Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8008321.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8008321.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8008321.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: 2.18, 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: 0.82 Conformation dependent library (CDL) restraints added in 304.1 milliseconds Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 533 0.92 - 1.17: 1104 1.17 - 1.43: 667 1.43 - 1.69: 824 1.69 - 1.94: 25 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 104 " pdb=" CA ALA A 104 " ideal model delta sigma weight residual 1.455 1.703 -0.248 1.25e-02 6.40e+03 3.95e+02 bond pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 1.246 1.419 -0.173 9.20e-03 1.18e+04 3.52e+02 bond pdb=" N THR A 34 " pdb=" CA THR A 34 " ideal model delta sigma weight residual 1.458 1.241 0.216 1.22e-02 6.72e+03 3.15e+02 bond pdb=" C ILE A 21 " pdb=" O ILE A 21 " ideal model delta sigma weight residual 1.242 1.091 0.151 8.60e-03 1.35e+04 3.07e+02 bond pdb=" C ARG A 98 " pdb=" N ALYS A 99 " ideal model delta sigma weight residual 1.333 1.566 -0.233 1.38e-02 5.25e+03 2.85e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 3184 4.72 - 9.43: 1852 9.43 - 14.15: 610 14.15 - 18.87: 118 18.87 - 23.59: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA AGLU A 90 " pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 120.82 137.50 -16.68 1.05e+00 9.07e-01 2.52e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.35 134.89 -13.54 9.20e-01 1.18e+00 2.17e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 121.53 109.25 12.28 8.70e-01 1.32e+00 1.99e+02 angle pdb=" O ALA A 165 " pdb=" C ALA A 165 " pdb=" N LEU A 166 " ideal model delta sigma weight residual 122.15 106.84 15.31 1.14e+00 7.69e-01 1.80e+02 angle pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 109.00 95.79 13.21 1.00e+00 1.00e+00 1.74e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.44: 949 18.44 - 36.88: 120 36.88 - 55.31: 30 55.31 - 73.75: 10 73.75 - 92.19: 2 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 -152.09 -27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+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 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.222: 95 0.222 - 0.440: 77 0.440 - 0.658: 49 0.658 - 0.877: 16 0.877 - 1.095: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA SER A 47 " pdb=" N SER A 47 " pdb=" C SER A 47 " pdb=" CB SER A 47 " both_signs ideal model delta sigma weight residual False 2.51 3.61 -1.09 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA ALA A 56 " pdb=" N ALA A 56 " pdb=" C ALA A 56 " pdb=" CB ALA A 56 " both_signs ideal model delta sigma weight residual False 2.48 3.48 -1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.58 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.057 2.00e-02 2.50e+03 7.67e-02 1.77e+02 pdb=" CG PHE A 162 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.102 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.076 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.080 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.126 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.066 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.072 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.098 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.111 2.00e-02 2.50e+03 6.98e-02 1.46e+02 pdb=" CG PHE A 119 " -0.094 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.074 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.137 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.022 2.00e-02 2.50e+03 6.61e-02 1.31e+02 pdb=" CG ATYR A 67 " -0.027 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.103 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.045 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.038 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.083 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.110 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.055 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.016 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.34: 1194 2.34 - 2.90: 8151 2.90 - 3.47: 10475 3.47 - 4.03: 15175 4.03 - 4.60: 21550 Nonbonded interactions: 56545 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.770 2.100 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.792 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.815 2.100 nonbonded pdb=" O ALA A 6 " pdb=" H THR A 34 " model vdw 1.830 2.450 nonbonded pdb=" H CYS A 46 " pdb=" O VAL A 50 " model vdw 1.849 2.450 ... (remaining 56540 