Starting phenix.refine on Sat Dec 28 21:06:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3473948.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3473948.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3473948.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" } 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: 2.13, per 1000 atoms: 0.63 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: 0.78 Conformation dependent library (CDL) restraints added in 239.1 milliseconds Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.89: 405 0.89 - 1.15: 1221 1.15 - 1.42: 638 1.42 - 1.69: 852 1.69 - 1.95: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.534 1.701 -0.166 6.80e-03 2.16e+04 5.97e+02 bond pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta sigma weight residual 1.458 1.683 -0.225 1.19e-02 7.06e+03 3.58e+02 bond pdb=" C THR A 154 " pdb=" O THR A 154 " ideal model delta sigma weight residual 1.234 1.018 0.216 1.28e-02 6.10e+03 2.84e+02 bond pdb=" CA GLU A 16 " pdb=" C GLU A 16 " ideal model delta sigma weight residual 1.523 1.750 -0.227 1.35e-02 5.49e+03 2.83e+02 bond pdb=" CA VAL A 50 " pdb=" CB VAL A 50 " ideal model delta sigma weight residual 1.538 1.727 -0.189 1.13e-02 7.83e+03 2.79e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.82: 3216 4.82 - 9.63: 1845 9.63 - 14.45: 610 14.45 - 19.26: 99 19.26 - 24.08: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O AGLY A 65 " pdb=" C AGLY A 65 " pdb=" N APRO A 66 " ideal model delta sigma weight residual 121.77 106.84 14.93 1.00e+00 1.00e+00 2.23e+02 angle pdb=" CA PHE A 164 " pdb=" CB PHE A 164 " pdb=" CG PHE A 164 " ideal model delta sigma weight residual 113.80 128.52 -14.72 1.00e+00 1.00e+00 2.17e+02 angle pdb=" CA AGLU A 90 " pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 120.82 135.89 -15.07 1.05e+00 9.07e-01 2.06e+02 angle pdb=" C ASP A 42 " pdb=" N PRO A 43 " pdb=" CA PRO A 43 " ideal model delta sigma weight residual 119.76 105.07 14.69 1.03e+00 9.43e-01 2.03e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 131.62 -12.42 9.00e-01 1.23e+00 1.90e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 924 15.61 - 31.21: 123 31.21 - 46.81: 37 46.81 - 62.42: 21 62.42 - 78.02: 6 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+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 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.217: 91 0.217 - 0.433: 82 0.433 - 0.649: 46 0.649 - 0.866: 18 0.866 - 1.082: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.93e+01 chirality pdb=" CA LEU A 7 " pdb=" N LEU A 7 " pdb=" C LEU A 7 " pdb=" CB LEU A 7 " both_signs ideal model delta sigma weight residual False 2.51 3.54 -1.03 2.00e-01 2.50e+01 2.67e+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 3.51 -1.00 2.00e-01 2.50e+01 2.52e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.003 2.00e-02 2.50e+03 7.23e-02 1.57e+02 pdb=" CG PHE A 164 " -0.095 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.128 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.073 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.061 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.075 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.084 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.109 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG ATYR A 67 " 0.097 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.030 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.009 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.091 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.058 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.035 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.042 2.00e-02 2.50e+03 5.38e-02 8.68e+01 pdb=" CG PHE A 119 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.124 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.039 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.061 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.019 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.080 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.017 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 1126 2.33 - 2.90: 8225 2.90 - 3.47: 10447 3.47 - 4.03: 15200 4.03 - 4.60: 21578 Nonbonded interactions: 56576 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.766 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.794 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.808 2.450 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.835 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.847 2.450 ... (remaining 56571 