEU A 58 " ideal model delta sigma weight residual 120.92 137.20 -16.28 1.12e+00 7.97e-01 2.11e+02 angle pdb=" O GLY A 120 " pdb=" C GLY A 120 " pdb=" N SER A 121 " ideal model delta sigma weight residual 122.77 110.06 12.71 9.40e-01 1.13e+00 1.83e+02 angle pdb=" N PRO A 43 " pdb=" CA PRO A 43 " pdb=" CB PRO A 43 " ideal model delta sigma weight residual 103.32 114.67 -11.35 8.40e-01 1.42e+00 1.83e+02 angle pdb=" O LYS A 130 " pdb=" C LYS A 130 " pdb=" N ASP A 131 " ideal model delta sigma weight residual 122.07 109.18 12.89 1.03e+00 9.43e-01 1.57e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.29: 943 17.29 - 34.58: 118 34.58 - 51.86: 32 51.86 - 69.15: 16 69.15 - 86.43: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+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 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 102 0.195 - 0.390: 66 0.390 - 0.585: 44 0.585 - 0.779: 22 0.779 - 0.974: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.74 0.97 2.00e-01 2.50e+01 2.37e+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 3.42 -0.91 2.00e-01 2.50e+01 2.05e+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 -1.74 -0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.076 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG PHE A 119 " -0.087 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.107 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.072 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.022 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.049 2.00e-02 2.50e+03 5.91e-02 1.05e+02 pdb=" CG PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.138 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.035 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.089 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.014 2.00e-02 2.50e+03 6.46e-02 9.40e+01 pdb=" CG HIS A 115 " 0.072 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.094 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.115 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.065 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 900 2.30 - 2.88: 8022 2.88 - 3.45: 10553 3.45 - 4.03: 15292 4.03 - 4.60: 21823 Nonbonded interactions: 56590 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.726 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.817 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.832 2.450 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.839 2.450 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.850 2.450 ... (remaining 56585 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_6017437_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= 0.2605 r_free= 0.1931 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.785659 | | target function (ml) not normalized (work): 232062.075368 | | target function (ml) not normalized (free): 11820.510947 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3041 0.2080 7.005 4.9586| | 2: 3.57 - 2.84 1.00 2876 122 0.2434 0.1802 4.3557 4.3551| | 3: 2.84 - 2.48 1.00 2833 165 0.2386 0.1603 4.1408 4.1475| | 4: 2.47 - 2.25 1.00 2825 136 0.2324 0.1501 3.8411 3.8338| | 5: 2.25 - 2.09 1.00 2756 127 0.2453 0.1565 3.806 3.8356| | 6: 2.09 - 1.97 1.00 2846 113 0.2574 0.1807 3.4626 3.5551| | 7: 1.97 - 1.87 1.00 2787 165 0.2541 0.1856 3.1208 3.1782| | 8: 1.87 - 1.79 1.00 2789 144 0.2453 0.1745 3.0487 3.1004| | 9: 1.79 - 1.72 1.00 2745 138 0.2468 0.1878 2.9015 2.9352| | 10: 1.72 - 1.66 1.00 2789 158 0.2379 0.1954 2.7833 2.8796| | 11: 1.66 - 1.61 1.00 2740 147 0.2464 0.1935 2.7407 2.8169| | 12: 1.61 - 1.56 1.00 2787 146 0.2538 0.1933 2.6342 2.676| | 13: 1.56 - 1.52 1.00 2745 130 0.2563 0.1781 2.5858 2.5926| | 14: 1.52 - 1.48 1.00 2803 134 0.2556 0.1726 2.502 2.5018| | 15: 1.48 - 1.45 1.00 2738 128 0.2578 0.2187 2.4183 2.5555| | 16: 1.45 - 1.42 1.00 2756 161 0.2585 0.2236 2.3706 2.455| | 17: 1.42 - 1.39 1.00 2785 139 0.2658 0.2062 2.325 2.3612| | 18: 1.39 - 1.36 1.00 2741 179 0.2632 0.2171 2.2557 2.3173| | 19: 1.36 - 1.34 1.00 2807 134 0.2644 0.2311 2.2548 2.2717| | 20: 1.34 - 1.32 1.00 2696 147 0.2611 0.2274 2.18 2.2556| | 21: 1.32 - 1.30 1.00 2785 112 0.2686 0.2050 2.178 2.1406| | 22: 1.29 - 1.27 1.00 2704 152 0.2723 0.2576 2.1214 2.1849| | 23: 1.27 - 1.26 1.00 2802 156 0.2778 0.2400 2.1115 2.1539| | 24: 1.26 - 1.24 1.00 2744 132 0.2738 0.2677 2.0666 2.1933| | 25: 