Starting phenix.refine on Sat Dec 28 21:06:35 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7798058.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7798058.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7798058.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 2.37, per 1000 atoms: 0.70 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 189.6 milliseconds Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.92: 590 0.92 - 1.21: 1105 1.21 - 1.49: 885 1.49 - 1.78: 562 1.78 - 2.06: 11 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 186 " pdb=" N LEU A 187 " ideal model delta sigma weight residual 1.330 1.069 0.262 1.38e-02 5.25e+03 3.59e+02 bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.235 1.417 -0.182 1.02e-02 9.61e+03 3.20e+02 bond pdb=" CA LYS A 182 " pdb=" C LYS A 182 " ideal model delta sigma weight residual 1.523 1.283 0.240 1.35e-02 5.49e+03 3.16e+02 bond pdb=" C ILE A 9 " pdb=" O ILE A 9 " ideal model delta sigma weight residual 1.236 1.043 0.193 1.09e-02 8.42e+03 3.13e+02 bond pdb=" N SER A 155 " pdb=" CA SER A 155 " ideal model delta sigma weight residual 1.457 1.668 -0.211 1.20e-02 6.94e+03 3.09e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 2906 4.17 - 8.33: 1891 8.33 - 12.49: 756 12.49 - 16.65: 197 16.65 - 20.81: 27 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 136.07 -13.40 1.02e+00 9.61e-01 1.73e+02 angle pdb=" O ALA A 114 " pdb=" C ALA A 114 " pdb=" N HIS A 115 " ideal model delta sigma weight residual 122.12 135.44 -13.32 1.06e+00 8.90e-01 1.58e+02 angle pdb=" CA AGLN A 80 " pdb=" C AGLN A 80 " pdb=" N ASN A 81 " ideal model delta sigma weight residual 117.39 102.01 15.38 1.24e+00 6.50e-01 1.54e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 109.34 12.16 1.00e+00 1.00e+00 1.48e+02 angle pdb=" O ALYS A 99 " pdb=" C ALYS A 99 " pdb=" N GLY A 100 " ideal model delta sigma weight residual 122.59 138.13 -15.54 1.33e+00 5.65e-01 1.37e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 927 16.49 - 32.99: 130 32.99 - 49.48: 36 49.48 - 65.97: 16 65.97 - 82.46: 2 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 180.00 155.97 24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA TYR A 139 " pdb=" C TYR A 139 " pdb=" N THR A 140 " pdb=" CA THR A 140 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta harmonic sigma weight residual 180.00 160.76 19.24 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.194: 104 0.194 - 0.384: 58 0.384 - 0.574: 37 0.574 - 0.764: 37 0.764 - 0.954: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.40 -0.95 2.00e-01 2.50e+01 2.28e+01 chirality pdb=" CG LEU A 72 " pdb=" CB LEU A 72 " pdb=" CD1 LEU A 72 " pdb=" CD2 LEU A 72 " both_signs ideal model delta sigma weight residual False -2.59 -1.68 -0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.39 -0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.037 2.00e-02 2.50e+03 6.63e-02 1.32e+02 pdb=" CG PHE A 162 " 0.111 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.063 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.109 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.075 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.046 2.00e-02 2.50e+03 6.51e-02 1.27e+02 pdb=" CG TYR A 139 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.057 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.090 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.087 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.104 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.075 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.024 2.00e-02 2.50e+03 6.37e-02 1.22e+02 pdb=" CG TYR A 141 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.097 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.080 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.118 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.033 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.103 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.004 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.32: 1068 2.32 - 2.89: 8155 2.89 - 3.46: 10516 3.46 - 4.03: 15147 4.03 - 4.60: 21742 Nonbonded interactions: 56628 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.756 2.100 nonbonded pdb=" HD2 LYS A 32 " pdb=" HZ2 LYS A 32 " model vdw 1.796 2.270 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.818 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.826 2.450 nonbonded pdb=" O ALA A 6 " pdb=" H THR A 34 " model vdw 1.830 2.450 ... (remaining 56623 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_7798058_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= 