Starting phenix.refine on Sat Dec 28 21:06:34 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3850167.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3850167.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3850167.pdb" } 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: 2.33, per 1000 atoms: 0.69 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 318.9 milliseconds Time building geometry restraints manager: 0.80 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: 601 0.92 - 1.19: 1081 1.19 - 1.46: 774 1.46 - 1.73: 684 1.73 - 2.00: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.339 1.486 -0.147 7.50e-03 1.78e+04 3.83e+02 bond pdb=" N GLU A 143 " pdb=" CA GLU A 143 " ideal model delta sigma weight residual 1.456 1.688 -0.232 1.22e-02 6.72e+03 3.61e+02 bond pdb=" C ALYS A 175 " pdb=" N GLU A 176 " ideal model delta sigma weight residual 1.334 1.114 0.220 1.20e-02 6.94e+03 3.38e+02 bond pdb=" N LEU A 151 " pdb=" CA LEU A 151 " ideal model delta sigma weight residual 1.456 1.235 0.221 1.26e-02 6.30e+03 3.08e+02 bond pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 1.236 1.419 -0.182 1.10e-02 8.26e+03 2.75e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 2932 4.25 - 8.50: 1862 8.50 - 12.74: 764 12.74 - 16.99: 190 16.99 - 21.24: 29 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ARG A 28 " pdb=" C ARG A 28 " pdb=" N ALA A 29 " ideal model delta sigma weight residual 122.12 138.52 -16.40 1.06e+00 8.90e-01 2.39e+02 angle pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 119.99 106.88 13.11 8.70e-01 1.32e+00 2.27e+02 angle pdb=" O ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 123.20 139.27 -16.07 1.08e+00 8.57e-01 2.21e+02 angle pdb=" O GLU A 16 " pdb=" C GLU A 16 " pdb=" N MET A 17 " ideal model delta sigma weight residual 122.22 105.67 16.55 1.17e+00 7.31e-01 2.00e+02 angle pdb=" O ASN A 81 " pdb=" C ASN A 81 " pdb=" N LEU A 82 " ideal model delta sigma weight residual 122.12 135.60 -13.48 1.06e+00 8.90e-01 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 943 16.94 - 33.88: 110 33.88 - 50.81: 40 50.81 - 67.75: 16 67.75 - 84.69: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -156.21 -23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA SER A 57 " pdb=" C SER A 57 " pdb=" N LEU A 58 " pdb=" CA LEU A 58 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual 180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.194: 76 0.194 - 0.387: 73 0.387 - 0.580: 61 0.580 - 0.773: 21 0.773 - 0.966: 12 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA GLU A 16 " pdb=" N GLU A 16 " pdb=" C GLU A 16 " pdb=" CB GLU A 16 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -3.53 0.94 2.00e-01 2.50e+01 2.21e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.001 2.00e-02 2.50e+03 5.84e-02 1.02e+02 pdb=" CG PHE A 162 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.104 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.090 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.070 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.043 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.059 2.00e-02 2.50e+03 6.54e-02 9.62e+01 pdb=" CG HIS A 126 " -0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.118 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.020 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.122 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 173 " -0.049 2.00e-02 2.50e+03 7.85e-02 9.24e+01 pdb=" CG ASN A 173 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 173 " 0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN A 173 " 0.075 2.00e-02 2.50e+03 pdb="HD21 ASN A 173 " -0.120 2.00e-02 2.50e+03 pdb="HD22 ASN A 173 " 0.075 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.38: 1486 2.38 - 2.93: 8395 2.93 - 3.49: 10385 3.49 - 4.04: 15036 4.04 - 4.60: 21272 Nonbonded interactions: 56574 Sorted by model distance: nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.823 2.450 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.829 2.450 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.832 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.845 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.863 2.450 ... (remaining 56569 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_3850167_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= 0.2613 r_free= 0.1929 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794039 | | target function (ml) not normalized (work): 232760.207845 | | target function (ml) not normalized (free): 11789.235816 