1.24 - 1.22 1.00 2734 148 0.2816 0.2682 2.038 2.0651| | 26: 1.22 - 1.21 1.00 2727 135 0.2843 0.2325 1.9962 2.0704| | 27: 1.21 - 1.19 1.00 2814 148 0.3009 0.2834 2.0091 2.0418| | 28: 1.19 - 1.18 1.00 2671 147 0.2964 0.2733 1.9716 2.0262| | 29: 1.18 - 1.16 1.00 2800 134 0.2942 0.2770 1.9569 2.0367| | 30: 1.16 - 1.15 1.00 2740 148 0.3064 0.2500 1.9321 1.9044| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.05 0.76 0.23 1525.77| | 2: 3.57 - 2.84 2876 122 0.80 26.44 1.27 0.23 1525.77| | 3: 2.84 - 2.48 2833 165 0.73 32.39 1.24 0.24 1264.11| | 4: 2.47 - 2.25 2825 136 0.81 25.74 1.25 0.25 585.06| | 5: 2.25 - 2.09 2756 127 0.77 29.57 1.28 0.25 585.06| | 6: 2.09 - 1.97 2846 113 0.83 22.94 1.30 0.25 318.32| | 7: 1.97 - 1.87 2787 165 0.90 16.48 1.29 0.26 90.82| | 8: 1.87 - 1.79 2789 144 0.86 20.98 1.25 0.26 90.82| | 9: 1.79 - 1.72 2745 138 0.88 18.84 1.24 0.25 55.33| | 10: 1.72 - 1.66 2789 158 0.86 20.30 1.22 0.25 48.22| | 11: 1.66 - 1.61 2740 147 0.85 21.45 1.23 0.25 46.56| | 12: 1.61 - 1.56 2787 146 0.88 18.73 1.24 0.25 29.75| | 13: 1.56 - 1.52 2745 130 0.86 20.64 1.24 0.25 29.75| | 14: 1.52 - 1.48 2803 134 0.86 20.93 1.23 0.25 26.46| | 15: 1.48 - 1.45 2738 128 0.87 19.96 1.23 0.25 20.43| | 16: 1.45 - 1.42 2756 161 0.86 21.54 1.23 0.25 20.43| | 17: 1.42 - 1.39 2785 139 0.87 20.72 1.23 0.25 17.49| | 18: 1.39 - 1.36 2741 179 0.87 20.92 1.23 0.25 15.78| | 19: 1.36 - 1.34 2807 134 0.85 22.12 1.21 0.25 15.78| | 20: 1.34 - 1.32 2696 147 0.87 20.91 1.20 0.25 13.19| | 21: 1.32 - 1.30 2785 112 0.86 21.92 1.19 0.24 13.01| | 22: 1.29 - 1.27 2704 152 0.85 22.55 1.22 0.24 12.72| | 23: 1.27 - 1.26 2802 156 0.85 22.48 1.21 0.24 11.29| | 24: 1.26 - 1.24 2744 132 0.85 23.00 1.20 0.24 11.29| | 25: 1.24 - 1.22 2734 148 0.84 23.51 1.20 0.24 10.66| | 26: 1.22 - 1.21 2727 135 0.84 23.95 1.21 0.23 9.96| | 27: 1.21 - 1.19 2814 148 0.83 24.90 1.21 0.23 9.96| | 28: 1.19 - 1.18 2671 147 0.83 24.78 1.18 0.23 9.01| | 29: 1.18 - 1.16 2800 134 0.83 24.81 1.16 0.23 8.66| | 30: 1.16 - 1.15 2740 148 0.82 26.36 1.15 0.23 8.66| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.66 max = 1525.77 mean = 220.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.93 mean = 22.63| |phase err.(test): min = 0.00 max = 89.85 mean = 22.49| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.273 1557 Z= 5.355 Angle : 5.322 17.136 2118 Z= 3.696 Chirality : 0.367 0.974 243 Planarity : 0.032 0.088 284 Dihedral : 13.812 86.433 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 4.35 % Favored : 95.03 % Cbeta Deviations : 32.97 % 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: -2.79 (0.45), residues: 224 helix: -2.86 (0.34), residues: 106 sheet: -2.09 (0.75), residues: 28 loop : -0.04 (0.57), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.083 0.017 ARG A 48 TYR 0.064 0.030 TYR A 141 PHE 0.103 0.044 PHE A 119 HIS 0.073 0.031 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= 0.2605 r_free= 0.1931 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.785659 | | target function (ml) not normalized (work): 232062.075368 | | target function (ml) not normalized (free): 11820.510947 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2564 0.2606 0.1931 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2564 0.2606 0.1931 n_refl.: 87602 remove outliers: r(all,work,free)=0.1975 0.1980 0.1931 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.1999 0.2004 0.1945 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1639 0.1632 0.1765 n_refl.: 87594 remove outliers: r(all,work,free)=0.1638 0.1632 0.1765 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 0.3794 386.428 360.028 0.669 1.003 0.407 11.894-9.307 99.02 97 4 0.1810 613.822 597.327 0.921 1.004 0.390 9.237-7.194 100.00 213 7 0.2154 502.031 490.818 0.955 1.004 0.360 7.162-5.571 100.00 427 22 0.2209 376.746 364.935 0.927 1.004 0.330 5.546-4.326 100.00 867 58 0.1296 517.179 510.956 0.959 1.004 0.230 4.315-3.360 100.00 1859 96 0.1160 491.841 487.941 1.006 1.004 0.199 3.356-2.611 100.00 3867 181 0.1456 323.114 319.407 0.996 1.003 0.043 2.608-2.026 99.99 8198 413 0.1352 214.195 211.981 1.005 1.001 0.000 2.025-1.573 100.00 17313 902 0.1620 104.602 104.014 1.015 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2046 46.385 45.121 1.003 0.996 0.000 1.221-1.150 99.97 13689 708 0.2566 29.226 26.987 0.978 