0.2603 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.781375 | | target function (ml) not normalized (work): 231705.259508 | | target function (ml) not normalized (free): 11816.983228 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2115 7.0178 4.956| | 2: 3.57 - 2.84 1.00 2876 122 0.2442 0.1788 4.3525 4.3468| | 3: 2.84 - 2.48 1.00 2833 165 0.2334 0.1599 4.131 4.159| | 4: 2.47 - 2.25 1.00 2825 136 0.2352 0.1485 3.839 3.8298| | 5: 2.25 - 2.09 1.00 2756 127 0.2473 0.1519 3.8057 3.8205| | 6: 2.09 - 1.97 1.00 2846 113 0.2543 0.1690 3.4502 3.5376| | 7: 1.97 - 1.87 1.00 2787 165 0.2560 0.1718 3.1262 3.1709| | 8: 1.87 - 1.79 1.00 2789 144 0.2453 0.1747 3.0349 3.096| | 9: 1.79 - 1.72 1.00 2745 138 0.2428 0.1825 2.8812 2.9387| | 10: 1.72 - 1.66 1.00 2789 158 0.2435 0.2006 2.7955 2.8858| | 11: 1.66 - 1.61 1.00 2740 147 0.2483 0.1865 2.7336 2.7597| | 12: 1.61 - 1.56 1.00 2787 146 0.2516 0.2122 2.6354 2.7387| | 13: 1.56 - 1.52 1.00 2745 130 0.2540 0.1847 2.5587 2.6164| | 14: 1.52 - 1.48 1.00 2803 134 0.2599 0.1782 2.4888 2.4966| | 15: 1.48 - 1.45 1.00 2738 128 0.2531 0.2090 2.4098 2.4656| | 16: 1.45 - 1.42 1.00 2756 161 0.2621 0.2187 2.3755 2.4786| | 17: 1.42 - 1.39 1.00 2785 139 0.2671 0.2044 2.3323 2.3652| | 18: 1.39 - 1.36 1.00 2741 179 0.2685 0.2357 2.2697 2.3617| | 19: 1.36 - 1.34 1.00 2807 134 0.2660 0.2449 2.2361 2.3653| | 20: 1.34 - 1.32 1.00 2696 147 0.2653 0.2284 2.1894 2.2046| | 21: 1.32 - 1.30 1.00 2785 112 0.2652 0.2195 2.1392 2.184| | 22: 1.29 - 1.27 1.00 2704 152 0.2720 0.2651 2.1098 2.2435| | 23: 1.27 - 1.26 1.00 2802 156 0.2761 0.2561 2.1022 2.2087| | 24: 1.26 - 1.24 1.00 2744 132 0.2792 0.2497 2.0692 2.1653| | 25: 1.24 - 1.22 1.00 2734 148 0.2833 0.2699 2.0398 2.0754| | 26: 1.22 - 1.21 1.00 2727 135 0.2777 0.2220 1.9923 2.0484| | 27: 1.21 - 1.19 1.00 2814 148 0.2920 0.2326 1.9913 1.909| | 28: 1.19 - 1.18 1.00 2671 147 0.2949 0.2810 1.983 2.0056| | 29: 1.18 - 1.16 1.00 2800 134 0.2938 0.2729 1.9567 2.0088| | 30: 1.16 - 1.15 1.00 2740 148 0.3108 0.2633 1.9395 1.9125| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.07 0.76 0.23 1514.80| | 2: 3.57 - 2.84 2876 122 0.80 26.35 1.27 0.23 1514.80| | 3: 2.84 - 2.48 2833 165 0.74 32.33 1.24 0.24 1254.39| | 4: 2.47 - 2.25 2825 136 0.81 25.67 1.26 0.25 578.58| | 5: 2.25 - 2.09 2756 127 0.77 29.43 1.28 0.25 578.58| | 6: 2.09 - 1.97 2846 113 0.83 22.66 1.29 0.25 313.61| | 7: 1.97 - 1.87 2787 165 0.90 16.20 1.29 0.26 87.63| | 8: 1.87 - 1.79 2789 144 0.86 20.71 1.25 0.26 87.63| | 9: 1.79 - 1.72 2745 138 0.88 18.45 1.24 0.25 53.54| | 10: 1.72 - 1.66 2789 158 0.87 19.76 1.23 0.25 46.71| | 11: 1.66 - 1.61 2740 147 0.86 21.27 1.24 0.25 45.18| | 12: 1.61 - 1.56 2787 146 0.88 18.73 1.23 0.25 29.66| | 13: 1.56 - 1.52 2745 130 0.86 20.56 1.24 0.25 29.66| | 14: 1.52 - 1.48 2803 134 0.86 20.89 1.25 0.25 26.52| | 15: 1.48 - 1.45 2738 128 0.87 20.20 1.22 0.25 20.78| | 16: 1.45 - 1.42 2756 161 0.86 21.48 1.23 0.25 20.78| | 17: 1.42 - 1.39 2785 139 0.86 21.29 1.23 0.25 17.80| | 18: 1.39 - 1.36 2741 179 0.86 21.46 1.23 0.25 16.07| | 19: 1.36 - 1.34 2807 134 0.85 22.39 1.22 0.25 16.07| | 20: 1.34 - 1.32 2696 147 0.87 21.10 1.21 0.24 13.28| | 21: 1.32 - 1.30 2785 112 0.85 22.57 1.20 0.24 13.08| | 22: 1.29 - 1.27 2704 152 0.85 22.88 1.22 0.24 12.76| | 23: 1.27 - 1.26 2802 156 0.85 22.42 1.21 0.24 11.16| | 24: 1.26 - 1.24 2744 132 0.85 23.05 1.21 0.24 11.16| | 25: 1.24 - 1.22 2734 148 0.84 23.62 1.20 0.24 10.49| | 26: 1.22 - 1.21 2727 135 0.84 23.58 1.20 0.23 9.74| | 27: 1.21 - 1.19 2814 148 0.83 24.52 1.20 0.23 9.74| | 28: 1.19 - 1.18 2671 147 0.84 24.41 1.18 0.23 8.97| | 29: 1.18 - 1.16 2800 134 0.84 24.66 1.17 0.23 8.68| | 30: 1.16 - 1.15 2740 148 0.82 26.35 1.16 0.23 8.68| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.68 max = 1514.80 mean = 218.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.60| |phase err.(test): min = 0.00 max = 89.94 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 : 0.081 0.262 1557 Z= 5.405 Angle : 5.160 17.447 2118 Z= 3.572 Chirality : 0.380 0.954 243 Planarity : 0.030 0.097 284 Dihedral : 13.674 82.465 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 24.86 % 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: -2.66 (0.47), residues: 224 helix: -2.44 (0.36), residues: 108 sheet: -1.19 (0.71), residues: 38 loop : -0.58 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.101 0.025 ARG A 98 TYR 0.098 0.044 TYR A 141 PHE 0.121 0.043 PHE A 162 HIS 0.060 0.029 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= 0.2603 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.781375 | | target function (ml) not normalized (work): 231705.259508 | | target function (ml) not normalized (free): 11816.983228 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2561 0.2604 0.1927 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2561 0.2604 0.1927 n_refl.: 87602 remove outliers: r(all,work,free)=0.1971 0.1975 0.1927 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.1998 0.2003 0.1939 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1633 0.1627 0.1759 n_refl.: 87594 remove outliers: r(all,work,free)=0.1633 0.1626 0.1759 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 0.3893 386.331 357.759 0.739 0.911 0.407 11.894-9.307 99.02 97 4 0.1865 613.668 595.718 1.023 0.912 0.390 9.237-7.194 100.00 213 7 0.2131 501.905 491.090 1.043 0.913 0.354 7.162-5.571 100.00 427 22 0.2213 376.652 365.906 1.016 0.913 0.330 5.546-4.326 100.00 867 58 0.1298 517.050 509.693 1.055 0.914 0.224 4.315-3.360 100.00 1859 96 0.1125 491.718 488.109 1.100 0.915 0.199 3.356-2.611 100.00 3867 181 0.1416 323.033 319.536 1.087 0.917 0.099 2.608-2.026 99.99 8198 413 0.1370 214.142 211.703 1.093 0.920 0.000 2.025-1.573 100.00 17313 902 0.1628 104.576 103.862 1.094 0.925 0.000 1.573-1.221 100.00 36679 1900 0.2038 46.373 45.087 1.071 0.934 0.000 1.221-1.150 99.97 13689 708 0.2574 29.218 27.005 1.030 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0502 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1626 r_free=0.1759 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1626 r_free=0.1759 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.212563 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2026.074101 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 0.1210 0.1458 0.0248 0.007 0.9 1.3 0.5 0.0 0 12.106 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 14.58 2.48 3.013 19.078 2026.074 0.017 12.34 15.25 2.90 3.091 19.505 2026.074 0.016 Individual atomic B min max mean iso aniso Overall: 8.51 118.35 20.91 2.87 0 1785 Protein: 8.51 118.35 17.81 2.88 0 1519 Water: 11.08 114.85 38.94 N/A 0 258 Other: 22.36 35.44 28.41 N/A 0 8 Chain A: 8.51 118.35 20.91 N/A 0 1785 Histogram: Values Number of atoms 8.51 - 19.50 1210 19.50 - 30.48 229 30.48 - 41.46 168 41.46 - 52.45 96 52.45 - 63.43 53 63.43 - 74.41 18 74.41 - 85.40 4 85.40 - 96.38 4 96.38 - 107.36 0 107.36 - 118.35 3 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1525 r_work=0.1239 r_free=0.1527 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1527 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 = 0.1239 r_free = 0.1532 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 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= 0.1239 r_free= 0.1532 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015401 | | target function (ls_wunit_k1) not normalized (work): 1282.880269 | | target function (ls_wunit_k1) not normalized (free): 112.152756 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1253 0.1239 0.1532 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1698 0.1697 0.1763 n_refl.: 87593 remove outliers: r(all,work,free)=0.1698 0.1697 0.1763 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1719 0.1718 0.1777 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1251 0.1237 0.1525 n_refl.: 87593 remove outliers: r(all,work,free)=0.1251 0.1237 0.1525 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 0.3608 298.454 277.824 0.690 0.924 0.380 11.894-9.307 99.02 97 4 0.1633 478.107 466.546 0.987 0.924 0.380 9.237-7.194 100.00 213 7 0.1825 391.033 386.334 1.028 0.925 0.319 7.162-5.571 100.00 427 22 0.1738 293.448 287.962 0.997 0.925 0.300 5.546-4.326 100.00 867 58 0.0932 402.832 400.156 1.029 0.926 0.209 4.315-3.360 100.00 1859 96 0.0780 383.096 382.104 1.076 0.927 0.200 3.356-2.611 100.00 3867 181 0.1023 251.674 250.978 1.076 0.930 0.052 2.608-2.026 99.99 8198 413 0.0972 166.837 166.285 1.083 0.933 0.000 2.025-1.573 100.00 17313 902 0.1195 81.475 81.674 1.085 0.939 0.000 1.573-1.221 100.00 36679 1900 0.1629 36.129 35.597 1.059 0.948 0.000 1.221-1.150 99.97 13689 708 0.2351 22.764 21.292 1.014 0.955 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0486 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1237 r_free=0.1525 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=0.1238 r_free=0.1528 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1238 r_free=0.1528 | n_water=258 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1248 r_free=0.1526 | n_water=252 | time (s): 26.510 (total time: 29.020) Filter (q & B) r_work=0.1250 r_free=0.1525 | n_water=249 | time (s): 3.810 (total time: 32.830) Compute maps r_work=0.1250 r_free=0.1525 | n_water=249 | time (s): 1.910 (total time: 34.740) Filter (map) r_work=0.1269 r_free=0.1533 | n_water=235 | time (s): 3.920 (total time: 38.660) Find peaks r_work=0.1269 r_free=0.1533 | n_water=235 | time (s): 0.720 (total time: 39.380) Add new water r_work=0.1426 r_free=0.1695 | n_water=454 | time (s): 3.760 (total time: 43.140) Refine new water occ: r_work=0.1336 r_free=0.1550 adp: r_work=0.1252 r_free=0.1507 occ: r_work=0.1266 r_free=0.1486 adp: r_work=0.1229 r_free=0.1481 occ: r_work=0.1231 r_free=0.1463 adp: r_work=0.1221 r_free=0.1464 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1464 r_work=0.1221 r_free=0.1464 | n_water=454 | time (s): 82.870 (total time: 126.010) Filter (q & B) r_work=0.1226 r_free=0.1469 | n_water=433 | time (s): 4.150 (total time: 130.160) Filter (dist only) r_work=0.1226 r_free=0.1469 | n_water=433 | time (s): 41.330 (total time: 171.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.654307 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1523.110782 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 0.1502 0.0278 0.007 0.9 2.6 0.5 0.0 0 12.327 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.24 15.02 2.78 3.772 23.130 1523.111 0.015 11.98 14.81 2.83 4.156 22.985 1523.111 0.015 Individual atomic B min max mean iso aniso Overall: 8.81 113.67 23.23 2.59 198 1762 Protein: 8.81 113.67 17.62 2.59 0 1519 Water: 10.96 73.31 42.79 N/A 198 235 Other: 25.74 37.47 31.08 N/A 0 8 Chain A: 8.81 113.67 20.32 N/A 0 1762 Chain S: 16.57 72.74 49.21 N/A 198 0 Histogram: Values Number of atoms 8.81 - 19.29 1209 19.29 - 29.78 244 29.78 - 40.27 188 40.27 - 50.75 145 50.75 - 61.24 106 61.24 - 71.72 56 71.72 - 82.21 6 82.21 - 92.70 3 92.70 - 103.18 1 103.18 - 113.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1481 r_work=0.1198 r_free=0.1481 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1481 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 = 0.1200 r_free = 0.1473 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 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= 0.1200 r_free= 0.1473 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014019 | | target function (ls_wunit_k1) not normalized (work): 1167.692772 | | target function (ls_wunit_k1) not normalized (free): 101.003109 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1200 0.1473 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1614 0.1611 0.1721 n_refl.: 87592 remove outliers: r(all,work,free)=0.1614 0.1611 0.1721 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1619 0.1616 0.1724 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1198 0.1469 n_refl.: 87592 remove outliers: r(all,work,free)=0.1209 0.1196 0.1469 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 0.3323 291.163 269.045 0.581 1.003 0.350 11.894-9.307 99.02 97 4 0.1537 478.107 475.501 0.921 1.003 0.333 9.237-7.194 100.00 213 7 0.1623 391.033 391.945 0.982 1.003 0.270 7.162-5.571 100.00 427 22 0.1467 293.448 290.080 0.941 1.003 0.260 5.546-4.326 100.00 867 58 0.0843 402.832 400.307 0.958 1.003 0.210 4.315-3.360 100.00 1859 96 0.0719 383.096 381.961 1.001 1.003 0.210 3.356-2.611 100.00 3867 181 0.0959 251.674 251.001 1.010 1.002 0.072 2.608-2.026 99.99 8198 413 0.0967 166.837 166.430 1.018 1.002 0.000 2.025-1.573 100.00 17313 902 0.1173 81.475 81.681 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1608 36.129 35.635 1.018 0.998 0.000 1.221-1.150 99.97 13689 708 0.2334 22.764 21.291 0.978 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0494 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1469 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=0.1196 r_free=0.1471 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1471 | n_water=433 | time (s): 1.900 (total time: 1.900) Filter (dist) r_work=0.1196 r_free=0.1472 | n_water=430 | time (s): 34.620 (total time: 36.520) Filter (q & B) r_work=0.1196 r_free=0.1472 | n_water=430 | time (s): 1.330 (total time: 37.850) Compute maps r_work=0.1196 r_free=0.1472 | n_water=430 | time (s): 1.170 (total time: 39.020) Filter (map) r_work=0.1244 r_free=0.1469 | n_water=285 | time (s): 2.880 (total time: 41.900) Find peaks r_work=0.1244 r_free=0.1469 | n_water=285 | time (s): 0.460 (total time: 42.360) Add new water r_work=0.1373 r_free=0.1592 | n_water=482 | time (s): 2.670 (total time: 45.030) Refine new water occ: r_work=0.1268 r_free=0.1495 adp: r_work=0.1269 r_free=0.1497 occ: r_work=0.1246 r_free=0.1471 adp: r_work=0.1242 r_free=0.1473 occ: r_work=0.1231 r_free=0.1454 adp: r_work=0.1223 r_free=0.1452 ADP+occupancy (water only), MIN, final r_work=0.1223 r_free=0.1452 r_work=0.1223 r_free=0.1452 | n_water=482 | time (s): 205.640 (total time: 250.670) Filter (q & B) r_work=0.1227 r_free=0.1458 | n_water=448 | time (s): 3.250 (total time: 253.920) Filter (dist only) r_work=0.1227 r_free=0.1456 | n_water=447 | time (s): 36.730 (total time: 290.