Starting phenix.refine on Sat Dec 28 21:06:34 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8569971.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8569971.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8569971.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.25, per 1000 atoms: 0.67 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: 0.73 Conformation dependent library (CDL) restraints added in 183.3 milliseconds Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.91: 530 0.91 - 1.19: 1154 1.19 - 1.47: 771 1.47 - 1.74: 684 1.74 - 2.02: 14 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 1.332 1.512 -0.180 6.60e-03 2.30e+04 7.43e+02 bond pdb=" C GLN A 180 " pdb=" N VAL A 181 " ideal model delta sigma weight residual 1.335 1.581 -0.246 1.20e-02 6.94e+03 4.22e+02 bond pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 1.230 0.984 0.246 1.22e-02 6.72e+03 4.07e+02 bond pdb=" C GLY A 37 " pdb=" O GLY A 37 " ideal model delta sigma weight residual 1.234 1.027 0.207 1.05e-02 9.07e+03 3.88e+02 bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.236 1.025 0.212 1.15e-02 7.56e+03 3.40e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.98: 3327 4.98 - 9.97: 1831 9.97 - 14.95: 525 14.95 - 19.94: 86 19.94 - 24.92: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH1 ARG A 98 " ideal model delta sigma weight residual 121.50 136.19 -14.69 1.00e+00 1.00e+00 2.16e+02 angle pdb=" CA ALYS A 132 " pdb=" C ALYS A 132 " pdb=" O ALYS A 132 " ideal model delta sigma weight residual 120.70 135.34 -14.64 1.03e+00 9.43e-01 2.02e+02 angle pdb=" CA GLY A 37 " pdb=" C GLY A 37 " pdb=" O GLY A 37 " ideal model delta sigma weight residual 120.76 132.10 -11.34 8.10e-01 1.52e+00 1.96e+02 angle pdb=" CA GLY A 37 " pdb=" C GLY A 37 " pdb=" N LEU A 38 " ideal model delta sigma weight residual 115.86 100.57 15.29 1.13e+00 7.83e-01 1.83e+02 angle pdb=" CA PHE A 164 " pdb=" C PHE A 164 " pdb=" O PHE A 164 " ideal model delta sigma weight residual 120.42 107.20 13.22 1.06e+00 8.90e-01 1.56e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 919 16.75 - 33.49: 135 33.49 - 50.24: 40 50.24 - 66.99: 16 66.99 - 83.73: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 -157.78 -22.22 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ARG A 48 " pdb=" C ARG A 48 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.207: 93 0.207 - 0.411: 73 0.411 - 0.615: 46 0.615 - 0.818: 24 0.818 - 1.022: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PHE A 164 " pdb=" N PHE A 164 " pdb=" C PHE A 164 " pdb=" CB PHE A 164 " both_signs ideal model delta sigma weight residual False 2.51 3.53 -1.02 2.00e-01 2.50e+01 2.61e+01 chirality pdb=" CA GLN A 180 " pdb=" N GLN A 180 " pdb=" C GLN A 180 " pdb=" CB GLN A 180 " both_signs ideal model delta sigma weight residual False 2.51 3.48 -0.97 2.00e-01 2.50e+01 2.36e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -1.69 -0.94 2.00e-01 2.50e+01 2.20e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.000 2.00e-02 2.50e+03 6.53e-02 1.28e+02 pdb=" CG PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.090 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.128 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " 0.040 9.50e-02 1.11e+02 6.74e-02 9.83e+01 pdb=" NE ARG A 145 " 0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.065 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " 0.147 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " 0.044 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " -0.081 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.043 2.00e-02 2.50e+03 5.45e-02 8.90e+01 pdb=" CG TYR A 139 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.106 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.048 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.063 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.062 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.059 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.035 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 951 2.31 - 2.88: 8124 2.88 - 3.46: 10582 3.46 - 4.03: 15177 4.03 - 4.60: 21855 Nonbonded interactions: 56689 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.742 2.100 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.807 2.270 nonbonded pdb="HE21 GLN A 45 " pdb=" OD1 ASP A 49 " model vdw 1.809 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.820 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.844 2.100 ... (remaining 56684 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_8569971_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795464 | | target function (ml) not normalized (work): 232878.907119 | | target function (ml) not normalized (free): 11865.045426 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3023 0.2047 7.0595 4.9394| | 2: 3.57 - 2.84 1.00 2876 122 0.2433 0.1812 4.3473 4.3473| | 3: 2.84 - 2.48 1.00 2833 165 0.2359 0.1619 4.1251 4.1765| | 4: 2.47 - 2.25 1.00 2825 136 0.2352 0.1453 3.8335 3.8238| | 5: 2.25 - 2.09 1.00 2756 127 0.2452 0.1597 3.8016 3.8184| | 6: 2.09 - 1.97 1.00 2846 113 0.2539 0.1686 3.4897 3.537| | 7: 1.97 - 1.87 1.00 2787 165 0.2572 0.1933 3.1614 3.2655| | 8: 1.87 - 1.79 1.00 2789 144 0.2476 0.1959 3.0759 3.1596| | 9: 1.79 - 1.72 1.00 2745 138 0.2428 0.1989 2.8995 3.0022| | 10: 1.72 - 1.66 1.00 2789 158 0.2396 0.1835 2.8237 2.8353| | 11: 1.66 - 1.61 1.00 2740 147 0.2491 0.2062 2.7438 2.8356| | 12: 1.61 - 1.56 1.00 2787 146 0.2572 0.1777 2.6271 2.6288| | 13: 1.56 - 1.52 1.00 2745 130 0.2572 0.2028 2.5829 2.6881| | 14: 1.52 - 1.48 1.00 2803 134 0.2587 0.2001 2.5292 2.6019| | 15: 1.48 - 1.45 1.00 2738 128 0.2588 0.2280 2.4232 2.5818| | 16: 1.45 - 1.42 1.00 2756 161 0.2681 0.2050 2.3884 2.4277| | 17: 1.42 - 1.39 1.00 2785 139 0.2743 0.2102 2.343 2.3621| | 18: 1.39 - 1.36 1.00 2741 179 0.2671 0.2166 2.2658 2.3385| | 19: 1.36 - 1.34 1.00 2807 134 0.2638 0.2343 2.2387 2.2743| | 20: 1.34 - 1.32 1.00 2696 147 0.2672 0.2299 2.1928 2.2174| | 21: 1.32 - 1.30 1.00 2785 112 0.2694 0.2255 2.1576 2.1793| | 22: 1.29 - 1.27 1.00 2704 152 0.2765 0.2346 2.1578 2.1492| | 23: 1.27 - 1.26 1.00 2802 156 0.2765 0.2465 2.0956 2.1615| | 24: 1.26 - 1.24 1.00 2744 132 0.2792 0.2536 2.0865 2.1458| | 25: 1.24 - 1.22 1.00 2734 148 0.2821 0.2524 2.0516 2.0476| | 26: 1.22 - 1.21 1.00 2727 135 0.2905 0.2265 2.0199 2.0886| | 27: 1.21 - 1.19 1.00 2814 148 0.2976 0.2738 2.0045 2.0531| | 28: 1.19 - 1.18 1.00 2671 147 0.3030 0.2867 1.9996 2.0128| | 29: 1.18 - 1.16 1.00 2800 134 0.2947 0.2851 1.9567 2.0584| | 30: 1.16 - 1.15 1.00 2740 148 0.3013 0.2818 1.9265 1.9641| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.84 0.76 0.23 1477.36| | 2: 3.57 - 2.84 2876 122 0.80 26.05 1.27 0.23 1477.36| | 3: 2.84 - 2.48 2833 165 0.74 32.08 1.24 0.24 1225.80| | 4: 2.47 - 2.25 2825 136 0.81 25.69 1.26 0.25 572.96| | 5: 2.25 - 2.09 2756 127 0.77 29.26 1.28 0.25 572.96| | 6: 2.09 - 1.97 2846 113 0.83 22.79 1.29 0.25 315.10| | 7: 1.97 - 1.87 2787 165 0.90 17.01 1.28 0.25 95.18| | 8: 1.87 - 1.79 2789 144 0.85 21.57 1.25 0.25 95.18| | 9: 1.79 - 1.72 2745 138 0.87 19.25 1.24 0.25 58.61| | 10: 1.72 - 1.66 2789 158 0.86 20.63 1.22 0.25 51.28| | 11: 1.66 - 1.61 2740 147 0.84 22.46 1.24 0.25 49.50| | 12: 1.61 - 1.56 2787 146 0.88 19.33 1.25 0.25 31.42| | 13: 1.56 - 1.52 2745 130 0.86 21.27 1.24 0.25 31.42| | 14: 1.52 - 1.48 2803 134 0.86 21.61 1.23 0.25 28.11| | 15: 1.48 - 1.45 2738 128 0.87 20.74 1.24 0.25 22.04| | 16: 1.45 - 1.42 2756 161 0.85 22.26 1.24 0.25 22.04| | 17: 1.42 - 1.39 2785 139 0.86 21.51 1.24 0.25 18.34| | 18: 1.39 - 1.36 2741 179 0.86 21.73 1.23 0.25 16.20| | 19: 1.36 - 1.34 2807 134 0.85 22.34 1.22 0.25 16.20| | 20: 1.34 - 1.32 2696 147 0.87 21.10 1.22 0.25 13.27| | 21: 1.32 - 1.30 2785 112 0.85 22.19 1.21 0.25 13.07| | 22: 1.29 - 1.27 2704 152 0.85 22.57 1.20 0.25 12.75| | 23: 1.27 - 1.26 2802 156 0.86 22.28 1.21 0.24 11.13| | 24: 1.26 - 1.24 2744 132 0.85 22.85 1.20 0.24 11.13| | 25: 1.24 - 1.22 2734 148 0.84 23.77 1.19 0.24 10.70| | 26: 1.22 - 1.21 2727 135 0.84 24.39 1.20 0.23 10.22| | 27: 1.21 - 1.19 2814 148 0.83 25.12 1.21 0.23 10.22| | 28: 1.19 - 1.18 2671 147 0.82 26.02 1.19 0.23 9.77| | 29: 1.18 - 1.16 2800 134 0.81 26.58 1.16 0.22 9.60| | 30: 1.16 - 1.15 2740 148 0.80 28.20 1.15 0.22 9.60| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.60 max = 1477.36 mean = 215.82| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 23.05| |phase err.(test): min = 0.00 max = 89.94 mean = 22.93| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.266 1557 Z= 5.641 Angle : 5.182 20.690 2118 Z= 3.682 Chirality : 0.386 1.022 243 Planarity : 0.032 0.094 284 Dihedral : 14.037 83.732 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.54 % Allowed : 0.54 % Favored : 98.92 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 30.27 % 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: -2.63 (0.45), residues: 224 helix: -2.81 (0.33), residues: 109 sheet: -0.30 (0.68), residues: 38 loop : -0.38 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.087 0.025 ARG A 28 TYR 0.080 0.032 TYR A 141 PHE 0.098 0.039 PHE A 119 HIS 0.026 0.012 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795464 | | target function (ml) not