Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2226169.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_2226169.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2226169.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 =============================================================================== 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: 2.07, per 1000 atoms: 0.61 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: 0.52 Conformation dependent library (CDL) restraints added in 188.3 milliseconds Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 0.94: 722 0.94 - 1.20: 976 1.20 - 1.46: 712 1.46 - 1.71: 720 1.71 - 1.97: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.515 -0.194 1.00e-02 1.00e+04 3.77e+02 bond pdb=" CA VAL A 181 " pdb=" CB VAL A 181 " ideal model delta sigma weight residual 1.540 1.775 -0.235 1.29e-02 6.01e+03 3.33e+02 bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.237 1.424 -0.187 1.13e-02 7.83e+03 2.74e+02 bond pdb=" C LYS A 32 " pdb=" O LYS A 32 " ideal model delta sigma weight residual 1.235 1.430 -0.194 1.19e-02 7.06e+03 2.67e+02 bond pdb=" N HIS A 115 " pdb=" CA HIS A 115 " ideal model delta sigma weight residual 1.456 1.250 0.205 1.26e-02 6.30e+03 2.65e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.76: 3198 4.76 - 9.52: 1843 9.52 - 14.28: 618 14.28 - 19.03: 108 19.03 - 23.79: 10 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH2 ARG A 98 " ideal model delta sigma weight residual 119.20 104.39 14.81 9.00e-01 1.23e+00 2.71e+02 angle pdb=" OE1BGLN A 80 " pdb=" CD BGLN A 80 " pdb=" NE2BGLN A 80 " ideal model delta sigma weight residual 122.60 137.81 -15.21 1.00e+00 1.00e+00 2.31e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH2 ARG A 28 " ideal model delta sigma weight residual 119.20 132.19 -12.99 9.00e-01 1.23e+00 2.08e+02 angle pdb=" CA ALA A 103 " pdb=" C ALA A 103 " pdb=" N ALA A 104 " ideal model delta sigma weight residual 116.37 132.58 -16.21 1.19e+00 7.06e-01 1.85e+02 angle pdb=" CA LEU A 38 " pdb=" C LEU A 38 " pdb=" O LEU A 38 " ideal model delta sigma weight residual 120.63 106.13 14.50 1.08e+00 8.57e-01 1.80e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 923 16.26 - 32.51: 127 32.51 - 48.77: 36 48.77 - 65.03: 21 65.03 - 81.28: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 180.00 158.99 21.01 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA VAL A 70 " pdb=" C VAL A 70 " pdb=" N VAL A 71 " pdb=" CA VAL A 71 " ideal model delta harmonic sigma weight residual -180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ARG A 27 " pdb=" C ARG A 27 " pdb=" N ARG A 28 " pdb=" CA ARG A 28 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.185: 66 0.185 - 0.368: 79 0.368 - 0.551: 54 0.551 - 0.734: 30 0.734 - 0.917: 14 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 103 " pdb=" N ALA A 103 " pdb=" C ALA A 103 " pdb=" CB ALA A 103 " both_signs ideal model delta sigma weight residual False 2.48 1.57 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CA LEU A 77 " pdb=" N LEU A 77 " pdb=" C LEU A 77 " pdb=" CB LEU A 77 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb=" CA VAL A 169 " pdb=" N VAL A 169 " pdb=" C VAL A 169 " pdb=" CB VAL A 169 " both_signs ideal model delta sigma weight residual False 2.44 3.35 -0.91 2.00e-01 2.50e+01 2.08e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.062 2.00e-02 2.50e+03 6.70e-02 1.35e+02 pdb=" CG TYR A 139 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.072 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.017 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.114 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.133 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.029 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.040 2.00e-02 2.50e+03 5.91e-02 1.05e+02 pdb=" CG ATYR A 67 " 0.094 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.023 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.082 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.017 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.023 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.087 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.009 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.087 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.060 2.00e-02 2.50e+03 5.74e-02 9.89e+01 pdb=" CG PHE A 162 " 0.113 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.070 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.060 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.050 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.053 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.039 