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_6197065.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_6197065.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6197065.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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 2.26, per 1000 atoms: 0.67 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: 0.84 Conformation dependent library (CDL) restraints added in 204.4 milliseconds Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.92: 546 0.92 - 1.18: 1113 1.18 - 1.45: 756 1.45 - 1.72: 725 1.72 - 1.99: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 52 " pdb=" C ILE A 52 " ideal model delta sigma weight residual 1.522 1.303 0.219 1.19e-02 7.06e+03 3.38e+02 bond pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 1.237 1.439 -0.202 1.11e-02 8.12e+03 3.30e+02 bond pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 1.331 1.567 -0.236 1.38e-02 5.25e+03 2.93e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.150 0.171 1.00e-02 1.00e+04 2.92e+02 bond pdb=" C PRO A 184 " pdb=" O PRO A 184 " ideal model delta sigma weight residual 1.238 0.996 0.242 1.42e-02 4.96e+03 2.91e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 2838 4.18 - 8.35: 1931 8.35 - 12.52: 780 12.52 - 16.70: 196 16.70 - 20.87: 32 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1 GLN A 45 " pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 122.60 107.47 15.13 1.00e+00 1.00e+00 2.29e+02 angle pdb=" CA GLY A 120 " pdb=" C GLY A 120 " pdb=" O GLY A 120 " ideal model delta sigma weight residual 119.27 133.52 -14.25 1.01e+00 9.80e-01 1.99e+02 angle pdb=" O VAL A 51 " pdb=" C VAL A 51 " pdb=" N ILE A 52 " ideal model delta sigma weight residual 123.10 106.77 16.33 1.17e+00 7.31e-01 1.95e+02 angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.12 136.84 -14.72 1.06e+00 8.90e-01 1.93e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.91 108.45 13.46 9.80e-01 1.04e+00 1.89e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.81: 948 17.81 - 35.60: 111 35.60 - 53.39: 40 53.39 - 71.18: 10 71.18 - 88.97: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+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 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.209: 97 0.209 - 0.415: 87 0.415 - 0.620: 36 0.620 - 0.826: 18 0.826 - 1.031: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 20 " pdb=" N VAL A 20 " pdb=" C VAL A 20 " pdb=" CB VAL A 20 " both_signs ideal model delta sigma weight residual False 2.44 1.41 1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" CA AASN A 76 " pdb=" N AASN A 76 " pdb=" C AASN A 76 " pdb=" CB AASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 3.48 -0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CG LEU A 101 " pdb=" CB LEU A 101 " pdb=" CD1 LEU A 101 " pdb=" CD2 LEU A 101 " both_signs ideal model delta sigma weight residual False -2.59 -1.66 -0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.050 2.00e-02 2.50e+03 7.04e-02 1.49e+02 pdb=" CG PHE A 162 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.101 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.119 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.081 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.034 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.049 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.076 2.00e-02 2.50e+03 6.09e-02 1.11e+02 pdb=" CG PHE A 119 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.080 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.096 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.070 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.046 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.096 2.00e-02 2.50e+03 5.59e-02 9.37e+01 pdb=" CG PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.083 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.011 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.100 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.053 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.023 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 588 2.24 - 2.83: 7474 2.83 - 3.42: 10735 3.42 - 4.01: 15411 4.01 - 4.60: 22349 Nonbonded interactions: 56557 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.647 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.732 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.800 2.100 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.851 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.864 2.450 ... (remaining 56552 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_6197065_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1949 