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_8530424.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_8530424.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530424.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: 2.15, 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: 0.78 Conformation dependent library (CDL) restraints added in 336.2 milliseconds Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.91: 556 0.91 - 1.16: 1074 1.16 - 1.40: 593 1.40 - 1.65: 869 1.65 - 1.89: 61 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.204 0.256 1.19e-02 7.06e+03 4.61e+02 bond pdb=" N LYS A 63 " pdb=" CA LYS A 63 " ideal model delta sigma weight residual 1.457 1.729 -0.272 1.33e-02 5.65e+03 4.18e+02 bond pdb=" CA HIS A 126 " pdb=" C HIS A 126 " ideal model delta sigma weight residual 1.528 1.729 -0.200 1.11e-02 8.12e+03 3.25e+02 bond pdb=" N THR A 154 " pdb=" CA THR A 154 " ideal model delta sigma weight residual 1.454 1.688 -0.234 1.33e-02 5.65e+03 3.09e+02 bond pdb=" CA BGLU A 90 " pdb=" C BGLU A 90 " ideal model delta sigma weight residual 1.523 1.757 -0.234 1.35e-02 5.49e+03 3.00e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 2729 4.02 - 8.04: 1893 8.04 - 12.06: 872 12.06 - 16.08: 230 16.08 - 20.10: 53 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 181 " pdb=" C VAL A 181 " pdb=" N LYS A 182 " ideal model delta sigma weight residual 121.83 138.67 -16.84 1.03e+00 9.43e-01 2.67e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH1 ARG A 28 " ideal model delta sigma weight residual 121.50 135.63 -14.13 1.00e+00 1.00e+00 2.00e+02 angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH1 ARG A 98 " ideal model delta sigma weight residual 121.50 134.91 -13.41 1.00e+00 1.00e+00 1.80e+02 angle pdb=" OE1 GLN A 180 " pdb=" CD GLN A 180 " pdb=" NE2 GLN A 180 " ideal model delta sigma weight residual 122.60 135.98 -13.38 1.00e+00 1.00e+00 1.79e+02 angle pdb=" CA LYS A 130 " pdb=" C LYS A 130 " pdb=" O LYS A 130 " ideal model delta sigma weight residual 120.82 134.78 -13.96 1.05e+00 9.07e-01 1.77e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 935 16.66 - 33.32: 125 33.32 - 49.98: 33 49.98 - 66.63: 14 66.63 - 83.29: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+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 180.00 152.08 27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " pdb=" CE1 HIS A 138 " pdb=" HE1 HIS A 138 " ideal model delta harmonic sigma weight residual -180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.211: 100 0.211 - 0.422: 81 0.422 - 0.633: 41 0.633 - 0.843: 16 0.843 - 1.054: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 166 " pdb=" N LEU A 166 " pdb=" C LEU A 166 " pdb=" CB LEU A 166 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.78e+01 chirality pdb=" CB ILE A 117 " pdb=" CA ILE A 117 " pdb=" CG1 ILE A 117 " pdb=" CG2 ILE A 117 " both_signs ideal model delta sigma weight residual False 2.64 1.62 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA BLEU A 153 " pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CB BLEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.51 -1.00 2.00e-01 2.50e+01 2.48e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.067 2.00e-02 2.50e+03 6.69e-02 1.34e+02 pdb=" CG PHE A 119 " -0.095 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.100 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.104 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.062 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.048 2.00e-02 2.50e+03 6.63e-02 9.88e+01 pdb=" CG HIS A 138 " 0.001 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " -0.129 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.036 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.046 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.031 2.00e-02 2.50e+03 5.53e-02 9.18e+01 pdb=" CG TYR A 141 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.082 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.049 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.086 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1010 2.32 - 2.89: 8126 2.89 - 3.46: 10504 3.46 - 4.03: 15263 4.03 - 4.60: 21626 Nonbonded interactions: 56529 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.748 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.755 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.812 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.826 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.832 2.270 ... (remaining 56524 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_8530424_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= 