Starting phenix.refine on Sat Dec 28 21:06:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6943566.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6943566.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6943566.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.35, per 1000 atoms: 0.70 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: 0.77 Conformation dependent library (CDL) restraints added in 444.4 milliseconds Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 616 0.93 - 1.20: 1079 1.20 - 1.47: 792 1.47 - 1.74: 655 1.74 - 2.01: 11 Bond restraints: 3153 Sorted by residual: bond pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 1.523 1.298 0.226 1.27e-02 6.20e+03 3.16e+02 bond pdb=" N VAL A 177 " pdb=" CA VAL A 177 " ideal model delta sigma weight residual 1.461 1.666 -0.206 1.19e-02 7.06e+03 2.99e+02 bond pdb=" CA VAL A 181 " pdb=" CB VAL A 181 " ideal model delta sigma weight residual 1.540 1.755 -0.215 1.25e-02 6.40e+03 2.96e+02 bond pdb=" N GLU A 147 " pdb=" CA GLU A 147 " ideal model delta sigma weight residual 1.455 1.248 0.207 1.21e-02 6.83e+03 2.93e+02 bond pdb=" N ASP A 60 " pdb=" CA ASP A 60 " ideal model delta sigma weight residual 1.458 1.673 -0.215 1.27e-02 6.20e+03 2.87e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.71: 3185 4.71 - 9.41: 1875 9.41 - 14.12: 592 14.12 - 18.82: 111 18.82 - 23.53: 14 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.07 115.47 5.60 3.60e-01 7.72e+00 2.42e+02 angle pdb=" OE1BGLN A 80 " pdb=" CD BGLN A 80 " pdb=" NE2BGLN A 80 " ideal model delta sigma weight residual 122.60 109.44 13.16 1.00e+00 1.00e+00 1.73e+02 angle pdb=" O MET A 17 " pdb=" C MET A 17 " pdb=" N GLU A 18 " ideal model delta sigma weight residual 122.12 135.79 -13.67 1.06e+00 8.90e-01 1.66e+02 angle pdb=" OE1 GLN A 180 " pdb=" CD GLN A 180 " pdb=" NE2 GLN A 180 " ideal model delta sigma weight residual 122.60 109.83 12.77 1.00e+00 1.00e+00 1.63e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.90 134.09 -13.19 1.07e+00 8.73e-01 1.52e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 960 17.65 - 35.30: 98 35.30 - 52.95: 41 52.95 - 70.59: 8 70.59 - 88.24: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ILE A 9 " pdb=" C ILE A 9 " pdb=" N LEU A 10 " pdb=" CA LEU A 10 " ideal model delta harmonic sigma weight residual -180.00 -158.95 -21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 122 0.248 - 0.495: 81 0.495 - 0.742: 30 0.742 - 0.989: 9 0.989 - 1.237: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.35 -1.24 2.00e-01 2.50e+01 3.82e+01 chirality pdb=" CA BLYS A 93 " pdb=" N BLYS A 93 " pdb=" C BLYS A 93 " pdb=" CB BLYS A 93 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CG ALEU A 153 " pdb=" CB ALEU A 153 " pdb=" CD1ALEU A 153 " pdb=" CD2ALEU A 153 " both_signs ideal model delta sigma weight residual False -2.59 -3.56 0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.017 2.00e-02 2.50e+03 6.32e-02 1.20e+02 pdb=" CG TYR A 141 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.121 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.071 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.080 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.092 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.016 2.00e-02 2.50e+03 6.74e-02 1.02e+02 pdb=" CG HIS A 115 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.103 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.053 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.125 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.057 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.012 2.00e-02 2.50e+03 5.62e-02 9.46e+01 pdb=" CG PHE A 162 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.105 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.077 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.032 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.049 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.040 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.091 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.015 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.050 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 854 2.29 - 2.87: 7943 2.87 - 3.45: 10608 3.45 - 4.02: 15268 4.02 - 4.60: 21947 Nonbonded interactions: 56620 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.715 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.785 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.800 2.270 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.825 2.100 nonbonded pdb="HH22 ARG A 5 " pdb=" O AGLU A 64 " model vdw 1.843 2.450 ... (remaining 56615 