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788271 | | target function (ml) not normalized (work): 232279.691607 | | target function (ml) not normalized (free): 11804.334416 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3022 0.2079 7.0391 4.9438| | 2: 3.57 - 2.84 1.00 2876 122 0.2410 0.1816 4.3499 4.3437| | 3: 2.84 - 2.48 1.00 2833 165 0.2367 0.1738 4.1311 4.1589| | 4: 2.47 - 2.25 1.00 2825 136 0.2347 0.1367 3.8368 3.8168| | 5: 2.25 - 2.09 1.00 2756 127 0.2487 0.1581 3.8063 3.8196| | 6: 2.09 - 1.97 1.00 2846 113 0.2546 0.1927 3.4703 3.6489| | 7: 1.97 - 1.87 1.00 2787 165 0.2529 0.1887 3.1377 3.221| | 8: 1.87 - 1.79 1.00 2789 144 0.2473 0.2074 3.0675 3.1489| | 9: 1.79 - 1.72 1.00 2745 138 0.2406 0.1853 2.9106 2.9395| | 10: 1.72 - 1.66 1.00 2789 158 0.2399 0.1907 2.8084 2.8528| | 11: 1.66 - 1.61 1.00 2740 147 0.2524 0.1896 2.7492 2.7896| | 12: 1.61 - 1.56 1.00 2787 146 0.2559 0.1947 2.6331 2.6347| | 13: 1.56 - 1.52 1.00 2745 130 0.2547 0.1944 2.5773 2.6514| | 14: 1.52 - 1.48 1.00 2803 134 0.2601 0.2005 2.5088 2.5351| | 15: 1.48 - 1.45 1.00 2738 128 0.2583 0.1962 2.4143 2.4654| | 16: 1.45 - 1.42 1.00 2756 161 0.2618 0.2045 2.3615 2.3674| | 17: 1.42 - 1.39 1.00 2785 139 0.2599 0.1976 2.3047 2.3659| | 18: 1.39 - 1.36 1.00 2741 179 0.2640 0.2047 2.2668 2.2962| | 19: 1.36 - 1.34 1.00 2807 134 0.2730 0.2488 2.2288 2.3664| | 20: 1.34 - 1.32 1.00 2696 147 0.2671 0.2139 2.1821 2.1723| | 21: 1.32 - 1.30 1.00 2785 112 0.2715 0.2181 2.1569 2.1202| | 22: 1.29 - 1.27 1.00 2704 152 0.2752 0.2512 2.1322 2.1961| | 23: 1.27 - 1.26 1.00 2802 156 0.2833 0.2323 2.1204 2.1231| | 24: 1.26 - 1.24 1.00 2744 132 0.2816 0.2323 2.0702 2.0983| | 25: 1.24 - 1.22 1.00 2734 148 0.2814 0.2642 2.0334 2.1041| | 26: 1.22 - 1.21 1.00 2727 135 0.2862 0.2297 2.0081 2.0556| | 27: 1.21 - 1.19 1.00 2814 148 0.3005 0.2834 2.0141 2.0679| | 28: 1.19 - 1.18 1.00 2671 147 0.3017 0.2812 1.9924 2.0267| | 29: 1.18 - 1.16 1.00 2800 134 0.2965 0.2733 1.952 2.0497| | 30: 1.16 - 1.15 1.00 2740 148 0.3059 0.2803 1.9285 1.9314| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.88 0.76 0.23 1490.71| | 2: 3.57 - 2.84 2876 122 0.80 26.12 1.27 0.23 1490.71| | 3: 2.84 - 2.48 2833 165 0.74 32.06 1.25 0.23 1236.86| | 4: 2.47 - 2.25 2825 136 0.81 25.82 1.26 0.25 578.09| | 5: 2.25 - 2.09 2756 127 0.77 29.37 1.28 0.25 578.09| | 6: 2.09 - 1.97 2846 113 0.83 23.06 1.30 0.25 317.73| | 7: 1.97 - 1.87 2787 165 0.90 16.98 1.28 0.26 95.68| | 8: 1.87 - 1.79 2789 144 0.85 21.73 1.25 0.26 95.68| | 9: 1.79 - 1.72 2745 138 0.88 18.95 1.23 0.26 57.36| | 10: 1.72 - 1.66 2789 158 0.86 20.55 1.22 0.26 49.69| | 11: 1.66 - 1.61 2740 147 0.85 21.63 1.24 0.25 47.90| | 12: 1.61 - 1.56 2787 146 0.89 18.35 1.24 0.25 29.81| | 13: 1.56 - 1.52 2745 130 0.87 20.39 1.24 0.25 29.81| | 14: 1.52 - 1.48 2803 134 0.86 20.86 1.24 0.25 26.41| | 15: 1.48 - 1.45 2738 128 0.87 19.80 1.23 0.25 20.16| | 16: 1.45 - 1.42 2756 161 0.86 21.40 1.23 0.25 20.16| | 17: 1.42 - 1.39 2785 139 0.87 20.19 1.22 0.25 17.13| | 18: 1.39 - 1.36 2741 179 0.87 20.59 1.23 0.25 15.38| | 19: 1.36 - 1.34 2807 134 0.86 21.90 1.24 0.25 15.38| | 20: 1.34 - 1.32 2696 147 0.87 20.69 1.21 0.25 12.72| | 21: 1.32 - 1.30 2785 112 0.86 21.69 1.20 0.25 12.54| | 22: 1.29 - 1.27 2704 152 0.85 22.32 1.21 0.24 12.28| | 23: 1.27 - 1.26 2802 156 0.86 22.08 1.21 0.24 10.96| | 24: 1.26 - 1.24 2744 132 0.85 22.81 1.21 0.24 10.96| | 25: 1.24 - 1.22 2734 148 0.85 23.44 1.20 0.24 10.46| | 26: 1.22 - 1.21 2727 135 0.84 24.12 1.20 0.23 9.91| | 27: 1.21 - 1.19 2814 148 0.83 24.92 1.21 0.23 9.91| | 28: 1.19 - 1.18 2671 147 0.82 25.72 1.17 0.23 9.34| | 29: 1.18 - 1.16 2800 134 0.82 25.87 1.16 0.22 9.13| | 30: 1.16 - 1.15 2740 148 0.81 27.34 1.15 0.22 9.13| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.13 max = 1490.71 mean = 216.93| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.92 mean = 22.66| |phase err.(test): min = 0.00 max = 89.55 mean = 22.52| |-----------------------------------------------------------------------------| ----------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 0.248 1557 Z= 5.480 Angle : 5.477 18.164 2118 Z= 3.848 Chirality : 0.364 1.031 243 Planarity : 0.029 0.081 284 Dihedral : 13.920 88.967 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 1.62 % Allowed : 1.62 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Cbeta Deviations : 26.49 % 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: -2.94 (0.46), residues: 224 helix: -2.72 (0.35), residues: 109 sheet: -1.48 (0.69), residues: 38 loop : -0.50 (0.67), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.076 0.019 ARG