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_8008321_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= 0.2613 r_free= 0.1952 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794815 | | target function (ml) not normalized (work): 232824.818337 | | target function (ml) not normalized (free): 11876.937492 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3032 0.2090 7.0691 4.9474| | 2: 3.57 - 2.84 1.00 2876 122 0.2427 0.1709 4.3461 4.3296| | 3: 2.84 - 2.48 1.00 2833 165 0.2342 0.1781 4.127 4.1822| | 4: 2.47 - 2.25 1.00 2825 136 0.2337 0.1369 3.8288 3.8421| | 5: 2.25 - 2.09 1.00 2756 127 0.2519 0.1379 3.7969 3.8051| | 6: 2.09 - 1.97 1.00 2846 113 0.2562 0.1741 3.4585 3.549| | 7: 1.97 - 1.87 1.00 2787 165 0.2604 0.1899 3.1494 3.1835| | 8: 1.87 - 1.79 1.00 2789 144 0.2463 0.2053 3.048 3.1722| | 9: 1.79 - 1.72 1.00 2745 138 0.2418 0.1781 2.9081 2.9368| | 10: 1.72 - 1.66 1.00 2789 158 0.2435 0.2018 2.8188 2.91| | 11: 1.66 - 1.61 1.00 2740 147 0.2493 0.2015 2.751 2.8205| | 12: 1.61 - 1.56 1.00 2787 146 0.2558 0.1942 2.6507 2.6445| | 13: 1.56 - 1.52 1.00 2745 130 0.2555 0.2022 2.5787 2.651| | 14: 1.52 - 1.48 1.00 2803 134 0.2552 0.1792 2.5144 2.487| | 15: 1.48 - 1.45 1.00 2738 128 0.2600 0.2265 2.4437 2.5492| | 16: 1.45 - 1.42 1.00 2756 161 0.2684 0.2249 2.3873 2.4291| | 17: 1.42 - 1.39 1.00 2785 139 0.2639 0.2322 2.3354 2.4593| | 18: 1.39 - 1.36 1.00 2741 179 0.2689 0.2051 2.2763 2.2963| | 19: 1.36 - 1.34 1.00 2807 134 0.2686 0.2414 2.2493 2.2562| | 20: 1.34 - 1.32 1.00 2696 147 0.2687 0.2279 2.1998 2.1957| | 21: 1.32 - 1.30 1.00 2785 112 0.2751 0.2406 2.1845 2.2095| | 22: 1.29 - 1.27 1.00 2704 152 0.2747 0.2437 2.1367 2.1821| | 23: 1.27 - 1.26 1.00 2802 156 0.2727 0.2571 2.1006 2.2086| | 24: 1.26 - 1.24 1.00 2744 132 0.2765 0.2624 2.065 2.1648| | 25: 1.24 - 1.22 1.00 2734 148 0.2803 0.2692 2.0369 2.1188| | 26: 1.22 - 1.21 1.00 2727 135 0.2878 0.2428 2.0192 2.1504| | 27: 1.21 - 1.19 1.00 2814 148 0.2985 0.2672 2.016 2.0397| | 28: 1.19 - 1.18 1.00 2671 147 0.2989 0.2756 1.9901 2.015| | 29: 1.18 - 1.16 1.00 2800 134 0.2980 0.2975 1.9647 2.0796| | 30: 1.16 - 1.15 1.00 2740 148 0.3064 0.2825 1.9376 1.9912| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.76 0.76 0.23 1469.95| | 2: 3.57 - 2.84 2876 122 0.80 25.99 1.27 0.23 1469.95| | 3: 2.84 - 2.48 2833 165 0.74 31.93 1.24 0.23 1219.61| | 4: 2.47 - 2.25 2825 136 0.81 25.70 1.25 0.25 569.92| | 5: 2.25 - 2.09 2756 127 0.77 29.52 1.28 0.25 569.92| | 6: 2.09 - 1.97 2846 113 0.83 22.76 1.30 0.25 313.40| | 7: 1.97 - 1.87 2787 165 0.90 17.01 1.29 0.26 94.61| | 8: 1.87 - 1.79 2789 144 0.85 21.71 1.25 0.26 94.61| | 9: 1.79 - 1.72 2745 138 0.88 18.84 1.23 0.25 56.95| | 10: 1.72 - 1.66 2789 158 0.87 20.21 1.23 0.25 49.41| | 11: 1.66 - 1.61 2740 147 0.85 21.61 1.24 0.25 47.70| | 12: 1.61 - 1.56 2787 146 0.88 18.51 1.24 0.25 30.31| | 13: 1.56 - 1.52 2745 130 0.86 20.57 1.24 0.25 30.31| | 14: 1.52 - 1.48 2803 134 0.86 20.83 1.23 0.25 26.92| | 15: 1.48 - 1.45 2738 128 0.87 19.99 1.22 0.25 20.73| | 16: 1.45 - 1.42 2756 161 0.85 21.73 1.24 0.25 20.73| | 17: 1.42 - 1.39 2785 139 0.87 20.82 1.21 0.25 17.91| | 18: 1.39 - 1.36 2741 179 0.86 21.78 1.22 0.25 16.27| | 19: 1.36 - 1.34 2807 134 0.85 22.49 1.22 0.25 16.27| | 20: 1.34 - 1.32 2696 147 0.86 21.51 1.21 0.25 13.61| | 21: 1.32 - 1.30 2785 112 0.85 22.31 1.20 0.25 13.42| | 22: 1.29 - 1.27 2704 152 0.85 22.90 1.21 0.25 13.17| | 23: 1.27 - 1.26 2802 156 0.85 22.74 1.21 0.24 11.91| | 24: 1.26 - 1.24 2744 132 0.84 23.91 1.20 0.24 11.91| | 25: 1.24 - 1.22 2734 148 0.83 24.85 1.20 0.24 11.44| | 26: 1.22 - 1.21 2727 135 0.83 25.26 1.20 0.23 10.92| | 27: 1.21 - 1.19 2814 148 0.81 26.29 1.21 0.23 10.92| | 28: 1.19 - 1.18 2671 147 0.81 27.17 1.18 0.23 10.47| | 29: 1.18 - 1.16 2800 134 0.80 27.83 1.17 0.22 10.30| | 30: 1.16 - 1.15 2740 148 0.78 29.27 1.16 0.22 10.30| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 10.30 max = 1469.95 mean = 214.64| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.97 mean = 23.16| |phase err.