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_6943566_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= 0.2607 r_free= 0.1912 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790819 | | target function (ml) not normalized (work): 232491.997603 | | target function (ml) not normalized (free): 11807.322548 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3015 0.2024 7.0679 4.9435| | 2: 3.57 - 2.84 1.00 2876 122 0.2437 0.1700 4.3454 4.3336| | 3: 2.84 - 2.48 1.00 2833 165 0.2335 0.1716 4.1262 4.1555| | 4: 2.47 - 2.25 1.00 2825 136 0.2308 0.1465 3.8347 3.8388| | 5: 2.25 - 2.09 1.00 2756 127 0.2493 0.1621 3.797 3.8273| | 6: 2.09 - 1.97 1.00 2846 113 0.2524 0.1796 3.4617 3.5726| | 7: 1.97 - 1.87 1.00 2787 165 0.2554 0.1716 3.1375 3.1501| | 8: 1.87 - 1.79 1.00 2789 144 0.2463 0.1852 3.0547 3.1512| | 9: 1.79 - 1.72 1.00 2745 138 0.2446 0.1754 2.9036 2.896| | 10: 1.72 - 1.66 1.00 2789 158 0.2502 0.1967 2.8083 2.8997| | 11: 1.66 - 1.61 1.00 2740 147 0.2484 0.1777 2.7276 2.73| | 12: 1.61 - 1.56 1.00 2787 146 0.2515 0.1901 2.6284 2.6441| | 13: 1.56 - 1.52 1.00 2745 130 0.2518 0.1763 2.5501 2.5632| | 14: 1.52 - 1.48 1.00 2803 134 0.2591 0.1900 2.5064 2.5198| | 15: 1.48 - 1.45 1.00 2738 128 0.2572 0.2096 2.4249 2.5084| | 16: 1.45 - 1.42 1.00 2756 161 0.2662 0.2251 2.382 2.466| | 17: 1.42 - 1.39 1.00 2785 139 0.2619 0.2081 2.3273 2.3777| | 18: 1.39 - 1.36 1.00 2741 179 0.2675 0.2223 2.2832 2.3244| | 19: 1.36 - 1.34 1.00 2807 134 0.2647 0.2590 2.2525 2.3722| | 20: 1.34 - 1.32 1.00 2696 147 0.2760 0.2166 2.2069 2.2044| | 21: 1.32 - 1.30 1.00 2785 112 0.2786 0.2041 2.178 2.1094| | 22: 1.29 - 1.27 1.00 2704 152 0.2738 0.2471 2.1406 2.1995| | 23: 1.27 - 1.26 1.00 2802 156 0.2810 0.2546 2.1017 2.2271| | 24: 1.26 - 1.24 1.00 2744 132 0.2811 0.2412 2.0764 2.1122| | 25: 1.24 - 1.22 1.00 2734 148 0.2884 0.2595 2.04 2.1034| | 26: 1.22 - 1.21 1.00 2727 135 0.2855 0.2383 2.0108 2.1362| | 27: 1.21 - 1.19 1.00 2814 148 0.2987 0.2547 2.0047 1.9638| | 28: 1.19 - 1.18 1.00 2671 147 0.3064 0.2775 1.9947 1.9901| | 29: 1.18 - 1.16 1.00 2800 134 0.3008 0.2611 1.9658 2.0176| | 30: 1.16 - 1.15 1.00 2740 148 0.3078 0.2841 1.9292 1.9564| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.70 0.76 0.23 1483.75| | 2: 3.57 - 2.84 2876 122 0.80 26.08 1.27 0.23 1483.75| | 3: 2.84 - 2.48 2833 165 0.74 31.97 1.24 0.24 1230.42| | 4: 2.47 - 2.25 2825 136 0.81 25.51 1.25 0.25 572.98| | 5: 2.25 - 2.09 2756 127 0.77 29.39 1.29 0.25 572.98| | 6: 2.09 - 1.97 2846 113 0.83 22.78 1.29 0.25 313.06| | 7: 1.97 - 1.87 2787 165 0.90 16.64 1.28 0.26 91.38| | 8: 1.87 - 1.79 2789 144 0.86 21.16 1.25 0.26 91.38| | 9: 1.79 - 1.72 2745 138 0.88 18.20 1.23 0.25 53.96| | 10: 1.72 - 1.66 2789 158 0.87 19.99 1.24 0.25 46.46| | 11: 1.66 - 1.61 2740 147 0.86 20.88 1.24 0.25 44.79| | 12: 1.61 - 1.56 2787 146 0.89 17.88 1.23 0.25 27.84| | 13: 1.56 - 1.52 2745 130 0.87 19.74 1.23 0.25 27.84| | 14: 1.52 - 1.48 2803 134 0.87 20.08 1.24 0.25 25.04| | 15: 1.48 - 1.45 2738 128 0.87 19.75 1.22 0.25 19.93| | 16: 1.45 - 1.42 2756 161 0.86 21.06 1.23 0.25 19.93| | 17: 1.42 - 1.39 2785 139 0.87 20.37 1.22 0.25 17.17| | 18: 1.39 - 1.36 2741 179 0.86 21.01 1.23 0.25 15.57| | 19: 1.36 - 1.34 2807 134 0.86 21.61 1.21 0.25 15.57| | 20: 1.34 - 1.32 2696 147 0.87 21.14 1.22 0.25 13.21| | 21: 1.32 - 1.30 2785 112 0.86 22.21 1.21 0.25 13.04| | 22: 1.29 - 1.27 2704 152 0.86 22.31 1.21 0.25 12.74| | 23: 1.27 - 1.26 2802 156 0.85 22.36 1.22 0.24 11.24| | 24: 1.26 - 1.24 2744 132 0.85 22.97 1.21 0.24 11.24| | 25: 1.24 - 1.22 2734 148 0.84 23.78 1.21 0.24 10.62| | 26: 1.22 - 1.21 2727 135 0.84 23.86 1.20 0.24 9.93| | 27: 1.21 - 1.19 2814 148 0.83 24.63 1.21 0.24 9.93| | 28: 1.19 - 1.18 2671 147 0.83 24.88 1.20 0.23 9.04| | 29: 1.18 - 1.16 2800 134 0.83 24.93 1.18 0.23 8.70| | 30: 1.16 - 1.15 2740 148 0.81 26.49 1.16 0.23 8.70| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.70 max = 1483.75 mean = 214.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 22.41| |phase err.