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3041 0.2086 7.1037 4.9396| | 2: 3.57 - 2.84 1.00 2876 122 0.2456 0.1789 4.3442 4.3365| | 3: 2.84 - 2.48 1.00 2833 165 0.2343 0.1698 4.1209 4.1577| | 4: 2.47 - 2.25 1.00 2825 136 0.2331 0.1412 3.8313 3.8175| | 5: 2.25 - 2.09 1.00 2756 127 0.2447 0.1562 3.7937 3.7903| | 6: 2.09 - 1.97 1.00 2846 113 0.2578 0.1623 3.4684 3.5421| | 7: 1.97 - 1.87 1.00 2787 165 0.2519 0.1613 3.1211 3.092| | 8: 1.87 - 1.79 1.00 2789 144 0.2530 0.2038 3.0597 3.1596| | 9: 1.79 - 1.72 1.00 2745 138 0.2408 0.1979 2.9037 2.9491| | 10: 1.72 - 1.66 1.00 2789 158 0.2416 0.2077 2.8279 2.9512| | 11: 1.66 - 1.61 1.00 2740 147 0.2534 0.1842 2.754 2.8065| | 12: 1.61 - 1.56 1.00 2787 146 0.2557 0.1961 2.6419 2.6624| | 13: 1.56 - 1.52 1.00 2745 130 0.2560 0.1918 2.5832 2.6149| | 14: 1.52 - 1.48 1.00 2803 134 0.2529 0.2192 2.5006 2.6243| | 15: 1.48 - 1.45 1.00 2738 128 0.2517 0.1948 2.4077 2.4397| | 16: 1.45 - 1.42 1.00 2756 161 0.2730 0.2130 2.4141 2.4193| | 17: 1.42 - 1.39 1.00 2785 139 0.2680 0.1967 2.3565 2.329| | 18: 1.39 - 1.36 1.00 2741 179 0.2636 0.2169 2.2612 2.3321| | 19: 1.36 - 1.34 1.00 2807 134 0.2688 0.2030 2.2498 2.2014| | 20: 1.34 - 1.32 1.00 2696 147 0.2659 0.2268 2.1961 2.1672| | 21: 1.32 - 1.30 1.00 2785 112 0.2790 0.2298 2.1816 2.1586| | 22: 1.29 - 1.27 1.00 2704 152 0.2820 0.2414 2.1386 2.1544| | 23: 1.27 - 1.26 1.00 2802 156 0.2771 0.2643 2.0928 2.276| | 24: 1.26 - 1.24 1.00 2744 132 0.2807 0.2223 2.0756 2.0739| | 25: 1.24 - 1.22 1.00 2734 148 0.2885 0.2706 2.056 2.1244| | 26: 1.22 - 1.21 1.00 2727 135 0.2817 0.2481 2.0029 2.1216| | 27: 1.21 - 1.19 1.00 2814 148 0.2943 0.2582 2.0005 2.0035| | 28: 1.19 - 1.18 1.00 2671 147 0.3022 0.2575 1.9895 1.9604| | 29: 1.18 - 1.16 1.00 2800 134 0.2946 0.2712 1.9562 2.004| | 30: 1.16 - 1.15 1.00 2740 148 0.3035 0.2842 1.9296 1.9512| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.78 0.76 0.23 1471.09| | 2: 3.57 - 2.84 2876 122 0.80 26.04 1.28 0.23 1471.09| | 3: 2.84 - 2.48 2833 165 0.74 31.92 1.24 0.24 1218.59| | 4: 2.47 - 2.25 2825 136 0.81 25.31 1.25 0.25 563.31| | 5: 2.25 - 2.09 2756 127 0.78 28.97 1.28 0.25 563.31| | 6: 2.09 - 1.97 2846 113 0.84 22.29 1.30 0.25 306.37| | 7: 1.97 - 1.87 2787 165 0.90 16.12 1.28 0.26 87.23| | 8: 1.87 - 1.79 2789 144 0.86 20.75 1.26 0.26 87.23| | 9: 1.79 - 1.72 2745 138 0.88 18.47 1.23 0.25 54.99| | 10: 1.72 - 1.66 2789 158 0.87 20.08 1.22 0.25 48.53| | 11: 1.66 - 1.61 2740 147 0.85 21.64 1.24 0.25 46.88| | 12: 1.61 - 1.56 2787 146 0.88 18.76 1.24 0.25 30.14| | 13: 1.56 - 1.52 2745 130 0.86 20.99 1.23 0.25 30.14| | 14: 1.52 - 1.48 2803 134 0.86 20.74 1.23 0.25 26.80| | 15: 1.48 - 1.45 2738 128 0.87 20.09 1.23 0.25 20.69| | 16: 1.45 - 1.42 2756 161 0.85 21.76 1.24 0.25 20.69| | 17: 1.42 - 1.39 2785 139 0.87 20.23 1.23 0.25 17.30| | 18: 1.39 - 1.36 2741 179 0.87 20.62 1.23 0.25 15.34| | 19: 1.36 - 1.34 2807 134 0.86 21.33 1.22 0.25 15.34| | 20: 1.34 - 1.32 2696 147 0.87 20.37 1.21 0.25 12.66| | 21: 1.32 - 1.30 2785 112 0.86 21.49 1.21 0.25 12.47| | 22: 1.29 - 1.27 2704 152 0.86 21.98 1.22 0.25 12.22| | 23: 1.27 - 1.26 2802 156 0.86 21.93 1.22 0.24 10.92| | 24: 1.26 - 1.24 2744 132 0.85 22.70 1.20 0.24 10.92| | 25: 1.24 - 1.22 2734 148 0.85 23.26 1.21 0.24 10.39| | 26: 1.22 - 1.21 2727 135 0.85 23.51 1.19 0.24 9.79| | 27: 1.21 - 1.19 2814 148 0.84 24.34 1.21 0.24 9.79| | 28: 1.19 - 1.18 2671 147 0.83 24.77 1.19 0.23 9.00| | 29: 1.18 - 1.16 2800 134 0.83 24.89 1.16 0.23 8.69| | 30: 1.16 - 1.15 2740 148 0.82 26.45 1.15 0.23 8.69| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.69 max = 1471.09 mean = 212.86| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.36| |phase err.(test): min = 0.00 max = 90.00 mean = 22.34| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.233 1557 Z= 5.612 Angle : 5.255 16.549 2118 Z= 3.695 Chirality : 0.399 0.966 243 Planarity : 0.030 0.087 284 Dihedral : 13.955 84.687 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 30.27 % 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: -2.58 (0.46), residues: 224 helix: -2.82 (0.34), residues: 115 sheet: -0.73 (0.81), residues: 28 loop : 0.16 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.112 0.018 ARG A 98 TYR 0.084 0.034 TYR A 141 PHE 0.101 0.038 PHE A 162 HIS 0.086 0.052 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= 0.2613 r_free= 0.1929 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794039 | | target function (ml) not normalized (work): 232760.207845 | | target function (ml) not normalized (free): 11789.235816 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2571 