A 5 TYR 0.067 0.032 TYR A 139 PHE 0.122 0.051 PHE A 162 HIS 0.014 0.008 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1949 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788271 | | target function (ml) not normalized (work): 232279.691607 | | target function (ml) not normalized (free): 11804.334416 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2606 0.1949 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2606 0.1949 n_refl.: 87602 remove outliers: r(all,work,free)=0.1979 0.1983 0.1949 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2004 0.2008 0.1965 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1636 0.1629 0.1772 n_refl.: 87594 remove outliers: r(all,work,free)=0.1636 0.1629 0.1772 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 0.3781 386.383 359.849 0.675 1.003 0.414 11.894-9.307 99.02 97 4 0.1795 613.750 594.255 0.922 1.004 0.400 9.237-7.194 100.00 213 7 0.2159 501.972 489.766 0.955 1.004 0.360 7.162-5.571 100.00 427 22 0.2224 376.702 365.536 0.930 1.004 0.310 5.546-4.326 100.00 867 58 0.1277 517.119 511.669 0.962 1.003 0.234 4.315-3.360 100.00 1859 96 0.1116 491.784 487.993 1.005 1.003 0.219 3.356-2.611 100.00 3867 181 0.1427 323.077 319.764 0.995 1.002 0.080 2.608-2.026 99.99 8198 413 0.1354 214.170 212.017 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1642 104.590 103.866 1.012 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2048 46.379 45.051 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2603 29.222 26.925 0.975 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0464 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1629 r_free=0.1772 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.1631 r_free=0.1776 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.801249 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2014.087296 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 0.1458 0.0246 0.007 0.9 1.3 0.5 0.0 0 12.401 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.58 2.46 3.013 19.061 2014.087 0.017 12.39 15.33 2.94 3.199 19.555 2014.087 0.016 Individual atomic B min max mean iso aniso Overall: 8.51 118.52 21.02 2.87 0 1785 Protein: 8.51 118.52 17.90 2.87 0 1519 Water: 11.02 114.60 39.15 N/A 0 258 Other: 22.68 36.62 29.29 N/A 0 8 Chain A: 8.51 118.52 21.02 N/A 0 1785 Histogram: Values Number of atoms 8.51 - 19.51 1208 19.51 - 30.51 230 30.51 - 41.51 162 41.51 - 52.51 104 52.51 - 63.52 52 63.52 - 74.52 16 74.52 - 85.52 6 85.52 - 96.52 4 96.52 - 107.52 0 107.52 - 118.52 3 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1533 r_work=0.1243 r_free=0.1538 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1243 r_free = 0.1538 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1244 r_free = 0.1543 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 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= 0.1244 r_free= 0.1543 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015415 | | target function (ls_wunit_k1) not normalized (work): 1284.052244 | | target function (ls_wunit_k1) not normalized (free): 113.339566 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1258 0.1244 0.1543 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1705 0.1704 0.1771 n_refl.: 87593 remove outliers: r(all,work,free)=0.1705 0.1704 0.1771 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1727 0.1726 0.1787 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1256 0.1241 0.1536 n_refl.: 87593 remove outliers: r(all,work,free)=0.1255 0.1241 0.1536 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 0.3572 298.370 277.756 0.635 1.001 0.380 11.894-9.307 99.02 97 4 0.1598 477.973 465.662 0.906 1.001 0.380 9.237-7.194 100.00 213 7 0.1831 390.923 385.764 0.949 1.002 0.330 7.162-5.571 100.00 427 22 0.1688 293.366 288.673 0.927 1.002 0.263 5.546-4.326 100.00 867 58 0.0909 402.719 400.443 0.950 1.002 0.214 4.315-3.360 100.00 1859 96 0.0776 382.989 381.701 0.994 1.002 0.200 3.356-2.611 100.00 3867 181 0.1023 251.604 250.900 0.997 1.002 0.100 2.608-2.026 99.99 8198 413 0.0975 166.790 166.269 1.009 1.002 0.000 2.025-1.573 100.00 17313 902 0.1207 81.452 81.668 1.015 1.003 0.000 1.573-1.221 100.00 36679 1900 0.1649 36.119 35.569 1.003 1.003 0.000 1.221-1.150 99.97 13689 708 0.2359 22.757 21.159 0.960 1.004 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 ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1241 r_free=0.1536 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1241 r_free=0.1536 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1241 r_free=0.1536 | n_water=258 | time (s): 2.220 (total time: 2.220) Filter (dist) r_work=0.1249 