Starting phenix.refine on Sat Dec 28 21:06:34 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4811713.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4811713.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4811713.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.32, per 1000 atoms: 0.69 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: 0.79 Conformation dependent library (CDL) restraints added in 411.5 milliseconds Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 408 0.89 - 1.16: 1214 1.16 - 1.42: 658 1.42 - 1.68: 840 1.68 - 1.95: 33 Bond restraints: 3153 Sorted by residual: bond pdb=" CA THR A 34 " pdb=" C THR A 34 " ideal model delta sigma weight residual 1.523 1.283 0.240 1.23e-02 6.61e+03 3.80e+02 bond pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 1.334 1.099 0.236 1.33e-02 5.65e+03 3.14e+02 bond pdb=" C GLN A 180 " pdb=" N VAL A 181 " ideal model delta sigma weight residual 1.335 1.528 -0.193 1.09e-02 8.42e+03 3.13e+02 bond pdb=" C LEU A 112 " pdb=" O LEU A 112 " ideal model delta sigma weight residual 1.237 1.439 -0.203 1.16e-02 7.43e+03 3.06e+02 bond pdb=" CA TYR A 141 " pdb=" C TYR A 141 " ideal model delta sigma weight residual 1.524 1.741 -0.217 1.25e-02 6.40e+03 3.01e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 3236 4.88 - 9.75: 1905 9.75 - 14.63: 533 14.63 - 19.51: 98 19.51 - 24.38: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLU A 16 " pdb=" C GLU A 16 " pdb=" N MET A 17 " ideal model delta sigma weight residual 122.12 139.86 -17.74 1.06e+00 8.90e-01 2.80e+02 angle pdb=" OD1AASN A 97 " pdb=" CG AASN A 97 " pdb=" ND2AASN A 97 " ideal model delta sigma weight residual 122.60 138.54 -15.94 1.00e+00 1.00e+00 2.54e+02 angle pdb=" OD1 ASN A 135 " pdb=" CG ASN A 135 " pdb=" ND2 ASN A 135 " ideal model delta sigma weight residual 122.60 108.18 14.42 1.00e+00 1.00e+00 2.08e+02 angle pdb=" C LEU A 72 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " ideal model delta sigma weight residual 120.21 107.69 12.52 9.60e-01 1.09e+00 1.70e+02 angle pdb=" CA LYS A 89 " pdb=" C LYS A 89 " pdb=" O LYS A 89 " ideal model delta sigma weight residual 120.98 107.15 13.84 1.10e+00 8.26e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 940 17.50 - 35.00: 118 35.00 - 52.49: 37 52.49 - 69.99: 14 69.99 - 87.48: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual -180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -155.34 -24.66 0 5.00e+00 4.00e-02 2.43e+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 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.215: 98 0.215 - 0.429: 75 0.429 - 0.643: 43 0.643 - 0.857: 20 0.857 - 1.071: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -3.70 1.07 2.00e-01 2.50e+01 2.87e+01 chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.47 -1.02 2.00e-01 2.50e+01 2.62e+01 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.71 -0.92 2.00e-01 2.50e+01 2.13e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 45 " -0.018 2.00e-02 2.50e+03 8.86e-02 1.18e+02 pdb=" CD GLN A 45 " -0.135 2.00e-02 2.50e+03 pdb=" OE1 GLN A 45 " 0.100 2.00e-02 2.50e+03 pdb=" NE2 GLN A 45 " 0.065 2.00e-02 2.50e+03 pdb="HE21 GLN A 45 " 0.079 2.00e-02 2.50e+03 pdb="HE22 GLN A 45 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.030 2.00e-02 2.50e+03 5.99e-02 1.08e+02 pdb=" CG TYR A 141 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.112 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.072 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.066 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.084 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.092 2.00e-02 2.50e+03 5.81e-02 1.01e+02 pdb=" CG PHE A 119 " -0.122 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.090 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.060 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.045 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.008 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 705 2.26 - 2.85: 7714 2.85 - 3.43: 10703 3.43 - 4.02: 15316 4.02 - 4.60: 22151 Nonbonded interactions: 56589 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.681 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.753 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.824 2.100 nonbonded pdb=" O VAL A 51 " pdb=" H ACYS A 53 " model vdw sym.op. 1.826 2.450 x-y,-y,-z-4/3 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.835 2.450 ... (remaining 56584 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_4811713_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2605 r_free= 0.1946 