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_3473948_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= 0.2606 r_free= 0.1957 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795734 | | target function (ml) not normalized (work): 232901.437821 | | target function (ml) not normalized (free): 11833.313609 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3035 0.2003 7.1008 4.9264| | 2: 3.57 - 2.84 1.00 2876 122 0.2416 0.1757 4.3428 4.3396| | 3: 2.84 - 2.48 1.00 2833 165 0.2366 0.1789 4.1227 4.1514| | 4: 2.47 - 2.25 1.00 2825 136 0.2328 0.1380 3.8273 3.8266| | 5: 2.25 - 2.09 1.00 2756 127 0.2449 0.1716 3.7933 3.8162| | 6: 2.09 - 1.97 1.00 2846 113 0.2551 0.1610 3.4712 3.5574| | 7: 1.97 - 1.87 1.00 2787 165 0.2513 0.1854 3.1448 3.2081| | 8: 1.87 - 1.79 1.00 2789 144 0.2472 0.2096 3.0941 3.1943| | 9: 1.79 - 1.72 1.00 2745 138 0.2437 0.2146 2.9088 3.0194| | 10: 1.72 - 1.66 1.00 2789 158 0.2411 0.2056 2.8204 2.924| | 11: 1.66 - 1.61 1.00 2740 147 0.2486 0.1997 2.7644 2.7924| | 12: 1.61 - 1.56 1.00 2787 146 0.2505 0.1954 2.6467 2.6549| | 13: 1.56 - 1.52 1.00 2745 130 0.2617 0.2049 2.585 2.6502| | 14: 1.52 - 1.48 1.00 2803 134 0.2607 0.1982 2.5037 2.5547| | 15: 1.48 - 1.45 1.00 2738 128 0.2583 0.2281 2.4207 2.5137| | 16: 1.45 - 1.42 1.00 2756 161 0.2619 0.2141 2.3629 2.3884| | 17: 1.42 - 1.39 1.00 2785 139 0.2647 0.1924 2.3274 2.2936| | 18: 1.39 - 1.36 1.00 2741 179 0.2641 0.2248 2.2666 2.3374| | 19: 1.36 - 1.34 1.00 2807 134 0.2721 0.2229 2.248 2.2905| | 20: 1.34 - 1.32 1.00 2696 147 0.2749 0.2317 2.1979 2.1832| | 21: 1.32 - 1.30 1.00 2785 112 0.2718 0.2401 2.1726 2.2033| | 22: 1.29 - 1.27 1.00 2704 152 0.2739 0.2599 2.1248 2.2347| | 23: 1.27 - 1.26 1.00 2802 156 0.2782 0.2477 2.1007 2.1543| | 24: 1.26 - 1.24 1.00 2744 132 0.2771 0.2259 2.0805 2.0658| | 25: 1.24 - 1.22 1.00 2734 148 0.2922 0.2364 2.0799 2.0615| | 26: 1.22 - 1.21 1.00 2727 135 0.2860 0.2307 2.0092 2.0767| | 27: 1.21 - 1.19 1.00 2814 148 0.2982 0.2606 2.0154 2.0287| | 28: 1.19 - 1.18 1.00 2671 147 0.2949 0.2933 1.9816 2.0022| | 29: 1.18 - 1.16 1.00 2800 134 0.2954 0.2977 1.964 2.1028| | 30: 1.16 - 1.15 1.00 2740 148 0.3062 0.2688 1.9354 1.9469| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.58 0.76 0.23 1444.95| | 2: 3.57 - 2.84 2876 122 0.81 25.72 1.27 0.23 1444.95| | 3: 2.84 - 2.48 2833 165 0.74 31.75 1.24 0.23 1200.93| | 4: 2.47 - 2.25 2825 136 0.81 25.54 1.26 0.25 567.67| | 5: 2.25 - 2.09 2756 127 0.77 29.16 1.28 0.25 567.67| | 6: 2.09 - 1.97 2846 113 0.83 23.09 1.29 0.25 315.85| | 7: 1.97 - 1.87 2787 165 0.89 17.63 1.28 0.26 101.08| | 8: 1.87 - 1.79 2789 144 0.85 22.13 1.24 0.26 101.08| | 9: 1.79 - 1.72 2745 138 0.87 19.48 1.24 0.25 61.07| | 10: 1.72 - 1.66 2789 158 0.86 21.20 1.22 0.25 53.06| | 11: 1.66 - 1.61 2740 147 0.84 22.56 1.24 0.25 51.08| | 12: 1.61 - 1.56 2787 146 0.88 18.80 1.23 0.25 31.01| | 13: 1.56 - 1.52 2745 130 0.86 21.21 1.25 0.25 31.01| | 14: 1.52 - 1.48 2803 134 0.86 21.14 1.25 0.25 27.42| | 15: 1.48 - 1.45 2738 128 0.87 20.35 1.23 0.25 20.86| | 16: 1.45 - 1.42 2756 161 0.85 21.89 1.24 0.25 20.86| | 17: 1.42 - 1.39 2785 139 0.86 20.98 1.22 0.25 17.62| | 18: 1.39 - 1.36 2741 179 0.86 21.14 1.23 0.25 15.75| | 19: 1.36 - 1.34 2807 134 0.86 21.94 1.23 0.25 15.75| | 20: 1.34 - 1.32 2696 147 0.87 20.99 1.22 0.25 12.94| | 21: 1.32 - 1.30 2785 112 0.86 21.88 1.20 0.25 12.74| | 22: 1.29 - 1.27 2704 152 0.86 22.25 1.22 0.24 12.48| | 23: 1.27 - 1.26 2802 156 0.86 22.16 1.21 0.24 11.15| | 24: 1.26 - 1.24 2744 132 0.85 22.57 1.20 0.24 11.15| | 25: 1.24 - 1.22 2734 148 0.84 23.61 1.20 0.24 10.68| | 26: 1.22 - 1.21 2727 135 0.83 24.46 1.20 0.23 10.15| | 27: 1.21 - 1.19 2814 148 0.83 24.98 1.21 0.23 10.15| | 28: 1.19 - 1.18 2671 147 0.82 26.30 1.18 0.23 9.78| | 29: 1.18 - 1.16 2800 134 0.81 26.69 1.16 0.22 9.64| | 30: 1.16 - 1.15 2740 148 0.80 28.16 1.15 0.22 9.64| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.64 max = 1444.95 mean = 212.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.97 mean = 22.94| |phase err.