0.2614 0.1929 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2571 0.2614 0.1929 n_refl.: 87602 remove outliers: r(all,work,free)=0.1986 0.1992 0.1929 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2012 0.2017 0.1942 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1652 0.1647 0.1748 n_refl.: 87594 remove outliers: r(all,work,free)=0.1651 0.1646 0.1748 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 0.3833 386.293 369.115 0.688 1.001 0.401 11.894-9.307 99.02 97 4 0.1759 613.608 596.323 0.928 1.002 0.380 9.237-7.194 100.00 213 7 0.2154 501.856 489.639 0.960 1.002 0.360 7.162-5.571 100.00 427 22 0.2214 376.615 364.151 0.928 1.002 0.320 5.546-4.326 100.00 867 58 0.1321 516.999 511.502 0.962 1.002 0.224 4.315-3.360 100.00 1859 96 0.1175 491.670 486.152 1.005 1.002 0.199 3.356-2.611 100.00 3867 181 0.1434 323.002 319.213 0.998 1.002 0.048 2.608-2.026 99.99 8198 413 0.1352 214.121 211.864 1.004 1.002 0.000 2.025-1.573 100.00 17313 902 0.1668 104.565 103.991 1.010 1.002 0.000 1.573-1.221 100.00 36679 1900 0.2074 46.369 45.087 0.999 1.002 0.000 1.221-1.150 99.97 13689 708 0.2566 29.215 26.868 0.964 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0476 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1646 r_free=0.1748 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=0.1646 r_free=0.1748 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.394034 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1973.775896 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 0.1213 0.1463 0.0250 0.007 0.9 1.0 0.5 0.0 0 12.697 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 14.63 2.50 3.013 19.066 1973.776 0.017 12.38 15.31 2.93 3.051 19.464 1973.776 0.016 Individual atomic B min max mean iso aniso Overall: 8.47 118.20 20.85 2.87 0 1785 Protein: 8.47 118.20 17.75 2.87 0 1519 Water: 11.06 115.11 38.86 N/A 0 258 Other: 22.41 35.01 28.21 N/A 0 8 Chain A: 8.47 118.20 20.85 N/A 0 1785 Histogram: Values Number of atoms 8.47 - 19.45 1209 19.45 - 30.42 236 30.42 - 41.39 160 41.39 - 52.36 96 52.36 - 63.34 55 63.34 - 74.31 18 74.31 - 85.28 4 85.28 - 96.26 4 96.26 - 107.23 0 107.23 - 118.20 3 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1531 r_work=0.1242 r_free=0.1536 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1242 r_free = 0.1536 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 = 0.1242 r_free = 0.1539 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 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= 0.1242 r_free= 0.1539 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015442 | | target function (ls_wunit_k1) not normalized (work): 1286.282683 | | target function (ls_wunit_k1) not normalized (free): 113.203130 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1257 0.1242 0.1539 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1696 0.1695 0.1761 n_refl.: 87593 remove outliers: r(all,work,free)=0.1696 0.1695 0.1761 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1718 0.1717 0.1776 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1254 0.1240 0.1533 n_refl.: 87593 remove outliers: r(all,work,free)=0.1253 0.1239 0.1533 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 0.3614 298.979 278.016 0.639 1.002 0.380 11.894-9.307 99.02 97 4 0.1633 478.948 467.751 0.909 1.003 0.367 9.237-7.194 100.00 213 7 0.1810 391.721 386.530 0.952 1.003 0.340 7.162-5.571 100.00 427 22 0.1748 293.965 288.373 0.921 1.003 0.290 5.546-4.326 100.00 867 58 0.0930 403.541 400.643 0.950 1.003 0.214 4.315-3.360 100.00 1859 96 0.0784 383.770 382.686 0.995 1.003 0.200 3.356-2.611 100.00 3867 181 0.1024 252.117 251.410 0.999 1.002 0.052 2.608-2.026 99.99 8198 413 0.0970 167.131 166.596 1.009 1.002 0.000 2.025-1.573 100.00 17313 902 0.1196 81.618 81.813 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1639 36.193 35.655 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2357 22.804 21.315 0.970 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0499 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1239 r_free=0.1533 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1241 r_free=0.1534 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1241 r_free=0.1534 | n_water=258 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1249 r_free=0.1534 | n_water=252 | time (s): 26.350 (total time: 28.890) Filter (q & B) r_work=0.1253 r_free=0.1532 | n_water=249 | time (s): 3.780 (total time: 32.670) Compute maps r_work=0.1253 r_free=0.1532 | n_water=249 | time (s): 1.880 (total time: 34.550) Filter (map) r_work=0.1263 