(test): min = 0.00 max = 89.60 mean = 22.15| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.249 1557 Z= 5.539 Angle : 5.281 19.516 2118 Z= 3.691 Chirality : 0.371 1.237 243 Planarity : 0.032 0.103 284 Dihedral : 13.797 88.242 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 27.57 % 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: -2.61 (0.47), residues: 224 helix: -2.85 (0.32), residues: 108 sheet: -1.43 (0.67), residues: 40 loop : 0.44 (0.70), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.107 0.030 ARG A 145 TYR 0.088 0.047 TYR A 141 PHE 0.120 0.035 PHE A 164 HIS 0.065 0.032 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2607 r_free= 0.1912 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790819 | | target function (ml) not normalized (work): 232491.997603 | | target function (ml) not normalized (free): 11807.322548 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2565 0.2607 0.1913 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2565 0.2607 0.1913 n_refl.: 87602 remove outliers: r(all,work,free)=0.1973 0.1978 0.1913 n_refl.: 87594 overall B=0.17 to atoms: r(all,work,free)=0.1995 0.2000 0.1925 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1639 0.1634 0.1749 n_refl.: 87594 remove outliers: r(all,work,free)=0.1639 0.1633 0.1749 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.87 87 5 0.3836 382.322 354.267 0.663 1.001 0.397 11.894-9.307 99.02 97 4 0.1852 614.119 592.856 0.930 1.003 0.375 9.237-7.194 100.00 213 7 0.2159 502.274 492.138 0.958 1.003 0.344 7.162-5.571 100.00 427 22 0.2168 376.928 365.139 0.935 1.003 0.320 5.546-4.326 100.00 867 58 0.1265 517.430 511.608 0.960 1.003 0.219 4.315-3.360 100.00 1859 96 0.1142 492.079 488.652 1.005 1.003 0.199 3.356-2.611 100.00 3867 181 0.1426 323.271 319.876 0.997 1.002 0.029 2.608-2.026 99.99 8198 413 0.1351 214.299 212.020 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1643 104.652 104.009 1.014 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2066 46.407 45.084 1.002 0.996 0.000 1.221-1.150 99.97 13689 708 0.2594 29.240 26.983 0.979 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0401 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1633 r_free=0.1749 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1635 r_free=0.1753 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.956766 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2004.155187 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 0.1464 0.0252 0.008 1.0 1.3 0.5 0.0 0 13.478 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.64 2.52 3.013 19.033 2004.155 0.017 12.34 15.28 2.93 3.031 19.430 2004.155 0.016 Individual atomic B min max mean iso aniso Overall: 8.42 118.13 20.81 2.90 0 1785 Protein: 8.42 118.13 17.72 2.90 0 1519 Water: 11.08 114.87 38.81 N/A 0 258 Other: 22.36 34.64 28.02 N/A 0 8 Chain A: 8.42 118.13 20.81 N/A 0 1785 Histogram: Values Number of atoms 8.42 - 19.39 1204 19.39 - 30.36 242 30.36 - 41.33 159 41.33 - 52.30 100 52.30 - 63.27 51 63.27 - 74.24 18 74.24 - 85.21 4 85.21 - 96.18 4 96.18 - 107.15 0 107.15 - 118.13 3 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1528 r_work=0.1239 r_free=0.1531 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1531 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 = 0.1240 r_free = 0.1540 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1240 r_free= 0.1540 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015333 | | target function (ls_wunit_k1) not normalized (work): 1277.184376 | | target function (ls_wunit_k1) not normalized (free): 113.200942 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1254 0.1240 0.1540 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1696 0.1695 0.1758 n_refl.: 87592 remove outliers: r(all,work,free)=0.1696 0.1695 0.1758 n_refl.: 87592 overall B=0.13 to atoms: r(all,work,free)=0.1717 0.1717 0.1773 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1251 0.1237 0.1535 n_refl.: 87592 remove outliers: r(all,work,free)=0.1251 0.1237 0.1535 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 0.3611 298.427 279.351 0.695 0.924 0.393 11.894-9.307 99.02 97 4 0.1628 479.360 467.114 0.985 0.925 0.380 9.237-7.194 100.00 213 7 0.1818 392.057 387.520 1.027 0.925 0.330 7.162-5.571 100.00 427 22 0.1735 294.217 288.869 0.999 0.926 0.290 5.546-4.326 100.00 867 58 0.0935 403.888 400.937 1.028 0.926 0.220 4.315-3.360 100.00 1859 96 0.0782 384.100 383.234 1.075 0.928 0.190 3.356-2.611 100.00 3867 181 0.1027 252.334 251.626 1.077 0.929 0.048 2.608-2.026 99.99 8198 413 0.0972 167.274 166.706 1.083 0.932 0.000 2.025-1.573 100.00 17313 902 0.1193 81.688 81.893 1.086 0.937 0.000 1.573-1.221 100.00 36679 1900 0.1630 36.224 35.694 1.062 0.945 0.000 1.221-1.150 99.97 13689 708 0.2354 22.824 21.354 1.017 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0498 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1237 r_free=0.1535 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** A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1238 r_free=0.1535 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1238 r_free=0.1535 | n_water=258 | time (s): 2.230 (total time: 2.230) Filter (dist) r_work=0.1246 r_free=0.1532 | n_water=252 | time (s): 28.740 (total time: 30.970) Filter (q & B) r_work=0.1249 r_free=0.1530 | n_water=249 | time (s): 3.660 (total time: 34.630) Compute maps r_work=0.1249 r_free=0.1530 | n_water=249 | time (s): 1.880 (total time: 36.510) Filter (map) r_work=0.1262 r_free=0.1537 | n_water=236 | time (s): 3.720 (total time: 40.230) Find peaks r_work=0.1262 r_free=0.1537 | n_water=236 | time (s): 0.670 (total time: 40.900) Add new water r_work=0.1418 r_free=0.1691 | n_water=459 | time (s): 3.710 (total time: 44.610) Refine new water occ: r_work=0.1325 r_free=0.1540 adp: r_work=0.1245 r_free=0.1496 occ: r_work=0.1257 r_free=0.1482 adp: r_work=0.1222 r_free=0.1474 occ: r_work=0.1225 r_free=0.1464 adp: r_work=0.1215 r_free=0.1469 ADP+occupancy (water only), MIN, final r_work=0.1215 r_free=0.1469 r_work=0.1215 r_free=0.1469 | n_water=459 | time (s): 77.200 (total time: 121.810) Filter (q & B) r_work=0.1222 r_free=0.1473 | n_water=431 | time (s): 4.140 (total time: 125.950) Filter (dist only) r_work=0.1222 r_free=0.1471 | n_water=430 | time (s): 45.740 (total time: 171.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.685338 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1651.470522 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 0.1218 0.1521 0.0303 0.007 0.9 1.9 0.5 0.0 0 12.843 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.18 15.21 3.03 3.763 22.978 1651.471 0.015 11.87 15.03 3.16 4.053 22.817 1651.471 0.014 Individual atomic B min max mean iso aniso Overall: 8.79 114.29 23.03 2.62 194 1763 Protein: 8.79 114.29 17.59 2.62 0 1519 Water: 10.90 74.14 42.21 N/A 194 236 Other: 21.55 32.13 26.12 N/A 0 8 Chain A: 8.79 114.29 20.23 N/A 0 1763 Chain S: 14.32 69.29 48.52 N/A 194 0 Histogram: Values Number of atoms 8.79 - 19.34 1215 19.34 - 29.89 244 29.89 - 40.44 184 40.44 - 50.99 150 50.99 - 61.54 111 61.54 - 72.09 43 72.09 - 82.64 4 82.64 - 93.19 3 93.19 - 103.74 1 103.74 - 114.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1503 r_work=0.1187 r_free=0.1503 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1503 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1489 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 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= 0.1187 r_free= 0.1489 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013626 | | target function (ls_wunit_k1) not normalized (work): 1135.030083 | | target function (ls_wunit_k1) not normalized (free): 108.294269 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1187 0.1489 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1603 0.1600 0.1709 n_refl.: 87592 remove outliers: r(all,work,free)=0.1603 0.1600 0.1709 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1610 0.1607 0.1713 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1184 0.1484 n_refl.: 87592 remove outliers: r(all,work,free)=0.1198 0.1183 0.1484 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 0.3488 297.795 269.582 0.592 1.000 0.370 11.894-9.307 99.02 97 4 0.1504 479.360 475.356 0.913 1.001 0.360 9.237-7.194 100.00 213 7 0.1650 392.057 392.630 0.970 1.002 0.280 7.162-5.571 100.00 427 22 0.1506 294.217 290.237 0.940 1.002 0.260 5.546-4.326 100.00 867 58 0.0808 403.888 401.009 0.957 1.002 0.215 4.315-3.360 100.00 1859 96 0.0706 384.100 382.961 1.002 1.002 0.210 3.356-2.611 100.00 3867 181 0.0950 252.334 251.786 1.009 1.002 0.062 2.608-2.026 99.99 8198 413 0.0937 167.274 167.006 1.016 1.002 0.000 2.025-1.573 100.00 17313 902 0.1165 81.688 81.934 1.026 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1598 36.224 35.716 1.014 1.001 0.000 1.221-1.150 99.97 13689 708 0.2330 22.824 21.243 0.969 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0644 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1183 r_free=0.1484 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1183 r_free=0.1484 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1484 | n_water=430 | time (s): 1.690 (total time: 1.690) Filter (dist) r_work=0.1183 r_free=0.1485 | n_water=429 | time (s): 40.720 (total time: 42.410) Filter (q & B) r_work=0.1184 r_free=0.1487 | n_water=428 | time (s): 3.550 (total time: 45.960) Compute maps r_work=0.1184 r_free=0.1487 | n_water=428 | time (s): 1.630 (total time: 47.590) Filter (map) r_work=0.1229 r_free=0.1484 | n_water=292 | time (s): 3.420 (total time: 51.010) Find peaks r_work=0.1229 r_free=0.1484 | n_water=292 | time (s): 0.730 (total time: 51.740) Add new water r_work=0.1354 r_free=0.1603 | n_water=482 | time (s): 3.480 (total time: 55.220) Refine new water occ: r_work=0.1251 r_free=0.1516 adp: r_work=0.1252 r_free=0.1517 occ: r_work=0.1230 r_free=0.1499 adp: r_work=0.1227 r_free=0.1497 occ: r_work=0.1215 r_free=0.1490 adp: r_work=0.1208 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1208 r_free=0.1485 r_work=0.1208 r_free=0.1485 | n_water=482 | time (s): 217.800 (total time: 273.020) Filter (q & B) r_work=0.1213 r_free=0.1486 | n_water=445 | time (s): 3.580 (total time: 276.600) Filter (dist only) r_work=0.1213 r_free=0.1484 | n_water=444 | time (s): 39.590 (total time: 316.