(test): min = 0.00 max = 89.62 mean = 22.91| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.246 1557 Z= 5.496 Angle : 5.302 19.071 2118 Z= 3.752 Chirality : 0.400 1.082 243 Planarity : 0.033 0.096 284 Dihedral : 13.800 78.020 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 32.97 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.45), residues: 224 helix: -2.90 (0.38), residues: 102 sheet: -0.55 (0.68), residues: 38 loop : -1.43 (0.56), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.012 ARG A 5 TYR 0.088 0.042 TYR A 141 PHE 0.108 0.043 PHE A 164 HIS 0.104 0.029 HIS A 126 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= 0.2606 r_free= 0.1957 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795734 | | target function (ml) not normalized (work): 232901.437821 | | target function (ml) not normalized (free): 11833.313609 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2606 0.1958 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2606 0.1958 n_refl.: 87602 remove outliers: r(all,work,free)=0.1978 0.1981 0.1958 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2003 0.2007 0.1973 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1645 0.1638 0.1780 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1637 0.1780 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 97.87 87 5 0.3703 389.766 370.079 0.760 0.918 0.401 11.894-9.307 99.02 97 4 0.1881 613.927 592.064 1.005 0.919 0.380 9.237-7.194 100.00 213 7 0.2217 502.117 488.953 1.039 0.919 0.354 7.162-5.571 100.00 427 22 0.2202 376.811 364.115 1.007 0.920 0.288 5.546-4.326 100.00 867 58 0.1269 517.268 510.758 1.045 0.920 0.229 4.315-3.360 100.00 1859 96 0.1148 491.925 488.902 1.092 0.921 0.209 3.356-2.611 100.00 3867 181 0.1439 323.170 319.932 1.083 0.922 0.038 2.608-2.026 99.99 8198 413 0.1346 214.232 212.104 1.089 0.924 0.000 2.025-1.573 100.00 17313 902 0.1648 104.620 104.018 1.089 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2067 46.393 45.106 1.074 0.933 0.000 1.221-1.150 99.97 13689 708 0.2602 29.231 26.897 1.030 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0479 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1637 r_free=0.1780 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1639 r_free=0.1784 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.587517 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2007.473208 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1208 0.1453 0.0245 0.007 1.0 1.3 0.5 0.0 0 12.794 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 14.53 2.45 3.013 19.067 2007.473 0.017 12.37 15.29 2.92 3.140 19.528 2007.473 0.016 Individual atomic B min max mean iso aniso Overall: 8.52 118.45 20.97 2.87 0 1785 Protein: 8.52 118.45 17.85 2.87 0 1519 Water: 11.01 114.51 39.07 N/A 0 258 Other: 22.82 35.93 28.95 N/A 0 8 Chain A: 8.52 118.45 20.97 N/A 0 1785 Histogram: Values Number of atoms 8.52 - 19.51 1212 19.51 - 30.51 227 30.51 - 41.50 166 41.50 - 52.49 97 52.49 - 63.49 54 63.49 - 74.48 17 74.48 - 85.47 5 85.47 - 96.47 4 96.47 - 107.46 0 107.46 - 118.45 3 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1529 r_work=0.1242 r_free=0.1534 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1242 r_free = 0.1534 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 = 0.1241 r_free = 0.1532 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1241 r_free= 0.1532 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015384 | | target function (ls_wunit_k1) not normalized (work): 1281.451079 | | target function (ls_wunit_k1) not normalized (free): 111.940103 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1255 0.1241 0.1532 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1697 0.1696 0.1760 n_refl.: 87592 remove outliers: r(all,work,free)=0.1697 0.1696 0.1760 n_refl.: 87592 overall B=0.13 to atoms: r(all,work,free)=0.1718 0.1718 0.1775 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1254 0.1240 0.1529 n_refl.: 87592 remove outliers: r(all,work,free)=0.1254 0.1240 0.1529 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3557 300.748 279.271 0.640 1.002 0.380 11.894-9.307 99.02 97 4 0.1619 477.703 465.545 0.906 1.003 0.380 9.237-7.194 100.00 213 7 0.1836 390.702 384.993 0.947 1.003 0.340 7.162-5.571 100.00 427 22 0.1751 293.200 287.569 0.920 1.003 0.258 5.546-4.326 100.00 867 58 0.0930 402.492 399.718 0.949 1.003 0.209 4.315-3.360 100.00 1859 96 0.0780 382.772 381.718 0.995 1.003 0.190 3.356-2.611 100.00 3867 181 0.1016 251.462 250.788 0.999 1.002 0.048 2.608-2.026 99.99 8198 413 0.0968 166.696 166.112 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1201 81.406 81.601 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1646 36.099 35.563 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2358 22.745 21.261 0.969 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0510 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1240 r_free=0.1529 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1242 r_free=0.1531 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1242 r_free=0.1531 | n_water=258 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1250 r_free=0.1531 | n_water=252 | time (s): 26.430 (total time: 28.960) Filter (q & B) r_work=0.1253 