r_free=0.1539 | n_water=238 | time (s): 3.790 (total time: 38.340) Find peaks r_work=0.1263 r_free=0.1539 | n_water=238 | time (s): 0.710 (total time: 39.050) Add new water r_work=0.1420 r_free=0.1703 | n_water=452 | time (s): 3.740 (total time: 42.790) Refine new water occ: r_work=0.1330 r_free=0.1565 adp: r_work=0.1251 r_free=0.1520 occ: r_work=0.1264 r_free=0.1501 adp: r_work=0.1229 r_free=0.1496 occ: r_work=0.1233 r_free=0.1479 adp: r_work=0.1222 r_free=0.1484 ADP+occupancy (water only), MIN, final r_work=0.1222 r_free=0.1484 r_work=0.1222 r_free=0.1484 | n_water=452 | time (s): 158.870 (total time: 201.660) Filter (q & B) r_work=0.1227 r_free=0.1489 | n_water=434 | time (s): 3.880 (total time: 205.540) Filter (dist only) r_work=0.1227 r_free=0.1489 | n_water=434 | time (s): 41.940 (total time: 247.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.891444 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1508.616379 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 0.1224 0.1500 0.0276 0.007 0.9 1.9 0.5 0.0 0 12.446 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.24 15.00 2.76 3.759 23.018 1508.616 0.015 12.01 14.87 2.86 4.132 22.840 1508.616 0.015 Individual atomic B min max mean iso aniso Overall: 8.69 113.42 23.04 2.59 196 1765 Protein: 8.69 113.42 17.55 2.59 0 1519 Water: 10.94 72.44 42.14 N/A 196 238 Other: 24.73 35.89 29.78 N/A 0 8 Chain A: 8.69 113.42 20.28 N/A 0 1765 Chain S: 14.88 72.10 47.91 N/A 196 0 Histogram: Values Number of atoms 8.69 - 19.16 1205 19.16 - 29.63 254 29.63 - 40.11 192 40.11 - 50.58 137 50.58 - 61.05 109 61.05 - 71.53 52 71.53 - 82.00 6 82.00 - 92.47 3 92.47 - 102.94 1 102.94 - 113.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1487 r_work=0.1201 r_free=0.1487 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1487 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1485 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1202 r_free= 0.1485 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014083 | | target function (ls_wunit_k1) not normalized (work): 1173.043304 | | target function (ls_wunit_k1) not normalized (free): 101.530836 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1202 0.1485 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1600 0.1596 0.1711 n_refl.: 87592 remove outliers: r(all,work,free)=0.1600 0.1596 0.1711 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1605 0.1601 0.1714 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1197 0.1485 n_refl.: 87592 remove outliers: r(all,work,free)=0.1210 0.1196 0.1485 n_refl.: 87589 ======================== 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 92.71 84 5 0.3351 294.364 272.279 0.588 1.002 0.364 11.894-9.307 99.02 97 4 0.1529 478.948 474.983 0.916 1.003 0.360 9.237-7.194 100.00 213 7 0.1677 391.721 393.806 0.983 1.003 0.260 7.162-5.571 100.00 427 22 0.1513 293.965 290.394 0.938 1.003 0.234 5.546-4.326 100.00 867 58 0.0829 403.541 400.819 0.958 1.003 0.215 4.315-3.360 100.00 1859 96 0.0702 383.770 382.803 1.002 1.002 0.210 3.356-2.611 100.00 3867 181 0.0964 252.117 251.460 1.010 1.002 0.072 2.608-2.026 99.99 8198 413 0.0959 167.131 166.710 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1179 81.618 81.804 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1611 36.193 35.688 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2338 22.804 21.325 0.979 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0546 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1485 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=0.1196 r_free=0.1485 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1485 | n_water=434 | time (s): 1.950 (total time: 1.950) Filter (dist) r_work=0.1197 r_free=0.1484 | n_water=431 | time (s): 41.650 (total time: 43.600) Filter (q & B) r_work=0.1197 r_free=0.1484 | n_water=431 | time (s): 1.240 (total time: 44.840) Compute maps r_work=0.1197 r_free=0.1484 | n_water=431 | time (s): 1.710 (total time: 46.550) Filter (map) r_work=0.1239 r_free=0.1482 | n_water=298 | time (s): 3.320 (total time: 49.870) Find peaks r_work=0.1239 r_free=0.1482 | n_water=298 | time (s): 0.780 (total time: 50.650) Add new water r_work=0.1364 r_free=0.1611 | n_water=480 | time (s): 3.790 (total time: 54.440) Refine new water occ: r_work=0.1264 r_free=0.1529 adp: r_work=0.1265 r_free=0.1529 occ: r_work=0.1241 r_free=0.1509 adp: r_work=0.1240 r_free=0.1508 occ: r_work=0.1226 r_free=0.1493 adp: r_work=0.1220 r_free=0.1490 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1490 r_work=0.1220 r_free=0.1490 | n_water=480 | time (s): 174.090 (total time: 228.530) Filter (q & B) r_work=0.1224 r_free=0.1483 | n_water=450 | time (s): 2.870 (total time: 231.400) Filter (dist only) r_work=0.1224 r_free=0.1483 | n_water=450 | time (s): 35.400 (total time: 266.