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791021 | | target function (ml) not normalized (work): 232508.831690 | | target function (ml) not normalized (free): 11810.494274 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3031 0.2102 7.1064 4.9319| | 2: 3.57 - 2.84 1.00 2876 122 0.2438 0.1842 4.3423 4.3481| | 3: 2.84 - 2.48 1.00 2833 165 0.2322 0.1592 4.1221 4.1469| | 4: 2.47 - 2.25 1.00 2825 136 0.2330 0.1513 3.8192 3.8424| | 5: 2.25 - 2.09 1.00 2756 127 0.2501 0.1541 3.7937 3.8087| | 6: 2.09 - 1.97 1.00 2846 113 0.2513 0.1739 3.4544 3.5281| | 7: 1.97 - 1.87 1.00 2787 165 0.2583 0.1748 3.1442 3.1666| | 8: 1.87 - 1.79 1.00 2789 144 0.2468 0.1688 3.0502 3.0597| | 9: 1.79 - 1.72 1.00 2745 138 0.2396 0.2167 2.8966 3.041| | 10: 1.72 - 1.66 1.00 2789 158 0.2411 0.1992 2.8114 2.9156| | 11: 1.66 - 1.61 1.00 2740 147 0.2519 0.1765 2.7636 2.762| | 12: 1.61 - 1.56 1.00 2787 146 0.2505 0.2099 2.6228 2.6987| | 13: 1.56 - 1.52 1.00 2745 130 0.2518 0.1726 2.5468 2.5634| | 14: 1.52 - 1.48 1.00 2803 134 0.2564 0.1957 2.5001 2.5651| | 15: 1.48 - 1.45 1.00 2738 128 0.2622 0.2232 2.4389 2.4763| | 16: 1.45 - 1.42 1.00 2756 161 0.2639 0.2264 2.3947 2.5084| | 17: 1.42 - 1.39 1.00 2785 139 0.2734 0.2106 2.3338 2.3617| | 18: 1.39 - 1.36 1.00 2741 179 0.2664 0.2418 2.283 2.3263| | 19: 1.36 - 1.34 1.00 2807 134 0.2727 0.2202 2.2627 2.2532| | 20: 1.34 - 1.32 1.00 2696 147 0.2687 0.2352 2.1953 2.2162| | 21: 1.32 - 1.30 1.00 2785 112 0.2664 0.2415 2.1614 2.1816| | 22: 1.29 - 1.27 1.00 2704 152 0.2704 0.2417 2.1241 2.1457| | 23: 1.27 - 1.26 1.00 2802 156 0.2828 0.2692 2.112 2.2615| | 24: 1.26 - 1.24 1.00 2744 132 0.2835 0.2474 2.0855 2.1431| | 25: 1.24 - 1.22 1.00 2734 148 0.2758 0.2395 2.0341 2.0442| | 26: 1.22 - 1.21 1.00 2727 135 0.2838 0.2347 2.0033 2.0825| | 27: 1.21 - 1.19 1.00 2814 148 0.2975 0.2682 1.9981 2.006| | 28: 1.19 - 1.18 1.00 2671 147 0.2989 0.2706 1.9806 1.9654| | 29: 1.18 - 1.16 1.00 2800 134 0.2981 0.2717 1.9614 2.0193| | 30: 1.16 - 1.15 1.00 2740 148 0.3027 0.2751 1.9295 1.9434| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.65 0.76 0.23 1461.62| | 2: 3.57 - 2.84 2876 122 0.81 25.95 1.27 0.23 1461.62| | 3: 2.84 - 2.48 2833 165 0.74 31.63 1.24 0.24 1211.48| | 4: 2.47 - 2.25 2825 136 0.81 25.42 1.26 0.25 562.34| | 5: 2.25 - 2.09 2756 127 0.77 29.07 1.29 0.25 562.34| | 6: 2.09 - 1.97 2846 113 0.84 22.42 1.29 0.25 306.88| | 7: 1.97 - 1.87 2787 165 0.90 16.39 1.29 0.26 89.01| | 8: 1.87 - 1.79 2789 144 0.86 20.72 1.25 0.26 89.01| | 9: 1.79 - 1.72 2745 138 0.88 18.66 1.23 0.25 55.37| | 10: 1.72 - 1.66 2789 158 0.87 20.13 1.22 0.25 48.63| | 11: 1.66 - 1.61 2740 147 0.86 21.42 1.24 0.25 46.93| | 12: 1.61 - 1.56 2787 146 0.89 18.35 1.24 0.25 29.69| | 13: 1.56 - 1.52 2745 130 0.87 20.47 1.24 0.25 29.69| | 14: 1.52 - 1.48 2803 134 0.86 20.82 1.24 0.25 26.57| | 15: 1.48 - 1.45 2738 128 0.87 20.23 1.24 0.25 20.88| | 16: 1.45 - 1.42 2756 161 0.86 21.37 1.23 0.25 20.88| | 17: 1.42 - 1.39 2785 139 0.87 20.73 1.24 0.25 17.73| | 18: 1.39 - 1.36 2741 179 0.86 21.12 1.22 0.25 15.90| | 19: 1.36 - 1.34 2807 134 0.86 21.97 1.22 0.25 15.90| | 20: 1.34 - 1.32 2696 147 0.87 20.98 1.21 0.25 13.08| | 21: 1.32 - 1.30 2785 112 0.86 21.84 1.20 0.25 12.88| | 22: 1.29 - 1.27 2704 152 0.85 22.33 1.21 0.25 12.58| | 23: 1.27 - 1.26 2802 156 0.86 22.11 1.22 0.24 11.05| | 24: 1.26 - 1.24 2744 132 0.85 22.63 1.21 0.24 11.05| | 25: 1.24 - 1.22 2734 148 0.85 23.29 1.20 0.24 10.41| | 26: 1.22 - 1.21 2727 135 0.84 23.52 1.20 0.24 9.70| | 27: 1.21 - 1.19 2814 148 0.84 24.43 1.20 0.24 9.70| | 28: 1.19 - 1.18 2671 147 0.84 24.57 1.19 0.23 8.94| | 29: 1.18 - 1.16 2800 134 0.83 24.91 1.16 0.23 8.65| | 30: 1.16 - 1.15 2740 148 0.82 26.16 1.15 0.23 8.65| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.65 max = 1461.62 mean = 212.11| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.41| |phase err.(test): min = 0.00 max = 89.97 mean = 22.48| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.246 1557 Z= 5.331 Angle : 5.362 18.216 2118 Z= 3.708 Chirality : 0.400 1.071 243 Planarity : 0.032 0.088 284 Dihedral : 13.917 87.482 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 1.86 % Favored : 96.89 % Cbeta Deviations : 35.14 % 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: -2.40 (0.47), residues: 224 helix: -2.61 (0.39), residues: 109 sheet: -0.63 (0.78), residues: 28 loop : -0.13 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.105 0.033 ARG A 156 TYR 0.093 0.036 TYR A 141 PHE 0.115 0.031 PHE A 119 HIS 0.077 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= 0.2605 r_free= 0.1946 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791021 | | target function (ml) not normalized (work): 232508.831690 | | target function (ml) not normalized (free): 11810.494274 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2564 0.2606 0.1946 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2564 0.2606 0.1946 n_refl.: 87602 remove outliers: r(all,work,free)=0.1975 0.1979 0.1946 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2000 0.2005 0.1960 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1634 0.1627 0.1773 n_refl.: 87594 remove outliers: r(all,work,free)=0.1633 0.1626 0.1773 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3785 386.510 369.685 0.687 1.000 0.401 11.894-9.307 99.02 97 4 0.1797 613.953 593.270 0.921 1.001 0.375 9.237-7.194 100.00 213 7 0.2165 502.138 488.963 0.951 1.002 0.370 7.162-5.571 100.00 427 22 0.2148 376.827 365.576 0.930 1.002 0.308 5.546-4.326 100.00 867 58 0.1260 517.290 512.829 0.962 1.002 0.233 4.315-3.360 100.00 1859 96 0.1129 491.946 488.141 1.005 1.002 0.199 3.356-2.611 100.00 3867 181 0.1430 323.183 319.721 0.996 1.002 0.043 2.608-2.026 99.99 8198 413 0.1325 214.241 212.129 1.006 1.002 0.000 2.025-1.573 100.00 17313 902 0.1649 104.624 104.141 1.010 1.002 0.000 1.573-1.221 100.00 36679 1900 0.2064 46.395 45.108 1.000 1.002 0.000 1.221-1.150 99.97 13689 708 0.2581 29.232 26.844 0.963 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0469 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1626 r_free=0.1773 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1626 r_free=0.1773 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.201611 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2016.807295 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 0.1212 0.1460 0.0248 0.007 0.9 1.0 0.5 0.0 0 11.601 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.60 2.48 3.013 19.063 2016.807 0.017 12.44 15.37 2.94 3.303 19.620 2016.807 0.016 Individual atomic B min max mean iso aniso Overall: 8.57 118.65 21.15 2.88 0 1785 Protein: 8.57 118.65 17.99 2.88 0 1519 Water: 11.10 114.60 39.47 N/A 0 258 Other: 23.32 37.23 29.83 N/A 0 8 Chain A: 8.57 118.65 21.15 N/A 0 1785 Histogram: Values Number of atoms 8.57 - 19.58 1203 19.58 - 30.59 234 30.59 - 41.60 160 41.60 - 52.60 103 52.60 - 63.61 53 63.61 - 74.62 16 74.62 - 85.63 9 85.63 - 96.63 3 96.63 - 107.64 1 107.64 - 118.65 3 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1538 r_work=0.1248 r_free=0.1542 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1248 r_free = 0.1542 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 = 0.1251 r_free = 0.1545 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1251 r_free= 0.1545 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015613 | | target function (ls_wunit_k1) not normalized (work): 1300.516078 | | target function (ls_wunit_k1) not normalized (free): 113.077774 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1266 0.1251 0.1545 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1712 0.1711 0.1774 n_refl.: 87593 remove outliers: r(all,work,free)=0.1712 0.1711 0.1774 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1732 0.1732 0.1788 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1264 0.1249 0.1539 n_refl.: 87593 remove outliers: r(all,work,free)=0.1263 0.1249 0.1539 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3702 297.785 278.771 0.627 1.002 0.380 11.894-9.307 99.02 97 4 0.1653 477.036 464.192 0.902 1.002 0.380 9.237-7.194 100.00 213 7 0.1815 390.156 384.682 0.944 1.003 0.340 7.162-5.571 100.00 427 22 0.1755 292.791 287.046 0.924 1.003 0.290 5.546-4.326 100.00 867 58 0.0926 401.929 399.176 0.948 1.003 0.209 4.315-3.360 100.00 1859 96 0.0771 382.238 381.271 0.996 1.003 0.190 3.356-2.611 100.00 3867 181 0.1027 251.110 250.378 0.999 1.002 0.048 2.608-2.026 99.99 8198 413 0.0985 166.463 165.842 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1218 81.292 81.459 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1653 36.048 35.511 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2361 22.713 21.233 0.970 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0466 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1249 r_free=0.1539 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1251 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1251 r_free=0.1541 | n_water=258 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1259 r_free=0.1540 | n_water=252 | time (s): 26.560 (total time: 29.070) Filter (q & B) r_work=0.1262 r_free=0.1539 | n_water=249 | time (s): 3.850 (total time: 32.920) Compute maps r_work=0.1262 r_free=0.1539 | n_water=249 | time (s): 1.920 (total time: 34.840) Filter (map) r_work=0.1276 r_free=0.1549 | n_water=236 | time (s): 4.010 (total time: 38.850) Find peaks r_work=0.1276 r_free=0.1549 | n_water=236 | time (s): 0.750 (total time: 39.600) Add new water r_work=0.1437 r_free=0.1706 | n_water=460 | time (s): 3.850 (total time: 43.450) Refine new water occ: r_work=0.1348 r_free=0.1574 adp: r_work=0.1261 r_free=0.1521 occ: r_work=0.1274 r_free=0.1506 adp: r_work=0.1238 r_free=0.1490 occ: r_work=0.1243 r_free=0.1477 adp: r_work=0.1232 r_free=0.1477 ADP+occupancy (water only), MIN, final r_work=0.1232 r_free=0.1477 r_work=0.1232 r_free=0.1477 | n_water=460 | time (s): 87.400 (total time: 130.850) Filter (q & B) r_work=0.1237 r_free=0.1477 | n_water=441 | time (s): 4.050 (total time: 134.900) Filter (dist only) r_work=0.1237 r_free=0.1477 | n_water=441 | time (s): 42.480 (total time: 177.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.303441 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1573.655539 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 0.1232 0.1509 0.0277 0.007 0.9 2.6 0.5 0.0 0 13.152 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 15.09 2.77 3.812 23.370 1573.656 0.016 11.98 14.89 2.90 4.291 23.150 1573.656 0.015 Individual atomic B min max mean iso aniso Overall: 8.79 113.77 23.35 2.62 205 1763 Protein: 8.79 113.77 17.72 2.62 0 1519 Water: 11.12 72.45 42.70 N/A 205 236 Other: 18.44 32.35 25.22 N/A 0 8 Chain A: 8.79 113.77 20.41 N/A 0 1763 Chain S: 15.13 70.87 48.64 N/A 205 0 Histogram: Values Number of atoms 8.79 - 19.28 1207 19.28 - 29.78 250 29.78 - 40.28 183 40.28 - 50.78 142 50.78 - 61.28 117 61.28 - 71.78 56 71.78 - 82.27 7 82.27 - 92.77 3 92.77 - 103.27 1 103.27 - 113.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1489 r_work=0.1198 r_free=0.1488 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 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 = 0.1202 r_free = 0.1484 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1202 r_free= 0.1484 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014068 | | target function (ls_wunit_k1) not normalized (work): 1171.813972 | | target function (ls_wunit_k1) not normalized (free): 104.214351 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1202 0.1484 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1614 0.1611 0.1718 n_refl.: 87592 remove outliers: r(all,work,free)=0.1614 0.1611 0.1718 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1619 0.1616 0.1721 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1198 0.1483 n_refl.: 87592 remove outliers: r(all,work,free)=0.1211 0.1197 0.1483 n_refl.: 87590 ======================== 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 93.75 85 5 0.3381 296.351 271.551 0.590 1.001 0.370 11.894-9.307 99.02 97 4 0.1553 477.036 473.858 0.912 1.002 0.370 9.237-7.194 100.00 213 7 0.1676 390.156 389.849 0.970 1.003 0.290 7.162-5.571 100.00 427 22 0.1526 292.791 288.255 0.941 1.003 0.240 5.546-4.326 100.00 867 58 0.0826 401.929 399.283 0.957 1.003 0.216 4.315-3.360 100.00 1859 96 0.0717 382.238 381.389 1.003 1.002 0.213 3.356-2.611 100.00 3867 181 0.0954 251.110 250.635 1.009 1.002 0.062 2.608-2.026 99.99 8198 413 0.0964 166.463 166.081 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1176 81.292 81.479 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1611 36.048 35.548 1.019 0.998 0.000 1.221-1.150 99.97 13689 708 0.2340 22.713 21.260 0.979 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0466 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1483 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=0.1197 r_free=0.1483 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1483 | n_water=441 | time (s): 1.640 (total time: 1.640) Filter (dist) r_work=0.1197 r_free=0.1484 | n_water=440 | time (s): 37.730 (total time: 39.370) Filter (q & B) r_work=0.1197 r_free=0.1484 | n_water=440 | time (s): 1.060 (total time: 40.430) Compute maps r_work=0.1197 r_free=0.1484 | n_water=440 | time (s): 1.850 (total time: 42.280) Filter (map) r_work=0.1234 r_free=0.1479 | n_water=294 | time (s): 3.460 (total time: 45.740) Find peaks r_work=0.1234 r_free=0.1479 | n_water=294 | time (s): 0.650 (total time: 46.390) Add new water r_work=0.1365 r_free=0.1600 | n_water=484 | time (s): 3.370 (total time: 49.760) Refine new water occ: r_work=0.1269 r_free=0.1525 adp: r_work=0.1270 r_free=0.1526 occ: r_work=0.1245 r_free=0.1510 adp: r_work=0.1243 r_free=0.1509 occ: r_work=0.1229 r_free=0.1498 adp: r_work=0.1222 r_free=0.1493 ADP+occupancy (water only), MIN, final r_work=0.1222 r_free=0.1493 r_work=0.1222 r_free=0.1493 | n_water=484 | time (s): 175.370 (total time: 225.130) Filter (q & B) r_work=0.1227 r_free=0.1491 | n_water=446 | time (s): 3.780 (total time: 228.910) Filter (dist only) r_work=0.1226 r_free=0.1489 | n_water=445 | time (s): 39.200 (total time: 268.