r_free=0.1531 | n_water=249 | time (s): 3.860 (total time: 32.820) Compute maps r_work=0.1253 r_free=0.1531 | n_water=249 | time (s): 1.850 (total time: 34.670) Filter (map) r_work=0.1265 r_free=0.1539 | n_water=237 | time (s): 3.800 (total time: 38.470) Find peaks r_work=0.1265 r_free=0.1539 | n_water=237 | time (s): 0.730 (total time: 39.200) Add new water r_work=0.1425 r_free=0.1706 | n_water=457 | time (s): 3.920 (total time: 43.120) Refine new water occ: r_work=0.1340 r_free=0.1559 adp: r_work=0.1255 r_free=0.1514 occ: r_work=0.1270 r_free=0.1493 adp: r_work=0.1231 r_free=0.1485 occ: r_work=0.1235 r_free=0.1468 adp: r_work=0.1224 r_free=0.1470 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1470 r_work=0.1224 r_free=0.1470 | n_water=457 | time (s): 82.210 (total time: 125.330) Filter (q & B) r_work=0.1229 r_free=0.1474 | n_water=440 | time (s): 3.900 (total time: 129.230) Filter (dist only) r_work=0.1229 r_free=0.1473 | n_water=439 | time (s): 45.480 (total time: 174.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.733235 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1483.617578 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1230 0.1510 0.0279 0.006 0.9 1.6 0.5 0.0 0 11.867 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 15.10 2.79 3.778 23.210 1483.618 0.016 12.06 14.92 2.86 4.135 23.042 1483.618 0.015 Individual atomic B min max mean iso aniso Overall: 8.73 114.43 23.30 2.59 202 1764 Protein: 8.73 114.43 17.66 2.59 0 1519 Water: 10.88 73.76 42.72 N/A 202 237 Other: 23.29 34.13 27.80 N/A 0 8 Chain A: 8.73 114.43 20.34 N/A 0 1764 Chain S: 16.56 70.49 49.12 N/A 202 0 Histogram: Values Number of atoms 8.73 - 19.30 1203 19.30 - 29.87 254 29.87 - 40.44 188 40.44 - 51.01 141 51.01 - 61.58 108 61.58 - 72.15 60 72.15 - 82.72 6 82.72 - 93.29 3 93.29 - 103.86 1 103.86 - 114.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1492 r_work=0.1206 r_free=0.1492 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1492 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1490 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1207 r_free= 0.1490 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014075 | | target function (ls_wunit_k1) not normalized (work): 1172.337639 | | target function (ls_wunit_k1) not normalized (free): 104.286272 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1207 0.1490 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1607 0.1604 0.1706 n_refl.: 87591 remove outliers: r(all,work,free)=0.1607 0.1604 0.1706 n_refl.: 87591 overall B=0.03 to atoms: r(all,work,free)=0.1613 0.1609 0.1709 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1217 0.1203 0.1488 n_refl.: 87591 remove outliers: r(all,work,free)=0.1215 0.1201 0.1488 n_refl.: 87588 ======================== 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 91.67 83 5 0.3286 296.736 272.481 0.590 1.002 0.360 11.894-9.307 99.02 97 4 0.1447 477.703 476.578 0.917 1.002 0.350 9.237-7.194 100.00 213 7 0.1681 390.702 390.390 0.981 1.003 0.290 7.162-5.571 100.00 427 22 0.1543 293.200 289.851 0.939 1.003 0.229 5.546-4.326 100.00 867 58 0.0826 402.492 399.956 0.958 1.003 0.210 4.315-3.360 100.00 1859 96 0.0710 382.772 381.759 1.003 1.002 0.200 3.356-2.611 100.00 3867 181 0.0963 251.462 250.709 1.009 1.002 0.140 2.608-2.026 99.99 8198 413 0.0961 166.696 166.264 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1185 81.406 81.586 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1624 36.099 35.591 1.018 0.998 0.000 1.221-1.150 99.97 13689 708 0.2352 22.745 21.267 0.977 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0525 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1488 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1488 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1488 | n_water=439 | time (s): 1.930 (total time: 1.930) Filter (dist) r_work=0.1201 r_free=0.1489 | n_water=437 | time (s): 40.460 (total time: 42.390) Filter (q & B) r_work=0.1201 r_free=0.1489 | n_water=437 | time (s): 0.860 (total time: 43.250) Compute maps r_work=0.1201 r_free=0.1489 | n_water=437 | time (s): 1.840 (total time: 45.090) Filter (map) r_work=0.1248 r_free=0.1493 | n_water=292 | time (s): 3.500 (total time: 48.590) Find peaks r_work=0.1248 r_free=0.1493 | n_water=292 | time (s): 0.730 (total time: 49.320) Add new water r_work=0.1378 r_free=0.1627 | n_water=480 | time (s): 3.620 (total time: 52.940) Refine new water occ: r_work=0.1269 r_free=0.1540 adp: r_work=0.1270 r_free=0.1541 occ: r_work=0.1247 r_free=0.1518 adp: r_work=0.1245 r_free=0.1519 occ: r_work=0.1231 r_free=0.1501 adp: r_work=0.1224 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1499 r_work=0.1224 r_free=0.1499 | n_water=480 | time (s): 184.810 (total time: 237.750) Filter (q & B) r_work=0.1228 r_free=0.1504 | n_water=449 | time (s): 3.690 (total time: 241.440) Filter (dist only) r_work=0.1229 r_free=0.1503 | n_water=447 | time (s): 38.120 (total time: 279.