normalized (work): 232878.907119 | | target function (ml) not normalized (free): 11865.045426 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2568 0.2610 0.1942 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2568 0.2610 0.1942 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1985 0.1942 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2005 0.2009 0.1956 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1648 0.1642 0.1756 n_refl.: 87594 remove outliers: r(all,work,free)=0.1647 0.1642 0.1756 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 0.3819 386.300 356.639 0.669 1.003 0.401 11.894-9.307 99.02 97 4 0.1844 613.619 593.824 0.924 1.003 0.380 9.237-7.194 100.00 213 7 0.2167 501.865 490.910 0.964 1.003 0.352 7.162-5.571 100.00 427 22 0.2221 376.622 364.726 0.934 1.003 0.295 5.546-4.326 100.00 867 58 0.1277 517.008 511.095 0.962 1.003 0.224 4.315-3.360 100.00 1859 96 0.1136 491.679 487.418 1.003 1.002 0.158 3.356-2.611 100.00 3867 181 0.1419 323.007 319.810 0.999 1.002 0.057 2.608-2.026 99.99 8198 413 0.1373 214.124 211.929 1.006 1.000 0.000 2.025-1.573 100.00 17313 902 0.1653 104.567 103.917 1.014 0.998 0.000 1.573-1.221 100.00 36679 1900 0.2077 46.369 45.002 1.006 0.994 0.000 1.221-1.150 99.97 13689 708 0.2594 29.216 26.958 0.977 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0443 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1642 r_free=0.1756 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1643 r_free=0.1754 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.362160 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2018.379591 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 0.1209 0.1461 0.0252 0.007 1.0 1.3 0.5 0.0 0 12.681 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 14.61 2.52 3.013 19.052 2018.380 0.017 12.38 15.37 2.99 3.172 19.528 2018.380 0.016 Individual atomic B min max mean iso aniso Overall: 8.60 118.43 20.98 2.89 0 1785 Protein: 8.60 118.43 17.84 2.89 0 1519 Water: 11.07 114.63 39.21 N/A 0 258 Other: 22.94 36.16 28.92 N/A 0 8 Chain A: 8.60 118.43 20.98 N/A 0 1785 Histogram: Values Number of atoms 8.60 - 19.58 1214 19.58 - 30.57 224 30.57 - 41.55 162 41.55 - 52.53 100 52.53 - 63.51 56 63.51 - 74.50 17 74.50 - 85.48 5 85.48 - 96.46 4 96.46 - 107.45 0 107.45 - 118.43 3 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1538 r_work=0.1243 r_free=0.1543 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1243 r_free = 0.1543 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 = 0.1243 r_free = 0.1547 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 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= 0.1243 r_free= 0.1547 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015389 | | target function (ls_wunit_k1) not normalized (work): 1281.869218 | | target function (ls_wunit_k1) not normalized (free): 112.583858 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1258 0.1243 0.1547 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1692 0.1691 0.1767 n_refl.: 87593 remove outliers: r(all,work,free)=0.1692 0.1691 0.1767 n_refl.: 87593 overall B=0.17 to atoms: r(all,work,free)=0.1720 0.1719 0.1787 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1257 0.1242 0.1542 n_refl.: 87593 remove outliers: r(all,work,free)=0.1256 0.1242 0.1542 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 0.3588 299.092 279.300 0.633 1.003 0.380 11.894-9.307 99.02 97 4 0.1596 479.129 467.770 0.905 1.003 0.380 9.237-7.194 100.00 213 7 0.1837 391.869 386.588 0.947 1.003 0.340 7.162-5.571 100.00 427 22 0.1705 294.076 289.059 0.924 1.003 0.258 5.546-4.326 100.00 867 58 0.0912 403.693 401.160 0.946 1.003 0.204 4.315-3.360 100.00 1859 96 0.0776 383.915 382.852 0.991 1.002 0.179 3.356-2.611 100.00 3867 181 0.1023 252.212 251.472 0.997 1.002 0.109 2.608-2.026 99.99 8198 413 0.0973 167.194 166.621 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1206 81.649 81.823 1.016 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1651 36.206 35.662 1.006 0.997 0.000 1.221-1.150 99.97 13689 708 0.2360 22.813 21.307 0.971 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0386 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1242 r_free=0.1542 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=0.1242 r_free=0.1542 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1242 r_free=0.1542 | n_water=258 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1252 r_free=0.1539 | n_water=252 | time (s): 26.010 (total time: 28.380) Filter (q & B) r_work=0.1255 r_free=0.1539 | n_water=249 | time (s): 3.690 (total time: 32.070) Compute maps