r_free=0.1533 | n_water=253 | time (s): 26.150 (total time: 28.370) Filter (q & B) r_work=0.1251 r_free=0.1532 | n_water=250 | time (s): 3.720 (total time: 32.090) Compute maps r_work=0.1251 r_free=0.1532 | n_water=250 | time (s): 1.900 (total time: 33.990) Filter (map) r_work=0.1276 r_free=0.1548 | n_water=234 | time (s): 3.840 (total time: 37.830) Find peaks r_work=0.1276 r_free=0.1548 | n_water=234 | time (s): 0.710 (total time: 38.540) Add new water r_work=0.1435 r_free=0.1704 | n_water=456 | time (s): 3.700 (total time: 42.240) Refine new water occ: r_work=0.1336 r_free=0.1558 adp: r_work=0.1253 r_free=0.1511 occ: r_work=0.1267 r_free=0.1510 adp: r_work=0.1231 r_free=0.1494 occ: r_work=0.1235 r_free=0.1492 adp: r_work=0.1224 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1489 r_work=0.1224 r_free=0.1489 | n_water=456 | time (s): 129.750 (total time: 171.990) Filter (q & B) r_work=0.1229 r_free=0.1492 | n_water=435 | time (s): 3.780 (total time: 175.770) Filter (dist only) r_work=0.1229 r_free=0.1492 | n_water=435 | time (s): 41.420 (total time: 217.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.367353 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1564.070179 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 0.1226 0.1514 0.0288 0.007 0.9 1.9 0.5 0.0 0 12.684 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 15.14 2.88 3.789 23.231 1564.070 0.015 11.99 14.89 2.90 4.148 23.063 1564.070 0.015 Individual atomic B min max mean iso aniso Overall: 8.71 114.44 23.27 2.61 201 1761 Protein: 8.71 114.44 17.73 2.61 0 1519 Water: 10.72 73.98 42.53 N/A 201 234 Other: 24.45 36.51 29.57 N/A 0 8 Chain A: 8.71 114.44 20.42 N/A 0 1761 Chain S: 16.99 69.83 48.31 N/A 201 0 Histogram: Values Number of atoms 8.71 - 19.28 1206 19.28 - 29.85 253 29.85 - 40.43 188 40.43 - 51.00 144 51.00 - 61.57 109 61.57 - 72.15 51 72.15 - 82.72 5 82.72 - 93.29 3 93.29 - 103.87 1 103.87 - 114.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1489 r_work=0.1199 r_free=0.1489 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1489 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1481 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.17 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= 0.1199 r_free= 0.1481 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013860 | | target function (ls_wunit_k1) not normalized (work): 1154.483865 | | target function (ls_wunit_k1) not normalized (free): 101.674072 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1199 0.1481 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1612 0.1608 0.1730 n_refl.: 87592 remove outliers: r(all,work,free)=0.1612 0.1608 0.1730 n_refl.: 87592 overall B=0.02 to atoms: r(all,work,free)=0.1616 0.1612 0.1732 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1197 0.1476 n_refl.: 87592 remove outliers: r(all,work,free)=0.1208 0.1195 0.1476 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3350 291.082 269.481 0.567 1.002 0.340 11.894-9.307 99.02 97 4 0.1588 477.973 476.487 0.915 1.002 0.330 9.237-7.194 100.00 213 7 0.1648 390.923 392.555 0.979 1.003 0.280 7.162-5.571 100.00 427 22 0.1476 293.366 289.782 0.944 1.003 0.229 5.546-4.326 100.00 867 58 0.0813 402.719 400.131 0.959 1.002 0.217 4.315-3.360 100.00 1859 96 0.0713 382.989 382.021 1.002 1.002 0.214 3.356-2.611 100.00 3867 181 0.0944 251.604 251.030 1.009 1.002 0.140 2.608-2.026 99.99 8198 413 0.0963 166.790 166.438 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1178 81.452 81.683 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1615 36.119 35.626 1.019 0.999 0.000 1.221-1.150 99.97 13689 708 0.2345 22.757 21.295 0.979 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0378 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1476 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1476 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1476 | n_water=435 | time (s): 1.680 (total time: 1.680) Filter (dist) r_work=0.1196 r_free=0.1473 | n_water=432 | time (s): 39.350 (total time: 41.030) Filter (q & B) r_work=0.1196 r_free=0.1473 | n_water=432 | time (s): 1.010 (total time: 42.040) Compute maps r_work=0.1196 r_free=0.1473 | n_water=432 | time (s): 1.630 (total time: 43.670) Filter (map) r_work=0.1237 r_free=0.1478 | n_water=289 | time (s): 3.630 (total time: 47.300) Find peaks r_work=0.1237 r_free=0.1478 | n_water=289 | time (s): 0.720 (total time: 48.020) Add new water r_work=0.1367 r_free=0.1614 | n_water=476 | time (s): 2.970 (total time: 50.990) Refine new water occ: r_work=0.1265 r_free=0.1516 adp: r_work=0.1266 r_free=0.1518 occ: r_work=0.1243 r_free=0.1496 adp: r_work=0.1241 r_free=0.1496 occ: r_work=0.1228 r_free=0.1483 adp: r_work=0.1221 r_free=0.1480 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1480 r_work=0.1221 r_free=0.1480 | n_water=476 | time (s): 202.970 (total time: 253.960) Filter (q & B) r_work=0.1225 r_free=0.1491 | n_water=439 | time (s): 2.620 (total time: 256.580) Filter (dist only) r_work=0.1225 r_free=0.1489 | n_water=438 | time (s): 37.090 (total time: 293.