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.998474 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 55.667953 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 0.1234 0.1458 0.0223 0.005 0.9 1.9 0.5 0.0 0 0.999 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.34 14.58 2.23 3.613 22.094 55.668 3.727 12.11 14.02 1.91 4.098 21.909 55.668 3.647 Individual atomic B min max mean iso aniso Overall: 9.24 109.86 21.66 2.35 213 1761 Protein: 9.24 109.86 17.23 2.36 0 1519 Water: 11.42 72.78 36.63 N/A 213 234 Other: 20.00 30.35 25.44 N/A 0 8 Chain A: 9.24 109.86 19.91 N/A 0 1761 Chain S: 15.94 65.43 36.13 N/A 213 0 Histogram: Values Number of atoms 9.24 - 19.30 1237 19.30 - 29.36 270 29.36 - 39.43 224 39.43 - 49.49 139 49.49 - 59.55 72 59.55 - 69.61 18 69.61 - 79.67 8 79.67 - 89.74 3 89.74 - 99.80 1 99.80 - 109.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1402 r_work=0.1212 r_free=0.1403 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1212 r_free = 0.1403 target_work(ml) = 3.648 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1404 target_work(ml) = 3.646 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1207 r_free= 0.1404 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.646117 | | target function (ml) not normalized (work): 303692.398079 | | target function (ml) not normalized (free): 16047.328018 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1207 0.1404 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1530 0.1529 0.1582 n_refl.: 87588 remove outliers: r(all,work,free)=0.1530 0.1529 0.1582 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1529 0.1527 0.1581 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1197 0.1370 n_refl.: 87588 remove outliers: r(all,work,free)=0.1201 0.1192 0.1370 n_refl.: 87578 ======================== 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 0.3898 293.517 259.986 0.478 1.000 0.322 11.894-9.307 96.08 94 4 0.2350 474.935 459.710 0.846 1.002 0.238 9.237-7.194 97.73 208 7 0.2292 383.339 384.645 0.948 1.002 0.170 7.162-5.571 100.00 427 22 0.2069 293.200 283.567 0.911 1.002 0.170 5.546-4.326 100.00 867 58 0.1109 402.492 398.112 0.952 1.002 0.150 4.315-3.360 100.00 1859 96 0.0920 382.772 380.097 0.992 1.002 0.143 3.356-2.611 100.00 3867 181 0.1156 251.462 249.563 0.998 1.002 0.130 2.608-2.026 99.99 8198 413 0.1045 166.696 165.669 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1007 81.406 81.556 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1281 36.099 35.673 1.019 0.998 0.000 1.221-1.150 99.97 13689 708 0.2125 22.745 21.360 0.977 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0242 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1370 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=0.1370 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1370 | n_water=447 | time (s): 1.910 (total time: 1.910) Filter (dist) r_work=0.1192 r_free=0.1370 | n_water=447 | time (s): 37.090 (total time: 39.000) Filter (q & B) r_work=0.1192 r_free=0.1372 | n_water=445 | time (s): 2.900 (total time: 41.900) Compute maps r_work=0.1192 r_free=0.1372 | n_water=445 | time (s): 1.230 (total time: 43.130) Filter (map) r_work=0.1218 r_free=0.1391 | n_water=310 | time (s): 2.730 (total time: 45.860) Find peaks r_work=0.1218 r_free=0.1391 | n_water=310 | time (s): 0.710 (total time: 46.570) Add new water r_work=0.1284 r_free=0.1456 | n_water=487 | time (s): 3.270 (total time: 49.840) Refine new water occ: r_work=0.1208 r_free=0.1372 adp: r_work=0.1208 r_free=0.1374 occ: r_work=0.1193 r_free=0.1362 adp: r_work=0.1192 r_free=0.1363 occ: r_work=0.1182 r_free=0.1353 adp: r_work=0.1180 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1353 r_work=0.1180 r_free=0.1353 | n_water=487 | time (s): 157.250 (total time: 207.090) Filter (q & B) r_work=0.1189 r_free=0.1359 | n_water=443 | time (s): 3.040 (total time: 210.130) Filter (dist only) r_work=0.1189 r_free=0.1358 | n_water=442 | time (s): 40.030 (total time: 250.