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0455 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1632 r_free=0.1765 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1642 r_free=0.1781 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.322228 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2024.532548 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 12.161 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.62 2.51 3.013 19.057 2024.533 0.017 12.44 15.40 2.97 3.177 19.540 2024.533 0.016 Individual atomic B min max mean iso aniso Overall: 8.47 118.68 21.00 2.88 0 1785 Protein: 8.47 118.68 17.88 2.88 0 1519 Water: 11.04 114.79 39.11 N/A 0 258 Other: 22.91 36.11 28.80 N/A 0 8 Chain A: 8.47 118.68 21.00 N/A 0 1785 Histogram: Values Number of atoms 8.47 - 19.49 1204 19.49 - 30.51 234 30.51 - 41.53 168 41.53 - 52.55 95 52.55 - 63.57 55 63.57 - 74.59 17 74.59 - 85.61 5 85.61 - 96.64 4 96.64 - 107.66 0 107.66 - 118.68 3 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1541 r_work=0.1249 r_free=0.1546 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1249 r_free = 0.1546 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 = 0.1248 r_free = 0.1550 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= 0.1248 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015429 | | target function (ls_wunit_k1) not normalized (work): 1285.226431 | | target function (ls_wunit_k1) not normalized (free): 114.318586 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1262 0.1248 0.1550 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1704 0.1703 0.1765 n_refl.: 87593 remove outliers: r(all,work,free)=0.1704 0.1703 0.1765 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1727 0.1726 0.1781 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1245 0.1540 n_refl.: 87593 remove outliers: r(all,work,free)=0.1259 0.1245 0.1540 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 0.3611 298.549 278.668 0.629 1.002 0.375 11.894-9.307 99.02 97 4 0.1625 478.259 465.840 0.905 1.003 0.372 9.237-7.194 100.00 213 7 0.1807 391.157 386.868 0.949 1.003 0.324 7.162-5.571 100.00 427 22 0.1722 293.541 288.070 0.923 1.003 0.300 5.546-4.326 100.00 867 58 0.0917 402.960 400.213 0.948 1.003 0.209 4.315-3.360 100.00 1859 96 0.0772 383.218 382.315 0.996 1.003 0.199 3.356-2.611 100.00 3867 181 0.1019 251.754 251.080 0.998 1.002 0.052 2.608-2.026 99.99 8198 413 0.0975 166.890 166.296 1.009 1.002 0.000 2.025-1.573 100.00 17313 902 0.1214 81.500 81.685 1.018 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1658 36.141 35.594 1.004 0.999 0.000 1.221-1.150 99.97 13689 708 0.2365 22.771 21.285 0.969 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0543 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1245 r_free=0.1540 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=0.1245 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1540 | n_water=258 | time (s): 2.220 (total time: 2.220) Filter (dist) r_work=0.1253 r_free=0.1538 | n_water=252 | time (s): 26.070 (total time: 28.290) Filter (q & B) r_work=0.1256 r_free=0.1537 | n_water=249 | time (s): 3.680 (total time: 31.970) Compute maps r_work=0.1256 r_free=0.1537 | n_water=249 | time (s): 1.780 (total time: 33.750) Filter (map) r_work=0.1268 r_free=0.1543 | n_water=237 | time (s): 3.820 (total time: 37.570) Find peaks r_work=0.1268 r_free=0.1543 | n_water=237 | time (s): 0.740 (total time: 38.310) Add new water r_work=0.1428 r_free=0.1696 | n_water=460 | time (s): 3.790 (total time: 42.100) Refine new water occ: r_work=0.1334 r_free=0.1559 adp: r_work=0.1253 r_free=0.1509 occ: r_work=0.1267 r_free=0.1494 adp: r_work=0.1231 r_free=0.1483 occ: r_work=0.1235 r_free=0.1472 adp: r_work=0.1223 r_free=0.1473 ADP+occupancy (water only), MIN, final r_work=0.1223 r_free=0.1473 r_work=0.1223 r_free=0.1473 | n_water=460 | time (s): 85.890 (total time: 127.990) Filter (q & B) r_work=0.1229 r_free=0.1480 | n_water=436 | time (s): 3.850 (total time: 131.840) Filter (dist only) r_work=0.1229 r_free=0.1480 | n_water=436 | time (s): 40.390 (total time: 172.