(test): min = 0.00 max = 89.63 mean = 23.00| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.248 1557 Z= 5.441 Angle : 5.290 21.328 2118 Z= 3.740 Chirality : 0.390 1.095 243 Planarity : 0.030 0.100 284 Dihedral : 14.300 92.188 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % 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: -2.21 (0.48), residues: 224 helix: -2.26 (0.39), residues: 108 sheet: -0.87 (0.87), residues: 28 loop : -0.24 (0.58), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.096 0.019 ARG A 156 TYR 0.064 0.029 TYR A 139 PHE 0.119 0.062 PHE A 164 HIS 0.045 0.027 HIS A 138 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= 0.2613 r_free= 0.1952 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794815 | | target function (ml) not normalized (work): 232824.818337 | | target function (ml) not normalized (free): 11876.937492 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2572 0.2614 0.1952 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2572 0.2614 0.1952 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1986 0.1952 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2008 0.2012 0.1967 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1644 0.1637 0.1769 n_refl.: 87594 remove outliers: r(all,work,free)=0.1643 0.1637 0.1769 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 0.3787 386.373 358.004 0.667 1.002 0.401 11.894-9.307 99.02 97 4 0.1804 613.735 591.609 0.928 1.003 0.380 9.237-7.194 100.00 213 7 0.2158 501.960 491.967 0.954 1.003 0.370 7.162-5.571 100.00 427 22 0.2171 376.693 364.251 0.936 1.003 0.310 5.546-4.326 100.00 867 58 0.1281 517.107 510.768 0.962 1.003 0.229 4.315-3.360 100.00 1859 96 0.1145 491.772 488.069 1.004 1.003 0.209 3.356-2.611 100.00 3867 181 0.1427 323.069 319.521 0.993 1.002 0.043 2.608-2.026 99.99 8198 413 0.1365 214.165 211.780 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1638 104.587 103.984 1.016 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2071 46.378 44.954 1.002 0.996 0.000 1.221-1.150 99.97 13689 708 0.2599 29.221 26.930 0.979 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0474 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1637 r_free=0.1769 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=0.1638 r_free=0.1770 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.438009 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1972.129387 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 0.1214 0.1470 0.0257 0.008 1.0 1.0 0.5 0.0 0 13.219 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 14.70 2.57 3.013 19.066 1972.129 0.017 12.43 15.45 3.02 3.183 19.544 1972.129 0.016 Individual atomic B min max mean iso aniso Overall: 8.52 118.57 21.00 2.87 0 1785 Protein: 8.52 118.57 17.89 2.87 0 1519 Water: 11.00 114.51 39.08 N/A 0 258 Other: 22.98 35.79 28.88 N/A 0 8 Chain A: 8.52 118.57 21.00 N/A 0 1785 Histogram: Values Number of atoms 8.52 - 19.53 1204 19.53 - 30.53 234 30.53 - 41.53 164 41.53 - 52.54 101 52.54 - 63.54 53 63.54 - 74.55 16 74.55 - 85.55 6 85.55 - 96.56 4 96.56 - 107.56 0 107.56 - 118.57 3 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1545 r_work=0.1248 r_free=0.1550 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1248 r_free = 0.1550 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 = 0.1249 r_free = 0.1552 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 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= 0.1249 r_free= 0.1552 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015462 | | target function (ls_wunit_k1) not normalized (work): 1287.978398 | | target function (ls_wunit_k1) not normalized (free): 114.786048 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1263 0.1249 0.1552 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1703 0.1701 0.1775 n_refl.: 87593 remove outliers: r(all,work,free)=0.1703 0.1701 0.1775 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1726 0.1725 0.1791 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1260 0.1245 0.1545 n_refl.: 87593 remove outliers: r(all,work,free)=0.1259 0.1245 0.1545 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 0.3613 298.678 277.973 0.691 0.923 0.380 11.894-9.307 99.02 97 4 0.1608 478.466 466.695 0.986 0.924 0.380 9.237-7.194 100.00 213 7 0.1815 391.326 386.139 1.029 0.924 0.340 7.162-5.571 100.00 427 22 0.1735 293.668 288.293 1.002 0.925 0.280 5.546-4.326 100.00 867 58 0.0926 403.134 400.287 1.029 0.926 0.209 4.315-3.360 100.00 1859 96 0.0781 383.383 382.372 1.076 0.927 0.199 3.356-2.611 100.00 3867 181 0.1021 251.863 251.118 1.075 0.929 0.052 2.608-2.026 99.99 8198 413 0.0977 166.962 166.369 1.084 0.932 0.000 2.025-1.573 100.00 17313 902 0.1211 81.536 81.718 1.085 0.938 0.000 1.573-1.221 100.00 36679 1900 0.1650 36.156 35.616 1.059 0.947 0.000 1.221-1.150 99.97 13689 708 0.2361 22.781 21.315 1.014 0.955 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0550 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1245 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1246 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1246 r_free=0.1546 | n_water=258 | time (s): 2.310 (total time: 2.310) Filter (dist) r_work=0.1254 r_free=0.1544 | n_water=252 | time (s): 25.870 (total time: 28.180) Filter (q & B) r_work=0.1258 r_free=0.1543 | n_water=249 | time (s): 3.770 (total time: 31.950) Compute maps r_work=0.1258 r_free=0.1543 | n_water=249 | time (s): 1.820 (total time: 33.770) Filter (map) r_work=0.1269 r_free=0.1550 | n_water=237 | time (s): 3.800 (total time: 37.570) Find peaks r_work=0.1269 r_free=0.1550 | n_water=237 | time (s): 0.710 (total time: 38.280) Add new water r_work=0.1422 r_free=0.1701 | n_water=451 | time (s): 3.730 (total time: 42.010) Refine new water occ: r_work=0.1331 r_free=0.1570 adp: r_work=0.1253 r_free=0.1512 occ: r_work=0.1265 r_free=0.1512 adp: r_work=0.1231 r_free=0.1494 occ: r_work=0.1234 r_free=0.1485 adp: r_work=0.1224 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1485 r_work=0.1224 r_free=0.1485 | n_water=451 | time (s): 81.830 (total time: 123.840) Filter (q & B) r_work=0.1229 r_free=0.1492 | n_water=431 | time (s): 3.880 (total time: 127.720) Filter (dist only) r_work=0.1229 r_free=0.1492 | n_water=431 | time (s): 39.950 (total time: 167.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.319418 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1517.191094 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 0.1526 0.0297 0.007 0.9 1.6 0.5 0.0 0 13.160 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 15.26 2.97 3.785 23.123 1517.191 0.015 11.96 14.96 3.00 4.161 22.942 1517.191 0.015 Individual atomic B min max mean iso aniso Overall: 8.70 114.27 23.06 2.60 194 1764 Protein: 8.70 114.27 17.68 2.60 0 1519 Water: 11.07 73.17 41.91 N/A 194 237 Other: 25.05 36.60 30.13 N/A 0 8 Chain A: 8.70 114.27 20.39 N/A 0 1764 Chain S: 16.61 73.17 47.42 N/A 194 0 Histogram: Values Number of atoms 8.70 - 19.25 1204 19.25 - 29.81 251 29.81 - 40.37 197 40.37 - 50.92 144 50.92 - 61.48 100 61.48 - 72.04 50 72.04 - 82.60 6 82.60 - 93.15 3 93.15 - 103.71 1 103.71 - 114.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1496 r_work=0.1196 r_free=0.1496 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1496 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 = 0.1197 r_free = 0.1494 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1197 r_free= 0.1494 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.013972 | | target function (ls_wunit_k1) not normalized (work): 1163.828281 | | target function (ls_wunit_k1) not normalized (free): 107.858369 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1197 0.1494 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1615 0.1610 0.1744 n_refl.: 87592 remove outliers: r(all,work,free)=0.1615 0.1610 0.1744 n_refl.: 87592 overall B=0.02 to atoms: r(all,work,free)=0.1619 0.1614 0.1747 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1193 0.1491 n_refl.: 87592 remove outliers: r(all,work,free)=0.1207 0.1192 0.1491 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 0.3408 294.619 271.370 0.639 0.938 0.370 11.894-9.307 99.02 97 4 0.1481 478.466 473.952 0.977 0.938 0.360 9.237-7.194 100.00 213 7 0.1685 391.326 392.642 1.049 0.939 0.280 7.162-5.571 100.00 427 22 0.1478 293.668 290.179 1.002 0.939 0.229 5.546-4.326 100.00 867 58 0.0821 403.134 400.016 1.024 0.939 0.215 4.315-3.360 100.00 1859 96 0.0701 383.383 382.446 1.069 0.939 0.210 3.356-2.611 100.00 3867 181 0.0958 251.863 251.179 1.075 0.940 0.072 2.608-2.026 99.99 8198 413 0.0961 166.962 166.509 1.084 0.941 0.000 2.025-1.573 100.00 17313 902 0.1175 81.536 81.723 1.092 0.942 0.000 1.573-1.221 100.00 36679 1900 0.1604 36.156 35.664 1.078 0.944 0.000 1.221-1.150 99.97 13689 708 0.2336 22.781 21.341 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=0.0348 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1491 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=0.1192 r_free=0.1491 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1491 | n_water=431 | time (s): 1.970 (total time: 1.970) Filter (dist) r_work=0.1194 r_free=0.1491 | n_water=429 | time (s): 37.410 (total time: 39.380) Filter (q & B) r_work=0.1194 r_free=0.1491 | n_water=429 | time (s): 1.030 (total time: 40.410) Compute maps r_work=0.1194 r_free=0.1491 | n_water=429 | time (s): 1.590 (total time: 42.000) Filter (map) r_work=0.1238 r_free=0.1462 | n_water=289 | time (s): 3.350 (total time: 45.350) Find peaks r_work=0.1238 r_free=0.1462 | n_water=289 | time (s): 0.700 (total time: 46.050) Add new water r_work=0.1364 r_free=0.1570 | n_water=471 | time (s): 2.320 (total time: 48.370) Refine new water occ: r_work=0.1264 r_free=0.1501 adp: r_work=0.1265 r_free=0.1502 occ: r_work=0.1241 r_free=0.1482 adp: r_work=0.1238 r_free=0.1481 occ: r_work=0.1224 r_free=0.1470 adp: r_work=0.1216 r_free=0.1466 ADP+occupancy (water only), MIN, final r_work=0.1216 r_free=0.1466 r_work=0.1216 r_free=0.1466 | n_water=471 | time (s): 179.300 (total time: 227.670) Filter (q & B) r_work=0.1220 r_free=0.1468 | n_water=442 | time (s): 2.860 (total time: 230.530) Filter (dist only) r_work=0.1220 r_free=0.1468 | n_water=442 | time (s): 34.540 (total time: 265.