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.079551 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.074953 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1232 0.1454 0.0222 0.006 0.9 1.9 0.5 0.0 0 1.040 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.54 2.22 3.593 21.976 47.075 3.726 12.09 14.05 1.95 4.039 21.819 47.075 3.654 Individual atomic B min max mean iso aniso Overall: 9.19 109.45 21.61 2.30 216 1761 Protein: 9.19 109.45 17.16 2.30 0 1519 Water: 11.42 71.41 36.54 N/A 216 234 Other: 20.14 31.76 26.34 N/A 0 8 Chain A: 9.19 109.45 19.83 N/A 0 1761 Chain S: 15.75 68.44 36.17 N/A 216 0 Histogram: Values Number of atoms 9.19 - 19.21 1235 19.21 - 29.24 277 29.24 - 39.27 214 39.27 - 49.29 149 49.29 - 59.32 70 59.32 - 69.34 19 69.34 - 79.37 7 79.37 - 89.40 3 89.40 - 99.42 1 99.42 - 109.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1405 r_work=0.1210 r_free=0.1406 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1406 target_work(ml) = 3.654 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1407 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1207 r_free= 0.1407 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.652467 | | target function (ml) not normalized (work): 304224.919169 | | target function (ml) not normalized (free): 16056.932330 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1207 0.1407 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1530 0.1528 0.1583 n_refl.: 87589 remove outliers: r(all,work,free)=0.1530 0.1528 0.1583 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1528 0.1527 0.1582 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1197 0.1371 n_refl.: 87589 remove outliers: r(all,work,free)=0.1201 0.1192 0.1371 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 0.3797 290.920 260.503 0.462 1.000 0.296 11.894-9.307 96.08 94 4 0.2362 468.654 457.385 0.852 1.001 0.280 9.237-7.194 97.73 208 7 0.2311 384.339 385.556 0.946 1.002 0.169 7.162-5.571 100.00 427 22 0.2096 293.965 283.140 0.907 1.002 0.157 5.546-4.326 100.00 867 58 0.1116 403.541 399.125 0.951 1.002 0.146 4.315-3.360 100.00 1859 96 0.0933 383.770 381.124 0.993 1.002 0.140 3.356-2.611 100.00 3867 181 0.1141 252.117 250.114 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1036 167.131 166.143 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1004 81.618 81.774 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1293 36.193 35.771 1.018 0.999 0.000 1.221-1.150 99.97 13689 708 0.2133 22.804 21.418 0.976 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0050 b_overall=-0.0206 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1371 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1371 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1371 | n_water=450 | time (s): 1.810 (total time: 1.810) Filter (dist) r_work=0.1195 r_free=0.1372 | n_water=448 | time (s): 40.870 (total time: 42.680) Filter (q & B) r_work=0.1195 r_free=0.1373 | n_water=445 | time (s): 2.920 (total time: 45.600) Compute maps r_work=0.1195 r_free=0.1373 | n_water=445 | time (s): 1.230 (total time: 46.830) Filter (map) r_work=0.1223 r_free=0.1384 | n_water=311 | time (s): 3.000 (total time: 49.830) Find peaks r_work=0.1223 r_free=0.1384 | n_water=311 | time (s): 0.680 (total time: 50.510) Add new water r_work=0.1285 r_free=0.1440 | n_water=477 | time (s): 3.150 (total time: 53.660) Refine new water occ: r_work=0.1210 r_free=0.1370 adp: r_work=0.1210 r_free=0.1372 occ: r_work=0.1195 r_free=0.1358 adp: r_work=0.1193 r_free=0.1359 occ: r_work=0.1183 r_free=0.1348 adp: r_work=0.1180 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1348 r_work=0.1180 r_free=0.1348 | n_water=477 | time (s): 199.180 (total time: 252.840) Filter (q & B) r_work=0.1185 r_free=0.1352 | n_water=443 | time (s): 3.230 (total time: 256.070) Filter (dist only) r_work=0.1185 r_free=0.1351 | n_water=441 | time (s): 38.400 (total time: 294.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.951100 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.039526 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 0.1191 0.1360 0.0169 0.006 1.0 1.9 0.5 0.0 0 0.976 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.60 1.69 3.405 21.387 40.040 3.636 11.89 13.62 1.73 3.750 21.283 40.040 3.626 Individual atomic B min max mean iso aniso Overall: 9.24 105.12 21.13 2.12 211 1757 Protein: 9.24 105.12 16.91 2.13 0 1519 Water: 11.61 70.42 35.60 N/A 211 230 Other: 20.27 29.15 24.89 N/A 0 8 Chain A: 9.24 105.12 19.48 N/A 0 1757 Chain S: 15.89 57.47 34.86 N/A 211 0 Histogram: Values Number of atoms 9.24 - 18.83 1238 18.83 - 28.42 272 28.42 - 38.00 210 38.00 - 47.59 148 47.59 - 57.18 61 57.18 - 66.77 26 66.77 - 76.36 8 76.36 - 85.94 2 85.94 - 95.53 1 95.53 - 105.