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.063 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 1001 2.31 - 2.88: 8055 2.88 - 3.46: 10524 3.46 - 4.03: 15242 4.03 - 4.60: 21875 Nonbonded interactions: 56697 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.739 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.768 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.792 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.812 2.450 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.821 2.270 ... (remaining 56692 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_2226169_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= 0.2595 r_free= 0.1930 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.784553 | | target function (ml) not normalized (work): 231969.967499 | | target function (ml) not normalized (free): 11774.106116 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3030 0.2087 7.0825 4.9576| | 2: 3.57 - 2.84 1.00 2876 122 0.2435 0.1793 4.3449 4.3317| | 3: 2.84 - 2.48 1.00 2833 165 0.2367 0.1706 4.1332 4.1585| | 4: 2.47 - 2.25 1.00 2825 136 0.2302 0.1466 3.8284 3.8188| | 5: 2.25 - 2.09 1.00 2756 127 0.2449 0.1634 3.8 3.8198| | 6: 2.09 - 1.97 1.00 2846 113 0.2525 0.1655 3.4722 3.4798| | 7: 1.97 - 1.87 1.00 2787 165 0.2517 0.1871 3.1091 3.2356| | 8: 1.87 - 1.79 1.00 2789 144 0.2432 0.1815 3.0491 3.1207| | 9: 1.79 - 1.72 1.00 2745 138 0.2385 0.1858 2.8763 2.9341| | 10: 1.72 - 1.66 1.00 2789 158 0.2375 0.1704 2.7858 2.7693| | 11: 1.66 - 1.61 1.00 2740 147 0.2496 0.1953 2.7233 2.7733| | 12: 1.61 - 1.56 1.00 2787 146 0.2471 0.1784 2.5993 2.5734| | 13: 1.56 - 1.52 1.00 2745 130 0.2528 0.1825 2.5617 2.5662| | 14: 1.52 - 1.48 1.00 2803 134 0.2572 0.1947 2.4959 2.5582| | 15: 1.48 - 1.45 1.00 2738 128 0.2574 0.1962 2.4184 2.4754| | 16: 1.45 - 1.42 1.00 2756 161 0.2675 0.2187 2.3778 2.4679| | 17: 1.42 - 1.39 1.00 2785 139 0.2662 0.2313 2.3334 2.3777| | 18: 1.39 - 1.36 1.00 2741 179 0.2631 0.2153 2.2554 2.3023| | 19: 1.36 - 1.34 1.00 2807 134 0.2649 0.2162 2.2343 2.257| | 20: 1.34 - 1.32 1.00 2696 147 0.2679 0.2437 2.1873 2.286| | 21: 1.32 - 1.30 1.00 2785 112 0.2692 0.2204 2.1687 2.1588| | 22: 1.29 - 1.27 1.00 2704 152 0.2721 0.2490 2.1382 2.1933| | 23: 1.27 - 1.26 1.00 2802 156 0.2791 0.2350 2.1076 2.11| | 24: 1.26 - 1.24 1.00 2744 132 0.2772 0.2519 2.0727 2.1792| | 25: 1.24 - 1.22 1.00 2734 148 0.2781 0.2598 2.0343 2.1157| | 26: 1.22 - 1.21 1.00 2727 135 0.2900 0.2358 2.0179 2.1186| | 27: 1.21 - 1.19 1.00 2814 148 0.2893 0.2541 1.9892 1.9795| | 28: 1.19 - 1.18 1.00 2671 147 0.2990 0.2705 1.9888 1.9534| | 29: 1.18 - 1.16 1.00 2800 134 0.3033 0.2828 1.9593 2.0502| | 30: 1.16 - 1.15 1.00 2740 148 0.3099 0.2694 1.9334 1.941| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.80 0.76 0.23 1491.17| | 2: 3.57 - 2.84 2876 122 0.80 26.09 1.27 0.23 1491.17| | 3: 2.84 - 2.48 2833 165 0.74 31.97 1.24 0.24 1236.00| | 4: 2.47 - 2.25 2825 136 0.81 25.51 1.25 0.25 573.80| | 5: 2.25 - 2.09 2756 127 0.77 29.16 1.28 0.25 573.80| | 6: 2.09 - 1.97 2846 113 0.84 22.51 1.29 0.25 312.42| | 7: 1.97 - 1.87 2787 165 0.90 16.32 1.28 0.26 89.50| | 8: 1.87 - 1.79 2789 144 0.86 20.82 1.24 0.26 89.50| | 9: 1.79 - 1.72 2745 138 0.88 18.17 1.23 0.26 52.84| | 10: 1.72 - 1.66 2789 158 0.87 19.48 1.22 0.25 45.50| | 11: 1.66 - 1.61 2740 147 0.86 20.75 1.25 0.25 43.92| | 12: 1.61 - 1.56 2787 146 0.89 17.83 1.24 0.25 27.93| | 13: 1.56 - 1.52 2745 130 0.87 19.73 1.24 0.25 27.93| | 14: 1.52 - 1.48 2803 134 0.87 20.42 1.24 0.25 25.26| | 15: 1.48 - 1.45 2738 128 0.87 20.04 1.23 0.25 20.39| | 16: 1.45 - 1.42 2756 161 0.86 21.51 1.24 0.25 20.39| | 17: 1.42 - 1.39 2785 139 0.87 20.65 1.23 0.25 17.55| | 18: 1.39 - 1.36 2741 179 0.86 21.45 1.23 0.25 15.90| | 19: 1.36 - 1.34 2807 134 0.85 22.42 1.22 0.25 15.90| | 20: 1.34 - 1.32 2696 147 0.86 21.58 1.22 0.24 13.40| | 21: 1.32 - 1.30 2785 112 0.85 22.30 1.19 0.24 13.23| | 22: 1.29 - 1.27 2704 152 0.85 22.76 1.20 0.24 12.92| | 23: 1.27 - 1.26 2802 156 0.85 22.70 1.20 0.24 11.34| | 24: 1.26 - 1.24 2744 132 0.84 23.43 1.20 0.24 11.34| | 25: 1.24 - 1.22 2734 148 0.84 23.84 1.19 0.23 10.73| | 26: 1.22 - 1.21 2727 135 0.84 24.42 1.21 0.23 10.07| | 27: 1.21 - 1.19 2814 148 0.83 24.91 1.20 0.23 10.07| | 28: 1.19 - 1.18 2671 147 0.83 25.03 1.17 0.23 9.13| | 29: 1.18 - 1.16 2800 134 0.82 25.62 1.18 0.23 8.78| | 30: 1.16 - 1.15 2740 148 0.81 26.65 1.16 0.23 8.78| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.78 max = 1491.17 mean = 215.61| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.56| |phase err.