r_work=0.1255 r_free=0.1539 | n_water=249 | time (s): 1.810 (total time: 33.880) Filter (map) r_work=0.1278 r_free=0.1551 | n_water=234 | time (s): 3.690 (total time: 37.570) Find peaks r_work=0.1278 r_free=0.1551 | n_water=234 | time (s): 0.700 (total time: 38.270) Add new water r_work=0.1429 r_free=0.1709 | n_water=455 | time (s): 3.710 (total time: 41.980) Refine new water occ: r_work=0.1327 r_free=0.1553 adp: r_work=0.1247 r_free=0.1504 occ: r_work=0.1261 r_free=0.1498 adp: r_work=0.1226 r_free=0.1484 occ: r_work=0.1229 r_free=0.1475 adp: r_work=0.1219 r_free=0.1477 ADP+occupancy (water only), MIN, final r_work=0.1219 r_free=0.1477 r_work=0.1219 r_free=0.1477 | n_water=455 | time (s): 87.310 (total time: 129.290) Filter (q & B) r_work=0.1226 r_free=0.1482 | n_water=435 | time (s): 3.770 (total time: 133.060) Filter (dist only) r_work=0.1226 r_free=0.1482 | n_water=435 | time (s): 41.430 (total time: 174.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.397103 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1585.814612 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1225 0.1515 0.0290 0.007 0.9 3.8 0.5 0.0 0 12.699 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 15.15 2.90 3.787 23.192 1585.815 0.015 11.94 14.87 2.93 4.164 23.005 1585.815 0.015 Individual atomic B min max mean iso aniso Overall: 8.68 114.27 23.21 2.63 201 1761 Protein: 8.68 114.27 17.67 2.63 0 1519 Water: 10.95 72.26 42.43 N/A 201 234 Other: 23.63 35.45 28.65 N/A 0 8 Chain A: 8.68 114.27 20.38 N/A 0 1761 Chain S: 15.79 70.99 48.00 N/A 201 0 Histogram: Values Number of atoms 8.68 - 19.24 1204 19.24 - 29.80 254 29.80 - 40.36 189 40.36 - 50.92 145 50.92 - 61.47 107 61.47 - 72.03 51 72.03 - 82.59 6 82.59 - 93.15 3 93.15 - 103.71 1 103.71 - 114.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1487 r_work=0.1194 r_free=0.1486 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1486 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 = 0.1196 r_free = 0.1476 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.18 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= 0.1196 r_free= 0.1476 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013883 | | target function (ls_wunit_k1) not normalized (work): 1156.374582 | | target function (ls_wunit_k1) not normalized (free): 102.876889 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1196 0.1476 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1609 0.1605 0.1727 n_refl.: 87592 remove outliers: r(all,work,free)=0.1609 0.1605 0.1727 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1614 0.1609 0.1730 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1192 0.1474 n_refl.: 87592 remove outliers: r(all,work,free)=0.1204 0.1191 0.1474 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 0.3409 295.028 272.282 0.637 0.940 0.370 11.894-9.307 99.02 97 4 0.1526 479.129 476.851 0.980 0.940 0.360 9.237-7.194 100.00 213 7 0.1651 391.869 392.623 1.041 0.940 0.290 7.162-5.571 100.00 427 22 0.1481 294.076 290.424 1.006 0.941 0.229 5.546-4.326 100.00 867 58 0.0822 403.693 400.975 1.019 0.941 0.210 4.315-3.360 100.00 1859 96 0.0710 383.915 382.775 1.066 0.941 0.200 3.356-2.611 100.00 3867 181 0.0957 252.212 251.571 1.074 0.941 0.150 2.608-2.026 99.99 8198 413 0.0958 167.194 166.790 1.082 0.942 0.000 2.025-1.573 100.00 17313 902 0.1168 81.649 81.846 1.090 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1603 36.206 35.710 1.076 0.945 0.000 1.221-1.150 99.97 13689 708 0.2337 22.813 21.367 1.034 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0442 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1474 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1474 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1474 | n_water=435 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1192 r_free=0.1474 | n_water=433 | time (s): 37.720 (total time: 39.980) Filter (q & B) r_work=0.1193 r_free=0.1476 | n_water=431 | time (s): 2.400 (total time: 42.380) Compute maps r_work=0.1193 r_free=0.1476 | n_water=431 | time (s): 1.420 (total time: 43.800) Filter (map) r_work=0.1236 r_free=0.1474 | n_water=291 | time (s): 2.640 (total time: 46.440) Find peaks r_work=0.1236 r_free=0.1474 | n_water=291 | time (s): 0.570 (total time: 47.010) Add new water r_work=0.1361 r_free=0.1599 | n_water=479 | time (s): 2.620 (total time: 49.630) Refine new water occ: r_work=0.1257 r_free=0.1512 adp: r_work=0.1259 r_free=0.1513 occ: r_work=0.1235 r_free=0.1495 adp: r_work=0.1234 r_free=0.1494 occ: r_work=0.1220 r_free=0.1484 adp: r_work=0.1214 r_free=0.1480 ADP+occupancy (water only), MIN, final r_work=0.1214 r_free=0.1480 r_work=0.1214 r_free=0.1480 | n_water=479 | time (s): 200.960 (total time: 250.590) Filter (q & B) r_work=0.1217 r_free=0.1481 | n_water=444 | time (s): 2.940 (total time: 253.530) Filter (dist only) r_work=0.1217 r_free=0.1481 | n_water=444 | time (s): 35.440 (total time: 288.