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.973640 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.088023 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 0.1189 0.1376 0.0187 0.006 0.9 1.6 0.5 0.0 0 0.987 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.76 1.87 3.440 21.470 39.088 3.631 11.87 13.71 1.84 3.521 21.431 39.088 3.626 Individual atomic B min max mean iso aniso Overall: 9.27 107.87 21.31 2.24 210 1759 Protein: 9.27 107.87 17.14 2.24 0 1519 Water: 11.53 72.56 35.58 N/A 210 232 Other: 20.33 29.63 25.24 N/A 0 8 Chain A: 9.27 107.87 19.77 N/A 0 1759 Chain S: 16.02 58.92 34.23 N/A 210 0 Histogram: Values Number of atoms 9.27 - 19.13 1235 19.13 - 28.99 283 28.99 - 38.85 217 38.85 - 48.71 133 48.71 - 58.57 68 58.57 - 68.43 19 68.43 - 78.29 9 78.29 - 88.15 2 88.15 - 98.01 1 98.01 - 107.87 2 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1371 r_work=0.1188 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1371 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1185 r_free = 0.1377 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1185 r_free= 0.1377 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.626979 | | target function (ml) not normalized (work): 302062.050881 | | target function (ml) not normalized (free): 15972.746441 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1185 0.1377 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1498 0.1496 0.1573 n_refl.: 87578 remove outliers: r(all,work,free)=0.1498 0.1496 0.1573 n_refl.: 87578 overall B=-0.01 to atoms: r(all,work,free)=0.1496 0.1494 0.1572 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1185 0.1381 n_refl.: 87578 remove outliers: r(all,work,free)=0.1193 0.1183 0.1381 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 0.3971 288.891 254.676 0.456 0.999 0.301 11.894-9.307 93.14 91 4 0.2204 473.271 451.843 0.840 1.001 0.209 9.237-7.194 97.73 208 7 0.2387 383.339 378.304 0.921 1.002 0.140 7.162-5.571 100.00 427 22 0.2085 293.200 283.903 0.905 1.002 0.132 5.546-4.326 100.00 867 58 0.1131 402.492 397.953 0.954 1.002 0.130 4.315-3.360 100.00 1859 96 0.0941 382.772 380.139 0.993 1.002 0.130 3.356-2.611 100.00 3867 181 0.1157 251.462 249.811 1.000 1.002 0.100 2.608-2.026 99.99 8198 413 0.1033 166.696 165.726 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0988 81.406 81.682 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.099 35.718 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2124 22.745 21.372 0.980 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0284 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1183 r_free=0.1381 After: r_work=0.1184 r_free=0.1381 ================================== NQH flips ================================== r_work=0.1184 r_free=0.1381 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=0.1184 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1381 | n_water=442 | time (s): 1.710 (total time: 1.710) Filter (dist) r_work=0.1184 r_free=0.1381 | n_water=442 | time (s): 35.480 (total time: 37.190) Filter (q & B) r_work=0.1185 r_free=0.1383 | n_water=437 | time (s): 2.650 (total time: 39.840) Compute maps r_work=0.1185 r_free=0.1383 | n_water=437 | time (s): 1.320 (total time: 41.160) Filter (map) r_work=0.1208 r_free=0.1384 | n_water=327 | time (s): 3.620 (total time: 44.780) Find peaks r_work=0.1208 r_free=0.1384 | n_water=327 | time (s): 0.560 (total time: 45.340) Add new water r_work=0.1260 r_free=0.1425 | n_water=496 | time (s): 2.760 (total time: 48.100) Refine new water occ: r_work=0.1198 r_free=0.1370 adp: r_work=0.1198 r_free=0.1371 occ: r_work=0.1184 r_free=0.1360 adp: r_work=0.1182 r_free=0.1361 occ: r_work=0.1174 r_free=0.1354 adp: r_work=0.1171 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1171 r_free=0.1353 r_work=0.1171 r_free=0.1353 | n_water=496 | time (s): 180.860 (total time: 228.960) Filter (q & B) r_work=0.1178 r_free=0.1356 | n_water=460 | time (s): 3.990 (total time: 232.950) Filter (dist only) r_work=0.1178 r_free=0.1354 | n_water=459 | time (s): 39.670 (total time: 272.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.982111 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.177041 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1208 0.1385 0.0177 0.007 1.1 5.8 0.5 0.0 0 0.991 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.85 1.77 3.377 21.456 46.177 3.636 12.04 13.88 1.84 3.830 21.319 46.177 3.625 Individual atomic B min max mean iso aniso Overall: 9.24 102.86 21.21 2.07 227 1759 Protein: 9.24 102.86 16.79 2.08 0 1519 Water: 11.50 71.30 35.76 N/A 227 232 Other: 21.35 29.26 26.06 N/A 0 8 Chain A: 9.24 102.86 19.41 N/A 0 1759 Chain S: 13.93 60.44 35.19 N/A 227 0 Histogram: Values Number of atoms 9.24 - 18.60 1229 18.60 - 27.96 278 27.96 - 37.32 211 37.32 - 46.69 147 46.69 - 56.05 80 56.05 - 65.41 25 65.41 - 74.77 11 74.77 - 84.13 2 84.13 - 93.50 1 93.50 - 102.