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.669223 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1529.485936 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 0.1509 0.0280 0.007 0.9 1.6 0.5 0.0 0 13.335 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 15.09 2.80 3.789 23.191 1529.486 0.015 11.96 14.82 2.86 4.187 22.985 1529.486 0.015 Individual atomic B min max mean iso aniso Overall: 8.71 114.59 23.14 2.61 199 1764 Protein: 8.71 114.59 17.65 2.61 0 1519 Water: 11.06 71.93 42.19 N/A 199 237 Other: 23.47 34.57 28.13 N/A 0 8 Chain A: 8.71 114.59 20.36 N/A 0 1764 Chain S: 15.05 70.05 47.80 N/A 199 0 Histogram: Values Number of atoms 8.71 - 19.30 1209 19.30 - 29.89 254 29.89 - 40.47 185 40.47 - 51.06 143 51.06 - 61.65 117 61.65 - 72.24 45 72.24 - 82.82 4 82.82 - 93.41 3 93.41 - 104.00 1 104.00 - 114.59 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1482 r_work=0.1196 r_free=0.1482 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1482 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1480 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1195 r_free= 0.1480 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013865 | | target function (ls_wunit_k1) not normalized (work): 1154.887565 | | target function (ls_wunit_k1) not normalized (free): 103.196246 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1195 0.1480 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1606 0.1603 0.1705 n_refl.: 87592 remove outliers: r(all,work,free)=0.1606 0.1603 0.1705 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1612 0.1609 0.1708 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1192 0.1478 n_refl.: 87592 remove outliers: r(all,work,free)=0.1205 0.1191 0.1478 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3383 294.492 271.906 0.596 1.002 0.364 11.894-9.307 99.02 97 4 0.1524 478.259 474.551 0.914 1.003 0.360 9.237-7.194 100.00 213 7 0.1682 391.157 392.258 0.980 1.003 0.270 7.162-5.571 100.00 427 22 0.1499 293.541 289.843 0.937 1.003 0.260 5.546-4.326 100.00 867 58 0.0826 402.960 400.284 0.958 1.003 0.215 4.315-3.360 100.00 1859 96 0.0703 383.218 382.205 1.002 1.003 0.210 3.356-2.611 100.00 3867 181 0.0950 251.754 251.056 1.009 1.002 0.130 2.608-2.026 99.99 8198 413 0.0958 166.890 166.460 1.017 1.002 0.000 2.025-1.573 100.00 17313 902 0.1174 81.500 81.713 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1604 36.141 35.640 1.016 0.999 0.000 1.221-1.150 99.97 13689 708 0.2330 22.771 21.307 0.977 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0579 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1478 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1193 r_free=0.1478 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1478 | n_water=436 | time (s): 2.170 (total time: 2.170) Filter (dist) r_work=0.1193 r_free=0.1479 | n_water=435 | time (s): 37.740 (total time: 39.910) Filter (q & B) r_work=0.1193 r_free=0.1479 | n_water=435 | time (s): 0.900 (total time: 40.810) Compute maps r_work=0.1193 r_free=0.1479 | n_water=435 | time (s): 1.130 (total time: 41.940) Filter (map) r_work=0.1233 r_free=0.1477 | n_water=298 | time (s): 3.330 (total time: 45.270) Find peaks r_work=0.1233 r_free=0.1477 | n_water=298 | time (s): 0.650 (total time: 45.920) Add new water r_work=0.1358 r_free=0.1600 | n_water=495 | time (s): 2.920 (total time: 48.840) Refine new water occ: r_work=0.1254 r_free=0.1510 adp: r_work=0.1255 r_free=0.1513 occ: r_work=0.1231 r_free=0.1489 adp: r_work=0.1229 r_free=0.1491 occ: r_work=0.1216 r_free=0.1474 adp: r_work=0.1209 r_free=0.1472 ADP+occupancy (water only), MIN, final r_work=0.1209 r_free=0.1472 r_work=0.1209 r_free=0.1472 | n_water=495 | time (s): 215.580 (total time: 264.420) Filter (q & B) r_work=0.1214 r_free=0.1470 | n_water=450 | time (s): 3.370 (total time: 267.790) Filter (dist only) r_work=0.1214 r_free=0.1470 | n_water=450 | time (s): 35.910 (total time: 303.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.005626 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.040354 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 0.1219 0.1443 0.0225 0.006 0.9 2.2 0.5 0.0 0 1.003 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.19 14.43 2.25 3.620 22.140 51.040 3.719 12.01 13.96 1.95 4.087 21.957 51.040 3.648 Individual atomic B min max mean iso aniso Overall: 9.14 110.28 21.74 2.34 215 1762 Protein: 9.14 110.28 17.23 2.34 0 1519 Water: 11.44 71.07 36.91 N/A 215 235 Other: 19.59 30.74 25.37 N/A 0 8 Chain A: 9.14 110.28 19.91 N/A 0 1762 Chain S: 15.47 66.98 36.71 N/A 215 0 Histogram: Values Number of atoms 9.14 - 19.25 1234 19.25 - 29.37 270 29.37 - 39.48 227 39.48 - 49.59 135 49.59 - 59.71 79 59.71 - 69.82 18 69.82 - 79.94 8 79.94 - 90.05 3 90.05 - 100.17 1 100.17 - 110.