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.194568 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.910762 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1446 0.0217 0.006 0.9 2.6 0.5 0.0 0 1.097 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.46 2.17 3.631 22.128 48.911 3.723 12.11 14.02 1.91 4.199 21.918 48.911 3.649 Individual atomic B min max mean iso aniso Overall: 9.23 109.46 21.59 2.33 207 1758 Protein: 9.23 109.46 17.23 2.33 0 1519 Water: 11.40 72.80 36.65 N/A 207 231 Other: 20.09 32.25 26.18 N/A 0 8 Chain A: 9.23 109.46 19.87 N/A 0 1758 Chain S: 15.52 60.56 36.22 N/A 207 0 Histogram: Values Number of atoms 9.23 - 19.25 1232 19.25 - 29.28 273 29.28 - 39.30 221 39.30 - 49.32 132 49.32 - 59.35 72 59.35 - 69.37 22 69.37 - 79.39 7 79.39 - 89.42 3 89.42 - 99.44 1 99.44 - 109.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1402 r_work=0.1212 r_free=0.1403 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1212 r_free = 0.1403 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1396 target_work(ml) = 3.645 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1205 r_free= 0.1396 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.645435 | | target function (ml) not normalized (work): 303635.585764 | | target function (ml) not normalized (free): 16026.465981 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1205 0.1396 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1551 0.1548 0.1627 n_refl.: 87588 remove outliers: r(all,work,free)=0.1551 0.1548 0.1627 n_refl.: 87588 overall B=-0.02 to atoms: r(all,work,free)=0.1548 0.1545 0.1625 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1198 0.1380 n_refl.: 87588 remove outliers: r(all,work,free)=0.1204 0.1195 0.1380 n_refl.: 87581 ======================== 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 0.3727 287.725 259.994 0.478 1.000 0.308 11.894-9.307 97.06 95 4 0.2348 471.374 460.866 0.859 1.001 0.293 9.237-7.194 98.64 210 7 0.2256 383.480 385.194 0.948 1.001 0.210 7.162-5.571 100.00 427 22 0.2025 293.366 283.811 0.918 1.002 0.177 5.546-4.326 100.00 867 58 0.1061 402.719 398.449 0.953 1.002 0.165 4.315-3.360 100.00 1859 96 0.0943 382.989 380.169 0.994 1.002 0.157 3.356-2.611 100.00 3867 181 0.1159 251.604 249.796 0.999 1.001 0.062 2.608-2.026 99.99 8198 413 0.1051 166.790 165.784 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1009 81.452 81.595 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1293 36.119 35.692 1.021 0.999 0.000 1.221-1.150 99.97 13689 708 0.2134 22.757 21.373 0.980 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0414 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1380 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1380 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1380 | n_water=438 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1195 r_free=0.1378 | n_water=437 | time (s): 37.550 (total time: 39.850) Filter (q & B) r_work=0.1195 r_free=0.1377 | n_water=435 | time (s): 2.600 (total time: 42.450) Compute maps r_work=0.1195 r_free=0.1377 | n_water=435 | time (s): 1.480 (total time: 43.930) Filter (map) r_work=0.1216 r_free=0.1376 | n_water=311 | time (s): 2.630 (total time: 46.560) Find peaks r_work=0.1216 r_free=0.1376 | n_water=311 | time (s): 0.660 (total time: 47.220) Add new water r_work=0.1290 r_free=0.1435 | n_water=475 | time (s): 3.250 (total time: 50.470) Refine new water occ: r_work=0.1212 r_free=0.1368 adp: r_work=0.1212 r_free=0.1369 occ: r_work=0.1195 r_free=0.1355 adp: r_work=0.1193 r_free=0.1354 occ: r_work=0.1183 r_free=0.1347 adp: r_work=0.1179 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1345 r_work=0.1179 r_free=0.1345 | n_water=475 | time (s): 175.590 (total time: 226.060) Filter (q & B) r_work=0.1185 r_free=0.1350 | n_water=444 | time (s): 3.080 (total time: 229.140) Filter (dist only) r_work=0.1185 r_free=0.1350 | n_water=444 | time (s): 31.980 (total time: 261.