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.176616 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 61.105472 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 0.1451 0.0224 0.006 0.9 1.9 0.5 0.0 0 1.088 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.51 2.24 3.632 22.169 61.105 3.721 12.07 13.90 1.83 4.170 21.968 61.105 3.643 Individual atomic B min max mean iso aniso Overall: 9.25 108.80 21.71 2.37 210 1762 Protein: 9.25 108.80 17.24 2.37 0 1519 Water: 11.62 71.02 36.98 N/A 210 235 Other: 16.48 28.38 22.27 N/A 0 8 Chain A: 9.25 108.80 19.93 N/A 0 1762 Chain S: 14.98 64.81 36.69 N/A 210 0 Histogram: Values Number of atoms 9.25 - 19.21 1236 19.21 - 29.16 268 29.16 - 39.12 214 39.12 - 49.07 139 49.07 - 59.03 78 59.03 - 68.98 23 68.98 - 78.93 8 78.93 - 88.89 3 88.89 - 98.84 1 98.84 - 108.80 2 =========================== Idealize ADP of riding H ========================== r_work=0.1207 r_free=0.1390 r_work=0.1208 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1208 r_free = 0.1391 target_work(ml) = 3.643 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1390 target_work(ml) = 3.640 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1201 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.640104 | | target function (ml) not normalized (work): 303198.799712 | | target function (ml) not normalized (free): 16027.786210 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1201 0.1390 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1535 0.1534 0.1588 n_refl.: 87590 remove outliers: r(all,work,free)=0.1535 0.1534 0.1588 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1534 0.1533 0.1588 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1193 0.1365 n_refl.: 87590 remove outliers: r(all,work,free)=0.1197 0.1189 0.1365 n_refl.: 87580 ======================== 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 0.3811 288.115 262.454 0.480 0.998 0.324 11.894-9.307 96.08 94 4 0.2327 470.480 449.928 0.858 1.000 0.253 9.237-7.194 98.64 210 7 0.2353 385.794 382.714 0.949 1.001 0.190 7.162-5.571 100.00 427 22 0.2057 292.791 282.793 0.923 1.001 0.181 5.546-4.326 100.00 867 58 0.1089 401.929 397.254 0.959 1.001 0.166 4.315-3.360 100.00 1859 96 0.0928 382.238 379.580 1.004 1.002 0.160 3.356-2.611 100.00 3867 181 0.1163 251.110 249.292 1.007 1.002 0.072 2.608-2.026 99.99 8198 413 0.1037 166.463 165.639 1.021 1.002 0.000 2.025-1.573 100.00 17313 902 0.0996 81.292 81.485 1.035 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1279 36.048 35.617 1.026 1.001 0.000 1.221-1.150 99.97 13689 708 0.2123 22.713 21.259 0.979 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0143 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1189 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1365 | n_water=445 | time (s): 2.210 (total time: 2.210) Filter (dist) r_work=0.1189 r_free=0.1365 | n_water=445 | time (s): 37.020 (total time: 39.230) Filter (q & B) r_work=0.1189 r_free=0.1364 | n_water=444 | time (s): 2.620 (total time: 41.850) Compute maps r_work=0.1189 r_free=0.1364 | n_water=444 | time (s): 1.600 (total time: 43.450) Filter (map) r_work=0.1212 r_free=0.1367 | n_water=316 | time (s): 2.650 (total time: 46.100) Find peaks r_work=0.1212 r_free=0.1367 | n_water=316 | time (s): 0.580 (total time: 46.680) Add new water r_work=0.1286 r_free=0.1432 | n_water=494 | time (s): 3.390 (total time: 50.070) Refine new water occ: r_work=0.1208 r_free=0.1363 adp: r_work=0.1208 r_free=0.1363 occ: r_work=0.1192 r_free=0.1356 adp: r_work=0.1190 r_free=0.1354 occ: r_work=0.1180 r_free=0.1354 adp: r_work=0.1175 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1175 r_free=0.1349 r_work=0.1175 r_free=0.1349 | n_water=494 | time (s): 225.140 (total time: 275.210) Filter (q & B) r_work=0.1183 r_free=0.1354 | n_water=454 | time (s): 2.650 (total time: 277.860) Filter (dist only) r_work=0.1183 r_free=0.1353 | n_water=453 | time (s): 41.250 (total time: 319.