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.013507 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.193263 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1445 0.0216 0.006 0.9 1.6 0.5 0.0 0 1.007 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.45 2.16 3.603 22.073 49.193 3.718 12.11 13.98 1.87 4.137 21.882 49.193 3.648 Individual atomic B min max mean iso aniso Overall: 9.27 109.39 21.65 2.30 217 1757 Protein: 9.27 109.39 17.16 2.30 0 1519 Water: 11.48 71.95 36.83 N/A 217 230 Other: 21.17 33.36 27.31 N/A 0 8 Chain A: 9.27 109.39 19.76 N/A 0 1757 Chain S: 15.15 63.86 36.96 N/A 217 0 Histogram: Values Number of atoms 9.27 - 19.28 1238 19.28 - 29.29 271 29.29 - 39.31 227 39.31 - 49.32 128 49.32 - 59.33 77 59.33 - 69.34 20 69.34 - 79.36 7 79.36 - 89.37 3 89.37 - 99.38 1 99.38 - 109.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1399 r_work=0.1212 r_free=0.1399 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1212 r_free = 0.1399 target_work(ml) = 3.648 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1396 target_work(ml) = 3.646 | | 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= 0.1204 r_free= 0.1396 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.645836 | | target function (ml) not normalized (work): 303668.935840 | | target function (ml) not normalized (free): 16033.725726 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1204 0.1396 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1537 0.1536 0.1589 n_refl.: 87588 remove outliers: r(all,work,free)=0.1537 0.1536 0.1589 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1534 0.1533 0.1588 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1195 0.1376 n_refl.: 87588 remove outliers: r(all,work,free)=0.1200 0.1191 0.1376 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3874 290.409 251.542 0.467 1.000 0.323 11.894-9.307 97.06 95 4 0.2439 471.506 456.824 0.852 1.002 0.247 9.237-7.194 98.64 210 7 0.2291 383.588 384.690 0.944 1.002 0.180 7.162-5.571 100.00 427 22 0.2077 293.448 283.154 0.907 1.002 0.164 5.546-4.326 100.00 867 58 0.1098 402.832 398.234 0.950 1.002 0.156 4.315-3.360 100.00 1859 96 0.0939 383.096 380.498 0.992 1.002 0.150 3.356-2.611 100.00 3867 181 0.1137 251.674 249.827 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1029 166.837 165.885 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1006 81.475 81.647 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1292 36.129 35.710 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2136 22.764 21.373 0.979 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0327 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1376 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1191 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1376 | n_water=447 | time (s): 1.690 (total time: 1.690) Filter (dist) r_work=0.1191 r_free=0.1374 | n_water=446 | time (s): 40.090 (total time: 41.780) Filter (q & B) r_work=0.1190 r_free=0.1373 | n_water=445 | time (s): 3.850 (total time: 45.630) Compute maps r_work=0.1190 r_free=0.1373 | n_water=445 | time (s): 1.600 (total time: 47.230) Filter (map) r_work=0.1217 r_free=0.1383 | n_water=309 | time (s): 2.610 (total time: 49.840) Find peaks r_work=0.1217 r_free=0.1383 | n_water=309 | time (s): 0.510 (total time: 50.350) Add new water r_work=0.1284 r_free=0.1455 | n_water=474 | time (s): 3.200 (total time: 53.550) Refine new water occ: r_work=0.1210 r_free=0.1381 adp: r_work=0.1211 r_free=0.1383 occ: r_work=0.1195 r_free=0.1368 adp: r_work=0.1193 r_free=0.1368 occ: r_work=0.1184 r_free=0.1364 adp: r_work=0.1180 r_free=0.1361 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1361 r_work=0.1180 r_free=0.1361 | n_water=474 | time (s): 154.790 (total time: 208.340) Filter (q & B) r_work=0.1188 r_free=0.1370 | n_water=436 | time (s): 2.710 (total time: 211.050) Filter (dist only) r_work=0.1188 r_free=0.1370 | n_water=435 | time (s): 39.100 (total time: 250.