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.079934 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.373788 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 0.1227 0.1449 0.0222 0.006 0.9 3.8 0.5 0.0 0 1.040 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.49 2.22 3.630 22.068 50.374 3.724 12.10 14.02 1.92 4.121 21.875 50.374 3.653 Individual atomic B min max mean iso aniso Overall: 9.22 109.72 21.57 2.33 212 1759 Protein: 9.22 109.72 17.22 2.33 0 1519 Water: 11.35 71.16 36.38 N/A 212 232 Other: 19.79 31.53 25.79 N/A 0 8 Chain A: 9.22 109.72 19.89 N/A 0 1759 Chain S: 15.90 60.22 35.50 N/A 212 0 Histogram: Values Number of atoms 9.22 - 19.27 1236 19.27 - 29.32 271 29.32 - 39.37 226 39.37 - 49.42 133 49.42 - 59.47 71 59.47 - 69.52 21 69.52 - 79.57 7 79.57 - 89.62 3 89.62 - 99.67 1 99.67 - 109.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1402 r_work=0.1211 r_free=0.1403 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1211 r_free = 0.1403 target_work(ml) = 3.653 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1400 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.11 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= 0.1205 r_free= 0.1400 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.650664 | | target function (ml) not normalized (work): 304074.760824 | | target function (ml) not normalized (free): 16062.289083 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1205 0.1400 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1541 0.1541 0.1579 n_refl.: 87589 remove outliers: r(all,work,free)=0.1541 0.1541 0.1579 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1538 0.1538 0.1577 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1197 0.1371 n_refl.: 87589 remove outliers: r(all,work,free)=0.1202 0.1193 0.1371 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 0.3933 287.160 259.964 0.467 1.000 0.297 11.894-9.307 95.10 93 4 0.2312 468.824 456.374 0.856 1.002 0.280 9.237-7.194 98.64 210 7 0.2372 385.422 386.745 0.944 1.002 0.175 7.162-5.571 100.00 427 22 0.2023 294.076 283.637 0.914 1.002 0.165 5.546-4.326 100.00 867 58 0.1087 403.693 399.498 0.951 1.002 0.160 4.315-3.360 100.00 1859 96 0.0934 383.915 381.236 0.994 1.002 0.160 3.356-2.611 100.00 3867 181 0.1151 252.212 250.425 1.000 1.002 0.130 2.608-2.026 99.99 8198 413 0.1046 167.194 166.248 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1002 81.649 81.793 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1291 36.206 35.783 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2132 22.813 21.428 0.981 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0385 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 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=0.1193 r_free=0.1371 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1371 | n_water=444 | time (s): 2.030 (total time: 2.030) Filter (dist) r_work=0.1193 r_free=0.1372 | n_water=443 | time (s): 39.320 (total time: 41.350) Filter (q & B) r_work=0.1193 r_free=0.1372 | n_water=441 | time (s): 2.630 (total time: 43.980) Compute maps r_work=0.1193 r_free=0.1372 | n_water=441 | time (s): 1.570 (total time: 45.550) Filter (map) r_work=0.1220 r_free=0.1382 | n_water=311 | time (s): 2.860 (total time: 48.410) Find peaks r_work=0.1220 r_free=0.1382 | n_water=311 | time (s): 0.520 (total time: 48.930) Add new water r_work=0.1286 r_free=0.1452 | n_water=480 | time (s): 2.710 (total time: 51.640) Refine new water occ: r_work=0.1212 r_free=0.1383 adp: r_work=0.1212 r_free=0.1384 occ: r_work=0.1196 r_free=0.1372 adp: r_work=0.1195 r_free=0.1371 occ: r_work=0.1186 r_free=0.1363 adp: r_work=0.1182 r_free=0.1359 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1359 r_work=0.1182 r_free=0.1359 | n_water=480 | time (s): 133.980 (total time: 185.620) Filter (q & B) r_work=0.1189 r_free=0.1367 | n_water=443 | time (s): 2.770 (total time: 188.390) Filter (dist only) r_work=0.1189 r_free=0.1365 | n_water=442 | time (s): 37.900 (total time: 226.