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.958992 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 52.842805 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 0.1188 0.1362 0.0174 0.006 0.9 3.5 0.5 0.0 0 0.979 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 13.62 1.74 3.442 21.587 52.843 3.629 11.79 13.64 1.85 3.691 21.500 52.843 3.618 Individual atomic B min max mean iso aniso Overall: 9.28 105.02 21.45 2.22 219 1761 Protein: 9.28 105.02 17.06 2.22 0 1519 Water: 11.52 70.06 36.18 N/A 219 234 Other: 16.81 25.53 21.26 N/A 0 8 Chain A: 9.28 105.02 19.69 N/A 0 1761 Chain S: 15.27 55.86 35.55 N/A 219 0 Histogram: Values Number of atoms 9.28 - 18.86 1226 18.86 - 28.43 285 28.43 - 38.00 199 38.00 - 47.58 147 47.58 - 57.15 84 57.15 - 66.72 25 66.72 - 76.30 9 76.30 - 85.87 2 85.87 - 95.44 1 95.44 - 105.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1179 r_free=0.1364 r_work=0.1179 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1179 r_free = 0.1364 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1173 r_free = 0.1363 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1173 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.615758 | | target function (ml) not normalized (work): 301134.789603 | | target function (ml) not normalized (free): 15933.502079 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1182 0.1173 0.1363 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1492 0.1490 0.1568 n_refl.: 87580 remove outliers: r(all,work,free)=0.1492 0.1490 0.1568 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1490 0.1487 0.1566 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1182 0.1173 0.1366 n_refl.: 87580 remove outliers: r(all,work,free)=0.1181 0.1172 0.1366 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 0.4054 288.115 258.479 0.455 0.997 0.297 11.894-9.307 94.12 92 4 0.2356 476.330 450.624 0.837 1.000 0.207 9.237-7.194 98.64 210 7 0.2415 385.794 380.430 0.929 1.000 0.140 7.162-5.571 100.00 427 22 0.2137 292.791 281.592 0.909 1.000 0.130 5.546-4.326 100.00 867 58 0.1109 401.929 397.284 0.950 1.001 0.130 4.315-3.360 100.00 1859 96 0.0942 382.238 380.093 0.996 1.001 0.130 3.356-2.611 100.00 3867 181 0.1146 251.110 249.420 1.000 1.001 0.048 2.608-2.026 99.99 8198 413 0.1017 166.463 165.603 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0961 81.292 81.582 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1235 36.048 35.693 1.019 1.001 0.000 1.221-1.150 99.97 13689 708 0.2121 22.713 21.313 0.974 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0368 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1172 r_free=0.1366 After: r_work=0.1172 r_free=0.1366 ================================== NQH flips ================================== r_work=0.1172 r_free=0.1366 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=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1172 r_free=0.1366 | n_water=453 | time (s): 1.690 (total time: 1.690) Filter (dist) r_work=0.1172 r_free=0.1366 | n_water=452 | time (s): 37.700 (total time: 39.390) Filter (q & B) r_work=0.1172 r_free=0.1365 | n_water=450 | time (s): 2.750 (total time: 42.140) Compute maps r_work=0.1172 r_free=0.1365 | n_water=450 | time (s): 1.270 (total time: 43.410) Filter (map) r_work=0.1198 r_free=0.1368 | n_water=338 | time (s): 2.730 (total time: 46.140) Find peaks r_work=0.1198 r_free=0.1368 | n_water=338 | time (s): 0.450 (total time: 46.590) Add new water r_work=0.1251 r_free=0.1424 | n_water=509 | time (s): 2.830 (total time: 49.420) Refine new water occ: r_work=0.1186 r_free=0.1358 adp: r_work=0.1186 r_free=0.1362 occ: r_work=0.1173 r_free=0.1350 adp: r_work=0.1172 r_free=0.1351 occ: r_work=0.1163 r_free=0.1350 adp: r_work=0.1160 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1160 r_free=0.1347 r_work=0.1160 r_free=0.1347 | n_water=509 | time (s): 176.880 (total time: 226.300) Filter (q & B) r_work=0.1169 r_free=0.1349 | n_water=459 | time (s): 3.110 (total time: 229.410) Filter (dist only) r_work=0.1169 r_free=0.1348 | n_water=458 | time (s): 39.530 (total time: 268.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.971646 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.812706 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 0.1188 0.1361 0.0173 0.006 1.0 2.6 0.5 0.0 0 0.986 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 13.61 1.73 3.336 21.396 49.813 3.621 11.92 13.59 1.67 3.653 21.289 49.813 3.616 Individual atomic B min max mean iso aniso Overall: 9.32 100.98 21.29 2.07 224 1761 Protein: 9.32 100.98 16.80 2.07 0 1519 Water: 11.55 68.89 36.21 N/A 224 234 Other: 17.39 23.95 20.66 N/A 0 8 Chain A: 9.32 100.98 19.42 N/A 0 1761 Chain S: 15.51 60.04 36.02 N/A 224 0 Histogram: Values Number of atoms 9.32 - 18.48 1222 18.48 - 27.65 279 27.65 - 36.82 200 36.82 - 45.98 148 45.98 - 55.15 88 55.15 - 64.31 31 64.31 - 73.48 12 73.48 - 82.65 2 82.65 - 91.81 1 91.81 - 100.