(test): min = 0.00 max = 89.67 mean = 22.56| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.235 1557 Z= 5.403 Angle : 5.373 18.971 2118 Z= 3.821 Chirality : 0.404 0.917 243 Planarity : 0.031 0.107 284 Dihedral : 13.852 81.283 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 36.22 % 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: -2.43 (0.48), residues: 224 helix: -2.67 (0.36), residues: 108 sheet: 0.02 (0.93), residues: 28 loop : -0.40 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.071 0.019 ARG A 48 TYR 0.080 0.032 TYR A 141 PHE 0.117 0.042 PHE A 162 HIS 0.086 0.038 HIS A 138 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= 0.2595 r_free= 0.1930 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.784553 | | target function (ml) not normalized (work): 231969.967499 | | target function (ml) not normalized (free): 11774.106116 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2554 0.2595 0.1931 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2554 0.2595 0.1931 n_refl.: 87602 remove outliers: r(all,work,free)=0.1963 0.1967 0.1931 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.1987 0.1991 0.1942 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1630 0.1623 0.1756 n_refl.: 87594 remove outliers: r(all,work,free)=0.1629 0.1623 0.1756 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 0.3882 386.134 356.576 0.674 1.003 0.409 11.894-9.307 99.02 97 4 0.1836 613.356 596.841 0.925 1.004 0.401 9.237-7.194 100.00 213 7 0.2085 501.649 491.609 0.960 1.004 0.344 7.162-5.571 100.00 427 22 0.2188 376.460 364.210 0.927 1.004 0.283 5.546-4.326 100.00 867 58 0.1289 516.787 510.301 0.967 1.004 0.222 4.315-3.360 100.00 1859 96 0.1143 491.468 487.644 1.006 1.004 0.205 3.356-2.611 100.00 3867 181 0.1441 322.869 319.446 0.999 1.003 0.052 2.608-2.026 99.99 8198 413 0.1324 214.033 211.986 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1616 104.522 103.919 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2057 46.349 45.048 1.005 0.994 0.000 1.221-1.150 99.97 13689 708 0.2578 29.203 26.941 0.980 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0458 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1623 r_free=0.1756 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1623 r_free=0.1759 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.139569 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2053.650246 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 0.1461 0.0249 0.007 0.9 1.0 0.5 0.0 0 12.070 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 14.61 2.49 3.013 19.058 2053.650 0.017 12.38 15.31 2.92 3.041 19.441 2053.650 0.016 Individual atomic B min max mean iso aniso Overall: 8.50 118.14 20.81 2.88 0 1785 Protein: 8.50 118.14 17.71 2.88 0 1519 Water: 11.04 114.98 38.84 N/A 0 258 Other: 22.97 35.31 28.32 N/A 0 8 Chain A: 8.50 118.14 20.81 N/A 0 1785 Histogram: Values Number of atoms 8.50 - 19.47 1216 19.47 - 30.43 225 30.43 - 41.39 165 41.39 - 52.36 97 52.36 - 63.32 53 63.32 - 74.28 18 74.28 - 85.25 4 85.25 - 96.21 4 96.21 - 107.18 0 107.18 - 118.14 3 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1531 r_work=0.1243 r_free=0.1535 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1243 r_free = 0.1535 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 = 0.1241 r_free = 0.1538 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1241 r_free= 0.1538 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015432 | | target function (ls_wunit_k1) not normalized (work): 1285.464783 | | target function (ls_wunit_k1) not normalized (free): 113.790277 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1256 0.1241 0.1538 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1688 0.1687 0.1753 n_refl.: 87593 remove outliers: r(all,work,free)=0.1688 0.1687 0.1753 n_refl.: 87593 overall B=0.17 to atoms: r(all,work,free)=0.1716 0.1716 0.1772 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1254 0.1240 0.1532 n_refl.: 87593 remove outliers: r(all,work,free)=0.1253 0.1239 0.1532 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 0.3617 299.821 278.939 0.626 1.002 0.373 11.894-9.307 99.02 97 4 0.1657 480.297 468.529 0.902 1.003 0.368 9.237-7.194 100.00 213 7 0.1838 392.824 387.845 0.947 1.003 0.340 7.162-5.571 100.00 427 22 0.1759 294.792 289.382 0.920 1.003 0.280 5.546-4.326 100.00 867 58 0.0924 404.677 402.009 0.949 1.003 0.209 4.315-3.360 100.00 1859 96 0.0780 384.851 383.871 0.992 1.003 0.199 3.356-2.611 100.00 3867 181 0.1020 252.827 252.153 0.997 1.002 0.057 2.608-2.026 99.99 8198 413 0.0969 167.601 167.023 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1197 81.848 82.045 1.016 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1644 36.295 35.757 1.005 0.997 0.000 1.221-1.150 99.97 13689 708 0.2356 22.868 21.379 0.970 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0384 