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.306298 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.204198 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 0.1190 0.1362 0.0172 0.007 1.0 5.8 0.5 0.0 0 1.153 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.62 1.72 3.430 21.493 51.204 3.635 11.81 13.61 1.81 3.833 21.372 51.204 3.620 Individual atomic B min max mean iso aniso Overall: 9.29 105.58 21.22 2.19 213 1756 Protein: 9.29 105.58 16.93 2.19 0 1519 Water: 11.34 69.70 35.93 N/A 213 229 Other: 20.20 28.51 24.29 N/A 0 8 Chain A: 9.29 105.58 19.50 N/A 0 1756 Chain S: 15.26 60.08 35.41 N/A 213 0 Histogram: Values Number of atoms 9.29 - 18.92 1229 18.92 - 28.55 287 28.55 - 38.18 211 38.18 - 47.81 128 47.81 - 57.44 77 57.44 - 67.07 24 67.07 - 76.70 8 76.70 - 86.32 2 86.32 - 95.95 1 95.95 - 105.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.1181 r_free=0.1361 r_work=0.1181 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1181 r_free = 0.1362 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1177 r_free = 0.1358 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1177 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.618859 | | target function (ml) not normalized (work): 301389.439769 | | target function (ml) not normalized (free): 15931.965562 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1186 0.1177 0.1358 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1506 0.1504 0.1570 n_refl.: 87579 remove outliers: r(all,work,free)=0.1506 0.1504 0.1570 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1503 0.1501 0.1568 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1185 0.1176 0.1361 n_refl.: 87579 remove outliers: r(all,work,free)=0.1184 0.1174 0.1361 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4067 289.753 251.878 0.440 0.999 0.310 11.894-9.307 94.12 92 4 0.2412 472.704 450.054 0.832 1.001 0.246 9.237-7.194 97.73 208 7 0.2443 384.484 377.877 0.914 1.001 0.157 7.162-5.571 100.00 427 22 0.2254 294.076 281.839 0.903 1.002 0.130 5.546-4.326 100.00 867 58 0.1152 403.693 399.391 0.951 1.002 0.130 4.315-3.360 100.00 1859 96 0.0944 383.915 381.732 0.993 1.002 0.130 3.356-2.611 100.00 3867 181 0.1137 252.212 250.697 1.001 1.002 0.090 2.608-2.026 99.99 8198 413 0.1017 167.194 166.381 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0957 81.649 81.919 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1235 36.206 35.831 1.020 0.999 0.000 1.221-1.150 99.97 13689 708 0.2121 22.813 21.398 0.977 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0373 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1174 r_free=0.1361 After: r_work=0.1175 r_free=0.1361 ================================== NQH flips ================================== r_work=0.1175 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=0.1175 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1175 r_free=0.1361 | n_water=442 | time (s): 1.680 (total time: 1.680) Filter (dist) r_work=0.1175 r_free=0.1361 | n_water=442 | time (s): 35.380 (total time: 37.060) Filter (q & B) r_work=0.1175 r_free=0.1361 | n_water=442 | time (s): 0.810 (total time: 37.870) Compute maps r_work=0.1175 r_free=0.1361 | n_water=442 | time (s): 1.190 (total time: 39.060) Filter (map) r_work=0.1200 r_free=0.1375 | n_water=330 | time (s): 3.150 (total time: 42.210) Find peaks r_work=0.1200 r_free=0.1375 | n_water=330 | time (s): 0.670 (total time: 42.880) Add new water r_work=0.1249 r_free=0.1418 | n_water=490 | time (s): 3.010 (total time: 45.890) Refine new water occ: r_work=0.1186 r_free=0.1352 adp: r_work=0.1187 r_free=0.1355 occ: r_work=0.1174 r_free=0.1344 adp: r_work=0.1173 r_free=0.1345 occ: r_work=0.1165 r_free=0.1340 adp: r_work=0.1162 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1162 r_free=0.1339 r_work=0.1162 r_free=0.1339 | n_water=490 | time (s): 123.850 (total time: 169.740) Filter (q & B) r_work=0.1170 r_free=0.1346 | n_water=451 | time (s): 3.270 (total time: 173.010) Filter (dist only) r_work=0.1170 r_free=0.1345 | n_water=449 | time (s): 39.260 (total time: 212.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.975547 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.886446 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 0.1206 0.1372 0.0166 0.007 1.1 6.7 0.5 0.0 0 0.988 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.72 1.66 3.300 21.162 38.886 3.631 12.11 13.75 1.64 3.383 21.129 38.886 3.630 Individual atomic B min max mean iso aniso Overall: 9.25 103.20 21.13 2.07 221 1755 Protein: 9.25 103.20 16.82 2.07 0 1519 Water: 11.40 69.42 35.64 N/A 221 228 Other: 19.95 28.10 24.12 N/A 0 8 Chain A: 9.25 103.20 19.38 N/A 0 1755 Chain S: 14.86 59.40 35.04 N/A 221 0 Histogram: Values Number of atoms 9.25 - 18.64 1222 18.64 - 28.04 286 28.04 - 37.43 211 37.43 - 46.83 142 46.83 - 56.22 77 56.22 - 65.62 21 65.62 - 75.02 12 75.02 - 84.41 2 84.41 - 93.81 1 93.81 - 