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.979005 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.455553 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1361 0.0171 0.006 1.0 2.2 0.5 0.0 0 0.990 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.61 1.71 3.425 21.526 46.456 3.633 11.81 13.56 1.76 3.719 21.439 46.456 3.620 Individual atomic B min max mean iso aniso Overall: 9.31 105.17 21.35 2.17 214 1757 Protein: 9.31 105.17 17.01 2.17 0 1519 Water: 11.58 71.85 36.16 N/A 214 230 Other: 19.32 29.33 24.31 N/A 0 8 Chain A: 9.31 105.17 19.60 N/A 0 1757 Chain S: 16.03 60.79 35.71 N/A 214 0 Histogram: Values Number of atoms 9.31 - 18.89 1228 18.89 - 28.48 279 28.48 - 38.07 219 38.07 - 47.65 129 47.65 - 57.24 74 57.24 - 66.83 27 66.83 - 76.41 10 76.41 - 86.00 2 86.00 - 95.59 1 95.59 - 105.17 2 =========================== Idealize ADP of riding H ========================== r_work=0.1181 r_free=0.1357 r_work=0.1181 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1181 r_free = 0.1357 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1179 r_free = 0.1355 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1179 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.619837 | | target function (ml) not normalized (work): 301478.124323 | | target function (ml) not normalized (free): 15921.679702 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1188 0.1179 0.1355 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1516 0.1514 0.1580 n_refl.: 87581 remove outliers: r(all,work,free)=0.1516 0.1514 0.1580 n_refl.: 87581 overall B=-0.02 to atoms: r(all,work,free)=0.1513 0.1511 0.1577 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1187 0.1179 0.1359 n_refl.: 87581 remove outliers: r(all,work,free)=0.1186 0.1177 0.1359 n_refl.: 87577 ======================== 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 0.3887 283.027 260.740 0.457 0.999 0.304 11.894-9.307 96.08 94 4 0.2343 471.404 456.122 0.837 1.001 0.255 9.237-7.194 97.73 208 7 0.2386 383.556 376.059 0.914 1.001 0.185 7.162-5.571 100.00 427 22 0.2145 293.366 282.329 0.908 1.002 0.160 5.546-4.326 100.00 867 58 0.1122 402.719 398.738 0.953 1.002 0.141 4.315-3.360 100.00 1859 96 0.0944 382.989 380.511 0.994 1.002 0.133 3.356-2.611 100.00 3867 181 0.1139 251.604 249.854 1.000 1.002 0.120 2.608-2.026 99.99 8198 413 0.1029 166.790 165.860 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0970 81.452 81.729 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.119 35.752 1.024 0.998 0.000 1.221-1.150 99.97 13689 708 0.2123 22.757 21.394 0.982 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0515 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1177 r_free=0.1359 After: r_work=0.1178 r_free=0.1359 ================================== NQH flips ================================== r_work=0.1178 r_free=0.1359 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=0.1178 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1359 | n_water=444 | time (s): 1.650 (total time: 1.650) Filter (dist) r_work=0.1178 r_free=0.1359 | n_water=444 | time (s): 34.600 (total time: 36.250) Filter (q & B) r_work=0.1178 r_free=0.1359 | n_water=441 | time (s): 3.140 (total time: 39.390) Compute maps r_work=0.1178 r_free=0.1359 | n_water=441 | time (s): 1.260 (total time: 40.650) Filter (map) r_work=0.1203 r_free=0.1379 | n_water=336 | time (s): 2.560 (total time: 43.210) Find peaks r_work=0.1203 r_free=0.1379 | n_water=336 | time (s): 0.530 (total time: 43.740) Add new water r_work=0.1261 r_free=0.1424 | n_water=499 | time (s): 2.700 (total time: 46.440) Refine new water occ: r_work=0.1192 r_free=0.1367 adp: r_work=0.1192 r_free=0.1369 occ: r_work=0.1179 r_free=0.1358 adp: r_work=0.1178 r_free=0.1359 occ: r_work=0.1170 r_free=0.1351 adp: r_work=0.1167 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1167 r_free=0.1352 r_work=0.1167 r_free=0.1352 | n_water=499 | time (s): 183.940 (total time: 230.380) Filter (q & B) r_work=0.1174 r_free=0.1354 | n_water=462 | time (s): 2.840 (total time: 233.220) Filter (dist only) r_work=0.1174 r_free=0.1352 | n_water=461 | time (s): 39.370 (total time: 272.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.958979 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.496153 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1200 0.1371 0.0172 0.008 1.0 2.9 0.5 0.0 0 0.979 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.71 1.72 3.308 21.309 42.496 3.627 12.03 13.72 1.69 3.548 21.236 42.496 3.623 Individual atomic B min max mean iso aniso Overall: 9.27 100.91 21.25 2.03 232 1756 Protein: 9.27 100.91 16.80 2.03 0 1519 Water: 11.41 71.12 35.85 N/A 232 229 Other: 19.01 26.93 23.35 N/A 0 8 Chain A: 9.27 100.91 19.37 N/A 0 1756 Chain S: 15.09 61.00 35.45 N/A 232 0 Histogram: Values Number of atoms 9.27 - 18.43 1220 18.43 - 27.60 276 27.60 - 36.76 217 36.76 - 45.93 142 45.93 - 55.09 87 55.09 - 64.26 30 64.26 - 73.42 11 73.42 - 82.58 2 82.58 - 91.75 1 91.75 - 100.