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1396 r_work=0.1202 r_free=0.1396 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1396 target_work(ml) = 3.648 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1393 target_work(ml) = 3.647 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1197 r_free= 0.1393 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.646650 | | target function (ml) not normalized (work): 303740.442235 | | target function (ml) not normalized (free): 16045.817133 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1197 0.1393 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1527 0.1526 0.1571 n_refl.: 87589 remove outliers: r(all,work,free)=0.1527 0.1526 0.1571 n_refl.: 87589 overall B=0.00 to atoms: r(all,work,free)=0.1527 0.1526 0.1571 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1188 0.1363 n_refl.: 87589 remove outliers: r(all,work,free)=0.1194 0.1186 0.1363 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3939 291.651 263.924 0.500 0.999 0.360 11.894-9.307 99.02 97 4 0.2514 478.259 464.725 0.861 1.001 0.330 9.237-7.194 98.18 209 7 0.2275 382.712 384.239 0.960 1.001 0.190 7.162-5.571 100.00 427 22 0.2037 293.541 283.190 0.919 1.001 0.190 5.546-4.326 100.00 867 58 0.1071 402.960 397.881 0.960 1.001 0.151 4.315-3.360 100.00 1859 96 0.0906 383.218 380.676 1.002 1.001 0.140 3.356-2.611 100.00 3867 181 0.1130 251.754 250.049 1.008 1.002 0.120 2.608-2.026 99.99 8198 413 0.1035 166.890 166.059 1.019 1.002 0.000 2.025-1.573 100.00 17313 902 0.1005 81.500 81.693 1.032 1.003 0.000 1.573-1.221 100.00 36679 1900 0.1290 36.141 35.687 1.021 1.003 0.000 1.221-1.150 99.97 13689 708 0.2124 22.771 21.265 0.973 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0033 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1186 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1363 | n_water=450 | time (s): 1.810 (total time: 1.810) Filter (dist) r_work=0.1186 r_free=0.1363 | n_water=450 | time (s): 36.470 (total time: 38.280) Filter (q & B) r_work=0.1186 r_free=0.1363 | n_water=450 | time (s): 1.180 (total time: 39.460) Compute maps r_work=0.1186 r_free=0.1363 | n_water=450 | time (s): 1.590 (total time: 41.050) Filter (map) r_work=0.1211 r_free=0.1385 | n_water=322 | time (s): 3.040 (total time: 44.090) Find peaks r_work=0.1211 r_free=0.1385 | n_water=322 | time (s): 0.660 (total time: 44.750) Add new water r_work=0.1284 r_free=0.1444 | n_water=493 | time (s): 3.020 (total time: 47.770) Refine new water occ: r_work=0.1209 r_free=0.1372 adp: r_work=0.1209 r_free=0.1375 occ: r_work=0.1195 r_free=0.1364 adp: r_work=0.1193 r_free=0.1365 occ: r_work=0.1184 r_free=0.1361 adp: r_work=0.1180 r_free=0.1358 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1358 r_work=0.1180 r_free=0.1358 | n_water=493 | time (s): 236.930 (total time: 284.700) Filter (q & B) r_work=0.1185 r_free=0.1355 | n_water=450 | time (s): 2.790 (total time: 287.490) Filter (dist only) r_work=0.1185 r_free=0.1354 | n_water=448 | time (s): 36.990 (total time: 324.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.064245 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.390543 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 0.1370 0.0179 0.006 1.0 3.8 0.5 0.0 0 1.032 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.70 1.79 3.437 21.561 51.391 3.637 11.80 13.64 1.84 3.833 21.430 51.391 3.623 Individual atomic B min max mean iso aniso Overall: 9.24 106.05 21.31 2.19 217 1758 Protein: 9.24 106.05 16.94 2.19 0 1519 Water: 11.59 69.73 36.08 N/A 217 231 Other: 19.74 28.17 23.87 N/A 0 8 Chain A: 9.24 106.05 19.52 N/A 0 1758 Chain S: 15.75 67.30 35.86 N/A 217 0 Histogram: Values Number of atoms 9.24 - 18.92 1235 18.92 - 28.60 279 28.60 - 38.29 210 38.29 - 47.97 140 47.97 - 57.65 72 57.65 - 67.33 26 67.33 - 77.01 8 77.01 - 86.69 2 86.69 - 96.37 1 96.37 - 106.