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1388 r_work=0.1204 r_free=0.1388 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1388 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1384 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1201 r_free= 0.1384 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623976 | | target function (ml) not normalized (work): 301797.507602 | | target function (ml) not normalized (free): 15949.713366 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1420 0.1470 5.6763 5.6655| | 2: 3.57 - 2.84 1.00 2888 124 0.1111 0.1460 5.2039 5.264| | 3: 2.83 - 2.48 1.00 2820 163 0.1233 0.1252 5.0144 5.026| | 4: 2.47 - 2.25 1.00 2825 136 0.1041 0.1175 4.7174 4.7664| | 5: 2.25 - 2.09 1.00 2756 127 0.0999 0.1169 4.6588 4.7483| | 6: 2.09 - 1.97 1.00 2846 113 0.0979 0.1169 4.3584 4.4703| | 7: 1.97 - 1.87 1.00 2787 165 0.1003 0.1215 4.0827 4.1745| | 8: 1.87 - 1.79 1.00 2789 144 0.1025 0.1266 3.9945 4.0956| | 9: 1.79 - 1.72 1.00 2745 138 0.0957 0.1265 3.7216 3.8865| | 10: 1.72 - 1.66 1.00 2831 160 0.1006 0.1262 3.6393 3.7791| | 11: 1.66 - 1.61 1.00 2712 147 0.0960 0.1065 3.5702 3.5868| | 12: 1.61 - 1.56 1.00 2773 144 0.0926 0.1184 3.3522 3.4891| | 13: 1.56 - 1.52 1.00 2745 130 0.0989 0.1109 3.3474 3.467| | 14: 1.52 - 1.48 1.00 2803 134 0.1001 0.1125 3.2671 3.3469| | 15: 1.48 - 1.45 1.00 2738 128 0.1017 0.1334 3.1674 3.3137| | 16: 1.45 - 1.42 1.00 2756 161 0.1077 0.1282 3.1531 3.2539| | 17: 1.42 - 1.39 1.00 2785 139 0.1123 0.1318 3.116 3.2364| | 18: 1.39 - 1.36 1.00 2741 179 0.1155 0.1394 3.0868 3.2593| | 19: 1.36 - 1.34 1.00 2807 134 0.1218 0.1631 3.0938 3.2806| | 20: 1.34 - 1.32 1.00 2696 147 0.1320 0.1487 3.0867 3.1459| | 21: 1.32 - 1.30 1.00 2785 112 0.1427 0.1560 3.0906 3.144| | 22: 1.29 - 1.27 1.00 2704 152 0.1486 0.1893 3.0853 3.27| | 23: 1.27 - 1.26 1.00 2802 156 0.1579 0.1895 3.1035 3.219| | 24: 1.26 - 1.24 1.00 2744 132 0.1627 0.1737 3.093 3.1841| | 25: 1.24 - 1.22 1.00 2733 148 0.1803 0.2289 3.1108 3.2835| | 26: 1.22 - 1.21 1.00 2727 135 0.1866 0.1779 3.1203 3.1966| | 27: 1.21 - 1.19 1.00 2814 148 0.2012 0.2131 3.1369 3.1528| | 28: 1.19 - 1.18 1.00 2671 147 0.2151 0.2328 3.1386 3.1651| | 29: 1.18 - 1.16 1.00 2800 134 0.2223 0.2376 3.1256 3.2148| | 30: 1.16 - 1.15 1.00 2739 148 0.2377 0.2522 3.1146 3.1685| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2916 171 0.94 9.28 1.00 0.96 6461.25| | 2: 3.57 - 2.84 2888 124 0.92 13.69 1.01 0.96 6461.25| | 3: 2.83 - 2.48 2820 163 0.88 17.89 0.99 0.97 5414.60| | 4: 2.47 - 2.25 2825 136 0.91 14.92 1.00 0.97 2715.61| | 5: 2.25 - 2.09 2756 127 0.89 17.13 1.01 0.97 2715.61| | 6: 2.09 - 1.97 2846 113 0.91 13.82 1.02 0.97 1592.64| | 7: 1.97 - 1.87 2787 165 0.94 10.93 1.02 0.97 634.90| | 8: 1.87 - 1.79 2789 144 0.91 14.56 1.00 0.97 634.90| | 9: 1.79 - 1.72 2745 138 0.93 11.50 0.98 0.97 343.39| | 10: 1.72 - 1.66 2831 160 0.93 12.39 0.98 0.97 285.01| | 11: 1.66 - 1.61 2712 147 0.93 13.03 0.98 0.97 271.97| | 12: 1.61 - 1.56 2773 144 0.95 9.62 0.99 0.97 148.99| | 13: 1.56 - 1.52 2745 130 0.94 11.27 1.02 0.97 148.99| | 14: 1.52 - 1.48 2803 134 0.94 11.36 1.02 0.97 133.08| | 15: 1.48 - 1.45 2738 128 0.95 10.55 1.02 0.98 103.96| | 16: 1.45 - 1.42 2756 161 0.94 11.68 1.02 0.98 103.96| | 17: 1.42 - 1.39 2785 139 0.94 11.47 1.01 0.98 93.60| | 18: 1.39 - 1.36 2741 179 0.94 11.75 1.01 0.98 87.61| | 19: 1.36 - 1.34 2807 134 0.94 12.35 1.00 0.98 87.61| | 20: 1.34 - 1.32 2696 147 0.94 12.43 0.99 0.97 82.32| | 21: 1.32 - 1.30 2785 112 0.94 13.37 0.99 0.96 81.94| | 22: 1.29 - 1.27 2704 152 0.93 13.97 0.99 0.96 82.05| | 23: 1.27 - 1.26 2802 156 0.92 14.86 0.98 0.95 82.60| | 24: 1.26 - 1.24 2744 132 0.92 14.97 0.97 0.95 82.60| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.94 84.13| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.02 0.93 85.82| | 27: 1.21 - 1.19 2814 148 0.89 18.72 1.02 0.93 85.82| | 28: 1.19 - 1.18 2671 147 0.88 20.26 1.01 0.93 89.20| | 29: 1.18 - 1.16 2800 134 0.88 20.58 0.99 0.92 90.47| | 30: 1.16 - 1.15 2739 148 0.86 22.00 0.98 0.92 90.47| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.94 max = 6461.25 mean = 1003.55| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.15| |phase err.