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1239 r_free=0.1532 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1241 r_free=0.1534 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1241 r_free=0.1534 | n_water=258 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1250 r_free=0.1529 | n_water=252 | time (s): 25.570 (total time: 27.920) Filter (q & B) r_work=0.1253 r_free=0.1529 | n_water=249 | time (s): 3.550 (total time: 31.470) Compute maps r_work=0.1253 r_free=0.1529 | n_water=249 | time (s): 1.740 (total time: 33.210) Filter (map) r_work=0.1264 r_free=0.1538 | n_water=237 | time (s): 3.540 (total time: 36.750) Find peaks r_work=0.1264 r_free=0.1538 | n_water=237 | time (s): 0.650 (total time: 37.400) Add new water r_work=0.1420 r_free=0.1691 | n_water=455 | time (s): 3.290 (total time: 40.690) Refine new water occ: r_work=0.1329 r_free=0.1563 adp: r_work=0.1250 r_free=0.1511 occ: r_work=0.1263 r_free=0.1503 adp: r_work=0.1227 r_free=0.1489 occ: r_work=0.1231 r_free=0.1480 adp: r_work=0.1221 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1482 r_work=0.1221 r_free=0.1482 | n_water=455 | time (s): 97.230 (total time: 137.920) Filter (q & B) r_work=0.1227 r_free=0.1490 | n_water=432 | time (s): 4.060 (total time: 141.980) Filter (dist only) r_work=0.1227 r_free=0.1491 | n_water=431 | time (s): 44.510 (total time: 186.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.227236 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1580.886462 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 0.1223 0.1501 0.0278 0.007 0.9 2.9 0.5 0.0 0 12.614 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.23 15.01 2.78 3.759 23.037 1580.886 0.015 12.00 14.82 2.82 4.027 22.891 1580.886 0.015 Individual atomic B min max mean iso aniso Overall: 8.67 114.20 23.15 2.59 194 1764 Protein: 8.67 114.20 17.62 2.59 0 1519 Water: 11.01 73.10 42.51 N/A 194 237 Other: 25.15 36.73 29.72 N/A 0 8 Chain A: 8.67 114.20 20.30 N/A 0 1764 Chain S: 15.72 69.74 49.03 N/A 194 0 Histogram: Values Number of atoms 8.67 - 19.22 1205 19.22 - 29.77 252 29.77 - 40.33 184 40.33 - 50.88 144 50.88 - 61.43 118 61.43 - 71.99 45 71.99 - 82.54 4 82.54 - 93.09 3 93.09 - 103.65 1 103.65 - 114.20 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1483 r_work=0.1200 r_free=0.1483 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1483 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1479 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= 0.1479 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013832 | | target function (ls_wunit_k1) not normalized (work): 1152.113554 | | target function (ls_wunit_k1) not normalized (free): 103.869307 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1202 0.1479 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1606 0.1604 0.1697 n_refl.: 87592 remove outliers: r(all,work,free)=0.1606 0.1604 0.1697 n_refl.: 87592 overall B=0.05 to atoms: r(all,work,free)=0.1614 0.1611 0.1702 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1197 0.1480 n_refl.: 87592 remove outliers: r(all,work,free)=0.1209 0.1195 0.1480 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 0.3196 292.497 274.007 0.592 1.002 0.360 11.894-9.307 99.02 97 4 0.1489 480.297 476.123 0.920 1.003 0.350 9.237-7.194 100.00 213 7 0.1629 392.824 394.031 0.978 1.003 0.280 7.162-5.571 100.00 427 22 0.1499 294.792 292.023 0.939 1.003 0.234 5.546-4.326 100.00 867 58 0.0829 404.677 402.157 0.958 1.003 0.215 4.315-3.360 100.00 1859 96 0.0708 384.851 383.771 1.002 1.002 0.210 3.356-2.611 100.00 3867 181 0.0957 252.827 252.092 1.009 1.002 0.076 2.608-2.026 99.99 8198 413 0.0950 167.601 167.198 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1182 81.848 82.019 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1625 36.295 35.781 1.016 0.997 0.000 1.221-1.150 99.97 13689 708 0.2344 22.868 21.390 0.976 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0722 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1480 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=0.1195 r_free=0.1480 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1480 | n_water=431 | time (s): 2.030 (total time: 2.030) Filter (dist) r_work=0.1195 r_free=0.1480 | n_water=429 | time (s): 39.390 (total time: 41.420) Filter (q & B) r_work=0.1195 r_free=0.1480 | n_water=429 | time (s): 1.060 (total time: 42.480) Compute maps r_work=0.1195 r_free=0.1480 | n_water=429 | time (s): 1.300 (total time: 43.780) Filter (map) r_work=0.1234 r_free=0.1474 | n_water=292 | time (s): 2.700 (total time: 46.480) Find peaks r_work=0.1234 r_free=0.1474 | n_water=292 | time (s): 0.470 (total time: 46.950) Add new water r_work=0.1362 r_free=0.1610 | n_water=493 | time (s): 2.540 (total time: 49.490) Refine new water occ: r_work=0.1261 r_free=0.1526 adp: r_work=0.1262 r_free=0.1526 occ: r_work=0.1239 r_free=0.1504 adp: r_work=0.1237 r_free=0.1503 occ: r_work=0.1224 r_free=0.1487 adp: r_work=0.1216 r_free=0.1483 ADP+occupancy (water only), MIN, final r_work=0.1216 r_free=0.1483 r_work=0.1216 r_free=0.1483 | n_water=493 | time (s): 184.700 (total time: 234.190) Filter (q & B) r_work=0.1221 r_free=0.1488 | n_water=454 | time (s): 3.590 (total time: 237.780) Filter (dist only) r_work=0.1221 r_free=0.1488 | n_water=454 | time (s): 34.750 (total time: 272.