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1359 r_work=0.1192 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1359 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1356 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1188 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.614446 | | target function (ml) not normalized (work): 301018.264217 | | target function (ml) not normalized (free): 15925.330888 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1407 0.1416 5.6713 5.6583| | 2: 3.57 - 2.84 1.00 2888 124 0.1105 0.1387 5.1902 5.242| | 3: 2.83 - 2.48 1.00 2820 163 0.1222 0.1259 5.0025 5.0141| | 4: 2.47 - 2.25 1.00 2825 136 0.1019 0.1098 4.6988 4.7427| | 5: 2.25 - 2.09 1.00 2756 127 0.0981 0.1116 4.6406 4.728| | 6: 2.09 - 1.97 1.00 2846 113 0.0960 0.1150 4.3416 4.4537| | 7: 1.97 - 1.87 1.00 2787 165 0.0971 0.1197 4.0574 4.1709| | 8: 1.87 - 1.79 1.00 2789 144 0.1016 0.1280 3.9787 4.0826| | 9: 1.79 - 1.72 1.00 2745 138 0.0944 0.1259 3.7043 3.8713| | 10: 1.72 - 1.66 1.00 2831 160 0.0998 0.1259 3.6268 3.763| | 11: 1.66 - 1.61 1.00 2712 147 0.0963 0.1065 3.5633 3.597| | 12: 1.61 - 1.56 1.00 2773 144 0.0910 0.1195 3.3377 3.5006| | 13: 1.56 - 1.52 1.00 2745 130 0.0980 0.1071 3.3343 3.4264| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1101 3.2531 3.3387| | 15: 1.48 - 1.45 1.00 2738 128 0.1003 0.1379 3.1626 3.3402| | 16: 1.45 - 1.42 1.00 2756 161 0.1062 0.1241 3.1449 3.2333| | 17: 1.42 - 1.39 1.00 2785 139 0.1113 0.1306 3.1101 3.2332| | 18: 1.39 - 1.36 1.00 2741 179 0.1137 0.1378 3.0772 3.2642| | 19: 1.36 - 1.34 1.00 2807 134 0.1212 0.1568 3.0881 3.2506| | 20: 1.34 - 1.32 1.00 2696 147 0.1321 0.1490 3.0831 3.1385| | 21: 1.32 - 1.30 1.00 2785 112 0.1406 0.1631 3.0806 3.1587| | 22: 1.29 - 1.27 1.00 2704 152 0.1470 0.1943 3.0794 3.286| | 23: 1.27 - 1.26 1.00 2802 156 0.1561 0.1886 3.095 3.216| | 24: 1.26 - 1.24 1.00 2744 132 0.1622 0.1746 3.0898 3.1819| | 25: 1.24 - 1.22 1.00 2733 148 0.1786 0.2358 3.1041 3.2943| | 26: 1.22 - 1.21 1.00 2727 135 0.1860 0.1789 3.1196 3.2083| | 27: 1.21 - 1.19 1.00 2814 148 0.2010 0.2101 3.1364 3.1515| | 28: 1.19 - 1.18 1.00 2671 147 0.2139 0.2299 3.135 3.1562| | 29: 1.18 - 1.16 1.00 2800 134 0.2209 0.2373 3.1211 3.222| | 30: 1.16 - 1.15 1.00 2739 148 0.2376 0.2474 3.1118 3.156| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2920 171 0.95 9.07 1.00 0.97 6210.90| | 2: 3.57 - 2.84 2888 124 0.92 13.26 1.01 0.97 6210.90| | 3: 2.83 - 2.48 2820 163 0.89 17.43 0.99 0.97 5203.76| | 4: 2.47 - 2.25 2825 136 0.91 14.55 1.00 0.98 2606.68| | 5: 2.25 - 2.09 2756 127 0.89 16.77 1.01 0.98 2606.68| | 6: 2.09 - 1.97 2846 113 0.92 13.51 1.02 0.97 1528.11| | 7: 1.97 - 1.87 2787 165 0.94 10.69 1.02 0.97 608.25| | 8: 1.87 - 1.79 2789 144 0.91 14.24 0.99 0.97 608.25| | 9: 1.79 - 1.72 2745 138 0.93 11.32 0.98 0.97 333.56| | 10: 1.72 - 1.66 2831 160 0.93 12.22 0.98 0.97 278.55| | 11: 1.66 - 1.61 2712 147 0.93 12.88 0.98 0.97 265.95| | 12: 1.61 - 1.56 2773 144 0.95 9.61 0.99 0.97 147.19| | 13: 1.56 - 1.52 2745 130 0.94 11.12 1.02 0.97 147.19| | 14: 1.52 - 1.48 2803 134 0.94 11.31 1.02 0.97 131.63| | 15: 1.48 - 1.45 2738 128 0.95 10.48 1.01 0.98 103.13| | 16: 1.45 - 1.42 2756 161 0.94 11.61 1.02 0.98 103.13| | 17: 1.42 - 1.39 2785 139 0.94 11.50 1.01 0.98 93.18| | 18: 1.39 - 1.36 2741 179 0.94 11.85 1.01 0.98 87.42| | 19: 1.36 - 1.34 2807 134 0.94 12.40 1.00 0.98 87.42| | 20: 1.34 - 1.32 2696 147 0.94 12.52 0.99 0.96 82.35| | 21: 1.32 - 1.30 2785 112 0.94 13.39 0.98 0.96 82.00| | 22: 1.29 - 1.27 2704 152 0.93 13.91 0.98 0.96 82.19| | 23: 1.27 - 1.26 2802 156 0.92 14.90 0.97 0.95 83.15| | 24: 1.26 - 1.24 2744 132 0.92 15.03 0.97 0.95 83.15| | 25: 1.24 - 1.22 2733 148 0.91 16.41 0.96 0.94 84.52| | 26: 1.22 - 1.21 2727 135 0.90 18.16 1.03 0.93 86.03| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.02 0.93 86.03| | 28: 1.19 - 1.18 2671 147 0.88 20.22 1.01 0.93 88.70| | 29: 1.18 - 1.16 2800 134 0.88 20.47 0.99 0.93 89.71| | 30: 1.16 - 1.15 2739 148 0.86 21.86 0.98 0.93 89.71| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.00 max = 6210.90 mean = 966.94| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 14.03| |phase err.