(test): min = 0.00 max = 88.52 mean = 14.25| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1201 0.1384 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1505 0.1503 0.1575 n_refl.: 87574 remove outliers: r(all,work,free)=0.1505 0.1503 0.1575 n_refl.: 87574 overall B=-0.01 to atoms: r(all,work,free)=0.1504 0.1501 0.1574 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1201 0.1384 n_refl.: 87574 remove outliers: r(all,work,free)=0.1210 0.1201 0.1384 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 0.4030 288.891 252.773 0.428 1.000 0.291 11.894-9.307 93.14 91 4 0.2424 473.271 453.942 0.843 1.002 0.213 9.237-7.194 97.73 208 7 0.2552 383.339 376.136 0.905 1.002 0.145 7.162-5.571 100.00 427 22 0.2216 293.200 282.334 0.898 1.002 0.129 5.546-4.326 100.00 867 58 0.1204 402.492 397.598 0.954 1.002 0.108 4.315-3.360 100.00 1859 96 0.0998 382.772 379.998 0.994 1.002 0.106 3.356-2.611 100.00 3867 181 0.1185 251.462 249.320 1.000 1.001 0.090 2.608-2.026 99.99 8198 413 0.1049 166.696 165.699 1.014 1.000 0.000 2.025-1.573 100.00 17313 902 0.0979 81.406 81.667 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1233 36.099 35.721 1.022 0.996 0.000 1.221-1.150 99.97 13689 708 0.2121 22.745 21.371 0.980 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0286 ================= 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 : 0.2606 0.1957 0.082 5.302 8.8 119.3 19.9 258 0.000 1_bss: 0.1637 0.1780 0.082 5.302 9.1 119.5 20.1 258 0.000 1_settarget: 0.1637 0.1780 0.082 5.302 9.1 119.5 20.1 258 0.000 1_nqh: 0.1639 0.1784 0.082 5.302 9.1 119.5 20.1 258 0.006 1_weight: 0.1639 0.1784 0.082 5.302 9.1 119.5 20.1 258 0.006 1_xyzrec: 0.1208 0.1453 0.007 0.955 9.1 119.5 20.1 258 0.127 1_adp: 0.1237 0.1529 0.007 0.955 8.5 118.5 21.0 258 0.127 1_regHadp: 0.1242 0.1534 0.007 0.955 8.5 118.5 21.0 258 0.127 1_occ: 0.1241 0.1532 0.007 0.955 8.5 118.5 21.0 258 0.127 2_bss: 0.1240 0.1529 0.007 0.955 8.7 118.6 21.1 258 0.127 2_settarget: 0.1240 0.1529 0.007 0.955 8.7 118.6 21.1 258 0.127 2_updatecdl: 0.1240 0.1529 0.007 0.964 8.7 118.6 21.1 258 0.127 2_nqh: 0.1242 0.1531 0.007 0.964 8.7 118.6 21.1 258 0.127 2_sol: 0.1229 0.1473 0.007 0.964 8.7 118.6 23.6 439 n/a 2_weight: 0.1229 0.1473 0.007 0.964 8.7 118.6 23.6 439 n/a 2_xyzrec: 0.1230 0.1510 0.006 0.860 8.7 118.6 23.6 439 n/a 2_adp: 0.1206 0.1492 0.006 0.860 8.7 114.4 23.3 439 n/a 2_regHadp: 0.1206 0.1492 0.006 0.860 8.7 114.4 23.3 439 n/a 2_occ: 0.1207 0.1490 0.006 0.860 8.7 114.4 23.3 439 n/a 3_bss: 0.1201 0.1488 0.006 0.860 8.8 114.5 23.3 439 n/a 3_settarget: 0.1201 0.1488 0.006 0.860 8.8 114.5 23.3 439 n/a 3_updatecdl: 0.1201 0.1488 0.006 0.858 8.8 114.5 23.3 439 n/a 3_nqh: 0.1201 0.1488 0.006 0.858 8.8 114.5 23.3 439 n/a 3_sol: 0.1229 0.1503 0.006 0.858 8.8 114.5 22.0 447 n/a 3_weight: 0.1229 0.1503 0.006 0.858 8.8 114.5 22.0 447 n/a 3_xyzrec: 0.1234 0.1458 0.005 0.914 8.8 114.5 22.0 447 n/a 3_adp: 0.1211 0.1402 0.005 0.914 9.2 109.9 21.7 447 n/a 3_regHadp: 0.1212 0.1403 0.005 0.914 9.2 109.9 21.7 447 n/a 3_occ: 0.1207 0.1404 0.005 0.914 9.2 109.9 21.7 447 n/a 4_bss: 0.1192 0.1370 0.005 0.914 9.2 109.8 21.6 447 n/a 4_settarget: 0.1192 0.1370 0.005 0.914 9.2 109.8 21.6 447 n/a 4_updatecdl: 0.1192 0.1370 0.006 0.913 9.2 109.8 21.6 447 n/a 4_nqh: 0.1192 0.1370 0.006 0.913 9.2 109.8 21.6 447 n/a 4_sol: 0.1189 0.1358 0.006 0.913 9.2 109.8 21.4 442 n/a 4_weight: 0.1189 0.1358 0.006 0.913 9.2 109.8 21.4 442 n/a 4_xyzrec: 0.1189 0.1376 0.006 0.948 9.2 109.8 21.4 442 n/a 4_adp: 0.1187 0.1371 0.006 0.948 9.3 107.9 21.3 442 n/a 4_regHadp: 0.1188 0.1371 0.006 0.948 9.3 107.9 21.3 442 n/a 4_occ: 0.1185 0.1377 0.006 0.948 9.3 107.9 21.3 442 n/a 5_bss: 0.1183 0.1381 0.006 0.948 9.3 107.9 21.3 442 n/a 5_settarget: 0.1183 0.1381 0.006 0.948 9.3 107.9 21.3 442 n/a 5_updatecdl: 0.1183 0.1381 0.006 0.950 9.3 107.9 21.3 442 n/a 5_setrh: 0.1184 0.1381 0.006 0.950 9.3 107.9 21.3 442 n/a 5_nqh: 0.1184 0.1381 0.006 0.950 9.3 107.9 21.3 442 n/a 5_sol: 0.1178 0.1354 0.006 0.950 9.3 107.9 21.5 459 n/a 5_weight: 0.1178 0.1354 0.006 0.950 9.3 107.9 21.5 459 n/a 5_xyzrec: 0.1208 0.1385 0.007 1.058 9.3 107.9 21.5 459 n/a 5_adp: 0.1204 0.1388 0.007 1.058 9.2 102.9 21.2 459 n/a 5_regHadp: 0.1204 0.1388 0.007 1.058 9.2 102.9 21.2 459 n/a 5_occ: 0.1201 0.1384 0.007 1.058 9.2 102.9 21.2 459 n/a end: 0.1201 0.1384 0.007 1.058 9.2 102.8 21.2 459 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3473948_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3473948_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8800 Refinement macro-cycles (run) : 3541.0900 Write final files (write_after_run_outputs) : 69.8100 Total : 3615.7800 Total CPU time: 60.88 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:43 PST -0800 (1735452703.79 s) Start R-work = 0.1637, R-free = 0.1780 Final R-work = 0.1201, R-free = 0.1384 =============================================================================== Job complete usr+sys time: 3753.39 seconds wall clock time: 66 minutes 56.80 seconds (4016.80 seconds total)