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.984646 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.989309 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 0.1437 0.0211 0.005 0.9 2.2 0.5 0.0 0 0.992 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.37 2.11 3.623 22.147 46.989 3.720 12.18 13.91 1.73 4.170 21.947 46.989 3.651 Individual atomic B min max mean iso aniso Overall: 9.26 109.41 21.69 2.32 209 1760 Protein: 9.26 109.41 17.20 2.32 0 1519 Water: 11.55 71.50 37.03 N/A 209 233 Other: 20.66 32.48 26.79 N/A 0 8 Chain A: 9.26 109.41 19.85 N/A 0 1760 Chain S: 15.57 65.40 37.21 N/A 209 0 Histogram: Values Number of atoms 9.26 - 19.27 1235 19.27 - 29.29 263 29.29 - 39.30 221 39.30 - 49.32 145 49.32 - 59.33 71 59.33 - 69.35 20 69.35 - 79.36 8 79.36 - 89.38 3 89.38 - 99.39 1 99.39 - 109.41 2 =========================== Idealize ADP of riding H ========================== r_work=0.1218 r_free=0.1391 r_work=0.1219 r_free=0.1392 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1219 r_free = 0.1392 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1215 r_free = 0.1397 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.12 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= 0.1215 r_free= 0.1397 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.650787 | | target function (ml) not normalized (work): 304084.979442 | | target function (ml) not normalized (free): 16060.424440 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1224 0.1215 0.1397 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1551 0.1549 0.1606 n_refl.: 87589 remove outliers: r(all,work,free)=0.1551 0.1549 0.1606 n_refl.: 87589 overall B=-0.02 to atoms: r(all,work,free)=0.1548 0.1546 0.1603 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1206 0.1376 n_refl.: 87589 remove outliers: r(all,work,free)=0.1212 0.1204 0.1376 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 0.3706 299.456 263.379 0.494 0.999 0.330 11.894-9.307 99.02 97 4 0.2470 478.466 462.099 0.848 1.001 0.330 9.237-7.194 98.18 209 7 0.2350 382.877 384.122 0.946 1.002 0.184 7.162-5.571 100.00 427 22 0.2077 293.668 283.604 0.911 1.002 0.165 5.546-4.326 100.00 867 58 0.1118 403.134 398.284 0.950 1.002 0.150 4.315-3.360 100.00 1859 96 0.0937 383.383 380.675 0.992 1.002 0.140 3.356-2.611 100.00 3867 181 0.1166 251.863 249.836 1.001 1.002 0.110 2.608-2.026 99.99 8198 413 0.1053 166.962 165.911 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1019 81.536 81.689 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1289 36.156 35.727 1.023 0.999 0.000 1.221-1.150 99.97 13689 708 0.2129 22.781 21.403 0.983 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0519 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1204 r_free=0.1376 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=0.1204 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1204 r_free=0.1376 | n_water=442 | time (s): 2.140 (total time: 2.140) Filter (dist) r_work=0.1206 r_free=0.1377 | n_water=440 | time (s): 39.600 (total time: 41.740) Filter (q & B) r_work=0.1206 r_free=0.1377 | n_water=439 | time (s): 3.740 (total time: 45.480) Compute maps r_work=0.1206 r_free=0.1377 | n_water=439 | time (s): 1.720 (total time: 47.200) Filter (map) r_work=0.1230 r_free=0.1383 | n_water=307 | time (s): 2.490 (total time: 49.690) Find peaks r_work=0.1230 r_free=0.1383 | n_water=307 | time (s): 0.460 (total time: 50.150) Add new water r_work=0.1299 r_free=0.1439 | n_water=476 | time (s): 3.030 (total time: 53.180) Refine new water occ: r_work=0.1224 r_free=0.1374 adp: r_work=0.1225 r_free=0.1376 occ: r_work=0.1209 r_free=0.1364 adp: r_work=0.1207 r_free=0.1364 occ: r_work=0.1199 r_free=0.1360 adp: r_work=0.1194 r_free=0.1358 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1358 r_work=0.1194 r_free=0.1358 | n_water=476 | time (s): 215.800 (total time: 268.980) Filter (q & B) r_work=0.1200 r_free=0.1358 | n_water=444 | time (s): 3.160 (total time: 272.140) Filter (dist only) r_work=0.1200 r_free=0.1357 | n_water=443 | time (s): 38.870 (total time: 311.