0.1975 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792794 | | target function (ml) not normalized (work): 232656.523122 | | target function (ml) not normalized (free): 11819.249878 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3028 0.2055 7.1077 4.9209| | 2: 3.57 - 2.84 1.00 2876 122 0.2419 0.1872 4.3393 4.335| | 3: 2.84 - 2.48 1.00 2833 165 0.2348 0.1819 4.1239 4.1631| | 4: 2.47 - 2.25 1.00 2825 136 0.2321 0.1517 3.8224 3.8427| | 5: 2.25 - 2.09 1.00 2756 127 0.2462 0.1617 3.7958 3.8201| | 6: 2.09 - 1.97 1.00 2846 113 0.2571 0.1810 3.4696 3.5209| | 7: 1.97 - 1.87 1.00 2787 165 0.2589 0.1852 3.1471 3.2048| | 8: 1.87 - 1.79 1.00 2789 144 0.2487 0.1962 3.0618 3.1452| | 9: 1.79 - 1.72 1.00 2745 138 0.2422 0.1814 2.8887 2.9363| | 10: 1.72 - 1.66 1.00 2789 158 0.2397 0.2156 2.8086 2.9311| | 11: 1.66 - 1.61 1.00 2740 147 0.2492 0.1957 2.7627 2.7952| | 12: 1.61 - 1.56 1.00 2787 146 0.2567 0.2168 2.6366 2.7079| | 13: 1.56 - 1.52 1.00 2745 130 0.2553 0.1711 2.5963 2.5787| | 14: 1.52 - 1.48 1.00 2803 134 0.2530 0.2002 2.5005 2.6095| | 15: 1.48 - 1.45 1.00 2738 128 0.2600 0.2168 2.4297 2.4502| | 16: 1.45 - 1.42 1.00 2756 161 0.2639 0.2022 2.3807 2.3845| | 17: 1.42 - 1.39 1.00 2785 139 0.2680 0.2092 2.3374 2.3734| | 18: 1.39 - 1.36 1.00 2741 179 0.2703 0.2252 2.2668 2.3701| | 19: 1.36 - 1.34 1.00 2807 134 0.2631 0.2391 2.2535 2.3461| | 20: 1.34 - 1.32 1.00 2696 147 0.2739 0.2061 2.2184 2.1674| | 21: 1.32 - 1.30 1.00 2785 112 0.2737 0.2360 2.1693 2.2017| | 22: 1.29 - 1.27 1.00 2704 152 0.2733 0.2349 2.1337 2.1469| | 23: 1.27 - 1.26 1.00 2802 156 0.2745 0.2526 2.0947 2.184| | 24: 1.26 - 1.24 1.00 2744 132 0.2773 0.2438 2.0719 2.1498| | 25: 1.24 - 1.22 1.00 2734 148 0.2831 0.2818 2.0393 2.1188| | 26: 1.22 - 1.21 1.00 2727 135 0.2866 0.2242 1.9938 2.0448| | 27: 1.21 - 1.19 1.00 2814 148 0.2987 0.2566 2.009 1.9822| | 28: 1.19 - 1.18 1.00 2671 147 0.2989 0.2731 1.9827 1.9681| | 29: 1.18 - 1.16 1.00 2800 134 0.2936 0.2636 1.9496 2.023| | 30: 1.16 - 1.15 1.00 2740 148 0.3084 0.2861 1.9341 1.9578| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.60 0.76 0.23 1445.40| | 2: 3.57 - 2.84 2876 122 0.81 25.75 1.27 0.23 1445.40| | 3: 2.84 - 2.48 2833 165 0.74 31.64 1.24 0.24 1199.64| | 4: 2.47 - 2.25 2825 136 0.81 25.37 1.26 0.25 561.84| | 5: 2.25 - 2.09 2756 127 0.78 28.95 1.28 0.25 561.84| | 6: 2.09 - 1.97 2846 113 0.83 22.68 1.29 0.25 309.70| | 7: 1.97 - 1.87 2787 165 0.90 16.87 1.29 0.26 94.66| | 8: 1.87 - 1.79 2789 144 0.85 21.55 1.25 0.26 94.66| | 9: 1.79 - 1.72 2745 138 0.87 19.28 1.23 0.25 58.05| | 10: 1.72 - 1.66 2789 158 0.86 20.69 1.22 0.25 50.71| | 11: 1.66 - 1.61 2740 147 0.85 21.73 1.23 0.25 48.93| | 12: 1.61 - 1.56 2787 146 0.88 19.08 1.24 0.25 30.85| | 13: 1.56 - 1.52 2745 130 0.86 20.88 1.23 0.25 30.85| | 14: 1.52 - 1.48 2803 134 0.86 21.19 1.23 0.25 27.48| | 15: 1.48 - 1.45 2738 128 0.86 20.67 1.23 0.25 21.31| | 16: 1.45 - 1.42 2756 161 0.85 22.12 1.24 0.25 21.31| | 17: 1.42 - 1.39 2785 139 0.86 20.98 1.23 0.25 18.01| | 18: 1.39 - 1.36 2741 179 0.86 21.62 1.24 0.25 16.10| | 19: 1.36 - 1.34 2807 134 0.85 22.13 1.21 0.25 16.10| | 20: 1.34 - 1.32 2696 147 0.87 21.03 1.21 0.25 13.23| | 21: 1.32 - 1.30 2785 112 0.86 21.94 1.20 0.25 13.03| | 22: 1.29 - 1.27 2704 152 0.86 22.31 1.21 0.25 12.72| | 23: 1.27 - 1.26 2802 156 0.86 22.10 1.21 0.24 11.18| | 24: 1.26 - 1.24 2744 132 0.85 22.71 1.21 0.24 11.18| | 25: 1.24 - 1.22 2734 148 0.85 23.39 1.21 0.24 10.53| | 26: 1.22 - 1.21 2727 135 0.84 23.74 1.21 0.24 9.80| | 27: 1.21 - 1.19 2814 148 0.83 24.65 1.20 0.24 9.80| | 28: 1.19 - 1.18 2671 147 0.84 24.52 1.19 0.23 8.96| | 29: 1.18 - 1.16 2800 134 0.84 24.61 1.17 0.23 8.65| | 30: 1.16 - 1.15 2740 148 0.82 26.35 1.15 0.23 8.65| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.65 max = 1445.40 mean = 211.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.64| |phase err.(test): min = 0.00 max = 89.82 mean = 22.65| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.272 1557 Z= 5.609 Angle : 5.432 16.836 2118 Z= 3.905 Chirality : 0.375 1.054 243 Planarity : 0.030 0.083 284 Dihedral : 14.044 83.291 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 33.51 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.50), residues: 224 helix: -2.30 (0.39), residues: 109 sheet: -0.50 (0.86), residues: 30 loop : 0.07 (0.66), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.130 0.031 ARG A 27 TYR 0.116 0.039 TYR A 141 PHE 0.113 0.044 PHE A 119 HIS 0.072 0.030 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= 0.1975 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792794 | | target function (ml) not normalized (work): 232656.523122 | | target function (ml) not normalized (free): 11819.249878 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2607 0.1975 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2607 0.1975 n_refl.: 87602 remove outliers: r(all,work,free)=0.1979 0.1982 0.1975 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2004 0.2007 0.1990 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1641 0.1633 0.1789 n_refl.: 87594 remove outliers: r(all,work,free)=0.1640 0.1632 0.1789 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 98.94 88 5 0.3806 386.340 360.033 0.740 0.916 0.407 11.894-9.307 98.04 96 4 0.1735 616.173 590.293 1.013 0.917 0.390 9.237-7.194 100.00 213 7 0.2205 501.916 491.202 1.041 0.917 0.370 7.162-5.571 100.00 427 22 0.2233 376.660 364.544 1.023 0.918 0.288 5.546-4.326 100.00 867 58 0.1278 517.062 510.322 1.051 0.918 0.228 4.315-3.360 100.00 1859 96 0.1149 491.729 488.401 1.094 0.919 0.199 3.356-2.611 100.00 3867 181 0.1421 323.041 319.738 1.084 0.920 0.109 2.608-2.026 99.99 8198 413 0.1354 214.146 212.181 1.092 0.922 0.000 2.025-1.573 100.00 17313 902 0.1641 104.578 103.927 1.093 0.926 0.000 1.573-1.221 100.00 36679 1900 0.2055 46.374 45.008 1.071 0.932 0.000 1.221-1.150 99.97 13689 708 0.2583 29.219 26.977 1.038 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0464 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1632 r_free=0.1789 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1633 r_free=0.1792 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.358717 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2001.444807 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1211 0.1459 0.0248 0.007 0.9 1.3 0.5 0.0 0 12.179 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.59 2.48 3.013 19.061 2001.445 0.017 12.39 15.38 2.99 3.225 19.585 2001.445 0.015 Individual atomic B min max mean iso aniso Overall: 8.54 118.47 21.08 2.86 0 1785 Protein: 8.54 118.47 17.95 2.86 0 1519 Water: 11.14 114.50 39.29 N/A 0 258 Other: 23.14 36.24 29.19 N/A 0 8 Chain A: 8.54 118.47 21.08 N/A 0 1785 Histogram: Values Number of atoms 8.54 - 19.54 1200 19.54 - 30.53 237 30.53 - 41.52 162 41.52 - 52.52 104 52.52 - 63.51 52 63.51 - 74.50 16 74.50 - 85.50 7 85.50 - 96.49 4 96.49 - 107.48 0 107.48 - 118.47 3 =========================== Idealize ADP of riding H ========================== r_work=0.1240 r_free=0.1538 r_work=0.1244 r_free=0.1541 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1244 r_free = 0.1541 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 = 0.1244 r_free = 0.1544 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.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1244 r_free= 0.1544 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015291 | | target function (ls_wunit_k1) not normalized (work): 1273.648344 | | target function (ls_wunit_k1) not normalized (free): 114.064070 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1259 0.1244 0.1544 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1707 0.1706 0.1768 n_refl.: 87592 remove outliers: r(all,work,free)=0.1707 0.1706 0.1768 n_refl.: 87592 overall B=0.11 to atoms: r(all,work,free)=0.1725 0.1725 0.1780 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1257 0.1243 0.1537 n_refl.: 87592 remove outliers: r(all,work,free)=0.1257 0.1242 0.1537 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 95.83 87 5 0.3616 297.847 279.034 0.686 0.924 0.380 11.894-9.307 98.04 96 4 0.1541 479.071 467.557 0.994 0.924 0.380 9.237-7.194 100.00 213 7 0.1838 390.237 384.979 1.027 0.924 0.340 7.162-5.571 100.00 427 22 0.1719 292.851 287.717 1.001 0.925 0.253 5.546-4.326 100.00 867 58 0.0921 402.012 399.110 1.028 0.925 0.204 4.315-3.360 100.00 1859 96 0.0774 382.317 381.331 1.076 0.926 0.190 3.356-2.611 100.00 3867 181 0.1022 251.162 250.453 1.078 0.928 0.057 2.608-2.026 99.99 8198 413 0.0975 166.498 165.921 1.086 0.930 0.000 2.025-1.573 100.00 17313 902 0.1209 81.309 81.466 1.089 0.935 0.000 1.573-1.221 100.00 36679 1900 0.1648 36.056 35.524 1.067 0.942 0.000 1.221-1.150 99.97 13689 708 0.2363 22.718 21.251 1.022 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0423 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1242 r_free=0.1537 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1242 r_free=0.1537 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1242 r_free=0.1537 | n_water=258 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1251 r_free=0.1538 | n_water=252 | time (s): 25.610 (total time: 27.980) Filter (q & B) r_work=0.1254 r_free=0.1537 | n_water=249 | time (s): 3.420 (total time: 31.400) Compute maps r_work=0.1254 r_free=0.1537 | n_water=249 | time (s): 1.650 (total time: 33.050) Filter (map) r_work=0.1272 r_free=0.1541 | n_water=235 | time (s): 3.740 (total time: 36.790) Find peaks r_work=0.1272 r_free=0.1541 | n_water=235 | time (s): 0.730 (total time: 37.520) Add new water r_work=0.1427 r_free=0.1690 | n_water=455 | time (s): 3.670 (total time: 41.190) Refine new water occ: r_work=0.1336 r_free=0.1570 adp: r_work=0.1253 r_free=0.1504 occ: r_work=0.1266 r_free=0.1501 adp: r_work=0.1230 r_free=0.1480 occ: r_work=0.1233 r_free=0.1477 adp: r_work=0.1223 r_free=0.1476 ADP+occupancy (water only), MIN, final r_work=0.1223 r_free=0.1476 r_work=0.1223 r_free=0.1476 | n_water=455 | time (s): 76.710 (total time: 117.900) Filter (q & B) r_work=0.1229 r_free=0.1483 | n_water=437 | time (s): 3.710 (total time: 121.610) Filter (dist only) r_work=0.1229 r_free=0.1483 | n_water=437 | time (s): 40.840 (total time: 162.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.099222 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1607.326222 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 0.1518 0.0289 0.007 0.9 2.2 0.5 0.0 0 12.050 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 15.18 2.89 3.794 23.312 1607.326 0.015 11.99 14.88 2.89 4.257 23.101 1607.326 0.015 Individual atomic B min max mean iso aniso Overall: 8.76 113.58 23.32 2.63 202 1762 Protein: 8.76 113.58 17.66 2.63 0 1519 Water: 11.05 72.92 42.96 N/A 202 235 Other: 21.06 32.41 25.84 N/A 0 8 Chain A: 8.76 113.58 20.36 N/A 0 1762 Chain S: 12.78 72.92 49.19 N/A 202 0 Histogram: Values Number of atoms 8.76 - 19.24 1208 19.24 - 29.72 244 29.72 - 40.21 187 40.21 - 50.69 143 50.69 - 61.17 116 61.17 - 71.65 52 71.65 - 82.14 8 82.14 - 92.62 3 92.62 - 103.10 1 103.10 - 113.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1488 r_work=0.1199 r_free=0.1488 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1488 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 = 0.1198 r_free = 0.1485 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.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1198 r_free= 0.1485 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013956 | | target function (ls_wunit_k1) not normalized (work): 1162.473315 | | target function (ls_wunit_k1) not normalized (free): 102.955863 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1198 0.1485 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1605 0.1602 0.1706 n_refl.: 87591 remove outliers: r(all,work,free)=0.1605 0.1602 0.1706 n_refl.: 87591 overall B=0.03 to atoms: r(all,work,free)=0.1610 0.1606 0.1709 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1195 0.1477 n_refl.: 87591 remove outliers: r(all,work,free)=0.1207 0.1193 0.1477 n_refl.: 87587 ======================== 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 290.571 271.559 0.611 0.939 0.350 11.894-9.307 98.04 96 4 0.1558 479.071 474.764 0.980 0.940 0.330 9.237-7.194 100.00 213 7 0.1685 390.237 391.364 1.040 0.940 0.270 7.162-5.571 100.00 427 22 0.1487 292.851 289.432 0.998 0.940 0.240 5.546-4.326 100.00 867 58 0.0827 402.012 398.890 1.019 0.940 0.210 4.315-3.360 100.00 1859 96 0.0717 382.317 381.158 1.067 0.941 0.210 3.356-2.611 100.00 3867 181 0.0961 251.162 250.424 1.075 0.941 0.072 2.608-2.026 99.99 8198 413 0.0951 166.498 166.100 1.081 0.942 0.000 2.025-1.573 100.00 17313 902 0.1174 81.309 81.505 1.090 0.944 0.000 1.573-1.221 100.00 36679 1900 0.1607 36.056 35.563 1.075 0.946 0.000 1.221-1.150 99.97 13689 708 0.2342 22.718 21.277 1.030 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0468 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1477 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1477 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1477 | n_water=437 | time (s): 2.030 (total time: 2.030) Filter (dist) r_work=0.1193 r_free=0.1476 | n_water=435 | time (s): 38.570 (total time: 40.600) Filter (q & B) r_work=0.1195 r_free=0.1475 | n_water=434 | time (s): 3.270 (total time: 43.870) Compute maps r_work=0.1195 r_free=0.1475 | n_water=434 | time (s): 1.610 (total time: 45.480) Filter (map) r_work=0.1236 r_free=0.1480 | n_water=294 | time (s): 2.960 (total time: 48.440) Find peaks r_work=0.1236 r_free=0.1480 | n_water=294 | time (s): 0.460 (total time: 48.900) Add new water r_work=0.1363 r_free=0.1613 | n_water=481 | time (s): 3.040 (total time: 51.940) Refine new water occ: r_work=0.1264 r_free=0.1525 adp: r_work=0.1266 r_free=0.1526 occ: r_work=0.1240 r_free=0.1502 adp: r_work=0.1238 r_free=0.1500 occ: r_work=0.1223 r_free=0.1485 adp: r_work=0.1217 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1217 r_free=0.1482 r_work=0.1217 r_free=0.1482 | n_water=481 | time (s): 162.640 (total time: 214.580) Filter (q & B) r_work=0.1221 r_free=0.1491 | n_water=450 | time (s): 2.620 (total time: 217.200) Filter (dist only) r_work=0.1221 r_free=0.1491 | n_water=450 | time (s): 37.690 (total time: 254.