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1362 r_work=0.1190 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1362 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1186 r_free = 0.1360 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1186 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.625336 | | target function (ml) not normalized (work): 301921.586388 | | target function (ml) not normalized (free): 15948.187470 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1186 0.1360 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1508 0.1508 0.1545 n_refl.: 87577 remove outliers: r(all,work,free)=0.1508 0.1508 0.1545 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1506 0.1506 0.1543 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1185 0.1360 n_refl.: 87577 remove outliers: r(all,work,free)=0.1192 0.1184 0.1360 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3933 290.920 256.883 0.452 1.001 0.308 11.894-9.307 93.14 91 4 0.2256 471.843 450.447 0.838 1.002 0.300 9.237-7.194 97.73 208 7 0.2460 384.339 379.435 0.918 1.002 0.120 7.162-5.571 100.00 427 22 0.2189 293.965 283.360 0.900 1.003 0.118 5.546-4.326 100.00 867 58 0.1163 403.541 398.972 0.952 1.003 0.117 4.315-3.360 100.00 1859 96 0.0950 383.770 381.176 0.993 1.002 0.117 3.356-2.611 100.00 3867 181 0.1152 252.117 250.335 1.001 1.002 0.048 2.608-2.026 99.99 8198 413 0.1023 167.131 166.256 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0978 81.618 81.892 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.193 35.824 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2123 22.804 21.434 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0390 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1184 r_free=0.1360 After: r_work=0.1184 r_free=0.1360 ================================== NQH flips ================================== r_work=0.1184 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1184 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1360 | n_water=441 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1184 r_free=0.1360 | n_water=441 | time (s): 36.660 (total time: 39.010) Filter (q & B) r_work=0.1185 r_free=0.1359 | n_water=440 | time (s): 3.090 (total time: 42.100) Compute maps r_work=0.1185 r_free=0.1359 | n_water=440 | time (s): 1.320 (total time: 43.420) Filter (map) r_work=0.1214 r_free=0.1383 | n_water=330 | time (s): 2.790 (total time: 46.210) Find peaks r_work=0.1214 r_free=0.1383 | n_water=330 | time (s): 0.570 (total time: 46.780) Add new water r_work=0.1259 r_free=0.1423 | n_water=481 | time (s): 2.580 (total time: 49.360) Refine new water occ: r_work=0.1196 r_free=0.1367 adp: r_work=0.1196 r_free=0.1368 occ: r_work=0.1185 r_free=0.1359 adp: r_work=0.1184 r_free=0.1361 occ: r_work=0.1177 r_free=0.1354 adp: r_work=0.1174 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1174 r_free=0.1354 r_work=0.1174 r_free=0.1354 | n_water=481 | time (s): 198.360 (total time: 247.720) Filter (q & B) r_work=0.1180 r_free=0.1358 | n_water=448 | time (s): 3.040 (total time: 250.760) Filter (dist only) r_work=0.1180 r_free=0.1357 | n_water=447 | time (s): 36.610 (total time: 287.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.020139 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.960880 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 0.1205 0.1383 0.0178 0.007 1.0 3.2 0.5 0.0 0 1.010 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.83 1.78 3.274 21.079 37.961 3.635 12.09 13.80 1.71 3.521 21.002 37.961 3.630 Individual atomic B min max mean iso aniso Overall: 9.24 100.71 20.93 1.98 217 1757 Protein: 9.24 100.71 16.71 1.98 0 1519 Water: 11.49 69.66 35.22 N/A 217 230 Other: 20.15 28.37 24.38 N/A 0 8 Chain A: 9.24 100.71 19.28 N/A 0 1757 Chain S: 14.93 57.62 34.29 N/A 217 0 Histogram: Values Number of atoms 9.24 - 18.39 1226 18.39 - 27.54 278 27.54 - 36.68 206 36.68 - 45.83 151 45.83 - 54.98 69 54.98 - 64.12 29 64.12 - 73.27 11 73.27 - 82.42 1 82.42 - 91.56 1 91.56 - 100.71 2 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1380 r_work=0.1209 r_free=0.1380 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1380 