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1180 r_free=0.1364 r_work=0.1180 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1180 r_free = 0.1364 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1174 r_free = 0.1363 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1174 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621514 | | target function (ml) not normalized (work): 301625.022349 | | target function (ml) not normalized (free): 15954.895483 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1183 0.1174 0.1363 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1511 0.1509 0.1572 n_refl.: 87583 remove outliers: r(all,work,free)=0.1511 0.1509 0.1572 n_refl.: 87583 overall B=-0.01 to atoms: r(all,work,free)=0.1509 0.1507 0.1571 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1182 0.1173 0.1361 n_refl.: 87583 remove outliers: r(all,work,free)=0.1180 0.1171 0.1361 n_refl.: 87579 ======================== 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 0.4090 293.859 249.413 0.449 1.000 0.310 11.894-9.307 96.08 94 4 0.2197 477.342 461.322 0.851 1.002 0.264 9.237-7.194 98.18 209 7 0.2330 382.712 378.320 0.923 1.002 0.190 7.162-5.571 100.00 427 22 0.2061 293.541 284.664 0.909 1.002 0.163 5.546-4.326 100.00 867 58 0.1100 402.960 398.785 0.954 1.002 0.151 4.315-3.360 100.00 1859 96 0.0921 383.218 380.840 0.995 1.002 0.143 3.356-2.611 100.00 3867 181 0.1155 251.754 250.002 0.998 1.002 0.130 2.608-2.026 99.99 8198 413 0.1028 166.890 166.038 1.011 1.002 0.000 2.025-1.573 100.00 17313 902 0.0963 81.500 81.811 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1237 36.141 35.776 1.020 0.999 0.000 1.221-1.150 99.97 13689 708 0.2122 22.771 21.407 0.977 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0320 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1171 r_free=0.1361 After: r_work=0.1171 r_free=0.1361 ================================== NQH flips ================================== r_work=0.1171 r_free=0.1361 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=0.1171 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1171 r_free=0.1361 | n_water=448 | time (s): 1.680 (total time: 1.680) Filter (dist) r_work=0.1171 r_free=0.1361 | n_water=448 | time (s): 36.490 (total time: 38.170) Filter (q & B) r_work=0.1172 r_free=0.1364 | n_water=445 | time (s): 3.430 (total time: 41.600) Compute maps r_work=0.1172 r_free=0.1364 | n_water=445 | time (s): 1.350 (total time: 42.950) Filter (map) r_work=0.1195 r_free=0.1379 | n_water=327 | time (s): 2.480 (total time: 45.430) Find peaks r_work=0.1195 r_free=0.1379 | n_water=327 | time (s): 0.550 (total time: 45.980) Add new water r_work=0.1254 r_free=0.1435 | n_water=484 | time (s): 2.560 (total time: 48.540) Refine new water occ: r_work=0.1189 r_free=0.1363 adp: r_work=0.1189 r_free=0.1366 occ: r_work=0.1177 r_free=0.1353 adp: r_work=0.1176 r_free=0.1356 occ: r_work=0.1169 r_free=0.1346 adp: r_work=0.1165 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1165 r_free=0.1347 r_work=0.1165 r_free=0.1347 | n_water=484 | time (s): 167.370 (total time: 215.910) Filter (q & B) r_work=0.1172 r_free=0.1353 | n_water=441 | time (s): 2.750 (total time: 218.660) Filter (dist only) r_work=0.1172 r_free=0.1353 | n_water=439 | time (s): 37.530 (total time: 256.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.992023 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.090901 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 0.1197 0.1377 0.0180 0.007 1.1 2.9 0.5 0.0 0 0.996 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.77 1.80 3.308 21.147 40.091 3.628 12.00 13.75 1.75 3.385 21.112 40.091 3.625 Individual atomic B min max mean iso aniso Overall: 9.24 103.91 21.08 2.09 209 1757 Protein: 9.24 103.91 16.85 2.09 0 1519 Water: 11.22 69.44 35.68 N/A 209 230 Other: 18.63 26.92 23.34 N/A 0 8 Chain A: 9.24 103.91 19.40 N/A 0 1757 Chain S: 16.05 59.60 35.23 N/A 209 0 Histogram: Values Number of atoms 9.24 - 18.71 1231 18.71 - 28.18 283 28.18 - 37.64 196 37.64 - 47.11 147 47.11 - 56.58 68 56.58 - 66.04 27 66.04 - 75.51 10 75.51 - 84.97 1 84.97 - 94.44 1 94.44 - 103.