103.20 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1375 r_work=0.1211 r_free=0.1375 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1211 r_free = 0.1375 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1372 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1205 r_free= 0.1372 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.627994 | | target function (ml) not normalized (work): 302135.744101 | | target function (ml) not normalized (free): 15960.970303 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1425 0.1396 5.6891 5.6493| | 2: 3.57 - 2.84 1.00 2888 124 0.1113 0.1482 5.1969 5.2559| | 3: 2.83 - 2.48 1.00 2820 163 0.1237 0.1253 5.0115 5.024| | 4: 2.47 - 2.25 1.00 2825 136 0.1030 0.1147 4.7093 4.7645| | 5: 2.25 - 2.09 1.00 2756 127 0.1008 0.1178 4.6534 4.7393| | 6: 2.09 - 1.97 1.00 2846 113 0.0982 0.1187 4.3578 4.4965| | 7: 1.97 - 1.87 1.00 2787 165 0.1010 0.1206 4.0848 4.1633| | 8: 1.87 - 1.79 1.00 2789 144 0.1032 0.1226 3.9972 4.0712| | 9: 1.79 - 1.72 1.00 2745 138 0.0973 0.1269 3.7278 3.888| | 10: 1.72 - 1.66 1.00 2831 160 0.1021 0.1280 3.6419 3.7637| | 11: 1.66 - 1.61 1.00 2712 147 0.0972 0.1122 3.5732 3.6128| | 12: 1.61 - 1.56 1.00 2773 144 0.0926 0.1179 3.355 3.4865| | 13: 1.56 - 1.52 1.00 2745 130 0.0991 0.1097 3.3499 3.4465| | 14: 1.52 - 1.48 1.00 2803 134 0.0995 0.1098 3.2692 3.3424| | 15: 1.48 - 1.45 1.00 2738 128 0.1030 0.1346 3.1834 3.3152| | 16: 1.45 - 1.42 1.00 2756 161 0.1071 0.1307 3.1581 3.2729| | 17: 1.42 - 1.39 1.00 2785 139 0.1133 0.1321 3.1237 3.2593| | 18: 1.39 - 1.36 1.00 2741 179 0.1171 0.1386 3.0982 3.2848| | 19: 1.36 - 1.34 1.00 2807 134 0.1226 0.1614 3.102 3.2849| | 20: 1.34 - 1.32 1.00 2696 147 0.1324 0.1491 3.0935 3.144| | 21: 1.32 - 1.30 1.00 2785 112 0.1421 0.1651 3.094 3.1744| | 22: 1.29 - 1.27 1.00 2704 152 0.1484 0.1920 3.0934 3.2853| | 23: 1.27 - 1.26 1.00 2802 156 0.1582 0.1838 3.108 3.2121| | 24: 1.26 - 1.24 1.00 2744 132 0.1633 0.1791 3.0996 3.2079| | 25: 1.24 - 1.22 1.00 2733 148 0.1803 0.2322 3.1135 3.2956| | 26: 1.22 - 1.21 1.00 2727 135 0.1869 0.1770 3.1286 3.1965| | 27: 1.21 - 1.19 1.00 2814 148 0.2014 0.2099 3.1445 3.1524| | 28: 1.19 - 1.18 1.00 2671 147 0.2144 0.2332 3.1415 3.1639| | 29: 1.18 - 1.16 1.00 2800 134 0.2224 0.2359 3.1302 3.2203| | 30: 1.16 - 1.15 1.00 2739 148 0.2381 0.2498 3.1185 3.1679| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2917 171 0.95 9.06 1.00 0.97 6276.46| | 2: 3.57 - 2.84 2888 124 0.92 13.31 1.01 0.97 6276.46| | 3: 2.83 - 2.48 2820 163 0.89 17.46 0.98 0.97 5262.93| | 4: 2.47 - 2.25 2825 136 0.91 14.57 1.00 0.98 2649.34| | 5: 2.25 - 2.09 2756 127 0.89 16.84 1.01 0.98 2649.34| | 6: 2.09 - 1.97 2846 113 0.92 13.66 1.02 0.98 1559.79| | 7: 1.97 - 1.87 2787 165 0.94 10.84 1.02 0.97 630.54| | 8: 1.87 - 1.79 2789 144 0.91 14.42 0.99 0.97 630.54| | 9: 1.79 - 1.72 2745 138 0.93 11.44 0.98 0.97 340.40| | 10: 1.72 - 1.66 2831 160 0.93 12.21 0.97 0.97 282.29| | 11: 1.66 - 1.61 2712 147 0.93 12.88 0.98 0.97 269.58| | 12: 1.61 - 1.56 2773 144 0.95 9.64 0.99 0.97 149.69| | 13: 1.56 - 1.52 2745 130 0.94 11.20 1.02 0.97 149.69| | 14: 1.52 - 1.48 2803 134 0.94 11.32 1.02 0.98 133.92| | 15: 1.48 - 1.45 2738 128 0.95 10.59 1.01 0.98 105.04| | 16: 1.45 - 1.42 2756 161 0.94 11.71 1.01 0.98 105.04| | 17: 1.42 - 1.39 2785 139 0.94 11.60 1.01 0.98 95.31| | 18: 1.39 - 1.36 2741 179 0.94 11.99 1.01 0.98 89.69| | 19: 1.36 - 1.34 2807 134 0.94 12.51 1.00 0.98 89.69| | 20: 1.34 - 1.32 2696 147 0.94 12.61 0.99 0.97 84.36| | 21: 1.32 - 1.30 2785 112 0.93 13.53 0.98 0.97 83.98| | 22: 1.29 - 1.27 2704 152 0.93 14.02 0.98 0.96 84.03| | 23: 1.27 - 1.26 2802 156 0.92 14.99 0.97 0.95 84.28| | 24: 1.26 - 1.24 2744 132 0.92 15.11 0.97 0.95 84.28| | 25: 1.24 - 1.22 2733 148 0.91 16.47 0.96 0.94 85.54| | 26: 1.22 - 1.21 2727 135 0.90 18.20 1.02 0.93 86.93| | 27: 1.21 - 1.19 2814 148 0.89 18.85 1.02 0.93 86.93| | 28: 1.19 - 1.18 2671 147 0.88 20.27 1.01 0.93 89.97| | 29: 1.18 - 1.16 2800 134 0.88 20.59 0.99 0.93 91.11| | 30: 1.16 - 1.15 2739 148 0.86 22.04 0.98 0.93 91.11| |alpha: min = 0.93 max = 0.98 mean = 0.97| |beta: min = 83.98 max = 6276.46 mean = 980.32| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.91 mean = 14.12| |phase err.