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.939594 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 52.025288 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 0.1466 0.0239 0.006 0.9 2.2 0.5 0.0 0 0.970 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.66 2.39 3.628 22.134 52.025 3.720 12.14 14.13 1.99 4.129 21.951 52.025 3.648 Individual atomic B min max mean iso aniso Overall: 9.27 108.61 21.74 2.33 217 1760 Protein: 9.27 108.61 17.22 2.34 0 1519 Water: 11.56 71.09 36.97 N/A 217 233 Other: 17.90 28.78 23.35 N/A 0 8 Chain A: 9.27 108.61 19.89 N/A 0 1760 Chain S: 16.28 60.34 36.73 N/A 217 0 Histogram: Values Number of atoms 9.27 - 19.20 1235 19.20 - 29.14 268 29.14 - 39.07 215 39.07 - 49.01 143 49.01 - 58.94 83 58.94 - 68.88 20 68.88 - 78.81 7 78.81 - 88.74 3 88.74 - 98.68 1 98.68 - 108.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1214 r_free=0.1413 r_work=0.1215 r_free=0.1413 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1215 r_free = 0.1413 target_work(ml) = 3.648 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1209 r_free = 0.1407 target_work(ml) = 3.645 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1209 r_free= 0.1407 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.645044 | | target function (ml) not normalized (work): 303599.393364 | | target function (ml) not normalized (free): 16038.090947 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1209 0.1407 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1541 0.1542 0.1570 n_refl.: 87587 remove outliers: r(all,work,free)=0.1541 0.1542 0.1570 n_refl.: 87587 overall B=-0.02 to atoms: r(all,work,free)=0.1538 0.1538 0.1568 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1201 0.1376 n_refl.: 87587 remove outliers: r(all,work,free)=0.1206 0.1198 0.1376 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3736 282.530 259.322 0.456 1.001 0.295 11.894-9.307 96.08 94 4 0.2364 483.126 461.235 0.851 1.002 0.277 9.237-7.194 98.64 210 7 0.2353 383.817 384.815 0.944 1.002 0.179 7.162-5.571 100.00 427 22 0.2037 292.851 283.282 0.909 1.002 0.168 5.546-4.326 100.00 867 58 0.1096 402.012 397.216 0.951 1.002 0.151 4.315-3.360 100.00 1859 96 0.0933 382.317 379.826 0.995 1.002 0.143 3.356-2.611 100.00 3867 181 0.1163 251.162 249.253 1.001 1.002 0.062 2.608-2.026 99.99 8198 413 0.1050 166.498 165.525 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1016 81.309 81.495 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1287 36.056 35.641 1.022 0.999 0.000 1.221-1.150 99.97 13689 708 0.2126 22.718 21.348 0.981 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0477 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 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=0.1198 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1376 | n_water=450 | time (s): 2.210 (total time: 2.210) Filter (dist) r_work=0.1198 r_free=0.1376 | n_water=449 | time (s): 39.050 (total time: 41.260) Filter (q & B) r_work=0.1198 r_free=0.1377 | n_water=448 | time (s): 2.800 (total time: 44.060) Compute maps r_work=0.1198 r_free=0.1377 | n_water=448 | time (s): 1.600 (total time: 45.660) Filter (map) r_work=0.1224 r_free=0.1385 | n_water=308 | time (s): 3.140 (total time: 48.800) Find peaks r_work=0.1224 r_free=0.1385 | n_water=308 | time (s): 0.660 (total time: 49.460) Add new water r_work=0.1294 r_free=0.1450 | n_water=490 | time (s): 3.060 (total time: 52.520) Refine new water occ: r_work=0.1217 r_free=0.1371 adp: r_work=0.1218 r_free=0.1375 occ: r_work=0.1202 r_free=0.1357 adp: r_work=0.1200 r_free=0.1359 occ: r_work=0.1190 r_free=0.1350 adp: r_work=0.1186 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1349 r_work=0.1186 r_free=0.1349 | n_water=490 | time (s): 228.040 (total time: 280.560) Filter (q & B) r_work=0.1193 r_free=0.1351 | n_water=449 | time (s): 2.540 (total time: 283.100) Filter (dist only) r_work=0.1193 r_free=0.1350 | n_water=448 | time (s): 35.940 (total time: 319.