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.050298 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.346135 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 0.1455 0.0229 0.005 0.9 1.9 0.5 0.0 0 1.025 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.55 2.29 3.609 22.122 40.346 3.732 12.10 14.08 1.98 4.106 21.929 40.346 3.659 Individual atomic B min max mean iso aniso Overall: 9.16 109.57 21.68 2.29 217 1764 Protein: 9.16 109.57 17.20 2.29 0 1519 Water: 11.58 72.21 36.58 N/A 217 237 Other: 20.94 32.72 26.90 N/A 0 8 Chain A: 9.16 109.57 19.90 N/A 0 1764 Chain S: 15.58 63.27 36.16 N/A 217 0 Histogram: Values Number of atoms 9.16 - 19.20 1232 19.20 - 29.24 274 29.24 - 39.28 231 39.28 - 49.33 131 49.33 - 59.37 77 59.37 - 69.41 24 69.41 - 79.45 6 79.45 - 89.49 3 89.49 - 99.53 1 99.53 - 109.57 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1408 r_work=0.1211 r_free=0.1409 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1211 r_free = 0.1409 target_work(ml) = 3.659 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1209 r_free = 0.1413 target_work(ml) = 3.658 | | occupancies: max = 1.00 min = 0.18 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= 0.1209 r_free= 0.1413 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.658302 | | target function (ml) not normalized (work): 304707.276803 | | target function (ml) not normalized (free): 16077.258590 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1209 0.1413 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1531 0.1531 0.1575 n_refl.: 87588 remove outliers: r(all,work,free)=0.1531 0.1531 0.1575 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1530 0.1529 0.1575 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1196 0.1379 n_refl.: 87588 remove outliers: r(all,work,free)=0.1203 0.1193 0.1379 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 0.3773 289.124 259.061 0.472 0.998 0.314 11.894-9.307 99.02 97 4 0.2615 480.297 464.155 0.855 1.000 0.310 9.237-7.194 97.73 208 7 0.2318 385.421 386.444 0.951 1.001 0.180 7.162-5.571 100.00 427 22 0.2100 294.792 283.741 0.915 1.001 0.175 5.546-4.326 100.00 867 58 0.1088 404.677 400.466 0.963 1.001 0.161 4.315-3.360 100.00 1859 96 0.0911 384.851 382.103 1.004 1.001 0.153 3.356-2.611 100.00 3867 181 0.1130 252.827 250.854 1.009 1.002 0.062 2.608-2.026 99.99 8198 413 0.1032 167.601 166.718 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1015 81.848 82.018 1.035 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1304 36.295 35.859 1.027 1.001 0.000 1.221-1.150 99.97 13689 708 0.2140 22.868 21.397 0.980 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0185 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1379 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=0.1193 r_free=0.1379 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1379 | n_water=454 | time (s): 1.940 (total time: 1.940) Filter (dist) r_work=0.1194 r_free=0.1378 | n_water=452 | time (s): 40.050 (total time: 41.990) Filter (q & B) r_work=0.1193 r_free=0.1379 | n_water=449 | time (s): 3.180 (total time: 45.170) Compute maps r_work=0.1193 r_free=0.1379 | n_water=449 | time (s): 1.370 (total time: 46.540) Filter (map) r_work=0.1214 r_free=0.1385 | n_water=324 | time (s): 2.930 (total time: 49.470) Find peaks r_work=0.1214 r_free=0.1385 | n_water=324 | time (s): 0.590 (total time: 50.060) Add new water r_work=0.1277 r_free=0.1434 | n_water=484 | time (s): 2.710 (total time: 52.770) Refine new water occ: r_work=0.1209 r_free=0.1365 adp: r_work=0.1209 r_free=0.1367 occ: r_work=0.1194 r_free=0.1351 adp: r_work=0.1192 r_free=0.1352 occ: r_work=0.1184 r_free=0.1345 adp: r_work=0.1180 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1343 r_work=0.1180 r_free=0.1343 | n_water=484 | time (s): 143.190 (total time: 195.960) Filter (q & B) r_work=0.1187 r_free=0.1347 | n_water=450 | time (s): 3.430 (total time: 199.390) Filter (dist only) r_work=0.1188 r_free=0.1347 | n_water=449 | time (s): 38.250 (total time: 237.