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.956843 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.119138 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1371 0.0181 0.006 1.0 1.6 0.5 0.0 0 0.978 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.71 1.81 3.400 21.370 39.119 3.635 11.93 13.71 1.78 3.674 21.282 39.119 3.625 Individual atomic B min max mean iso aniso Overall: 9.30 105.38 21.15 2.12 207 1755 Protein: 9.30 105.38 16.95 2.12 0 1519 Water: 11.67 71.08 35.70 N/A 207 228 Other: 20.50 30.54 25.92 N/A 0 8 Chain A: 9.30 105.38 19.49 N/A 0 1755 Chain S: 15.57 61.19 35.20 N/A 207 0 Histogram: Values Number of atoms 9.30 - 18.91 1231 18.91 - 28.52 279 28.52 - 38.13 207 38.13 - 47.73 144 47.73 - 57.34 63 57.34 - 66.95 26 66.95 - 76.55 7 76.55 - 86.16 2 86.16 - 95.77 1 95.77 - 105.38 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1371 r_work=0.1194 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1371 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1369 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1189 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623967 | | target function (ml) not normalized (work): 301818.466099 | | target function (ml) not normalized (free): 15947.461515 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1189 0.1369 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1521 0.1520 0.1573 n_refl.: 87580 remove outliers: r(all,work,free)=0.1521 0.1520 0.1573 n_refl.: 87580 overall B=-0.02 to atoms: r(all,work,free)=0.1517 0.1516 0.1571 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1189 0.1368 n_refl.: 87580 remove outliers: r(all,work,free)=0.1194 0.1186 0.1368 n_refl.: 87573 ======================== 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 0.3992 285.684 254.846 0.444 0.999 0.293 11.894-9.307 94.12 92 4 0.2428 477.400 448.923 0.829 1.001 0.233 9.237-7.194 97.27 207 7 0.2445 384.205 374.804 0.913 1.001 0.174 7.162-5.571 100.00 427 22 0.2179 293.448 282.908 0.901 1.002 0.160 5.546-4.326 100.00 867 58 0.1144 402.832 398.623 0.952 1.002 0.135 4.315-3.360 100.00 1859 96 0.0945 383.096 380.871 0.994 1.002 0.130 3.356-2.611 100.00 3867 181 0.1154 251.674 249.825 1.001 1.002 0.110 2.608-2.026 99.99 8198 413 0.1035 166.837 166.013 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0978 81.475 81.778 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.129 35.778 1.024 0.998 0.000 1.221-1.150 99.97 13689 708 0.2122 22.764 21.404 0.982 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0554 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1186 r_free=0.1368 After: r_work=0.1186 r_free=0.1368 ================================== NQH flips ================================== r_work=0.1186 r_free=0.1368 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=0.1186 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1368 | n_water=435 | time (s): 1.740 (total time: 1.740) Filter (dist) r_work=0.1186 r_free=0.1368 | n_water=435 | time (s): 32.980 (total time: 34.720) Filter (q & B) r_work=0.1186 r_free=0.1368 | n_water=435 | time (s): 1.180 (total time: 35.900) Compute maps r_work=0.1186 r_free=0.1368 | n_water=435 | time (s): 1.310 (total time: 37.210) Filter (map) r_work=0.1208 r_free=0.1375 | n_water=332 | time (s): 3.280 (total time: 40.490) Find peaks r_work=0.1208 r_free=0.1375 | n_water=332 | time (s): 0.580 (total time: 41.070) Add new water r_work=0.1258 r_free=0.1414 | n_water=481 | time (s): 3.480 (total time: 44.550) Refine new water occ: r_work=0.1200 r_free=0.1360 adp: r_work=0.1200 r_free=0.1362 occ: r_work=0.1188 r_free=0.1351 adp: r_work=0.1187 r_free=0.1352 occ: r_work=0.1180 r_free=0.1347 adp: r_work=0.1176 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1176 r_free=0.1346 r_work=0.1176 r_free=0.1346 | n_water=481 | time (s): 157.020 (total time: 201.570) Filter (q & B) r_work=0.1184 r_free=0.1354 | n_water=446 | time (s): 2.630 (total time: 204.200) Filter (dist only) r_work=0.1184 r_free=0.1353 | n_water=445 | time (s): 38.230 (total time: 242.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.830926 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 34.150511 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 0.1203 0.1369 0.0166 0.008 1.0 3.5 0.5 0.0 0 0.915 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.69 1.66 3.279 21.152 34.151 3.630 12.03 13.69 1.66 3.483 21.081 34.151 3.627 Individual atomic B min max mean iso aniso Overall: 9.28 101.37 21.04 1.98 219 1753 Protein: 9.28 101.37 16.78 1.98 0 1519 Water: 11.52 70.46 35.51 N/A 219 226 Other: 20.57 29.29 25.31 N/A 0 8 Chain A: 9.28 101.37 19.26 N/A 0 1753 Chain S: 15.20 60.47 35.27 N/A 219 0 Histogram: Values Number of atoms 9.28 - 18.49 1223 18.49 - 27.70 281 27.70 - 36.91 205 36.91 - 46.12 148 46.12 - 55.33 73 55.33 - 64.54 27 64.54 - 73.75 11 73.75 - 82.96 1 82.96 - 92.17 1 92.17 - 101.37 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1369 r_work=0.1203 