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.973856 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.443172 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1358 0.0168 0.006 0.9 1.9 0.5 0.0 0 0.987 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.58 1.68 3.427 21.496 49.443 3.630 11.77 13.55 1.78 3.722 21.396 49.443 3.617 Individual atomic B min max mean iso aniso Overall: 9.27 105.12 21.29 2.19 219 1756 Protein: 9.27 105.12 17.00 2.19 0 1519 Water: 11.56 70.01 35.82 N/A 219 229 Other: 18.07 25.97 22.03 N/A 0 8 Chain A: 9.27 105.12 19.55 N/A 0 1756 Chain S: 16.04 59.57 35.21 N/A 219 0 Histogram: Values Number of atoms 9.27 - 18.85 1226 18.85 - 28.44 287 28.44 - 38.02 202 38.02 - 47.61 149 47.61 - 57.19 74 57.19 - 66.78 23 66.78 - 76.36 9 76.36 - 85.95 2 85.95 - 95.53 1 95.53 - 105.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.1177 r_free=0.1355 r_work=0.1178 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1178 r_free = 0.1355 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1174 r_free = 0.1354 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1174 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.615487 | | target function (ml) not normalized (work): 301108.644820 | | target function (ml) not normalized (free): 15911.703153 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1183 0.1174 0.1354 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1494 0.1492 0.1550 n_refl.: 87579 remove outliers: r(all,work,free)=0.1494 0.1492 0.1550 n_refl.: 87579 overall B=-0.02 to atoms: r(all,work,free)=0.1490 0.1489 0.1548 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1182 0.1173 0.1358 n_refl.: 87579 remove outliers: r(all,work,free)=0.1180 0.1171 0.1358 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 0.4155 282.530 246.915 0.439 0.954 0.304 11.894-9.307 93.14 91 4 0.2216 477.041 463.722 0.896 0.956 0.238 9.237-7.194 98.18 209 7 0.2460 381.812 376.300 0.955 0.956 0.150 7.162-5.571 100.00 427 22 0.2155 292.851 282.164 0.945 0.956 0.121 5.546-4.326 100.00 867 58 0.1126 402.012 397.150 0.996 0.956 0.120 4.315-3.360 100.00 1859 96 0.0941 382.317 379.733 1.041 0.956 0.110 3.356-2.611 100.00 3867 181 0.1136 251.162 249.351 1.050 0.956 0.043 2.608-2.026 99.99 8198 413 0.1013 166.498 165.585 1.063 0.955 0.000 2.025-1.573 100.00 17313 902 0.0963 81.309 81.561 1.078 0.954 0.000 1.573-1.221 100.00 36679 1900 0.1238 36.056 35.673 1.073 0.951 0.000 1.221-1.150 99.97 13689 708 0.2122 22.718 21.347 1.030 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0495 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1171 r_free=0.1358 After: r_work=0.1172 r_free=0.1358 ================================== NQH flips ================================== r_work=0.1172 r_free=0.1358 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=0.1172 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1172 r_free=0.1358 | n_water=448 | time (s): 1.640 (total time: 1.640) Filter (dist) r_work=0.1172 r_free=0.1358 | n_water=448 | time (s): 36.100 (total time: 37.740) Filter (q & B) r_work=0.1172 r_free=0.1359 | n_water=446 | time (s): 2.800 (total time: 40.540) Compute maps r_work=0.1172 r_free=0.1359 | n_water=446 | time (s): 1.350 (total time: 41.890) Filter (map) r_work=0.1198 r_free=0.1377 | n_water=334 | time (s): 3.010 (total time: 44.900) Find peaks r_work=0.1198 r_free=0.1377 | n_water=334 | time (s): 0.490 (total time: 45.390) Add new water r_work=0.1242 r_free=0.1410 | n_water=490 | time (s): 2.700 (total time: 48.090) Refine new water occ: r_work=0.1183 r_free=0.1355 adp: r_work=0.1183 r_free=0.1356 occ: r_work=0.1172 r_free=0.1347 adp: r_work=0.1171 r_free=0.1348 occ: r_work=0.1164 r_free=0.1343 adp: r_work=0.1161 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1161 r_free=0.1343 r_work=0.1161 r_free=0.1343 | n_water=490 | time (s): 223.450 (total time: 271.540) Filter (q & B) r_work=0.1169 r_free=0.1349 | n_water=447 | time (s): 3.460 (total time: 275.000) Filter (dist only) r_work=0.1169 r_free=0.1347 | n_water=446 | time (s): 38.950 (total time: 313.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.038365 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.737493 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 0.1196 0.1379 0.0182 0.007 1.1 3.8 0.5 0.0 0 1.019 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.79 1.82 3.315 21.190 45.737 3.625 12.02 13.80 1.79 3.587 21.107 45.737 3.620 Individual atomic B min max mean iso aniso Overall: 9.32 101.01 21.02 2.03 217 1756 Protein: 9.32 101.01 16.77 2.04 0 1519 Water: 11.52 69.04 35.49 N/A 217 229 Other: 18.21 25.56 21.83 N/A 0 8 Chain A: 9.32 101.01 19.32 N/A 0 1756 Chain S: 15.50 57.44 34.83 N/A 217 0 Histogram: Values Number of atoms 9.32 - 18.49 1223 18.49 - 27.65 283 27.65 - 36.82 206 36.82 - 45.99 140 45.99 - 55.16 77 55.16 - 64.33 27 64.33 - 73.50 12 73.50 - 82.67 2 82.67 - 91.84 1 91.84 - 101.