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1375 r_work=0.1201 r_free=0.1375 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1375 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1371 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1197 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623295 | | target function (ml) not normalized (work): 301758.843009 | | target function (ml) not normalized (free): 15948.039671 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1405 0.1474 5.6635 5.6621| | 2: 3.57 - 2.84 1.00 2888 124 0.1124 0.1398 5.2074 5.2596| | 3: 2.83 - 2.48 1.00 2820 163 0.1218 0.1286 5.0091 5.0415| | 4: 2.47 - 2.25 1.00 2825 136 0.1020 0.1091 4.7104 4.7405| | 5: 2.25 - 2.09 1.00 2756 127 0.0997 0.1091 4.6531 4.7192| | 6: 2.09 - 1.97 1.00 2846 113 0.0982 0.1195 4.3578 4.4887| | 7: 1.97 - 1.87 1.00 2787 165 0.0989 0.1202 4.0731 4.1824| | 8: 1.87 - 1.79 1.00 2789 144 0.1028 0.1224 3.9906 4.0765| | 9: 1.79 - 1.72 1.00 2745 138 0.0967 0.1270 3.7199 3.8928| | 10: 1.72 - 1.66 1.00 2831 160 0.1011 0.1281 3.6379 3.7779| | 11: 1.66 - 1.61 1.00 2712 147 0.0969 0.1079 3.5716 3.5988| | 12: 1.61 - 1.56 1.00 2773 144 0.0926 0.1227 3.3552 3.4888| | 13: 1.56 - 1.52 1.00 2745 130 0.0985 0.1101 3.3443 3.443| | 14: 1.52 - 1.48 1.00 2803 134 0.0993 0.1136 3.2646 3.3612| | 15: 1.48 - 1.45 1.00 2738 128 0.1014 0.1362 3.1726 3.3338| | 16: 1.45 - 1.42 1.00 2756 161 0.1071 0.1274 3.1561 3.2529| | 17: 1.42 - 1.39 1.00 2785 139 0.1124 0.1315 3.1172 3.2372| | 18: 1.39 - 1.36 1.00 2741 179 0.1161 0.1351 3.0902 3.2505| | 19: 1.36 - 1.34 1.00 2807 134 0.1222 0.1588 3.0962 3.2771| | 20: 1.34 - 1.32 1.00 2696 147 0.1322 0.1457 3.0871 3.1299| | 21: 1.32 - 1.30 1.00 2785 112 0.1420 0.1654 3.0885 3.1745| | 22: 1.29 - 1.27 1.00 2704 152 0.1480 0.1899 3.0843 3.2773| | 23: 1.27 - 1.26 1.00 2802 156 0.1586 0.1836 3.1044 3.2032| | 24: 1.26 - 1.24 1.00 2744 132 0.1627 0.1779 3.0941 3.1954| | 25: 1.24 - 1.22 1.00 2733 148 0.1798 0.2323 3.1089 3.2881| | 26: 1.22 - 1.21 1.00 2727 135 0.1859 0.1789 3.1229 3.2032| | 27: 1.21 - 1.19 1.00 2814 148 0.2014 0.2092 3.1409 3.142| | 28: 1.19 - 1.18 1.00 2671 147 0.2142 0.2309 3.1393 3.1603| | 29: 1.18 - 1.16 1.00 2800 134 0.2217 0.2387 3.1264 3.2251| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2493 3.1159 3.1684| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2921 171 0.94 9.26 1.00 0.97 6407.00| | 2: 3.57 - 2.84 2888 124 0.92 13.58 1.01 0.97 6407.00| | 3: 2.83 - 2.48 2820 163 0.88 17.71 0.99 0.97 5366.92| | 4: 2.47 - 2.25 2825 136 0.91 14.76 1.00 0.98 2684.87| | 5: 2.25 - 2.09 2756 127 0.89 17.04 1.01 0.98 2684.87| | 6: 2.09 - 1.97 2846 113 0.92 13.71 1.02 0.97 1571.55| | 7: 1.97 - 1.87 2787 165 0.94 10.77 1.02 0.97 622.04| | 8: 1.87 - 1.79 2789 144 0.91 14.34 1.00 0.97 622.04| | 9: 1.79 - 1.72 2745 138 0.93 11.41 0.98 0.97 339.28| | 10: 1.72 - 1.66 2831 160 0.93 12.29 0.98 0.97 282.65| | 11: 1.66 - 1.61 2712 147 0.93 12.91 0.98 0.97 269.84| | 12: 1.61 - 1.56 2773 144 0.95 9.61 0.99 0.97 149.01| | 13: 1.56 - 1.52 2745 130 0.94 11.19 1.02 0.97 149.01| | 14: 1.52 - 1.48 2803 134 0.94 11.31 1.02 0.97 133.21| | 15: 1.48 - 1.45 2738 128 0.95 10.53 1.01 0.98 104.29| | 16: 1.45 - 1.42 2756 161 0.94 11.68 1.02 0.98 104.29| | 17: 1.42 - 1.39 2785 139 0.94 11.51 1.01 0.98 93.77| | 18: 1.39 - 1.36 2741 179 0.94 11.82 1.01 0.98 87.69| | 19: 1.36 - 1.34 2807 134 0.94 12.34 1.00 0.98 87.69| | 20: 1.34 - 1.32 2696 147 0.94 12.45 0.99 0.96 82.39| | 21: 1.32 - 1.30 2785 112 0.94 13.36 0.98 0.96 82.01| | 22: 1.29 - 1.27 2704 152 0.93 13.85 0.98 0.96 82.11| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.94 82.61| | 24: 1.26 - 1.24 2744 132 0.92 14.94 0.97 0.94 82.61| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.94 84.16| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.02 0.93 85.88| | 27: 1.21 - 1.19 2814 148 0.89 18.73 1.02 0.93 85.88| | 28: 1.19 - 1.18 2671 147 0.88 20.22 1.01 0.93 89.12| | 29: 1.18 - 1.16 2800 134 0.88 20.52 0.99 0.92 90.34| | 30: 1.16 - 1.15 2739 148 0.86 21.97 0.98 0.92 90.34| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 82.01 max = 6407.00 mean = 994.60| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 14.09| |phase err.(test): min = 0.00 max = 89.01 mean = 14.20| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1197 0.1371 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1516 0.1516 0.1558 n_refl.: 87579 remove outliers: r(all,work,free)=0.1516 0.1516 0.1558 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1515 0.1515 0.1557 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1197 0.1371 n_refl.: 87579 remove outliers: r(all,work,free)=0.1205 0.1196 0.1371 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 0.4150 293.859 256.424 0.448 1.001 0.289 11.894-9.307 95.10 93 4 0.2446 477.460 458.916 0.847 1.002 0.267 9.237-7.194 97.73 208 7 0.2474 383.785 376.093 0.919 1.002 