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.166236 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.078937 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 0.1218 0.1440 0.0223 0.006 0.9 1.9 0.5 0.0 0 1.083 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.18 14.40 2.23 3.608 22.038 46.079 3.717 12.10 13.96 1.86 4.152 21.852 46.079 3.649 Individual atomic B min max mean iso aniso Overall: 9.29 109.61 21.62 2.30 211 1760 Protein: 9.29 109.61 17.14 2.31 0 1519 Water: 11.61 73.07 36.89 N/A 211 233 Other: 17.71 28.10 22.89 N/A 0 8 Chain A: 9.29 109.61 19.75 N/A 0 1760 Chain S: 16.07 63.63 37.15 N/A 211 0 Histogram: Values Number of atoms 9.29 - 19.32 1238 19.32 - 29.35 273 29.35 - 39.39 218 39.39 - 49.42 132 49.42 - 59.45 79 59.45 - 69.48 19 69.48 - 79.51 6 79.51 - 89.54 3 89.54 - 99.58 1 99.58 - 109.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1396 r_work=0.1211 r_free=0.1397 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1211 r_free = 0.1397 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1389 target_work(ml) = 3.647 | | occupancies: max = 1.00 min = 0.16 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= 0.1204 r_free= 0.1389 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.646543 | | target function (ml) not normalized (work): 303735.165706 | | target function (ml) not normalized (free): 16039.089502 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1204 0.1389 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1537 0.1537 0.1572 n_refl.: 87590 remove outliers: r(all,work,free)=0.1537 0.1537 0.1572 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1535 0.1535 0.1571 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1195 0.1361 n_refl.: 87590 remove outliers: r(all,work,free)=0.1199 0.1191 0.1361 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 90.62 82 5 0.3912 291.917 264.908 0.474 0.999 0.297 11.894-9.307 96.08 94 4 0.2506 472.772 453.926 0.849 1.001 0.259 9.237-7.194 97.73 208 7 0.2306 384.669 384.549 0.937 1.002 0.210 7.162-5.571 100.00 427 22 0.2063 294.217 283.569 0.912 1.002 0.183 5.546-4.326 100.00 867 58 0.1109 403.888 399.317 0.952 1.002 0.170 4.315-3.360 100.00 1859 96 0.0924 384.100 381.710 0.995 1.002 0.170 3.356-2.611 100.00 3867 181 0.1144 252.334 250.474 0.999 1.002 0.100 2.608-2.026 99.99 8198 413 0.1033 167.274 166.362 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1007 81.688 81.872 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1283 36.224 35.809 1.021 0.999 0.000 1.221-1.150 99.97 13689 708 0.2134 22.824 21.436 0.978 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0373 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1191 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1361 | n_water=444 | time (s): 2.140 (total time: 2.140) Filter (dist) r_work=0.1193 r_free=0.1363 | n_water=442 | time (s): 38.730 (total time: 40.870) Filter (q & B) r_work=0.1192 r_free=0.1361 | n_water=441 | time (s): 2.800 (total time: 43.670) Compute maps r_work=0.1192 r_free=0.1361 | n_water=441 | time (s): 1.450 (total time: 45.120) Filter (map) r_work=0.1216 r_free=0.1374 | n_water=313 | time (s): 3.610 (total time: 48.730) Find peaks r_work=0.1216 r_free=0.1374 | n_water=313 | time (s): 0.500 (total time: 49.230) Add new water r_work=0.1287 r_free=0.1443 | n_water=480 | time (s): 2.980 (total time: 52.210) Refine new water occ: r_work=0.1211 r_free=0.1376 adp: r_work=0.1211 r_free=0.1378 occ: r_work=0.1195 r_free=0.1360 adp: r_work=0.1193 r_free=0.1360 occ: r_work=0.1184 r_free=0.1349 adp: r_work=0.1180 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1347 r_work=0.1180 r_free=0.1347 | n_water=480 | time (s): 206.120 (total time: 258.330) Filter (q & B) r_work=0.1187 r_free=0.1347 | n_water=446 | time (s): 3.490 (total time: 261.820) Filter (dist only) r_work=0.1187 r_free=0.1346 | n_water=445 | time (s): 39.820 (total time: 301.