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1369 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1363 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87573 (all), 4.91 % free)------------| | | | r_work= 0.1198 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.624518 | | target function (ml) not normalized (work): 301838.964239 | | target function (ml) not normalized (free): 15932.468728 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2915 171 0.1382 0.1386 5.6496 5.5998| | 2: 3.57 - 2.84 1.00 2888 124 0.1117 0.1468 5.188 5.2754| | 3: 2.83 - 2.48 1.00 2820 163 0.1222 0.1262 4.9945 5.0094| | 4: 2.47 - 2.25 1.00 2825 136 0.1034 0.1152 4.7001 4.7552| | 5: 2.25 - 2.09 1.00 2756 127 0.0994 0.1055 4.6377 4.6969| | 6: 2.09 - 1.97 1.00 2846 113 0.0981 0.1205 4.3471 4.4691| | 7: 1.97 - 1.87 1.00 2787 165 0.1010 0.1220 4.0809 4.1777| | 8: 1.87 - 1.79 1.00 2789 144 0.1034 0.1235 3.9914 4.071| | 9: 1.79 - 1.72 1.00 2745 138 0.0979 0.1253 3.7264 3.8663| | 10: 1.72 - 1.66 1.00 2831 160 0.1014 0.1295 3.636 3.779| | 11: 1.66 - 1.61 1.00 2712 147 0.0979 0.1107 3.5727 3.6202| | 12: 1.61 - 1.56 1.00 2773 144 0.0936 0.1167 3.3614 3.4827| | 13: 1.56 - 1.52 1.00 2745 130 0.0992 0.1095 3.349 3.4397| | 14: 1.52 - 1.48 1.00 2803 134 0.1012 0.1134 3.2739 3.3352| | 15: 1.48 - 1.45 1.00 2738 128 0.1034 0.1387 3.1829 3.3474| | 16: 1.45 - 1.42 1.00 2756 161 0.1084 0.1301 3.1644 3.2554| | 17: 1.42 - 1.39 1.00 2785 139 0.1139 0.1319 3.128 3.249| | 18: 1.39 - 1.36 1.00 2741 179 0.1178 0.1378 3.0982 3.2566| | 19: 1.36 - 1.34 1.00 2807 134 0.1233 0.1609 3.103 3.2772| | 20: 1.34 - 1.32 1.00 2696 147 0.1337 0.1480 3.0976 3.1433| | 21: 1.32 - 1.30 1.00 2785 112 0.1434 0.1618 3.0949 3.1686| | 22: 1.29 - 1.27 1.00 2704 152 0.1490 0.1933 3.0914 3.2898| | 23: 1.27 - 1.26 1.00 2802 156 0.1588 0.1880 3.107 3.2175| | 24: 1.26 - 1.24 1.00 2744 132 0.1644 0.1785 3.0994 3.1991| | 25: 1.24 - 1.22 1.00 2733 148 0.1813 0.2315 3.1142 3.2817| | 26: 1.22 - 1.21 1.00 2727 135 0.1867 0.1772 3.1257 3.1934| | 27: 1.21 - 1.19 1.00 2814 148 0.2019 0.2093 3.1424 3.1465| | 28: 1.19 - 1.18 1.00 2671 147 0.2157 0.2286 3.1432 3.1562| | 29: 1.18 - 1.16 1.00 2800 134 0.2229 0.2372 3.1289 3.2302| | 30: 1.16 - 1.15 1.00 2739 148 0.2380 0.2468 3.1178 3.1604| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2915 171 0.95 8.79 1.00 0.97 5995.86| | 2: 3.57 - 2.84 2888 124 0.92 12.98 1.01 0.97 5995.86| | 3: 2.83 - 2.48 2820 163 0.89 17.09 0.98 0.97 5031.65| | 4: 2.47 - 2.25 2825 136 0.91 14.32 1.00 0.98 2545.23| | 5: 2.25 - 2.09 2756 127 0.90 16.50 1.01 0.98 2545.23| | 6: 2.09 - 1.97 2846 113 0.92 13.48 1.02 0.97 1505.90| | 7: 1.97 - 1.87 2787 165 0.94 10.77 1.02 0.97 619.49| | 8: 1.87 - 1.79 2789 144 0.91 14.32 0.99 0.97 619.49| | 9: 1.79 - 1.72 2745 138 0.93 11.30 0.98 0.97 336.09| | 10: 1.72 - 1.66 2831 160 0.93 12.19 0.97 0.97 279.33| | 11: 1.66 - 1.61 2712 147 0.93 12.85 0.98 0.97 266.86| | 12: 1.61 - 1.56 2773 144 0.95 9.67 0.99 0.97 149.27| | 13: 1.56 - 1.52 2745 130 0.94 11.17 1.02 0.97 149.27| | 14: 1.52 - 1.48 2803 134 0.94 11.40 1.02 0.97 133.53| | 15: 1.48 - 1.45 2738 128 0.95 10.54 1.01 0.98 104.72| | 16: 1.45 - 1.42 2756 161 0.94 11.72 1.01 0.98 104.72| | 17: 1.42 - 1.39 2785 139 0.94 11.57 1.01 0.98 94.60| | 18: 1.39 - 1.36 2741 179 0.94 11.95 1.01 0.98 88.75| | 19: 1.36 - 1.34 2807 134 0.94 12.47 1.00 0.98 88.75| | 20: 1.34 - 1.32 2696 147 0.94 12.54 0.99 0.96 83.34| | 21: 1.32 - 1.30 2785 112 0.93 13.48 0.98 0.96 82.96| | 22: 1.29 - 1.27 2704 152 0.93 14.01 0.98 0.96 83.02| | 23: 1.27 - 1.26 2802 156 0.92 14.93 0.97 0.95 83.36| | 24: 1.26 - 1.24 2744 132 0.92 15.06 0.97 0.95 83.36| | 25: 1.24 - 1.22 2733 148 0.91 16.47 0.96 0.94 84.65| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.02 0.93 86.07| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.02 0.93 86.07| | 28: 1.19 - 1.18 2671 147 0.88 20.20 1.01 0.93 89.14| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.93 90.30| | 30: 1.16 - 1.15 2739 148 0.86 21.91 0.98 0.93 90.30| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.96 max = 5995.86 mean = 942.44| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 14.02| |phase err.