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.223151 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.339130 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 0.1189 0.1367 0.0178 0.006 1.0 4.2 0.5 0.0 0 1.112 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.67 1.78 3.408 21.542 45.339 3.643 11.76 13.53 1.77 3.849 21.404 45.339 3.624 Individual atomic B min max mean iso aniso Overall: 9.31 104.72 21.29 2.16 213 1763 Protein: 9.31 104.72 16.89 2.16 0 1519 Water: 11.58 70.86 36.11 N/A 213 236 Other: 20.67 29.82 25.21 N/A 0 8 Chain A: 9.31 104.72 19.55 N/A 0 1763 Chain S: 14.85 63.32 35.75 N/A 213 0 Histogram: Values Number of atoms 9.31 - 18.85 1232 18.85 - 28.39 274 28.39 - 37.93 225 37.93 - 47.47 126 47.47 - 57.01 79 57.01 - 66.55 26 66.55 - 76.10 9 76.10 - 85.64 2 85.64 - 95.18 1 95.18 - 104.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1176 r_free=0.1353 r_work=0.1177 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1177 r_free = 0.1353 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1174 r_free = 0.1352 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1174 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623257 | | target function (ml) not normalized (work): 301762.929701 | | target function (ml) not normalized (free): 15961.480355 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1182 0.1174 0.1352 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1500 0.1499 0.1552 n_refl.: 87581 remove outliers: r(all,work,free)=0.1500 0.1499 0.1552 n_refl.: 87581 overall B=-0.02 to atoms: r(all,work,free)=0.1497 0.1496 0.1550 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1181 0.1172 0.1355 n_refl.: 87581 remove outliers: r(all,work,free)=0.1179 0.1170 0.1355 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 0.4118 284.403 252.453 0.441 1.000 0.300 11.894-9.307 96.08 94 4 0.2344 475.587 456.895 0.841 1.002 0.250 9.237-7.194 97.73 208 7 0.2427 385.421 379.087 0.910 1.002 0.172 7.162-5.571 100.00 427 22 0.2184 294.792 284.059 0.903 1.002 0.143 5.546-4.326 100.00 867 58 0.1127 404.677 400.295 0.955 1.002 0.126 4.315-3.360 100.00 1859 96 0.0933 384.851 382.355 0.993 1.002 0.118 3.356-2.611 100.00 3867 181 0.1147 252.827 250.916 1.000 1.002 0.053 2.608-2.026 99.99 8198 413 0.1015 167.601 166.756 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0954 81.848 82.118 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1232 36.295 35.930 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2120 22.868 21.505 0.983 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0464 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1170 r_free=0.1355 After: r_work=0.1171 r_free=0.1355 ================================== NQH flips ================================== r_work=0.1171 r_free=0.1355 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=0.1171 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1171 r_free=0.1355 | n_water=449 | time (s): 1.940 (total time: 1.940) Filter (dist) r_work=0.1171 r_free=0.1355 | n_water=449 | time (s): 36.370 (total time: 38.310) Filter (q & B) r_work=0.1171 r_free=0.1355 | n_water=448 | time (s): 2.840 (total time: 41.150) Compute maps r_work=0.1171 r_free=0.1355 | n_water=448 | time (s): 1.150 (total time: 42.300) Filter (map) r_work=0.1190 r_free=0.1368 | n_water=345 | time (s): 2.560 (total time: 44.860) Find peaks r_work=0.1190 r_free=0.1368 | n_water=345 | time (s): 0.450 (total time: 45.310) Add new water r_work=0.1237 r_free=0.1406 | n_water=500 | time (s): 2.590 (total time: 47.900) Refine new water occ: r_work=0.1178 r_free=0.1338 adp: r_work=0.1178 r_free=0.1342 occ: r_work=0.1168 r_free=0.1328 adp: r_work=0.1167 r_free=0.1332 occ: r_work=0.1160 r_free=0.1323 adp: r_work=0.1158 r_free=0.1325 ADP+occupancy (water only), MIN, final r_work=0.1158 r_free=0.1325 r_work=0.1158 r_free=0.1325 | n_water=500 | time (s): 185.250 (total time: 233.150) Filter (q & B) r_work=0.1167 r_free=0.1330 | n_water=455 | time (s): 3.650 (total time: 236.800) Filter (dist only) r_work=0.1167 r_free=0.1329 | n_water=453 | time (s): 39.050 (total time: 275.