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.938104 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.230367 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 0.1194 0.1363 0.0169 0.006 1.0 2.6 0.5 0.0 0 0.969 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.63 1.69 3.395 21.393 47.230 3.635 11.79 13.58 1.79 3.718 21.301 47.230 3.619 Individual atomic B min max mean iso aniso Overall: 9.30 105.14 21.20 2.15 216 1756 Protein: 9.30 105.14 16.92 2.15 0 1519 Water: 11.56 71.93 35.81 N/A 216 229 Other: 17.62 25.17 21.25 N/A 0 8 Chain A: 9.30 105.14 19.43 N/A 0 1756 Chain S: 14.87 63.86 35.56 N/A 216 0 Histogram: Values Number of atoms 9.30 - 18.89 1235 18.89 - 28.47 277 28.47 - 38.06 217 38.06 - 47.64 134 47.64 - 57.22 70 57.22 - 66.81 27 66.81 - 76.39 7 76.39 - 85.97 2 85.97 - 95.56 1 95.56 - 105.14 2 =========================== Idealize ADP of riding H ========================== r_work=0.1179 r_free=0.1358 r_work=0.1180 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1180 r_free = 0.1358 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1175 r_free = 0.1355 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.18 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= 0.1175 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.617749 | | target function (ml) not normalized (work): 301296.984972 | | target function (ml) not normalized (free): 15922.049266 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1184 0.1175 0.1355 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1507 0.1506 0.1555 n_refl.: 87579 remove outliers: r(all,work,free)=0.1507 0.1506 0.1555 n_refl.: 87579 overall B=-0.02 to atoms: r(all,work,free)=0.1503 0.1502 0.1552 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1183 0.1174 0.1355 n_refl.: 87579 remove outliers: r(all,work,free)=0.1182 0.1174 0.1355 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 90.62 82 5 0.4208 291.917 256.832 0.450 1.000 0.308 11.894-9.307 95.10 93 4 0.2415 476.653 456.231 0.838 1.002 0.248 9.237-7.194 97.73 208 7 0.2507 384.669 378.223 0.909 1.002 0.168 7.162-5.571 100.00 427 22 0.2205 294.217 282.914 0.901 1.002 0.140 5.546-4.326 100.00 867 58 0.1132 403.888 399.175 0.951 1.002 0.126 4.315-3.360 100.00 1859 96 0.0954 384.100 381.638 0.995 1.002 0.117 3.356-2.611 100.00 3867 181 0.1136 252.334 250.659 1.002 1.002 0.090 2.608-2.026 99.99 8198 413 0.1010 167.274 166.396 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0954 81.688 81.963 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1235 36.224 35.858 1.024 0.998 0.000 1.221-1.150 99.97 13689 708 0.2125 22.824 21.448 0.982 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0501 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1174 r_free=0.1355 After: r_work=0.1174 r_free=0.1356 ================================== NQH flips ================================== r_work=0.1174 r_free=0.1356 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=0.1174 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1174 r_free=0.1356 | n_water=445 | time (s): 2.270 (total time: 2.270) Filter (dist) r_work=0.1174 r_free=0.1356 | n_water=445 | time (s): 34.410 (total time: 36.680) Filter (q & B) r_work=0.1175 r_free=0.1355 | n_water=444 | time (s): 2.610 (total time: 39.290) Compute maps r_work=0.1175 r_free=0.1355 | n_water=444 | time (s): 1.770 (total time: 41.060) Filter (map) r_work=0.1201 r_free=0.1379 | n_water=328 | time (s): 3.610 (total time: 44.670) Find peaks r_work=0.1201 r_free=0.1379 | n_water=328 | time (s): 0.700 (total time: 45.370) Add new water r_work=0.1250 r_free=0.1428 | n_water=482 | time (s): 3.680 (total time: 49.050) Refine new water occ: r_work=0.1186 r_free=0.1358 adp: r_work=0.1186 r_free=0.1361 occ: r_work=0.1173 r_free=0.1347 adp: r_work=0.1172 r_free=0.1350 occ: r_work=0.1164 r_free=0.1338 adp: r_work=0.1161 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1161 r_free=0.1339 r_work=0.1161 r_free=0.1339 | n_water=482 | time (s): 173.160 (total time: 222.210) Filter (q & B) r_work=0.1168 r_free=0.1343 | n_water=443 | time (s): 2.800 (total time: 225.010) Filter (dist only) r_work=0.1168 r_free=0.1342 | n_water=442 | time (s): 35.280 (total time: 260.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.249417 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.092875 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 0.1195 0.1383 0.0188 0.008 1.1 5.1 0.5 0.0 0 1.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.83 1.88 3.277 21.073 39.093 3.627 12.00 13.85 1.85 3.405 21.022 39.093 3.624 Individual atomic B min max mean iso aniso Overall: 9.30 102.29 20.98 2.03 213 1756 Protein: 9.30 102.29 16.78 2.03 0 1519 Water: 11.53 71.50 35.41 N/A 213 229 Other: 17.07 24.34 20.86 N/A 0 8 Chain A: 9.30 102.29 19.29 N/A 0 1756 Chain S: 14.38 58.98 34.91 N/A 213 0 Histogram: Values Number of atoms 9.30 - 18.60 1227 18.60 - 27.90 285 27.90 - 37.20 213 37.20 - 46.50 124 46.50 - 55.80 79 55.80 - 65.10 26 65.10 - 74.40 11 74.40 - 83.70 1 83.70 - 93.00 1 93.00 - 102.