(test): min = 0.00 max = 89.27 mean = 14.18| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1188 0.1356 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1493 0.1491 0.1552 n_refl.: 87578 remove outliers: r(all,work,free)=0.1493 0.1491 0.1552 n_refl.: 87578 overall B=-0.01 to atoms: r(all,work,free)=0.1490 0.1488 0.1550 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1188 0.1359 n_refl.: 87578 remove outliers: r(all,work,free)=0.1195 0.1187 0.1359 n_refl.: 87576 ======================== 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 0.4178 284.707 252.341 0.438 0.998 0.298 11.894-9.307 93.14 91 4 0.2429 470.113 455.969 0.853 1.000 0.197 9.237-7.194 98.64 210 7 0.2499 385.794 379.653 0.919 1.000 0.110 7.162-5.571 100.00 427 22 0.2249 292.791 281.017 0.900 1.001 0.110 5.546-4.326 100.00 867 58 0.1155 401.929 396.682 0.952 1.001 0.110 4.315-3.360 100.00 1859 96 0.0985 382.238 379.596 0.995 1.001 0.110 3.356-2.611 100.00 3867 181 0.1170 251.110 249.256 1.001 1.001 0.053 2.608-2.026 99.99 8198 413 0.1032 166.463 165.516 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0967 81.292 81.528 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1222 36.048 35.697 1.021 0.999 0.000 1.221-1.150 99.97 13689 708 0.2115 22.713 21.335 0.976 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0376 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2605 0.1946 0.081 5.362 8.8 119.3 19.9 258 0.000 1_bss: 0.1626 0.1773 0.081 5.362 9.1 119.5 20.1 258 0.000 1_settarget: 0.1626 0.1773 0.081 5.362 9.1 119.5 20.1 258 0.000 1_nqh: 0.1626 0.1773 0.081 5.362 9.1 119.5 20.1 258 0.000 1_weight: 0.1626 0.1773 0.081 5.362 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1212 0.1460 0.007 0.927 9.1 119.5 20.1 258 0.126 1_adp: 0.1244 0.1538 0.007 0.927 8.6 118.6 21.1 258 0.126 1_regHadp: 0.1248 0.1542 0.007 0.927 8.6 118.6 21.1 258 0.126 1_occ: 0.1251 0.1545 0.007 0.927 8.6 118.6 21.1 258 0.126 2_bss: 0.1249 0.1539 0.007 0.927 8.7 118.8 21.3 258 0.126 2_settarget: 0.1249 0.1539 0.007 0.927 8.7 118.8 21.3 258 0.126 2_updatecdl: 0.1249 0.1539 0.007 0.940 8.7 118.8 21.3 258 0.126 2_nqh: 0.1251 0.1541 0.007 0.940 8.7 118.8 21.3 258 0.129 2_sol: 0.1237 0.1477 0.007 0.940 8.7 118.8 23.8 441 n/a 2_weight: 0.1237 0.1477 0.007 0.940 8.7 118.8 23.8 441 n/a 2_xyzrec: 0.1232 0.1509 0.007 0.875 8.7 118.8 23.8 441 n/a 2_adp: 0.1198 0.1489 0.007 0.875 8.8 113.8 23.4 441 n/a 2_regHadp: 0.1198 0.1488 0.007 0.875 8.8 113.8 23.4 441 n/a 2_occ: 0.1202 0.1484 0.007 0.875 8.8 113.8 23.4 441 n/a 3_bss: 0.1197 0.1483 0.007 0.875 8.8 113.8 23.4 441 n/a 3_settarget: 0.1197 0.1483 0.007 0.875 8.8 113.8 23.4 441 n/a 3_updatecdl: 0.1197 0.1483 0.007 0.874 8.8 113.8 23.4 441 n/a 3_nqh: 0.1197 0.1483 0.007 0.874 8.8 113.8 23.4 441 n/a 3_sol: 0.1226 0.1489 0.007 0.874 8.8 113.8 22.1 445 n/a 3_weight: 0.1226 0.1489 0.007 0.874 8.8 113.8 22.1 445 n/a 3_xyzrec: 0.1227 0.1451 0.006 0.923 8.8 113.8 22.1 445 n/a 3_adp: 0.1207 0.1390 0.006 0.923 9.3 108.8 21.7 445 n/a 3_regHadp: 0.1208 0.1391 0.006 0.923 9.3 108.8 21.7 445 n/a 3_occ: 0.1201 0.1390 0.006 0.923 9.3 108.8 21.7 445 n/a 4_bss: 0.1189 0.1365 0.006 0.923 9.2 108.8 21.7 445 n/a 4_settarget: 0.1189 0.1365 0.006 0.923 9.2 108.8 21.7 445 n/a 4_updatecdl: 0.1189 0.1365 0.006 0.922 9.2 108.8 21.7 445 n/a 4_nqh: 0.1189 0.1365 0.006 0.922 9.2 108.8 21.7 445 n/a 4_sol: 0.1183 0.1353 0.006 0.922 9.2 108.8 21.6 453 n/a 4_weight: 0.1183 0.1353 0.006 0.922 9.2 108.8 21.6 453 n/a 4_xyzrec: 0.1188 0.1362 0.006 0.943 9.2 108.8 21.6 453 n/a 4_adp: 0.1179 0.1364 0.006 0.943 9.3 105.0 21.4 453 n/a 4_regHadp: 0.1179 0.1364 0.006 0.943 9.3 105.0 21.4 453 n/a 4_occ: 0.1173 0.1363 0.006 0.943 9.3 105.0 21.4 453 n/a 5_bss: 0.1172 0.1366 0.006 0.943 9.3 105.0 21.4 453 n/a 5_settarget: 0.1172 0.1366 0.006 0.943 9.3 105.0 21.4 453 n/a 5_updatecdl: 0.1172 0.1366 0.006 0.943 9.3 105.0 21.4 453 n/a 5_setrh: 0.1172 0.1366 0.006 0.943 9.3 105.0 21.4 453 n/a 5_nqh: 0.1172 0.1366 0.006 0.943 9.3 105.0 21.4 453 n/a 5_sol: 0.1169 0.1348 0.006 0.943 9.3 105.0 21.5 458 n/a 5_weight: 0.1169 0.1348 0.006 0.943 9.3 105.0 21.5 458 n/a 5_xyzrec: 0.1188 0.1361 0.006 1.001 9.3 105.0 21.5 458 n/a 5_adp: 0.1192 0.1359 0.006 1.001 9.3 101.0 21.3 458 n/a 5_regHadp: 0.1192 0.1359 0.006 1.001 9.3 101.0 21.3 458 n/a 5_occ: 0.1188 0.1356 0.006 1.001 9.3 101.0 21.3 458 n/a end: 0.1187 0.1359 0.006 1.001 9.3 101.0 21.3 458 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4811713_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4811713_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.5500 Refinement macro-cycles (run) : 3500.5500 Write final files (write_after_run_outputs) : 65.5400 Total : 3570.6400 Total CPU time: 60.13 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:25 PST -0800 (1735452685.71 s) Start R-work = 0.1626, R-free = 0.1773 Final R-work = 0.1187, R-free = 0.1359 =============================================================================== Job complete usr+sys time: 3697.72 seconds wall clock time: 66 minutes 27.32 seconds (3987.32 seconds total)