0.150 7.162-5.571 100.00 427 22 0.2242 293.541 282.625 0.904 1.003 0.150 5.546-4.326 100.00 867 58 0.1176 402.960 398.319 0.964 1.003 0.138 4.315-3.360 100.00 1859 96 0.0970 383.218 380.737 1.004 1.002 0.133 3.356-2.611 100.00 3867 181 0.1187 251.754 249.916 1.010 1.002 0.057 2.608-2.026 99.99 8198 413 0.1039 166.890 166.011 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0983 81.500 81.783 1.037 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1233 36.141 35.774 1.030 0.997 0.000 1.221-1.150 99.97 13689 708 0.2118 22.771 21.388 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0171 ================= 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 : 0.2605 0.1931 0.081 5.322 8.8 119.3 19.9 258 0.000 1_bss: 0.1632 0.1765 0.081 5.322 9.0 119.5 20.1 258 0.000 1_settarget: 0.1632 0.1765 0.081 5.322 9.0 119.5 20.1 258 0.000 1_nqh: 0.1642 0.1781 0.081 5.322 9.0 119.5 20.1 258 0.007 1_weight: 0.1642 0.1781 0.081 5.322 9.0 119.5 20.1 258 0.007 1_xyzrec: 0.1211 0.1462 0.007 0.931 9.0 119.5 20.1 258 0.130 1_adp: 0.1244 0.1541 0.007 0.931 8.5 118.7 21.0 258 0.130 1_regHadp: 0.1249 0.1546 0.007 0.931 8.5 118.7 21.0 258 0.130 1_occ: 0.1248 0.1550 0.007 0.931 8.5 118.7 21.0 258 0.130 2_bss: 0.1245 0.1540 0.007 0.931 8.6 118.8 21.1 258 0.130 2_settarget: 0.1245 0.1540 0.007 0.931 8.6 118.8 21.1 258 0.130 2_updatecdl: 0.1245 0.1540 0.007 0.948 8.6 118.8 21.1 258 0.130 2_nqh: 0.1245 0.1540 0.007 0.948 8.6 118.8 21.1 258 0.130 2_sol: 0.1229 0.1480 0.007 0.948 8.6 118.8 23.5 436 n/a 2_weight: 0.1229 0.1480 0.007 0.948 8.6 118.8 23.5 436 n/a 2_xyzrec: 0.1229 0.1509 0.007 0.891 8.6 118.8 23.5 436 n/a 2_adp: 0.1196 0.1482 0.007 0.891 8.7 114.6 23.1 436 n/a 2_regHadp: 0.1196 0.1482 0.007 0.891 8.7 114.6 23.1 436 n/a 2_occ: 0.1195 0.1480 0.007 0.891 8.7 114.6 23.1 436 n/a 3_bss: 0.1191 0.1478 0.007 0.891 8.7 114.6 23.2 436 n/a 3_settarget: 0.1191 0.1478 0.007 0.891 8.7 114.6 23.2 436 n/a 3_updatecdl: 0.1191 0.1478 0.007 0.890 8.7 114.6 23.2 436 n/a 3_nqh: 0.1193 0.1478 0.007 0.890 8.7 114.6 23.2 436 n/a 3_sol: 0.1214 0.1470 0.007 0.890 8.7 114.6 22.1 450 n/a 3_weight: 0.1214 0.1470 0.007 0.890 8.7 114.6 22.1 450 n/a 3_xyzrec: 0.1219 0.1443 0.006 0.926 8.7 114.6 22.1 450 n/a 3_adp: 0.1201 0.1396 0.006 0.926 9.1 110.3 21.7 450 n/a 3_regHadp: 0.1202 0.1396 0.006 0.926 9.1 110.3 21.7 450 n/a 3_occ: 0.1197 0.1393 0.006 0.926 9.1 110.3 21.7 450 n/a 4_bss: 0.1186 0.1363 0.006 0.926 9.1 110.3 21.7 450 n/a 4_settarget: 0.1186 0.1363 0.006 0.926 9.1 110.3 21.7 450 n/a 4_updatecdl: 0.1186 0.1363 0.006 0.926 9.1 110.3 21.7 450 n/a 4_nqh: 0.1186 0.1363 0.006 0.926 9.1 110.3 21.7 450 n/a 4_sol: 0.1185 0.1354 0.006 0.926 9.1 110.3 21.5 448 n/a 4_weight: 0.1185 0.1354 0.006 0.926 9.1 110.3 21.5 448 n/a 4_xyzrec: 0.1191 0.1370 0.006 0.961 9.1 110.3 21.5 448 n/a 4_adp: 0.1180 0.1364 0.006 0.961 9.2 106.1 21.3 448 n/a 4_regHadp: 0.1180 0.1364 0.006 0.961 9.2 106.1 21.3 448 n/a 4_occ: 0.1174 0.1363 0.006 0.961 9.2 106.1 21.3 448 n/a 5_bss: 0.1171 0.1361 0.006 0.961 9.2 106.0 21.3 448 n/a 5_settarget: 0.1171 0.1361 0.006 0.961 9.2 106.0 21.3 448 n/a 5_updatecdl: 0.1171 0.1361 0.006 0.962 9.2 106.0 21.3 448 n/a 5_setrh: 0.1171 0.1361 0.006 0.962 9.2 106.0 21.3 448 n/a 5_nqh: 0.1171 0.1361 0.006 0.962 9.2 106.0 21.3 448 n/a 5_sol: 0.1172 0.1353 0.006 0.962 9.2 106.0 21.1 439 n/a 5_weight: 0.1172 0.1353 0.006 0.962 9.2 106.0 21.1 439 n/a 5_xyzrec: 0.1197 0.1377 0.007 1.064 9.2 106.0 21.1 439 n/a 5_adp: 0.1200 0.1375 0.007 1.064 9.2 103.9 21.1 439 n/a 5_regHadp: 0.1201 0.1375 0.007 1.064 9.2 103.9 21.1 439 n/a 5_occ: 0.1197 0.1371 0.007 1.064 9.2 103.9 21.1 439 n/a end: 0.1196 0.1371 0.007 1.064 9.2 103.9 21.1 439 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6017437_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6017437_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.6800 Refinement macro-cycles (run) : 3373.8400 Write final files (write_after_run_outputs) : 72.5400 Total : 3451.0600 Total CPU time: 58.12 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:09:03 PST -0800 (1735452543.21 s) Start R-work = 0.1632, R-free = 0.1765 Final R-work = 0.1196, R-free = 0.1371 =============================================================================== Job complete usr+sys time: 3603.66 seconds wall clock time: 64 minutes 33.07 seconds (3873.07 seconds total)