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1385 r_work=0.1201 r_free=0.1385 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1385 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1384 target_work(ml) = 3.624 | | 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= 0.1197 r_free= 0.1384 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623533 | | target function (ml) not normalized (work): 301775.083376 | | target function (ml) not normalized (free): 15942.021813 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1433 0.1460 5.6939 5.6567| | 2: 3.57 - 2.84 1.00 2888 124 0.1118 0.1453 5.2041 5.2673| | 3: 2.83 - 2.48 1.00 2820 163 0.1207 0.1349 5.011 5.0433| | 4: 2.47 - 2.25 1.00 2825 136 0.1023 0.1164 4.71 4.7643| | 5: 2.25 - 2.09 1.00 2756 127 0.0984 0.1090 4.6549 4.7252| | 6: 2.09 - 1.97 1.00 2846 113 0.0971 0.1225 4.3536 4.4897| | 7: 1.97 - 1.87 1.00 2787 165 0.0999 0.1227 4.0791 4.1808| | 8: 1.87 - 1.79 1.00 2789 144 0.1024 0.1257 3.9931 4.088| | 9: 1.79 - 1.72 1.00 2745 138 0.0964 0.1247 3.7208 3.8735| | 10: 1.72 - 1.66 1.00 2831 160 0.1002 0.1257 3.633 3.7753| | 11: 1.66 - 1.61 1.00 2712 147 0.0966 0.1091 3.5697 3.6109| | 12: 1.61 - 1.56 1.00 2773 144 0.0932 0.1155 3.3522 3.4748| | 13: 1.56 - 1.52 1.00 2745 130 0.0978 0.1044 3.3362 3.4084| | 14: 1.52 - 1.48 1.00 2803 134 0.0987 0.1122 3.2589 3.3383| | 15: 1.48 - 1.45 1.00 2738 128 0.1017 0.1339 3.1706 3.3162| | 16: 1.45 - 1.42 1.00 2756 161 0.1060 0.1258 3.1485 3.2483| | 17: 1.42 - 1.39 1.00 2785 139 0.1122 0.1302 3.115 3.2413| | 18: 1.39 - 1.36 1.00 2741 179 0.1159 0.1373 3.0886 3.2547| | 19: 1.36 - 1.34 1.00 2807 134 0.1209 0.1637 3.0904 3.2867| | 20: 1.34 - 1.32 1.00 2696 147 0.1321 0.1421 3.0891 3.1167| | 21: 1.32 - 1.30 1.00 2785 112 0.1411 0.1624 3.0865 3.16| | 22: 1.29 - 1.27 1.00 2704 152 0.1468 0.1926 3.0842 3.2858| | 23: 1.27 - 1.26 1.00 2802 156 0.1576 0.1861 3.1021 3.2117| | 24: 1.26 - 1.24 1.00 2744 132 0.1616 0.1743 3.0926 3.1897| | 25: 1.24 - 1.22 1.00 2733 148 0.1789 0.2312 3.1094 3.2932| | 26: 1.22 - 1.21 1.00 2727 135 0.1865 0.1763 3.1271 3.1905| | 27: 1.21 - 1.19 1.00 2814 148 0.2010 0.2079 3.1421 3.1461| | 28: 1.19 - 1.18 1.00 2671 147 0.2147 0.2286 3.1425 3.16| | 29: 1.18 - 1.16 1.00 2800 134 0.2223 0.2380 3.1303 3.2274| | 30: 1.16 - 1.15 1.00 2739 148 0.2384 0.2523 3.1211 3.1767| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.14 1.00 0.97 6427.75| | 2: 3.57 - 2.84 2888 124 0.92 13.50 1.01 0.97 6427.75| | 3: 2.83 - 2.48 2820 163 0.88 17.69 0.98 0.97 5386.50| | 4: 2.47 - 2.25 2825 136 0.91 14.79 1.00 0.98 2701.45| | 5: 2.25 - 2.09 2756 127 0.89 17.00 1.01 0.98 2701.45| | 6: 2.09 - 1.97 2846 113 0.91 13.76 1.02 0.98 1583.56| | 7: 1.97 - 1.87 2787 165 0.94 10.84 1.02 0.98 630.15| | 8: 1.87 - 1.79 2789 144 0.91 14.45 1.00 0.98 630.15| | 9: 1.79 - 1.72 2745 138 0.93 11.36 0.98 0.97 338.63| | 10: 1.72 - 1.66 2831 160 0.93 12.18 0.98 0.97 280.25| | 11: 1.66 - 1.61 2712 147 0.93 12.78 0.98 0.97 267.35| | 12: 1.61 - 1.56 2773 144 0.95 9.44 0.99 0.97 145.67| | 13: 1.56 - 1.52 2745 130 0.94 10.95 1.02 0.97 145.67| | 14: 1.52 - 1.48 2803 134 0.94 11.15 1.02 0.98 130.32| | 15: 1.48 - 1.45 2738 128 0.95 10.28 1.01 0.98 102.22| | 16: 1.45 - 1.42 2756 161 0.94 11.47 1.02 0.98 102.22| | 17: 1.42 - 1.39 2785 139 0.94 11.37 1.01 0.99 92.47| | 18: 1.39 - 1.36 2741 179 0.94 11.65 1.01 0.99 86.83| | 19: 1.36 - 1.34 2807 134 0.94 12.20 1.00 0.99 86.83| | 20: 1.34 - 1.32 2696 147 0.94 12.35 0.99 0.97 82.06| | 21: 1.32 - 1.30 2785 112 0.94 13.28 0.99 0.97 81.72| | 22: 1.29 - 1.27 2704 152 0.93 13.78 0.98 0.96 81.88| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.98 0.95 82.69| | 24: 1.26 - 1.24 2744 132 0.93 14.89 0.97 0.95 82.69| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 84.42| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.02 0.93 86.33| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 86.33| | 28: 1.19 - 1.18 2671 147 0.88 20.31 1.01 0.93 90.17| | 29: 1.18 - 1.16 2800 134 0.88 20.67 0.99 0.93 91.62| | 30: 1.16 - 1.15 2739 148 0.86 22.09 0.98 0.93 91.62| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 81.72 max = 6427.75 mean = 998.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 14.03| |phase err.