(test): min = 0.00 max = 89.12 mean = 14.08| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1198 0.1363 n_refl.: 87573 re-set all scales: r(all,work,free)=0.1518 0.1517 0.1561 n_refl.: 87573 remove outliers: r(all,work,free)=0.1518 0.1517 0.1561 n_refl.: 87573 overall B=-0.02 to atoms: r(all,work,free)=0.1515 0.1514 0.1559 n_refl.: 87573 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1198 0.1365 n_refl.: 87573 remove outliers: r(all,work,free)=0.1207 0.1198 0.1365 n_refl.: 87573 ======================== 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 0.4135 285.684 251.323 0.437 1.000 0.298 11.894-9.307 94.12 92 4 0.2417 477.400 462.470 0.855 1.002 0.238 9.237-7.194 97.27 207 7 0.2465 384.205 375.980 0.915 1.002 0.171 7.162-5.571 100.00 427 22 0.2168 293.448 283.394 0.897 1.002 0.141 5.546-4.326 100.00 867 58 0.1151 402.832 398.662 0.952 1.002 0.125 4.315-3.360 100.00 1859 96 0.0982 383.096 380.378 0.995 1.002 0.120 3.356-2.611 100.00 3867 181 0.1180 251.674 249.556 1.001 1.002 0.100 2.608-2.026 99.99 8198 413 0.1043 166.837 165.892 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0992 81.475 81.725 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.129 35.754 1.024 0.996 0.000 1.221-1.150 99.97 13689 708 0.2124 22.764 21.387 0.984 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0456 ================= 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 : 0.2603 0.1926 0.081 5.160 8.8 119.3 19.9 258 0.000 1_bss: 0.1626 0.1759 0.081 5.160 9.1 119.5 20.1 258 0.000 1_settarget: 0.1626 0.1759 0.081 5.160 9.1 119.5 20.1 258 0.000 1_nqh: 0.1626 0.1759 0.081 5.160 9.1 119.5 20.1 258 0.000 1_weight: 0.1626 0.1759 0.081 5.160 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1210 0.1458 0.007 0.941 9.1 119.5 20.1 258 0.127 1_adp: 0.1235 0.1525 0.007 0.941 8.5 118.3 20.9 258 0.127 1_regHadp: 0.1239 0.1527 0.007 0.941 8.5 118.3 20.9 258 0.127 1_occ: 0.1239 0.1532 0.007 0.941 8.5 118.3 20.9 258 0.127 2_bss: 0.1237 0.1525 0.007 0.941 8.6 118.5 21.0 258 0.127 2_settarget: 0.1237 0.1525 0.007 0.941 8.6 118.5 21.0 258 0.127 2_updatecdl: 0.1237 0.1525 0.007 0.943 8.6 118.5 21.0 258 0.127 2_nqh: 0.1238 0.1528 0.007 0.943 8.6 118.5 21.0 258 0.130 2_sol: 0.1226 0.1469 0.007 0.943 8.6 118.5 23.5 433 n/a 2_weight: 0.1226 0.1469 0.007 0.943 8.6 118.5 23.5 433 n/a 2_xyzrec: 0.1224 0.1502 0.007 0.877 8.6 118.5 23.5 433 n/a 2_adp: 0.1198 0.1481 0.007 0.877 8.8 113.7 23.2 433 n/a 2_regHadp: 0.1198 0.1481 0.007 0.877 8.8 113.7 23.2 433 n/a 2_occ: 0.1200 0.1473 0.007 0.877 8.8 113.7 23.2 433 n/a 3_bss: 0.1196 0.1469 0.007 0.877 8.8 113.7 23.3 433 n/a 3_settarget: 0.1196 0.1469 0.007 0.877 8.8 113.7 23.3 433 n/a 3_updatecdl: 0.1196 0.1469 0.007 0.878 8.8 113.7 23.3 433 n/a 3_nqh: 0.1196 0.1471 0.007 0.878 8.8 113.7 23.3 433 n/a 3_sol: 0.1227 0.1456 0.007 0.878 8.8 113.7 22.0 447 n/a 3_weight: 0.1227 0.1456 0.007 0.878 8.8 113.7 22.0 447 n/a 3_xyzrec: 0.1229 0.1445 0.006 0.919 8.8 113.7 22.0 447 n/a 3_adp: 0.1211 0.1399 0.006 0.919 9.3 109.4 21.7 447 n/a 3_regHadp: 0.1212 0.1399 0.006 0.919 9.3 109.4 21.7 447 n/a 3_occ: 0.1204 0.1396 0.006 0.919 9.3 109.4 21.7 447 n/a 4_bss: 0.1191 0.1376 0.006 0.919 9.3 109.4 21.6 447 n/a 4_settarget: 0.1191 0.1376 0.006 0.919 9.3 109.4 21.6 447 n/a 4_updatecdl: 0.1191 0.1376 0.006 0.919 9.3 109.4 21.6 447 n/a 4_nqh: 0.1191 0.1376 0.006 0.919 9.3 109.4 21.6 447 n/a 4_sol: 0.1188 0.1370 0.006 0.919 9.3 109.4 21.3 435 n/a 4_weight: 0.1188 0.1370 0.006 0.919 9.3 109.4 21.3 435 n/a 4_xyzrec: 0.1190 0.1371 0.006 0.954 9.3 109.4 21.3 435 n/a 4_adp: 0.1193 0.1371 0.006 0.954 9.3 105.4 21.1 435 n/a 4_regHadp: 0.1194 0.1371 0.006 0.954 9.3 105.4 21.1 435 n/a 4_occ: 0.1189 0.1369 0.006 0.954 9.3 105.4 21.1 435 n/a 5_bss: 0.1186 0.1368 0.006 0.954 9.3 105.4 21.1 435 n/a 5_settarget: 0.1186 0.1368 0.006 0.954 9.3 105.4 21.1 435 n/a 5_updatecdl: 0.1186 0.1368 0.006 0.954 9.3 105.4 21.1 435 n/a 5_setrh: 0.1186 0.1368 0.006 0.954 9.3 105.4 21.1 435 n/a 5_nqh: 0.1186 0.1368 0.006 0.954 9.3 105.4 21.1 435 n/a 5_sol: 0.1184 0.1353 0.006 0.954 9.3 105.4 21.2 445 n/a 5_weight: 0.1184 0.1353 0.006 0.954 9.3 105.4 21.2 445 n/a 5_xyzrec: 0.1203 0.1369 0.008 1.033 9.3 105.4 21.2 445 n/a 5_adp: 0.1203 0.1369 0.008 1.033 9.3 101.4 21.0 445 n/a 5_regHadp: 0.1203 0.1369 0.008 1.033 9.3 101.4 21.0 445 n/a 5_occ: 0.1198 0.1363 0.008 1.033 9.3 101.4 21.0 445 n/a end: 0.1198 0.1365 0.008 1.033 9.3 101.4 21.0 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7798058_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7798058_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7900 Refinement macro-cycles (run) : 3452.4900 Write final files (write_after_run_outputs) : 73.2400 Total : 3530.5200 Total CPU time: 59.46 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:10:24 PST -0800 (1735452624.67 s) Start R-work = 0.1626, R-free = 0.1759 Final R-work = 0.1198, R-free = 0.1365 =============================================================================== Job complete usr+sys time: 3677.49 seconds wall clock time: 65 minutes 45.35 seconds (3945.35 seconds total)