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1376 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1205 r_free= 0.1376 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.628114 | | target function (ml) not normalized (work): 302142.066881 | | target function (ml) not normalized (free): 15959.357500 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1435 0.1434 5.7014 5.6444| | 2: 3.57 - 2.84 1.00 2888 124 0.1118 0.1449 5.2064 5.2634| | 3: 2.83 - 2.48 1.00 2820 163 0.1224 0.1244 5.0098 5.027| | 4: 2.47 - 2.25 1.00 2825 136 0.1032 0.1172 4.7131 4.7804| | 5: 2.25 - 2.09 1.00 2756 127 0.1007 0.1134 4.6566 4.7299| | 6: 2.09 - 1.97 1.00 2846 113 0.0982 0.1211 4.3554 4.4808| | 7: 1.97 - 1.87 1.00 2787 165 0.0997 0.1191 4.0749 4.1684| | 8: 1.87 - 1.79 1.00 2789 144 0.1027 0.1247 3.9922 4.0882| | 9: 1.79 - 1.72 1.00 2745 138 0.0963 0.1339 3.7237 3.9204| | 10: 1.72 - 1.66 1.00 2831 160 0.1008 0.1238 3.6428 3.7684| | 11: 1.66 - 1.61 1.00 2712 147 0.0976 0.1116 3.58 3.6233| | 12: 1.61 - 1.56 1.00 2773 144 0.0925 0.1203 3.3591 3.5009| | 13: 1.56 - 1.52 1.00 2745 130 0.0994 0.1093 3.3509 3.453| | 14: 1.52 - 1.48 1.00 2803 134 0.1001 0.1159 3.2713 3.352| | 15: 1.48 - 1.45 1.00 2738 128 0.1028 0.1392 3.1816 3.3401| | 16: 1.45 - 1.42 1.00 2756 161 0.1083 0.1257 3.1641 3.2401| | 17: 1.42 - 1.39 1.00 2785 139 0.1129 0.1312 3.1231 3.234| | 18: 1.39 - 1.36 1.00 2741 179 0.1162 0.1391 3.0926 3.2657| | 19: 1.36 - 1.34 1.00 2807 134 0.1231 0.1580 3.1015 3.2552| | 20: 1.34 - 1.32 1.00 2696 147 0.1335 0.1516 3.0973 3.1566| | 21: 1.32 - 1.30 1.00 2785 112 0.1426 0.1629 3.0924 3.1625| | 22: 1.29 - 1.27 1.00 2704 152 0.1491 0.1914 3.0926 3.2887| | 23: 1.27 - 1.26 1.00 2802 156 0.1579 0.1842 3.1048 3.2061| | 24: 1.26 - 1.24 1.00 2744 132 0.1635 0.1787 3.0979 3.1988| | 25: 1.24 - 1.22 1.00 2733 148 0.1796 0.2304 3.1115 3.2922| | 26: 1.22 - 1.21 1.00 2727 135 0.1864 0.1788 3.1257 3.2017| | 27: 1.21 - 1.19 1.00 2814 148 0.2017 0.2066 3.1422 3.1457| | 28: 1.19 - 1.18 1.00 2671 147 0.2146 0.2282 3.1421 3.1582| | 29: 1.18 - 1.16 1.00 2800 134 0.2216 0.2360 3.126 3.2247| | 30: 1.16 - 1.15 1.00 2739 148 0.2380 0.2486 3.118 3.1641| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2916 171 0.95 9.18 1.00 0.97 6357.56| | 2: 3.57 - 2.84 2888 124 0.92 13.47 1.01 0.97 6357.56| | 3: 2.83 - 2.48 2820 163 0.88 17.63 0.99 0.97 5327.67| | 4: 2.47 - 2.25 2825 136 0.91 14.71 1.00 0.98 2671.92| | 5: 2.25 - 2.09 2756 127 0.89 16.92 1.01 0.98 2671.92| | 6: 2.09 - 1.97 2846 113 0.92 13.72 1.02 0.97 1568.67| | 7: 1.97 - 1.87 2787 165 0.94 10.80 1.02 0.97 627.75| | 8: 1.87 - 1.79 2789 144 0.91 14.41 1.00 0.97 627.75| | 9: 1.79 - 1.72 2745 138 0.93 11.54 0.99 0.97 344.45| | 10: 1.72 - 1.66 2831 160 0.93 12.38 0.98 0.97 287.71| | 11: 1.66 - 1.61 2712 147 0.93 13.07 0.98 0.97 274.75| | 12: 1.61 - 1.56 2773 144 0.95 9.73 0.99 0.97 152.45| | 13: 1.56 - 1.52 2745 130 0.94 11.30 1.02 0.97 152.45| | 14: 1.52 - 1.48 2803 134 0.94 11.55 1.02 0.97 135.95| | 15: 1.48 - 1.45 2738 128 0.95 10.59 1.01 0.98 105.73| | 16: 1.45 - 1.42 2756 161 0.94 11.82 1.01 0.98 105.73| | 17: 1.42 - 1.39 2785 139 0.94 11.59 1.01 0.98 94.89| | 18: 1.39 - 1.36 2741 179 0.94 11.88 1.01 0.98 88.61| | 19: 1.36 - 1.34 2807 134 0.94 12.43 1.00 0.98 88.61| | 20: 1.34 - 1.32 2696 147 0.94 12.52 0.99 0.96 83.17| | 21: 1.32 - 1.30 2785 112 0.93 13.42 0.98 0.96 82.79| | 22: 1.29 - 1.27 2704 152 0.93 14.00 0.98 0.96 82.88| | 23: 1.27 - 1.26 2802 156 0.92 14.88 0.98 0.95 83.35| | 24: 1.26 - 1.24 2744 132 0.92 15.02 0.97 0.95 83.35| | 25: 1.24 - 1.22 2733 148 0.91 16.41 0.96 0.94 84.75| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.02 0.93 86.30| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.30| | 28: 1.19 - 1.18 2671 147 0.88 20.18 1.01 0.93 89.21| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.99 0.93 90.30| | 30: 1.16 - 1.15 2739 148 0.86 21.88 0.98 0.93 90.30| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.79 max = 6357.56 mean = 990.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.91 mean = 14.13| |phase err.