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.016040 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.070308 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 0.1198 0.1366 0.0168 0.007 1.0 4.5 0.5 0.0 0 1.008 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.66 1.68 3.278 21.172 49.070 3.631 12.01 13.66 1.65 3.530 21.092 49.070 3.624 Individual atomic B min max mean iso aniso Overall: 9.26 100.51 21.10 2.01 218 1762 Protein: 9.26 100.51 16.67 2.01 0 1519 Water: 11.74 69.82 35.91 N/A 218 235 Other: 20.90 29.21 25.03 N/A 0 8 Chain A: 9.26 100.51 19.31 N/A 0 1762 Chain S: 13.70 63.61 35.65 N/A 218 0 Histogram: Values Number of atoms 9.26 - 18.38 1219 18.38 - 27.51 272 27.51 - 36.63 224 36.63 - 45.76 138 45.76 - 54.88 77 54.88 - 64.01 35 64.01 - 73.13 11 73.13 - 82.26 1 82.26 - 91.38 1 91.38 - 100.51 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1366 r_work=0.1201 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1366 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1366 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1196 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.622619 | | target function (ml) not normalized (work): 301695.299921 | | target function (ml) not normalized (free): 15950.461804 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1395 0.1398 5.662 5.6334| | 2: 3.57 - 2.84 1.00 2888 124 0.1132 0.1455 5.203 5.2671| | 3: 2.83 - 2.48 1.00 2820 163 0.1244 0.1323 5.0127 5.0448| | 4: 2.47 - 2.25 1.00 2825 136 0.1039 0.1108 4.7128 4.7471| | 5: 2.25 - 2.09 1.00 2756 127 0.1000 0.1096 4.6509 4.7215| | 6: 2.09 - 1.97 1.00 2846 113 0.0969 0.1182 4.3514 4.4647| | 7: 1.97 - 1.87 1.00 2787 165 0.0991 0.1240 4.0777 4.2055| | 8: 1.87 - 1.79 1.00 2789 144 0.1017 0.1258 3.9924 4.0877| | 9: 1.79 - 1.72 1.00 2745 138 0.0949 0.1289 3.7139 3.9039| | 10: 1.72 - 1.66 1.00 2831 160 0.0990 0.1255 3.6312 3.7679| | 11: 1.66 - 1.61 1.00 2712 147 0.0966 0.1115 3.5689 3.6201| | 12: 1.61 - 1.56 1.00 2773 144 0.0916 0.1163 3.3507 3.4954| | 13: 1.56 - 1.52 1.00 2745 130 0.0975 0.1066 3.3396 3.443| | 14: 1.52 - 1.48 1.00 2803 134 0.0986 0.1144 3.264 3.3481| | 15: 1.48 - 1.45 1.00 2738 128 0.1011 0.1362 3.1699 3.3497| | 16: 1.45 - 1.42 1.00 2756 161 0.1075 0.1205 3.1565 3.2296| | 17: 1.42 - 1.39 1.00 2785 139 0.1122 0.1273 3.117 3.2147| | 18: 1.39 - 1.36 1.00 2741 179 0.1150 0.1345 3.0869 3.2571| | 19: 1.36 - 1.34 1.00 2807 134 0.1212 0.1596 3.095 3.2759| | 20: 1.34 - 1.32 1.00 2696 147 0.1320 0.1504 3.0892 3.1515| | 21: 1.32 - 1.30 1.00 2785 112 0.1412 0.1644 3.0873 3.1672| | 22: 1.29 - 1.27 1.00 2704 152 0.1483 0.1915 3.0878 3.2947| | 23: 1.27 - 1.26 1.00 2802 156 0.1573 0.1835 3.1037 3.1997| | 24: 1.26 - 1.24 1.00 2744 132 0.1624 0.1759 3.0949 3.1942| | 25: 1.24 - 1.22 1.00 2733 148 0.1796 0.2285 3.1103 3.2767| | 26: 1.22 - 1.21 1.00 2727 135 0.1852 0.1783 3.1228 3.2012| | 27: 1.21 - 1.19 1.00 2814 148 0.2008 0.2094 3.1423 3.1498| | 28: 1.19 - 1.18 1.00 2671 147 0.2146 0.2328 3.1428 3.166| | 29: 1.18 - 1.16 1.00 2800 134 0.2220 0.2351 3.1297 3.2205| | 30: 1.16 - 1.15 1.00 2739 148 0.2373 0.2491 3.1181 3.1674| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.10 1.00 0.97 6268.27| | 2: 3.57 - 2.84 2888 124 0.92 13.37 1.01 0.97 6268.27| | 3: 2.83 - 2.48 2820 163 0.89 17.49 0.99 0.97 5255.38| | 4: 2.47 - 2.25 2825 136 0.91 14.57 1.00 0.98 2643.48| | 5: 2.25 - 2.09 2756 127 0.89 16.83 1.01 0.98 2643.48| | 6: 2.09 - 1.97 2846 113 0.92 13.58 1.02 0.98 1555.84| | 7: 1.97 - 1.87 2787 165 0.94 10.78 1.02 0.97 628.23| | 8: 1.87 - 1.79 2789 144 0.91 14.36 1.00 0.97 628.23| | 9: 1.79 - 1.72 2745 138 0.93 11.42 0.98 0.97 341.25| | 10: 1.72 - 1.66 2831 160 0.93 12.30 0.98 0.97 283.77| | 11: 1.66 - 1.61 2712 147 0.93 12.92 0.98 0.97 270.96| | 12: 1.61 - 1.56 2773 144 0.95 9.59 0.99 0.97 150.10| | 13: 1.56 - 1.52 2745 130 0.94 11.22 1.02 0.97 150.10| | 14: 1.52 - 1.48 2803 134 0.94 11.31 1.02 0.98 133.75| | 15: 1.48 - 1.45 2738 128 0.95 10.42 1.01 0.98 103.81| | 16: 1.45 - 1.42 2756 161 0.94 11.65 1.02 0.98 103.81| | 17: 1.42 - 1.39 2785 139 0.94 11.40 1.01 0.98 93.47| | 18: 1.39 - 1.36 2741 179 0.94 11.70 1.01 0.98 87.48| | 19: 1.36 - 1.34 2807 134 0.94 12.25 1.00 0.98 87.48| | 20: 1.34 - 1.32 2696 147 0.94 12.39 0.99 0.97 82.37| | 21: 1.32 - 1.30 2785 112 0.94 13.28 0.98 0.97 82.01| | 22: 1.29 - 1.27 2704 152 0.93 13.86 0.98 0.96 82.16| | 23: 1.27 - 1.26 2802 156 0.92 14.79 0.97 0.95 82.89| | 24: 1.26 - 1.24 2744 132 0.92 14.91 0.97 0.95 82.89| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.94 84.48| | 26: 1.22 - 1.21 2727 135 0.90 18.01 1.02 0.93 86.23| | 27: 1.21 - 1.19 2814 148 0.89 18.65 1.02 0.93 86.23| | 28: 1.19 - 1.18 2671 147 0.88 20.19 1.01 0.93 89.59| | 29: 1.18 - 1.16 2800 134 0.88 20.51 0.99 0.93 90.85| | 30: 1.16 - 1.15 2739 148 0.86 21.83 0.98 0.93 90.85| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.01 max = 6268.27 mean = 978.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.02| |phase err.