(test): min = 0.00 max = 88.50 mean = 14.15| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1197 0.1384 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1521 0.1522 0.1556 n_refl.: 87578 remove outliers: r(all,work,free)=0.1521 0.1522 0.1556 n_refl.: 87578 overall B=-0.02 to atoms: r(all,work,free)=0.1518 0.1519 0.1554 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1198 0.1384 n_refl.: 87578 remove outliers: r(all,work,free)=0.1206 0.1197 0.1384 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 89.58 81 5 0.4123 294.535 255.408 0.445 1.000 0.308 11.894-9.307 95.10 93 4 0.2450 476.653 457.937 0.838 1.002 0.217 9.237-7.194 97.27 207 7 0.2572 384.195 377.739 0.901 1.002 0.140 7.162-5.571 100.00 427 22 0.2267 294.217 282.732 0.894 1.002 0.140 5.546-4.326 100.00 867 58 0.1200 403.888 399.243 0.953 1.002 0.123 4.315-3.360 100.00 1859 96 0.0995 384.100 381.382 0.995 1.002 0.115 3.356-2.611 100.00 3867 181 0.1176 252.334 250.602 1.001 1.002 0.090 2.608-2.026 99.99 8198 413 0.1033 167.274 166.286 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0980 81.688 81.949 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1226 36.224 35.861 1.024 0.996 0.000 1.221-1.150 99.97 13689 708 0.2121 22.824 21.442 0.983 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0413 ================= 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 : 0.2607 0.1912 0.083 5.281 8.8 119.3 19.9 258 0.000 1_bss: 0.1633 0.1749 0.083 5.281 9.0 119.5 20.1 258 0.000 1_settarget: 0.1633 0.1749 0.083 5.281 9.0 119.5 20.1 258 0.000 1_nqh: 0.1635 0.1753 0.083 5.281 9.0 119.5 20.1 258 0.006 1_weight: 0.1635 0.1753 0.083 5.281 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1212 0.1464 0.008 0.977 9.0 119.5 20.1 258 0.126 1_adp: 0.1235 0.1528 0.008 0.977 8.4 118.1 20.8 258 0.126 1_regHadp: 0.1239 0.1531 0.008 0.977 8.4 118.1 20.8 258 0.126 1_occ: 0.1240 0.1540 0.008 0.977 8.4 118.1 20.8 258 0.126 2_bss: 0.1237 0.1535 0.008 0.977 8.5 118.3 20.9 258 0.126 2_settarget: 0.1237 0.1535 0.008 0.977 8.5 118.3 20.9 258 0.126 2_updatecdl: 0.1237 0.1535 0.008 0.975 8.5 118.3 20.9 258 0.126 2_nqh: 0.1238 0.1535 0.008 0.975 8.5 118.3 20.9 258 0.123 2_sol: 0.1222 0.1471 0.008 0.975 8.5 118.3 23.3 430 n/a 2_weight: 0.1222 0.1471 0.008 0.975 8.5 118.3 23.3 430 n/a 2_xyzrec: 0.1218 0.1521 0.007 0.888 8.5 118.3 23.3 430 n/a 2_adp: 0.1187 0.1503 0.007 0.888 8.8 114.3 23.0 430 n/a 2_regHadp: 0.1187 0.1503 0.007 0.888 8.8 114.3 23.0 430 n/a 2_occ: 0.1187 0.1489 0.007 0.888 8.8 114.3 23.0 430 n/a 3_bss: 0.1183 0.1484 0.007 0.888 8.8 114.3 23.1 430 n/a 3_settarget: 0.1183 0.1484 0.007 0.888 8.8 114.3 23.1 430 n/a 3_updatecdl: 0.1183 0.1484 0.007 0.889 8.8 114.3 23.1 430 n/a 3_nqh: 0.1183 0.1484 0.007 0.889 8.8 114.3 23.1 430 n/a 3_sol: 0.1213 0.1484 0.007 0.889 8.8 114.3 22.0 444 n/a 3_weight: 0.1213 0.1484 0.007 0.889 8.8 114.3 22.0 444 n/a 3_xyzrec: 0.1218 0.1440 0.006 0.935 8.8 114.3 22.0 444 n/a 3_adp: 0.1210 0.1396 0.006 0.935 9.3 109.6 21.6 444 n/a 3_regHadp: 0.1211 0.1397 0.006 0.935 9.3 109.6 21.6 444 n/a 3_occ: 0.1204 0.1389 0.006 0.935 9.3 109.6 21.6 444 n/a 4_bss: 0.1191 0.1361 0.006 0.935 9.3 109.6 21.6 444 n/a 4_settarget: 0.1191 0.1361 0.006 0.935 9.3 109.6 21.6 444 n/a 4_updatecdl: 0.1191 0.1361 0.006 0.934 9.3 109.6 21.6 444 n/a 4_nqh: 0.1191 0.1361 0.006 0.934 9.3 109.6 21.6 444 n/a 4_sol: 0.1187 0.1346 0.006 0.934 9.3 109.6 21.4 445 n/a 4_weight: 0.1187 0.1346 0.006 0.934 9.3 109.6 21.4 445 n/a 4_xyzrec: 0.1194 0.1363 0.006 0.960 9.3 109.6 21.4 445 n/a 4_adp: 0.1179 0.1358 0.006 0.960 9.3 105.1 21.2 445 n/a 4_regHadp: 0.1180 0.1358 0.006 0.960 9.3 105.1 21.2 445 n/a 4_occ: 0.1175 0.1355 0.006 0.960 9.3 105.1 21.2 445 n/a 5_bss: 0.1174 0.1355 0.006 0.960 9.3 105.1 21.2 445 n/a 5_settarget: 0.1174 0.1355 0.006 0.960 9.3 105.1 21.2 445 n/a 5_updatecdl: 0.1174 0.1355 0.006 0.960 9.3 105.1 21.2 445 n/a 5_setrh: 0.1174 0.1356 0.006 0.960 9.3 105.1 21.2 445 n/a 5_nqh: 0.1174 0.1356 0.006 0.960 9.3 105.1 21.2 445 n/a 5_sol: 0.1168 0.1342 0.006 0.960 9.3 105.1 21.1 442 n/a 5_weight: 0.1168 0.1342 0.006 0.960 9.3 105.1 21.1 442 n/a 5_xyzrec: 0.1195 0.1383 0.008 1.116 9.3 105.1 21.1 442 n/a 5_adp: 0.1200 0.1385 0.008 1.116 9.3 102.3 21.0 442 n/a 5_regHadp: 0.1201 0.1385 0.008 1.116 9.3 102.3 21.0 442 n/a 5_occ: 0.1197 0.1384 0.008 1.116 9.3 102.3 21.0 442 n/a end: 0.1197 0.1384 0.008 1.116 9.3 102.3 21.0 442 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6943566_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6943566_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9300 Refinement macro-cycles (run) : 3497.0300 Write final files (write_after_run_outputs) : 66.5700 Total : 3568.5300 Total CPU time: 60.10 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:34 PST -0800 (1735452694.91 s) Start R-work = 0.1633, R-free = 0.1749 Final R-work = 0.1197, R-free = 0.1384 =============================================================================== Job complete usr+sys time: 3702.50 seconds wall clock time: 66 minutes 43.75 seconds (4003.75 seconds total)