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.175279 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.117345 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 0.1200 0.1377 0.0177 0.006 1.0 4.2 0.5 0.0 0 1.088 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.77 1.77 3.419 21.484 43.117 3.639 11.88 13.65 1.76 3.698 21.394 43.117 3.626 Individual atomic B min max mean iso aniso Overall: 9.05 105.65 21.30 2.15 213 1757 Protein: 9.05 105.65 16.99 2.16 0 1519 Water: 11.70 70.67 35.96 N/A 213 230 Other: 21.51 30.20 26.17 N/A 0 8 Chain A: 9.05 105.65 19.57 N/A 0 1757 Chain S: 16.15 59.23 35.54 N/A 213 0 Histogram: Values Number of atoms 9.05 - 18.71 1227 18.71 - 28.37 280 28.37 - 38.03 207 38.03 - 47.69 139 47.69 - 57.35 78 57.35 - 67.01 26 67.01 - 76.67 8 76.67 - 86.33 2 86.33 - 95.99 1 95.99 - 105.65 2 =========================== Idealize ADP of riding H ========================== r_work=0.1188 r_free=0.1365 r_work=0.1189 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1365 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1185 r_free = 0.1363 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1185 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.625276 | | target function (ml) not normalized (work): 301938.383706 | | target function (ml) not normalized (free): 15956.093524 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1185 0.1363 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1513 0.1512 0.1562 n_refl.: 87583 remove outliers: r(all,work,free)=0.1513 0.1512 0.1562 n_refl.: 87583 overall B=-0.02 to atoms: r(all,work,free)=0.1509 0.1507 0.1559 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1184 0.1365 n_refl.: 87583 remove outliers: r(all,work,free)=0.1190 0.1181 0.1365 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 0.3928 289.352 265.330 0.486 0.951 0.277 11.894-9.307 93.14 91 4 0.2473 461.682 452.091 0.876 0.953 0.253 9.237-7.194 98.18 209 7 0.2451 382.877 376.825 0.960 0.953 0.130 7.162-5.571 100.00 427 22 0.2190 293.668 282.568 0.948 0.954 0.122 5.546-4.326 100.00 867 58 0.1145 403.134 398.486 1.000 0.954 0.118 4.315-3.360 100.00 1859 96 0.0953 383.383 380.577 1.043 0.954 0.118 3.356-2.611 100.00 3867 181 0.1153 251.863 249.900 1.053 0.954 0.100 2.608-2.026 99.99 8198 413 0.1022 166.962 165.978 1.065 0.953 0.000 2.025-1.573 100.00 17313 902 0.0969 81.536 81.776 1.081 0.952 0.000 1.573-1.221 100.00 36679 1900 0.1244 36.156 35.767 1.075 0.951 0.000 1.221-1.150 99.97 13689 708 0.2116 22.781 21.410 1.033 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0612 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1181 r_free=0.1365 After: r_work=0.1182 r_free=0.1365 ================================== NQH flips ================================== r_work=0.1182 r_free=0.1365 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=0.1182 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1182 r_free=0.1365 | n_water=443 | time (s): 1.990 (total time: 1.990) Filter (dist) r_work=0.1182 r_free=0.1365 | n_water=443 | time (s): 38.190 (total time: 40.180) Filter (q & B) r_work=0.1182 r_free=0.1366 | n_water=440 | time (s): 2.960 (total time: 43.140) Compute maps r_work=0.1182 r_free=0.1366 | n_water=440 | time (s): 1.280 (total time: 44.420) Filter (map) r_work=0.1217 r_free=0.1374 | n_water=321 | time (s): 3.540 (total time: 47.960) Find peaks r_work=0.1217 r_free=0.1374 | n_water=321 | time (s): 0.500 (total time: 48.460) Add new water r_work=0.1267 r_free=0.1415 | n_water=494 | time (s): 2.900 (total time: 51.360) Refine new water occ: r_work=0.1196 r_free=0.1371 adp: r_work=0.1196 r_free=0.1372 occ: r_work=0.1183 r_free=0.1362 adp: r_work=0.1182 r_free=0.1361 occ: r_work=0.1173 r_free=0.1357 adp: r_work=0.1170 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1170 r_free=0.1355 r_work=0.1170 r_free=0.1355 | n_water=494 | time (s): 269.140 (total time: 320.500) Filter (q & B) r_work=0.1178 r_free=0.1352 | n_water=451 | time (s): 2.570 (total time: 323.070) Filter (dist only) r_work=0.1178 r_free=0.1351 | n_water=450 | time (s): 39.510 (total time: 362.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.883650 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 32.074674 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1213 0.1383 0.0171 0.007 1.0 2.2 0.5 0.0 0 0.942 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 13.83 1.71 3.304 21.194 32.075 3.637 12.13 13.82 1.69 3.332 21.179 32.075 3.635 Individual atomic B min max mean iso aniso Overall: 9.21 104.76 21.16 2.10 223 1754 Protein: 9.21 104.76 16.94 2.10 0 1519 Water: 11.46 70.57 35.30 N/A 223 227 Other: 21.06 29.94 26.02 N/A 0 8 Chain A: 9.21 104.76 19.45 N/A 0 1754 Chain S: 15.52 56.89 34.55 N/A 223 0 Histogram: Values Number of atoms 9.21 - 18.76 1231 18.76 - 28.32 277 28.32 - 37.87 219 37.87 - 47.43 143 47.43 - 56.98 70 56.98 - 66.54 22 66.54 - 76.09 10 76.09 - 85.65 2 85.65 - 95.20 1 95.20 - 104.