(test): min = 0.00 max = 88.78 mean = 14.09| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1196 0.1366 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1509 0.1508 0.1552 n_refl.: 87577 remove outliers: r(all,work,free)=0.1509 0.1508 0.1552 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1506 0.1506 0.1550 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1197 0.1368 n_refl.: 87577 remove outliers: r(all,work,free)=0.1205 0.1197 0.1368 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4162 284.403 251.629 0.426 1.001 0.271 11.894-9.307 94.12 92 4 0.2290 479.587 458.255 0.848 1.002 0.250 9.237-7.194 97.73 208 7 0.2442 385.421 378.216 0.909 1.002 0.173 7.162-5.571 100.00 427 22 0.2193 294.792 283.493 0.895 1.002 0.141 5.546-4.326 100.00 867 58 0.1166 404.677 400.711 0.955 1.002 0.132 4.315-3.360 100.00 1859 96 0.0989 384.851 382.281 0.995 1.002 0.123 3.356-2.611 100.00 3867 181 0.1208 252.827 250.514 0.999 1.001 0.120 2.608-2.026 99.99 8198 413 0.1049 167.601 166.667 1.014 1.000 0.000 2.025-1.573 100.00 17313 902 0.0973 81.848 82.117 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1227 36.295 35.938 1.023 0.996 0.000 1.221-1.150 99.97 13689 708 0.2115 22.868 21.500 0.980 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0311 ================= 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 : 0.2595 0.1930 0.081 5.373 8.8 119.3 19.9 258 0.000 1_bss: 0.1623 0.1756 0.081 5.373 9.0 119.5 20.1 258 0.000 1_settarget: 0.1623 0.1756 0.081 5.373 9.0 119.5 20.1 258 0.000 1_nqh: 0.1623 0.1759 0.081 5.373 9.0 119.5 20.1 258 0.003 1_weight: 0.1623 0.1759 0.081 5.373 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1213 0.1461 0.007 0.940 9.0 119.5 20.1 258 0.128 1_adp: 0.1239 0.1531 0.007 0.940 8.5 118.1 20.8 258 0.128 1_regHadp: 0.1243 0.1535 0.007 0.940 8.5 118.1 20.8 258 0.128 1_occ: 0.1241 0.1538 0.007 0.940 8.5 118.1 20.8 258 0.128 2_bss: 0.1239 0.1532 0.007 0.940 8.7 118.3 21.0 258 0.128 2_settarget: 0.1239 0.1532 0.007 0.940 8.7 118.3 21.0 258 0.128 2_updatecdl: 0.1239 0.1532 0.007 0.943 8.7 118.3 21.0 258 0.128 2_nqh: 0.1241 0.1534 0.007 0.943 8.7 118.3 21.0 258 0.131 2_sol: 0.1227 0.1491 0.007 0.943 8.7 118.3 23.4 431 n/a 2_weight: 0.1227 0.1491 0.007 0.943 8.7 118.3 23.4 431 n/a 2_xyzrec: 0.1223 0.1501 0.007 0.872 8.7 118.3 23.4 431 n/a 2_adp: 0.1200 0.1483 0.007 0.872 8.7 114.2 23.1 431 n/a 2_regHadp: 0.1200 0.1483 0.007 0.872 8.7 114.2 23.1 431 n/a 2_occ: 0.1202 0.1479 0.007 0.872 8.7 114.2 23.1 431 n/a 3_bss: 0.1195 0.1480 0.007 0.872 8.7 114.2 23.2 431 n/a 3_settarget: 0.1195 0.1480 0.007 0.872 8.7 114.2 23.2 431 n/a 3_updatecdl: 0.1195 0.1480 0.007 0.873 8.7 114.2 23.2 431 n/a 3_nqh: 0.1195 0.1480 0.007 0.873 8.7 114.2 23.2 431 n/a 3_sol: 0.1221 0.1488 0.007 0.873 8.7 114.2 22.0 454 n/a 3_weight: 0.1221 0.1488 0.007 0.873 8.7 114.2 22.0 454 n/a 3_xyzrec: 0.1226 0.1455 0.005 0.913 8.7 114.2 22.0 454 n/a 3_adp: 0.1210 0.1408 0.005 0.913 9.2 109.6 21.7 454 n/a 3_regHadp: 0.1211 0.1409 0.005 0.913 9.2 109.6 21.7 454 n/a 3_occ: 0.1209 0.1413 0.005 0.913 9.2 109.6 21.7 454 n/a 4_bss: 0.1193 0.1379 0.005 0.913 9.2 109.6 21.7 454 n/a 4_settarget: 0.1193 0.1379 0.005 0.913 9.2 109.6 21.7 454 n/a 4_updatecdl: 0.1193 0.1379 0.005 0.911 9.2 109.6 21.7 454 n/a 4_nqh: 0.1193 0.1379 0.005 0.911 9.2 109.6 21.7 454 n/a 4_sol: 0.1188 0.1347 0.005 0.911 9.2 109.6 21.5 449 n/a 4_weight: 0.1188 0.1347 0.005 0.911 9.2 109.6 21.5 449 n/a 4_xyzrec: 0.1189 0.1367 0.006 0.975 9.2 109.6 21.5 449 n/a 4_adp: 0.1176 0.1353 0.006 0.975 9.3 104.7 21.3 449 n/a 4_regHadp: 0.1177 0.1353 0.006 0.975 9.3 104.7 21.3 449 n/a 4_occ: 0.1174 0.1352 0.006 0.975 9.3 104.7 21.3 449 n/a 5_bss: 0.1170 0.1355 0.006 0.975 9.3 104.7 21.3 449 n/a 5_settarget: 0.1170 0.1355 0.006 0.975 9.3 104.7 21.3 449 n/a 5_updatecdl: 0.1170 0.1355 0.006 0.977 9.3 104.7 21.3 449 n/a 5_setrh: 0.1171 0.1355 0.006 0.977 9.3 104.7 21.3 449 n/a 5_nqh: 0.1171 0.1355 0.006 0.977 9.3 104.7 21.3 449 n/a 5_sol: 0.1167 0.1329 0.006 0.977 9.3 104.7 21.2 453 n/a 5_weight: 0.1167 0.1329 0.006 0.977 9.3 104.7 21.2 453 n/a 5_xyzrec: 0.1198 0.1366 0.007 1.033 9.3 104.7 21.2 453 n/a 5_adp: 0.1201 0.1366 0.007 1.033 9.3 100.5 21.1 453 n/a 5_regHadp: 0.1201 0.1366 0.007 1.033 9.3 100.5 21.1 453 n/a 5_occ: 0.1196 0.1366 0.007 1.033 9.3 100.5 21.1 453 n/a end: 0.1197 0.1368 0.007 1.033 9.2 100.5 21.1 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2226169_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2226169_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.5000 Refinement macro-cycles (run) : 3358.7800 Write final files (write_after_run_outputs) : 73.3400 Total : 3437.6200 Total CPU time: 57.89 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:09:36 PST -0800 (1735452576.05 s) Start R-work = 0.1623, R-free = 0.1756 Final R-work = 0.1197, R-free = 0.1368 =============================================================================== Job complete usr+sys time: 3588.81 seconds wall clock time: 65 minutes 3.75 seconds (3903.75 seconds total)