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1380 r_work=0.1202 r_free=0.1381 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1381 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1375 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1196 r_free= 0.1375 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.618685 | | target function (ml) not normalized (work): 301360.485013 | | target function (ml) not normalized (free): 15938.232590 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1381 0.1411 5.6242 5.6386| | 2: 3.57 - 2.84 1.00 2888 124 0.1136 0.1403 5.2043 5.2551| | 3: 2.83 - 2.48 1.00 2820 163 0.1240 0.1362 5.0141 5.0405| | 4: 2.47 - 2.25 1.00 2825 136 0.1036 0.1169 4.7113 4.7748| | 5: 2.25 - 2.09 1.00 2756 127 0.0999 0.1127 4.6541 4.7262| | 6: 2.09 - 1.97 1.00 2846 113 0.0978 0.1194 4.3555 4.479| | 7: 1.97 - 1.87 1.00 2787 165 0.1007 0.1230 4.0846 4.1869| | 8: 1.87 - 1.79 1.00 2789 144 0.1023 0.1270 3.9942 4.0912| | 9: 1.79 - 1.72 1.00 2745 138 0.0960 0.1285 3.7164 3.9036| | 10: 1.72 - 1.66 1.00 2831 160 0.1007 0.1261 3.634 3.7673| | 11: 1.66 - 1.61 1.00 2712 147 0.0970 0.1091 3.5703 3.6135| | 12: 1.61 - 1.56 1.00 2773 144 0.0922 0.1165 3.3479 3.4799| | 13: 1.56 - 1.52 1.00 2745 130 0.0983 0.1071 3.3377 3.4368| | 14: 1.52 - 1.48 1.00 2803 134 0.0991 0.1131 3.2596 3.3403| | 15: 1.48 - 1.45 1.00 2738 128 0.1009 0.1362 3.1646 3.3471| | 16: 1.45 - 1.42 1.00 2756 161 0.1066 0.1240 3.1493 3.2382| | 17: 1.42 - 1.39 1.00 2785 139 0.1119 0.1289 3.1117 3.2144| | 18: 1.39 - 1.36 1.00 2741 179 0.1147 0.1374 3.0797 3.2577| | 19: 1.36 - 1.34 1.00 2807 134 0.1222 0.1597 3.0918 3.2692| | 20: 1.34 - 1.32 1.00 2696 147 0.1320 0.1484 3.0828 3.1342| | 21: 1.32 - 1.30 1.00 2785 112 0.1414 0.1592 3.0838 3.1421| | 22: 1.29 - 1.27 1.00 2704 152 0.1474 0.1942 3.0802 3.283| | 23: 1.27 - 1.26 1.00 2802 156 0.1572 0.1856 3.098 3.1998| | 24: 1.26 - 1.24 1.00 2744 132 0.1625 0.1751 3.0896 3.1922| | 25: 1.24 - 1.22 1.00 2733 148 0.1788 0.2280 3.1039 3.2753| | 26: 1.22 - 1.21 1.00 2727 135 0.1859 0.1779 3.1188 3.1933| | 27: 1.21 - 1.19 1.00 2814 148 0.2010 0.2081 3.1374 3.1464| | 28: 1.19 - 1.18 1.00 2671 147 0.2147 0.2344 3.1375 3.167| | 29: 1.18 - 1.16 1.00 2800 134 0.2213 0.2390 3.1225 3.2216| | 30: 1.16 - 1.15 1.00 2739 148 0.2366 0.2488 3.1098 3.1639| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.27 1.00 0.97 6321.58| | 2: 3.57 - 2.84 2888 124 0.92 13.47 1.01 0.97 6321.58| | 3: 2.83 - 2.48 2820 163 0.89 17.62 0.98 0.97 5301.37| | 4: 2.47 - 2.25 2825 136 0.91 14.78 1.00 0.98 2670.57| | 5: 2.25 - 2.09 2756 127 0.89 16.97 1.01 0.98 2670.57| | 6: 2.09 - 1.97 2846 113 0.91 13.81 1.02 0.97 1572.20| | 7: 1.97 - 1.87 2787 165 0.94 10.94 1.02 0.97 635.45| | 8: 1.87 - 1.79 2789 144 0.91 14.57 1.00 0.97 635.45| | 9: 1.79 - 1.72 2745 138 0.93 11.57 0.98 0.97 342.62| | 10: 1.72 - 1.66 2831 160 0.93 12.38 0.98 0.97 283.97| | 11: 1.66 - 1.61 2712 147 0.93 13.00 0.98 0.97 270.90| | 12: 1.61 - 1.56 2773 144 0.95 9.58 0.99 0.97 147.59| | 13: 1.56 - 1.52 2745 130 0.94 11.21 1.02 0.97 147.59| | 14: 1.52 - 1.48 2803 134 0.94 11.33 1.02 0.97 131.93| | 15: 1.48 - 1.45 2738 128 0.95 10.47 1.01 0.98 103.25| | 16: 1.45 - 1.42 2756 161 0.94 11.62 1.02 0.98 103.25| | 17: 1.42 - 1.39 2785 139 0.94 11.44 1.01 0.98 92.72| | 18: 1.39 - 1.36 2741 179 0.94 11.66 1.01 0.98 86.62| | 19: 1.36 - 1.34 2807 134 0.94 12.30 1.00 0.98 86.62| | 20: 1.34 - 1.32 2696 147 0.94 12.41 0.99 0.96 81.32| | 21: 1.32 - 1.30 2785 112 0.94 13.28 0.98 0.96 80.95| | 22: 1.29 - 1.27 2704 152 0.93 13.88 0.98 0.96 81.08| | 23: 1.27 - 1.26 2802 156 0.93 14.75 0.98 0.95 81.79| | 24: 1.26 - 1.24 2744 132 0.92 14.92 0.97 0.95 81.79| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 83.60| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.02 0.93 85.60| | 27: 1.21 - 1.19 2814 148 0.89 18.73 1.02 0.93 85.60| | 28: 1.19 - 1.18 2671 147 0.88 20.32 1.01 0.93 89.48| | 29: 1.18 - 1.16 2800 134 0.88 20.66 0.99 0.92 90.94| | 30: 1.16 - 1.15 2739 148 0.86 22.05 0.98 0.92 90.94| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 80.95 max = 6321.58 mean = 985.86| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.89 mean = 14.10| |phase err.