(test): min = 0.00 max = 89.08 mean = 14.24| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1205 0.1376 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1519 0.1519 0.1563 n_refl.: 87574 remove outliers: r(all,work,free)=0.1519 0.1519 0.1563 n_refl.: 87574 overall B=-0.01 to atoms: r(all,work,free)=0.1517 0.1516 0.1562 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1205 0.1375 n_refl.: 87574 remove outliers: r(all,work,free)=0.1213 0.1205 0.1375 n_refl.: 87572 ======================== 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 87.50 79 5 0.3998 286.186 253.052 0.438 1.001 0.302 11.894-9.307 92.16 90 4 0.2411 474.419 450.320 0.837 1.003 0.290 9.237-7.194 97.73 208 7 0.2551 384.339 377.180 0.907 1.003 0.131 7.162-5.571 100.00 427 22 0.2316 293.965 282.924 0.892 1.003 0.114 5.546-4.326 100.00 867 58 0.1208 403.541 398.614 0.952 1.003 0.110 4.315-3.360 100.00 1859 96 0.0999 383.770 381.077 0.993 1.002 0.110 3.356-2.611 100.00 3867 181 0.1183 252.117 250.188 1.001 1.002 0.048 2.608-2.026 99.99 8198 413 0.1049 167.131 166.149 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0984 81.618 81.847 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1238 36.193 35.804 1.023 0.996 0.000 1.221-1.150 99.97 13689 708 0.2119 22.804 21.415 0.982 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0328 ================= 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 : 0.2613 0.1929 0.084 5.255 8.8 119.3 19.9 258 0.000 1_bss: 0.1646 0.1748 0.084 5.255 9.1 119.5 20.1 258 0.000 1_settarget: 0.1646 0.1748 0.084 5.255 9.1 119.5 20.1 258 0.000 1_nqh: 0.1646 0.1748 0.084 5.255 9.1 119.5 20.1 258 0.000 1_weight: 0.1646 0.1748 0.084 5.255 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1213 0.1463 0.007 0.944 9.1 119.5 20.1 258 0.124 1_adp: 0.1238 0.1531 0.007 0.944 8.5 118.2 20.8 258 0.124 1_regHadp: 0.1242 0.1536 0.007 0.944 8.5 118.2 20.8 258 0.124 1_occ: 0.1242 0.1539 0.007 0.944 8.5 118.2 20.8 258 0.124 2_bss: 0.1239 0.1533 0.007 0.944 8.6 118.3 21.0 258 0.124 2_settarget: 0.1239 0.1533 0.007 0.944 8.6 118.3 21.0 258 0.124 2_updatecdl: 0.1239 0.1533 0.008 0.953 8.6 118.3 21.0 258 0.124 2_nqh: 0.1241 0.1534 0.008 0.953 8.6 118.3 21.0 258 0.127 2_sol: 0.1227 0.1489 0.008 0.953 8.6 118.3 23.4 434 n/a 2_weight: 0.1227 0.1489 0.008 0.953 8.6 118.3 23.4 434 n/a 2_xyzrec: 0.1224 0.1500 0.007 0.876 8.6 118.3 23.4 434 n/a 2_adp: 0.1201 0.1487 0.007 0.876 8.7 113.4 23.0 434 n/a 2_regHadp: 0.1201 0.1487 0.007 0.876 8.7 113.4 23.0 434 n/a 2_occ: 0.1202 0.1485 0.007 0.876 8.7 113.4 23.0 434 n/a 3_bss: 0.1196 0.1485 0.007 0.876 8.7 113.5 23.1 434 n/a 3_settarget: 0.1196 0.1485 0.007 0.876 8.7 113.5 23.1 434 n/a 3_updatecdl: 0.1196 0.1485 0.007 0.876 8.7 113.5 23.1 434 n/a 3_nqh: 0.1196 0.1485 0.007 0.876 8.7 113.5 23.1 434 n/a 3_sol: 0.1224 0.1483 0.007 0.876 8.7 113.5 21.9 450 n/a 3_weight: 0.1224 0.1483 0.007 0.876 8.7 113.5 21.9 450 n/a 3_xyzrec: 0.1232 0.1454 0.006 0.917 8.7 113.5 21.9 450 n/a 3_adp: 0.1209 0.1405 0.006 0.917 9.2 109.5 21.6 450 n/a 3_regHadp: 0.1210 0.1406 0.006 0.917 9.2 109.5 21.6 450 n/a 3_occ: 0.1207 0.1407 0.006 0.917 9.2 109.5 21.6 450 n/a 4_bss: 0.1193 0.1371 0.006 0.917 9.2 109.4 21.6 450 n/a 4_settarget: 0.1193 0.1371 0.006 0.917 9.2 109.4 21.6 450 n/a 4_updatecdl: 0.1193 0.1371 0.006 0.916 9.2 109.4 21.6 450 n/a 4_nqh: 0.1193 0.1371 0.006 0.916 9.2 109.4 21.6 450 n/a 4_sol: 0.1185 0.1351 0.006 0.916 9.2 109.4 21.3 441 n/a 4_weight: 0.1185 0.1351 0.006 0.916 9.2 109.4 21.3 441 n/a 4_xyzrec: 0.1191 0.1360 0.006 0.958 9.2 109.4 21.3 441 n/a 4_adp: 0.1189 0.1362 0.006 0.958 9.2 105.1 21.1 441 n/a 4_regHadp: 0.1190 0.1362 0.006 0.958 9.2 105.1 21.1 441 n/a 4_occ: 0.1186 0.1360 0.006 0.958 9.2 105.1 21.1 441 n/a 5_bss: 0.1184 0.1360 0.006 0.958 9.2 105.1 21.1 441 n/a 5_settarget: 0.1184 0.1360 0.006 0.958 9.2 105.1 21.1 441 n/a 5_updatecdl: 0.1184 0.1360 0.006 0.959 9.2 105.1 21.1 441 n/a 5_setrh: 0.1184 0.1360 0.006 0.959 9.2 105.1 21.1 441 n/a 5_nqh: 0.1184 0.1360 0.006 0.959 9.2 105.1 21.1 441 n/a 5_sol: 0.1180 0.1357 0.006 0.959 9.2 105.1 21.1 447 n/a 5_weight: 0.1180 0.1357 0.006 0.959 9.2 105.1 21.1 447 n/a 5_xyzrec: 0.1205 0.1383 0.007 1.031 9.2 105.1 21.1 447 n/a 5_adp: 0.1209 0.1380 0.007 1.031 9.2 100.7 20.9 447 n/a 5_regHadp: 0.1209 0.1380 0.007 1.031 9.2 100.7 20.9 447 n/a 5_occ: 0.1205 0.1376 0.007 1.031 9.2 100.7 20.9 447 n/a end: 0.1205 0.1375 0.007 1.031 9.2 100.7 20.9 447 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3850167_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3850167_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7800 Refinement macro-cycles (run) : 3595.8700 Write final files (write_after_run_outputs) : 56.7100 Total : 3657.3600 Total CPU time: 61.58 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:37 PST -0800 (1735452757.75 s) Start R-work = 0.1646, R-free = 0.1748 Final R-work = 0.1205, R-free = 0.1375 =============================================================================== Job complete usr+sys time: 3790.03 seconds wall clock time: 67 minutes 44.66 seconds (4064.66 seconds total)