(test): min = 0.00 max = 88.59 mean = 14.23| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1205 0.1372 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1520 0.1517 0.1591 n_refl.: 87575 remove outliers: r(all,work,free)=0.1520 0.1517 0.1591 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1517 0.1515 0.1589 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1205 0.1375 n_refl.: 87575 remove outliers: r(all,work,free)=0.1213 0.1205 0.1375 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 0.4145 289.753 256.606 0.453 0.998 0.307 11.894-9.307 93.14 91 4 0.2476 466.399 453.436 0.843 1.000 0.202 9.237-7.194 97.73 208 7 0.2517 384.484 376.693 0.909 1.000 0.120 7.162-5.571 100.00 427 22 0.2255 294.076 281.151 0.898 1.001 0.120 5.546-4.326 100.00 867 58 0.1195 403.693 399.369 0.953 1.001 0.119 4.315-3.360 100.00 1859 96 0.0998 383.915 381.596 0.997 1.001 0.115 3.356-2.611 100.00 3867 181 0.1180 252.212 250.311 1.002 1.001 0.048 2.608-2.026 99.99 8198 413 0.1051 167.194 166.134 1.013 1.000 0.000 2.025-1.573 100.00 17313 902 0.0992 81.649 81.883 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1237 36.206 35.852 1.021 0.999 0.000 1.221-1.150 99.97 13689 708 0.2122 22.813 21.429 0.977 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0382 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2609 0.1941 0.083 5.182 8.8 119.3 19.9 258 0.000 1_bss: 0.1642 0.1756 0.083 5.182 9.0 119.5 20.1 258 0.000 1_settarget: 0.1642 0.1756 0.083 5.182 9.0 119.5 20.1 258 0.000 1_nqh: 0.1643 0.1754 0.083 5.182 9.0 119.5 20.1 258 0.003 1_weight: 0.1643 0.1754 0.083 5.182 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1209 0.1461 0.007 0.954 9.0 119.5 20.1 258 0.126 1_adp: 0.1239 0.1538 0.007 0.954 8.6 118.4 21.0 258 0.126 1_regHadp: 0.1243 0.1543 0.007 0.954 8.6 118.4 21.0 258 0.126 1_occ: 0.1243 0.1547 0.007 0.954 8.6 118.4 21.0 258 0.126 2_bss: 0.1242 0.1542 0.007 0.954 8.8 118.6 21.1 258 0.126 2_settarget: 0.1242 0.1542 0.007 0.954 8.8 118.6 21.1 258 0.126 2_updatecdl: 0.1242 0.1542 0.007 0.963 8.8 118.6 21.1 258 0.126 2_nqh: 0.1242 0.1542 0.007 0.963 8.8 118.6 21.1 258 0.126 2_sol: 0.1226 0.1482 0.007 0.963 8.8 118.6 23.5 435 n/a 2_weight: 0.1226 0.1482 0.007 0.963 8.8 118.6 23.5 435 n/a 2_xyzrec: 0.1225 0.1515 0.007 0.875 8.8 118.6 23.5 435 n/a 2_adp: 0.1194 0.1487 0.007 0.875 8.7 114.3 23.2 435 n/a 2_regHadp: 0.1194 0.1486 0.007 0.875 8.7 114.3 23.2 435 n/a 2_occ: 0.1196 0.1476 0.007 0.875 8.7 114.3 23.2 435 n/a 3_bss: 0.1191 0.1474 0.007 0.875 8.7 114.3 23.2 435 n/a 3_settarget: 0.1191 0.1474 0.007 0.875 8.7 114.3 23.2 435 n/a 3_updatecdl: 0.1191 0.1474 0.007 0.876 8.7 114.3 23.2 435 n/a 3_nqh: 0.1191 0.1474 0.007 0.876 8.7 114.3 23.2 435 n/a 3_sol: 0.1217 0.1481 0.007 0.876 8.7 114.3 21.9 444 n/a 3_weight: 0.1217 0.1481 0.007 0.876 8.7 114.3 21.9 444 n/a 3_xyzrec: 0.1227 0.1449 0.006 0.922 8.7 114.3 21.9 444 n/a 3_adp: 0.1210 0.1402 0.006 0.922 9.2 109.7 21.6 444 n/a 3_regHadp: 0.1211 0.1403 0.006 0.922 9.2 109.7 21.6 444 n/a 3_occ: 0.1205 0.1400 0.006 0.922 9.2 109.7 21.6 444 n/a 4_bss: 0.1193 0.1371 0.006 0.922 9.2 109.7 21.6 444 n/a 4_settarget: 0.1193 0.1371 0.006 0.922 9.2 109.7 21.6 444 n/a 4_updatecdl: 0.1193 0.1371 0.006 0.920 9.2 109.7 21.6 444 n/a 4_nqh: 0.1193 0.1371 0.006 0.920 9.2 109.7 21.6 444 n/a 4_sol: 0.1189 0.1365 0.006 0.920 9.2 109.7 21.4 442 n/a 4_weight: 0.1189 0.1365 0.006 0.920 9.2 109.7 21.4 442 n/a 4_xyzrec: 0.1190 0.1362 0.007 0.977 9.2 109.7 21.4 442 n/a 4_adp: 0.1181 0.1361 0.007 0.977 9.3 105.6 21.2 442 n/a 4_regHadp: 0.1181 0.1362 0.007 0.977 9.3 105.6 21.2 442 n/a 4_occ: 0.1177 0.1358 0.007 0.977 9.3 105.6 21.2 442 n/a 5_bss: 0.1174 0.1361 0.007 0.977 9.3 105.6 21.2 442 n/a 5_settarget: 0.1174 0.1361 0.007 0.977 9.3 105.6 21.2 442 n/a 5_updatecdl: 0.1174 0.1361 0.007 0.979 9.3 105.6 21.2 442 n/a 5_setrh: 0.1175 0.1361 0.007 0.979 9.3 105.6 21.2 442 n/a 5_nqh: 0.1175 0.1361 0.007 0.979 9.3 105.6 21.2 442 n/a 5_sol: 0.1170 0.1345 0.007 0.979 9.3 105.6 21.2 449 n/a 5_weight: 0.1170 0.1345 0.007 0.979 9.3 105.6 21.2 449 n/a 5_xyzrec: 0.1206 0.1372 0.007 1.060 9.3 105.6 21.2 449 n/a 5_adp: 0.1211 0.1375 0.007 1.060 9.2 103.2 21.1 449 n/a 5_regHadp: 0.1211 0.1375 0.007 1.060 9.2 103.2 21.1 449 n/a 5_occ: 0.1205 0.1372 0.007 1.060 9.2 103.2 21.1 449 n/a end: 0.1205 0.1375 0.007 1.060 9.2 103.2 21.1 449 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8569971_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8569971_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.0600 Refinement macro-cycles (run) : 3320.2100 Write final files (write_after_run_outputs) : 68.4500 Total : 3393.7200 Total CPU time: 57.17 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:08:50 PST -0800 (1735452530.09 s) Start R-work = 0.1642, R-free = 0.1756 Final R-work = 0.1205, R-free = 0.1375 =============================================================================== Job complete usr+sys time: 3541.59 seconds wall clock time: 64 minutes 12.18 seconds (3852.18 seconds total)