(test): min = 0.00 max = 89.44 mean = 14.21| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1196 0.1375 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1511 0.1509 0.1575 n_refl.: 87575 remove outliers: r(all,work,free)=0.1511 0.1509 0.1575 n_refl.: 87575 overall B=-0.02 to atoms: r(all,work,free)=0.1508 0.1506 0.1573 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1197 0.1377 n_refl.: 87575 remove outliers: r(all,work,free)=0.1205 0.1196 0.1377 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 0.4021 282.530 251.963 0.425 0.999 0.281 11.894-9.307 93.14 91 4 0.2238 477.041 461.637 0.855 1.001 0.198 9.237-7.194 97.73 208 7 0.2412 382.883 376.681 0.910 1.002 0.140 7.162-5.571 100.00 427 22 0.2117 292.851 283.230 0.899 1.002 0.127 5.546-4.326 100.00 867 58 0.1166 402.012 397.344 0.952 1.002 0.123 4.315-3.360 100.00 1859 96 0.0997 382.317 379.508 0.995 1.002 0.110 3.356-2.611 100.00 3867 181 0.1207 251.162 249.109 1.002 1.001 0.043 2.608-2.026 99.99 8198 413 0.1047 166.498 165.525 1.014 1.000 0.000 2.025-1.573 100.00 17313 902 0.0983 81.309 81.583 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1228 36.056 35.688 1.024 0.996 0.000 1.221-1.150 99.97 13689 708 0.2113 22.718 21.358 0.983 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0428 ================= 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 0.1975 0.084 5.432 8.8 119.3 19.9 258 0.000 1_bss: 0.1632 0.1789 0.084 5.432 9.0 119.5 20.1 258 0.000 1_settarget: 0.1632 0.1789 0.084 5.432 9.0 119.5 20.1 258 0.000 1_nqh: 0.1633 0.1792 0.084 5.432 9.0 119.5 20.1 258 0.003 1_weight: 0.1633 0.1792 0.084 5.432 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1211 0.1459 0.007 0.942 9.0 119.5 20.1 258 0.128 1_adp: 0.1240 0.1538 0.007 0.942 8.5 118.5 21.1 258 0.128 1_regHadp: 0.1244 0.1541 0.007 0.942 8.5 118.5 21.1 258 0.128 1_occ: 0.1244 0.1544 0.007 0.942 8.5 118.5 21.1 258 0.128 2_bss: 0.1242 0.1537 0.007 0.942 8.7 118.6 21.2 258 0.128 2_settarget: 0.1242 0.1537 0.007 0.942 8.7 118.6 21.2 258 0.128 2_updatecdl: 0.1242 0.1537 0.007 0.945 8.7 118.6 21.2 258 0.128 2_nqh: 0.1242 0.1537 0.007 0.945 8.7 118.6 21.2 258 0.128 2_sol: 0.1229 0.1483 0.007 0.945 8.7 118.6 23.7 437 n/a 2_weight: 0.1229 0.1483 0.007 0.945 8.7 118.6 23.7 437 n/a 2_xyzrec: 0.1229 0.1518 0.007 0.864 8.7 118.6 23.7 437 n/a 2_adp: 0.1199 0.1488 0.007 0.864 8.8 113.6 23.3 437 n/a 2_regHadp: 0.1199 0.1488 0.007 0.864 8.8 113.6 23.3 437 n/a 2_occ: 0.1198 0.1485 0.007 0.864 8.8 113.6 23.3 437 n/a 3_bss: 0.1193 0.1477 0.007 0.864 8.8 113.6 23.4 437 n/a 3_settarget: 0.1193 0.1477 0.007 0.864 8.8 113.6 23.4 437 n/a 3_updatecdl: 0.1193 0.1477 0.007 0.864 8.8 113.6 23.4 437 n/a 3_nqh: 0.1193 0.1477 0.007 0.864 8.8 113.6 23.4 437 n/a 3_sol: 0.1221 0.1491 0.007 0.864 8.8 113.6 22.1 450 n/a 3_weight: 0.1221 0.1491 0.007 0.864 8.8 113.6 22.1 450 n/a 3_xyzrec: 0.1227 0.1466 0.006 0.915 8.8 113.6 22.1 450 n/a 3_adp: 0.1214 0.1413 0.006 0.915 9.3 108.6 21.7 450 n/a 3_regHadp: 0.1215 0.1413 0.006 0.915 9.3 108.6 21.7 450 n/a 3_occ: 0.1209 0.1407 0.006 0.915 9.3 108.6 21.7 450 n/a 4_bss: 0.1198 0.1376 0.006 0.915 9.3 108.6 21.7 450 n/a 4_settarget: 0.1198 0.1376 0.006 0.915 9.3 108.6 21.7 450 n/a 4_updatecdl: 0.1198 0.1376 0.006 0.915 9.3 108.6 21.7 450 n/a 4_nqh: 0.1198 0.1376 0.006 0.915 9.3 108.6 21.7 450 n/a 4_sol: 0.1193 0.1350 0.006 0.915 9.3 108.6 21.5 448 n/a 4_weight: 0.1193 0.1350 0.006 0.915 9.3 108.6 21.5 448 n/a 4_xyzrec: 0.1190 0.1358 0.006 0.948 9.3 108.6 21.5 448 n/a 4_adp: 0.1177 0.1355 0.006 0.948 9.3 105.1 21.3 448 n/a 4_regHadp: 0.1178 0.1355 0.006 0.948 9.3 105.1 21.3 448 n/a 4_occ: 0.1174 0.1354 0.006 0.948 9.3 105.1 21.3 448 n/a 5_bss: 0.1171 0.1358 0.006 0.948 9.3 105.1 21.3 448 n/a 5_settarget: 0.1171 0.1358 0.006 0.948 9.3 105.1 21.3 448 n/a 5_updatecdl: 0.1171 0.1358 0.006 0.949 9.3 105.1 21.3 448 n/a 5_setrh: 0.1172 0.1358 0.006 0.949 9.3 105.1 21.3 448 n/a 5_nqh: 0.1172 0.1358 0.006 0.949 9.3 105.1 21.3 448 n/a 5_sol: 0.1169 0.1347 0.006 0.949 9.3 105.1 21.2 446 n/a 5_weight: 0.1169 0.1347 0.006 0.949 9.3 105.1 21.2 446 n/a 5_xyzrec: 0.1196 0.1379 0.007 1.060 9.3 105.1 21.2 446 n/a 5_adp: 0.1202 0.1380 0.007 1.060 9.3 101.0 21.0 446 n/a 5_regHadp: 0.1202 0.1381 0.007 1.060 9.3 101.0 21.0 446 n/a 5_occ: 0.1196 0.1375 0.007 1.060 9.3 101.0 21.0 446 n/a end: 0.1196 0.1377 0.007 1.060 9.3 101.0 21.0 446 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8530424_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8530424_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8600 Refinement macro-cycles (run) : 3430.0200 Write final files (write_after_run_outputs) : 70.4000 Total : 3505.2800 Total CPU time: 59.03 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:10:42 PST -0800 (1735452642.43 s) Start R-work = 0.1632, R-free = 0.1789 Final R-work = 0.1196, R-free = 0.1377 =============================================================================== Job complete usr+sys time: 3644.47 seconds wall clock time: 65 minutes 57.67 seconds (3957.67 seconds total)