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.1213 r_free=0.1382 r_work=0.1213 r_free=0.1382 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1213 r_free = 0.1382 target_work(ml) = 3.635 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1208 r_free = 0.1379 target_work(ml) = 3.633 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1208 r_free= 0.1379 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.633033 | | target function (ml) not normalized (work): 302555.320267 | | target function (ml) not normalized (free): 15973.554745 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1436 0.1431 5.6978 5.6525| | 2: 3.57 - 2.84 1.00 2888 124 0.1124 0.1447 5.2068 5.282| | 3: 2.83 - 2.48 1.00 2820 163 0.1216 0.1293 5.0135 5.0492| | 4: 2.47 - 2.25 1.00 2825 136 0.1020 0.1182 4.7164 4.7709| | 5: 2.25 - 2.09 1.00 2756 127 0.0994 0.1129 4.6588 4.7276| | 6: 2.09 - 1.97 1.00 2846 113 0.0985 0.1177 4.3689 4.4836| | 7: 1.97 - 1.87 1.00 2787 165 0.1010 0.1215 4.0909 4.1932| | 8: 1.87 - 1.79 1.00 2789 144 0.1024 0.1252 3.9998 4.0877| | 9: 1.79 - 1.72 1.00 2745 138 0.0976 0.1274 3.7316 3.9032| | 10: 1.72 - 1.66 1.00 2831 160 0.1025 0.1321 3.6497 3.7883| | 11: 1.66 - 1.61 1.00 2712 147 0.0988 0.1111 3.5839 3.6173| | 12: 1.61 - 1.56 1.00 2773 144 0.0947 0.1199 3.368 3.4881| | 13: 1.56 - 1.52 1.00 2745 130 0.1005 0.1054 3.358 3.4313| | 14: 1.52 - 1.48 1.00 2803 134 0.1003 0.1094 3.2755 3.344| | 15: 1.48 - 1.45 1.00 2738 128 0.1038 0.1300 3.1863 3.3108| | 16: 1.45 - 1.42 1.00 2756 161 0.1088 0.1287 3.1645 3.2741| | 17: 1.42 - 1.39 1.00 2785 139 0.1136 0.1337 3.1286 3.2629| | 18: 1.39 - 1.36 1.00 2741 179 0.1183 0.1391 3.1033 3.2748| | 19: 1.36 - 1.34 1.00 2807 134 0.1237 0.1611 3.1061 3.2905| | 20: 1.34 - 1.32 1.00 2696 147 0.1337 0.1438 3.0988 3.1177| | 21: 1.32 - 1.30 1.00 2785 112 0.1436 0.1628 3.0982 3.1647| | 22: 1.29 - 1.27 1.00 2704 152 0.1496 0.1965 3.0941 3.2919| | 23: 1.27 - 1.26 1.00 2802 156 0.1589 0.1873 3.1122 3.2195| | 24: 1.26 - 1.24 1.00 2744 132 0.1648 0.1789 3.104 3.1995| | 25: 1.24 - 1.22 1.00 2733 148 0.1816 0.2319 3.116 3.2892| | 26: 1.22 - 1.21 1.00 2727 135 0.1874 0.1768 3.1297 3.1939| | 27: 1.21 - 1.19 1.00 2814 148 0.2021 0.2121 3.1452 3.1533| | 28: 1.19 - 1.18 1.00 2671 147 0.2149 0.2328 3.144 3.1621| | 29: 1.18 - 1.16 1.00 2800 134 0.2227 0.2370 3.1302 3.218| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2505 3.1171 3.1733| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.94 9.28 1.00 0.97 6485.89| | 2: 3.57 - 2.84 2888 124 0.92 13.65 1.01 0.97 6485.89| | 3: 2.83 - 2.48 2820 163 0.88 17.85 0.99 0.98 5435.86| | 4: 2.47 - 2.25 2825 136 0.91 14.87 1.00 0.98 2728.17| | 5: 2.25 - 2.09 2756 127 0.89 17.14 1.01 0.98 2728.17| | 6: 2.09 - 1.97 2846 113 0.91 13.91 1.02 0.97 1601.22| | 7: 1.97 - 1.87 2787 165 0.94 10.98 1.02 0.97 640.08| | 8: 1.87 - 1.79 2789 144 0.91 14.58 1.00 0.97 640.08| | 9: 1.79 - 1.72 2745 138 0.93 11.58 0.98 0.97 346.38| | 10: 1.72 - 1.66 2831 160 0.93 12.42 0.98 0.97 287.56| | 11: 1.66 - 1.61 2712 147 0.93 13.08 0.98 0.97 274.40| | 12: 1.61 - 1.56 2773 144 0.95 9.62 0.99 0.97 150.32| | 13: 1.56 - 1.52 2745 130 0.94 11.25 1.02 0.97 150.32| | 14: 1.52 - 1.48 2803 134 0.94 11.39 1.02 0.97 134.20| | 15: 1.48 - 1.45 2738 128 0.95 10.55 1.01 0.98 104.69| | 16: 1.45 - 1.42 2756 161 0.94 11.70 1.01 0.98 104.69| | 17: 1.42 - 1.39 2785 139 0.94 11.58 1.01 0.98 94.70| | 18: 1.39 - 1.36 2741 179 0.94 11.90 1.01 0.98 88.92| | 19: 1.36 - 1.34 2807 134 0.94 12.44 1.00 0.98 88.92| | 20: 1.34 - 1.32 2696 147 0.94 12.53 0.99 0.96 83.35| | 21: 1.32 - 1.30 2785 112 0.93 13.51 0.98 0.96 82.96| | 22: 1.29 - 1.27 2704 152 0.93 13.99 0.98 0.96 83.10| | 23: 1.27 - 1.26 2802 156 0.92 14.95 0.98 0.95 83.79| | 24: 1.26 - 1.24 2744 132 0.92 15.09 0.97 0.95 83.79| | 25: 1.24 - 1.22 2733 148 0.91 16.50 0.96 0.94 85.06| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.93 86.47| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.02 0.93 86.47| | 28: 1.19 - 1.18 2671 147 0.88 20.25 1.01 0.92 89.47| | 29: 1.18 - 1.16 2800 134 0.88 20.55 0.99 0.92 90.60| | 30: 1.16 - 1.15 2739 148 0.86 21.98 0.98 0.92 90.60| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 82.96 max = 6485.89 mean = 1008.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.94 mean = 14.19| |phase err.