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1372 r_work=0.1203 r_free=0.1372 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1372 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1366 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1195 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.619977 | | target function (ml) not normalized (work): 301475.306754 | | target function (ml) not normalized (free): 15921.799727 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1398 0.1380 5.6561 5.6167| | 2: 3.57 - 2.84 1.00 2888 124 0.1112 0.1443 5.1864 5.2391| | 3: 2.83 - 2.48 1.00 2820 163 0.1221 0.1284 4.9939 5.0086| | 4: 2.47 - 2.25 1.00 2825 136 0.1032 0.1206 4.6998 4.7721| | 5: 2.25 - 2.09 1.00 2756 127 0.0999 0.1129 4.6384 4.7071| | 6: 2.09 - 1.97 1.00 2846 113 0.0974 0.1172 4.3426 4.4635| | 7: 1.97 - 1.87 1.00 2787 165 0.0998 0.1202 4.079 4.1657| | 8: 1.87 - 1.79 1.00 2789 144 0.1027 0.1269 3.9945 4.0867| | 9: 1.79 - 1.72 1.00 2745 138 0.0959 0.1296 3.7195 3.8813| | 10: 1.72 - 1.66 1.00 2831 160 0.0999 0.1281 3.6335 3.7788| | 11: 1.66 - 1.61 1.00 2712 147 0.0969 0.1131 3.5725 3.617| | 12: 1.61 - 1.56 1.00 2773 144 0.0927 0.1160 3.3503 3.4687| | 13: 1.56 - 1.52 1.00 2745 130 0.0982 0.1043 3.3386 3.4201| | 14: 1.52 - 1.48 1.00 2803 134 0.0997 0.1087 3.2632 3.3235| | 15: 1.48 - 1.45 1.00 2738 128 0.1020 0.1334 3.1699 3.3201| | 16: 1.45 - 1.42 1.00 2756 161 0.1075 0.1245 3.1519 3.2449| | 17: 1.42 - 1.39 1.00 2785 139 0.1123 0.1292 3.1147 3.2431| | 18: 1.39 - 1.36 1.00 2741 179 0.1161 0.1368 3.0882 3.2636| | 19: 1.36 - 1.34 1.00 2807 134 0.1223 0.1609 3.0941 3.2783| | 20: 1.34 - 1.32 1.00 2696 147 0.1326 0.1498 3.0909 3.1429| | 21: 1.32 - 1.30 1.00 2785 112 0.1426 0.1602 3.0905 3.1524| | 22: 1.29 - 1.27 1.00 2704 152 0.1490 0.1937 3.0886 3.285| | 23: 1.27 - 1.26 1.00 2802 156 0.1580 0.1878 3.1035 3.214| | 24: 1.26 - 1.24 1.00 2744 132 0.1633 0.1758 3.0958 3.1893| | 25: 1.24 - 1.22 1.00 2733 148 0.1789 0.2290 3.1067 3.2795| | 26: 1.22 - 1.21 1.00 2727 135 0.1865 0.1779 3.1219 3.2041| | 27: 1.21 - 1.19 1.00 2814 148 0.2021 0.2100 3.1424 3.1523| | 28: 1.19 - 1.18 1.00 2671 147 0.2141 0.2308 3.1385 3.1637| | 29: 1.18 - 1.16 1.00 2800 134 0.2223 0.2357 3.1262 3.2181| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2472 3.1154 3.1601| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2919 171 0.95 8.77 1.00 0.97 5986.19| | 2: 3.57 - 2.84 2888 124 0.92 12.93 1.01 0.97 5986.19| | 3: 2.83 - 2.48 2820 163 0.89 17.15 0.99 0.98 5027.03| | 4: 2.47 - 2.25 2825 136 0.91 14.38 1.00 0.98 2553.65| | 5: 2.25 - 2.09 2756 127 0.90 16.54 1.01 0.98 2553.65| | 6: 2.09 - 1.97 2846 113 0.92 13.47 1.02 0.98 1515.88| | 7: 1.97 - 1.87 2787 165 0.94 10.83 1.02 0.97 630.81| | 8: 1.87 - 1.79 2789 144 0.91 14.46 1.00 0.97 630.81| | 9: 1.79 - 1.72 2745 138 0.93 11.48 0.98 0.97 341.33| | 10: 1.72 - 1.66 2831 160 0.93 12.32 0.98 0.97 283.36| | 11: 1.66 - 1.61 2712 147 0.93 12.95 0.98 0.97 270.32| | 12: 1.61 - 1.56 2773 144 0.95 9.56 0.99 0.97 147.32| | 13: 1.56 - 1.52 2745 130 0.94 11.12 1.02 0.97 147.32| | 14: 1.52 - 1.48 2803 134 0.94 11.30 1.02 0.97 131.56| | 15: 1.48 - 1.45 2738 128 0.95 10.46 1.01 0.98 102.70| | 16: 1.45 - 1.42 2756 161 0.94 11.56 1.02 0.98 102.70| | 17: 1.42 - 1.39 2785 139 0.94 11.48 1.01 0.98 92.98| | 18: 1.39 - 1.36 2741 179 0.94 11.76 1.01 0.98 87.36| | 19: 1.36 - 1.34 2807 134 0.94 12.34 1.00 0.98 87.36| | 20: 1.34 - 1.32 2696 147 0.94 12.51 0.99 0.97 82.60| | 21: 1.32 - 1.30 2785 112 0.93 13.44 0.99 0.96 82.27| | 22: 1.29 - 1.27 2704 152 0.93 13.97 0.99 0.96 82.40| | 23: 1.27 - 1.26 2802 156 0.92 14.91 0.98 0.95 83.08| | 24: 1.26 - 1.24 2744 132 0.92 15.01 0.97 0.95 83.08| | 25: 1.24 - 1.22 2733 148 0.91 16.42 0.96 0.94 84.48| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.93 86.02| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.02| | 28: 1.19 - 1.18 2671 147 0.88 20.21 1.01 0.93 89.07| | 29: 1.18 - 1.16 2800 134 0.88 20.53 0.99 0.93 90.22| | 30: 1.16 - 1.15 2739 148 0.86 21.96 0.98 0.93 90.22| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.27 max = 5986.19 mean = 943.36| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.92 mean = 14.01| |phase err.