(test): min = 0.00 max = 89.53 mean = 14.25| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1208 0.1379 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1522 0.1521 0.1565 n_refl.: 87575 remove outliers: r(all,work,free)=0.1522 0.1521 0.1565 n_refl.: 87575 overall B=-0.02 to atoms: r(all,work,free)=0.1519 0.1518 0.1563 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1217 0.1208 0.1382 n_refl.: 87575 remove outliers: r(all,work,free)=0.1215 0.1207 0.1382 n_refl.: 87572 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4048 289.352 253.097 0.432 1.000 0.298 11.894-9.307 91.18 89 4 0.2426 467.520 438.662 0.819 1.002 0.227 9.237-7.194 97.73 208 7 0.2585 382.401 376.092 0.904 1.002 0.149 7.162-5.571 100.00 427 22 0.2315 293.668 282.138 0.895 1.002 0.119 5.546-4.326 100.00 867 58 0.1195 403.134 398.722 0.951 1.002 0.109 4.315-3.360 100.00 1859 96 0.0994 383.383 380.369 0.993 1.002 0.105 3.356-2.611 100.00 3867 181 0.1181 251.863 250.103 1.002 1.002 0.043 2.608-2.026 99.99 8198 413 0.1042 166.962 165.992 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0995 81.536 81.816 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.156 35.789 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2126 22.781 21.409 0.983 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0419 ================= 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 : 0.2613 0.1952 0.080 5.290 8.8 119.3 19.9 258 0.000 1_bss: 0.1637 0.1769 0.080 5.290 9.1 119.5 20.1 258 0.000 1_settarget: 0.1637 0.1769 0.080 5.290 9.1 119.5 20.1 258 0.000 1_nqh: 0.1638 0.1770 0.080 5.290 9.1 119.5 20.1 258 0.003 1_weight: 0.1638 0.1770 0.080 5.290 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1214 0.1470 0.008 0.970 9.1 119.5 20.1 258 0.124 1_adp: 0.1244 0.1545 0.008 0.970 8.5 118.6 21.0 258 0.124 1_regHadp: 0.1248 0.1550 0.008 0.970 8.5 118.6 21.0 258 0.124 1_occ: 0.1249 0.1552 0.008 0.970 8.5 118.6 21.0 258 0.124 2_bss: 0.1245 0.1545 0.008 0.970 8.7 118.7 21.1 258 0.124 2_settarget: 0.1245 0.1545 0.008 0.970 8.7 118.7 21.1 258 0.124 2_updatecdl: 0.1245 0.1545 0.008 0.974 8.7 118.7 21.1 258 0.124 2_nqh: 0.1246 0.1546 0.008 0.974 8.7 118.7 21.1 258 0.127 2_sol: 0.1229 0.1492 0.008 0.974 8.7 118.7 23.4 431 n/a 2_weight: 0.1229 0.1492 0.008 0.974 8.7 118.7 23.4 431 n/a 2_xyzrec: 0.1229 0.1526 0.007 0.887 8.7 118.7 23.4 431 n/a 2_adp: 0.1196 0.1496 0.007 0.887 8.7 114.3 23.1 431 n/a 2_regHadp: 0.1196 0.1496 0.007 0.887 8.7 114.3 23.1 431 n/a 2_occ: 0.1197 0.1494 0.007 0.887 8.7 114.3 23.1 431 n/a 3_bss: 0.1192 0.1491 0.007 0.887 8.7 114.3 23.1 431 n/a 3_settarget: 0.1192 0.1491 0.007 0.887 8.7 114.3 23.1 431 n/a 3_updatecdl: 0.1192 0.1491 0.007 0.887 8.7 114.3 23.1 431 n/a 3_nqh: 0.1192 0.1491 0.007 0.887 8.7 114.3 23.1 431 n/a 3_sol: 0.1220 0.1468 0.007 0.887 8.7 114.3 22.1 442 n/a 3_weight: 0.1220 0.1468 0.007 0.887 8.7 114.3 22.1 442 n/a 3_xyzrec: 0.1227 0.1437 0.005 0.909 8.7 114.3 22.1 442 n/a 3_adp: 0.1218 0.1391 0.005 0.909 9.3 109.4 21.7 442 n/a 3_regHadp: 0.1219 0.1392 0.005 0.909 9.3 109.4 21.7 442 n/a 3_occ: 0.1215 0.1397 0.005 0.909 9.3 109.4 21.7 442 n/a 4_bss: 0.1204 0.1376 0.005 0.909 9.2 109.4 21.7 442 n/a 4_settarget: 0.1204 0.1376 0.005 0.909 9.2 109.4 21.7 442 n/a 4_updatecdl: 0.1204 0.1376 0.006 0.907 9.2 109.4 21.7 442 n/a 4_nqh: 0.1204 0.1376 0.006 0.907 9.2 109.4 21.7 442 n/a 4_sol: 0.1200 0.1357 0.006 0.907 9.2 109.4 21.5 443 n/a 4_weight: 0.1200 0.1357 0.006 0.907 9.2 109.4 21.5 443 n/a 4_xyzrec: 0.1200 0.1377 0.006 0.972 9.2 109.4 21.5 443 n/a 4_adp: 0.1188 0.1365 0.006 0.972 9.1 105.7 21.3 443 n/a 4_regHadp: 0.1189 0.1365 0.006 0.972 9.1 105.7 21.3 443 n/a 4_occ: 0.1185 0.1363 0.006 0.972 9.1 105.7 21.3 443 n/a 5_bss: 0.1181 0.1365 0.006 0.972 9.0 105.6 21.3 443 n/a 5_settarget: 0.1181 0.1365 0.006 0.972 9.0 105.6 21.3 443 n/a 5_updatecdl: 0.1181 0.1365 0.006 0.973 9.0 105.6 21.3 443 n/a 5_setrh: 0.1182 0.1365 0.006 0.973 9.0 105.6 21.3 443 n/a 5_nqh: 0.1182 0.1365 0.006 0.973 9.0 105.6 21.3 443 n/a 5_sol: 0.1178 0.1351 0.006 0.973 9.0 105.6 21.2 450 n/a 5_weight: 0.1178 0.1351 0.006 0.973 9.0 105.6 21.2 450 n/a 5_xyzrec: 0.1213 0.1383 0.007 1.016 9.0 105.6 21.2 450 n/a 5_adp: 0.1213 0.1382 0.007 1.016 9.2 104.8 21.2 450 n/a 5_regHadp: 0.1213 0.1382 0.007 1.016 9.2 104.8 21.2 450 n/a 5_occ: 0.1208 0.1379 0.007 1.016 9.2 104.8 21.2 450 n/a end: 0.1207 0.1382 0.007 1.016 9.2 104.7 21.1 450 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8008321_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8008321_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7600 Refinement macro-cycles (run) : 3541.9000 Write final files (write_after_run_outputs) : 60.6200 Total : 3607.2800 Total CPU time: 60.74 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:18 PST -0800 (1735452738.12 s) Start R-work = 0.1637, R-free = 0.1769 Final R-work = 0.1207, R-free = 0.1382 =============================================================================== Job complete usr+sys time: 3741.92 seconds wall clock time: 67 minutes 28.85 seconds (4048.85 seconds total)