(test): min = 0.00 max = 89.55 mean = 14.12| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1195 0.1366 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1520 0.1518 0.1587 n_refl.: 87577 remove outliers: r(all,work,free)=0.1520 0.1518 0.1587 n_refl.: 87577 overall B=-0.02 to atoms: r(all,work,free)=0.1517 0.1514 0.1584 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1195 0.1367 n_refl.: 87577 remove outliers: r(all,work,free)=0.1203 0.1195 0.1367 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 0.3993 283.027 255.577 0.432 0.999 0.294 11.894-9.307 95.10 93 4 0.2341 475.274 457.654 0.839 1.001 0.218 9.237-7.194 97.73 208 7 0.2470 383.556 377.000 0.910 1.002 0.146 7.162-5.571 100.00 427 22 0.2207 293.366 281.958 0.900 1.002 0.140 5.546-4.326 100.00 867 58 0.1165 402.719 398.203 0.952 1.002 0.138 4.315-3.360 100.00 1859 96 0.0988 382.989 380.345 0.995 1.002 0.128 3.356-2.611 100.00 3867 181 0.1173 251.604 249.775 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1048 166.790 165.792 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0981 81.452 81.734 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1233 36.119 35.753 1.025 0.996 0.000 1.221-1.150 99.97 13689 708 0.2120 22.757 21.391 0.984 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0491 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2606 0.1949 0.083 5.477 8.8 119.3 19.9 258 0.000 1_bss: 0.1629 0.1772 0.083 5.477 9.0 119.5 20.1 258 0.000 1_settarget: 0.1629 0.1772 0.083 5.477 9.0 119.5 20.1 258 0.000 1_nqh: 0.1631 0.1776 0.083 5.477 9.0 119.5 20.1 258 0.006 1_weight: 0.1631 0.1776 0.083 5.477 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1212 0.1458 0.007 0.942 9.0 119.5 20.1 258 0.130 1_adp: 0.1239 0.1533 0.007 0.942 8.5 118.5 21.0 258 0.130 1_regHadp: 0.1243 0.1538 0.007 0.942 8.5 118.5 21.0 258 0.130 1_occ: 0.1244 0.1543 0.007 0.942 8.5 118.5 21.0 258 0.130 2_bss: 0.1241 0.1536 0.007 0.942 8.6 118.7 21.2 258 0.130 2_settarget: 0.1241 0.1536 0.007 0.942 8.6 118.7 21.2 258 0.130 2_updatecdl: 0.1241 0.1536 0.007 0.947 8.6 118.7 21.2 258 0.130 2_nqh: 0.1241 0.1536 0.007 0.947 8.6 118.7 21.2 258 0.130 2_sol: 0.1229 0.1492 0.007 0.947 8.6 118.7 23.6 435 n/a 2_weight: 0.1229 0.1492 0.007 0.947 8.6 118.7 23.6 435 n/a 2_xyzrec: 0.1226 0.1514 0.007 0.874 8.6 118.7 23.6 435 n/a 2_adp: 0.1199 0.1489 0.007 0.874 8.7 114.4 23.3 435 n/a 2_regHadp: 0.1199 0.1489 0.007 0.874 8.7 114.4 23.3 435 n/a 2_occ: 0.1199 0.1481 0.007 0.874 8.7 114.4 23.3 435 n/a 3_bss: 0.1195 0.1476 0.007 0.874 8.7 114.5 23.3 435 n/a 3_settarget: 0.1195 0.1476 0.007 0.874 8.7 114.5 23.3 435 n/a 3_updatecdl: 0.1195 0.1476 0.007 0.875 8.7 114.5 23.3 435 n/a 3_nqh: 0.1195 0.1476 0.007 0.875 8.7 114.5 23.3 435 n/a 3_sol: 0.1225 0.1489 0.007 0.875 8.7 114.5 22.0 438 n/a 3_weight: 0.1225 0.1489 0.007 0.875 8.7 114.5 22.0 438 n/a 3_xyzrec: 0.1229 0.1446 0.006 0.930 8.7 114.5 22.0 438 n/a 3_adp: 0.1211 0.1402 0.006 0.930 9.2 109.5 21.6 438 n/a 3_regHadp: 0.1212 0.1403 0.006 0.930 9.2 109.5 21.6 438 n/a 3_occ: 0.1205 0.1396 0.006 0.930 9.2 109.5 21.6 438 n/a 4_bss: 0.1195 0.1380 0.006 0.930 9.2 109.4 21.6 438 n/a 4_settarget: 0.1195 0.1380 0.006 0.930 9.2 109.4 21.6 438 n/a 4_updatecdl: 0.1195 0.1380 0.006 0.929 9.2 109.4 21.6 438 n/a 4_nqh: 0.1195 0.1380 0.006 0.929 9.2 109.4 21.6 438 n/a 4_sol: 0.1185 0.1350 0.006 0.929 9.2 109.4 21.5 444 n/a 4_weight: 0.1185 0.1350 0.006 0.929 9.2 109.4 21.5 444 n/a 4_xyzrec: 0.1190 0.1361 0.006 0.956 9.2 109.4 21.5 444 n/a 4_adp: 0.1181 0.1357 0.006 0.956 9.3 105.2 21.4 444 n/a 4_regHadp: 0.1181 0.1357 0.006 0.956 9.3 105.2 21.4 444 n/a 4_occ: 0.1179 0.1355 0.006 0.956 9.3 105.2 21.4 444 n/a 5_bss: 0.1177 0.1359 0.006 0.956 9.3 105.2 21.3 444 n/a 5_settarget: 0.1177 0.1359 0.006 0.956 9.3 105.2 21.3 444 n/a 5_updatecdl: 0.1177 0.1359 0.006 0.957 9.3 105.2 21.3 444 n/a 5_setrh: 0.1178 0.1359 0.006 0.957 9.3 105.2 21.3 444 n/a 5_nqh: 0.1178 0.1359 0.006 0.957 9.3 105.2 21.3 444 n/a 5_sol: 0.1174 0.1352 0.006 0.957 9.3 105.2 21.4 461 n/a 5_weight: 0.1174 0.1352 0.006 0.957 9.3 105.2 21.4 461 n/a 5_xyzrec: 0.1200 0.1371 0.008 1.043 9.3 105.2 21.4 461 n/a 5_adp: 0.1203 0.1372 0.008 1.043 9.3 100.9 21.2 461 n/a 5_regHadp: 0.1203 0.1372 0.008 1.043 9.3 100.9 21.2 461 n/a 5_occ: 0.1195 0.1366 0.008 1.043 9.3 100.9 21.2 461 n/a end: 0.1195 0.1367 0.008 1.043 9.3 100.9 21.2 461 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6197065_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6197065_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7100 Refinement macro-cycles (run) : 3512.7700 Write final files (write_after_run_outputs) : 65.8600 Total : 3583.3400 Total CPU time: 60.33 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:15 PST -0800 (1735452675.98 s) Start R-work = 0.1629, R-free = 0.1772 Final R-work = 0.1195, R-free = 0.1367 =============================================================================== Job complete usr+sys time: 3720.32 seconds wall clock time: 66 minutes 28.15 seconds (3988.15 seconds total)