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_1541177.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1541177.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1541177.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.26, per 1000 atoms: 0.67 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 221.1 milliseconds Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.92: 575 0.92 - 1.17: 1067 1.17 - 1.42: 625 1.42 - 1.66: 843 1.66 - 1.91: 43 Bond restraints: 3153 Sorted by residual: bond pdb=" N BGLN A 80 " pdb=" CA BGLN A 80 " ideal model delta sigma weight residual 1.459 1.694 -0.235 1.19e-02 7.06e+03 3.88e+02 bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.692 -0.233 1.19e-02 7.06e+03 3.82e+02 bond pdb=" CA ALA A 61 " pdb=" C ALA A 61 " ideal model delta sigma weight residual 1.523 1.284 0.239 1.35e-02 5.49e+03 3.13e+02 bond pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " ideal model delta sigma weight residual 1.326 1.518 -0.192 1.10e-02 8.26e+03 3.03e+02 bond pdb=" C ALA A 36 " pdb=" O ALA A 36 " ideal model delta sigma weight residual 1.236 1.436 -0.200 1.22e-02 6.72e+03 2.70e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 3146 4.72 - 9.44: 1861 9.44 - 14.16: 655 14.16 - 18.88: 105 18.88 - 23.60: 10 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 140.59 -19.36 8.10e-01 1.52e+00 5.71e+02 angle pdb=" O ILE A 152 " pdb=" C ILE A 152 " pdb=" N ALEU A 153 " ideal model delta sigma weight residual 123.10 142.90 -19.80 1.17e+00 7.31e-01 2.86e+02 angle pdb=" O ILE A 91 " pdb=" C ILE A 91 " pdb=" N LEU A 92 " ideal model delta sigma weight residual 121.83 138.06 -16.23 1.03e+00 9.43e-01 2.48e+02 angle pdb=" C ACYS A 53 " pdb=" N PRO A 54 " pdb=" CA PRO A 54 " ideal model delta sigma weight residual 120.03 104.54 15.49 9.90e-01 1.02e+00 2.45e+02 angle pdb=" CA BLEU A 153 " pdb=" C BLEU A 153 " pdb=" O BLEU A 153 " ideal model delta sigma weight residual 120.30 105.59 14.71 1.07e+00 8.73e-01 1.89e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 930 16.51 - 33.01: 116 33.01 - 49.52: 49 49.52 - 66.03: 12 66.03 - 82.53: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 160.19 19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.019 - 0.214: 92 0.214 - 0.410: 75 0.410 - 0.605: 43 0.605 - 0.800: 23 0.800 - 0.996: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG BLEU A 153 " pdb=" CB BLEU A 153 " pdb=" CD1BLEU A 153 " pdb=" CD2BLEU A 153 " both_signs ideal model delta sigma weight residual False -2.59 -3.59 1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.64 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CA ALA A 79 " pdb=" N ALA A 79 " pdb=" C ALA A 79 " pdb=" CB ALA A 79 " both_signs ideal model delta sigma weight residual False 2.48 1.56 0.93 2.00e-01 2.50e+01 2.14e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.029 2.00e-02 2.50e+03 7.00e-02 1.47e+02 pdb=" CG PHE A 164 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.121 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.085 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.058 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.121 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.123 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.025 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.025 2.00e-02 2.50e+03 5.95e-02 1.06e+02 pdb=" CG TYR A 139 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.078 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.118 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.078 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.026 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.107 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.059 2.00e-02 2.50e+03 5.87e-02 1.03e+02 pdb=" CG BTYR A 67 " 0.093 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.002 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.096 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.060 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.018 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.003 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.096 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.027 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.24: 583 2.24 - 2.83: 7551 2.83 - 3.42: 10765 3.42 - 4.01: 15326 4.01 - 4.60: 22349 Nonbonded interactions: 56574 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.655 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.770 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.797 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.847 2.100 nonbonded pdb=" HB2BGLN A 80 " pdb="HE21BGLN A 80 " model vdw 1.849 2.270 ... (remaining 56569 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_1541177_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2613 r_free= 0.1952 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794678 | | target function (ml) not normalized (work): 232813.404500 | | target function (ml) not normalized (free): 11845.770782 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3046 0.2073 7.0243 4.9328| | 2: 3.57 - 2.84 1.00 2876 122 0.2440 0.1792 4.3565 4.359| | 3: 2.84 - 2.48 1.00 2833 165 0.2370 0.1753 4.1311 4.178| | 4: 2.47 - 2.25 1.00 2825 136 0.2320 0.1465 3.8329 3.8388| | 5: 2.25 - 2.09 1.00 2756 127 0.2450 0.1645 3.7967 3.8413| | 6: 2.09 - 1.97 1.00 2846 113 0.2568 0.1718 3.477 3.5504| | 7: 1.97 - 1.87 1.00 2787 165 0.2519 0.1836 3.1351 3.1888| | 8: 1.87 - 1.79 1.00 2789 144 0.2546 0.1847 3.0693 3.1302| | 9: 1.79 - 1.72 1.00 2745 138 0.2480 0.1890 2.9161 2.9704| | 10: 1.72 - 1.66 1.00 2789 158 0.2421 0.1823 2.8039 2.8368| | 11: 1.66 - 1.61 1.00 2740 147 0.2511 0.1926 2.7407 2.7808| | 12: 1.61 - 1.56 1.00 2787 146 0.2550 0.2176 2.6535 2.7062| | 13: 1.56 - 1.52 1.00 2745 130 0.2608 0.1882 2.5889 2.5928| | 14: 1.52 - 1.48 1.00 2803 134 0.2583 0.1922 2.5187 2.6005| | 15: 1.48 - 1.45 1.00 2738 128 0.2587 0.2102 2.4264 2.4872| | 16: 1.45 - 1.42 1.00 2756 161 0.2658 0.2287 2.3885 2.4613| | 17: 1.42 - 1.39 1.00 2785 139 0.2605 0.2213 2.3348 2.4106| | 18: 1.39 - 1.36 1.00 2741 179 0.2657 0.2230 2.2773 2.3371| | 19: 1.36 - 1.34 1.00 2807 134 0.2687 0.2343 2.2736 2.2996| | 20: 1.34 - 1.32 1.00 2696 147 0.2676 0.2340 2.2023 2.2717| | 21: 1.32 - 1.30 1.00 2785 112 0.2679 0.2124 2.1651 2.1135| | 22: 1.29 - 1.27 1.00 2704 152 0.2758 0.2539 2.1458 2.1742| | 23: 1.27 - 1.26 1.00 2802 156 0.2751 0.2341 2.1094 2.1595| | 24: 1.26 - 1.24 1.00 2744 132 0.2782 0.2573 2.0813 2.1922| | 25: 1.24 - 1.22 1.00 2734 148 0.2822 0.2522 2.0546 2.08| | 26: 1.22 - 1.21 1.00 2727 135 0.2804 0.2279 2.0088 2.0693| | 27: 1.21 - 1.19 1.00 2814 148 0.2997 0.2647 2.0063 2.0429| | 28: 1.19 - 1.18 1.00 2671 147 0.2960 0.2579 1.9936 1.9598| | 29: 1.18 - 1.16 1.00 2800 134 0.2894 0.2741 1.9452 2.0575| | 30: 1.16 - 1.15 1.00 2740 148 0.3044 0.2783 1.9291 1.9499| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.96 0.76 0.23 1493.56| | 2: 3.57 - 2.84 2876 122 0.80 26.28 1.27 0.23 1493.56| | 3: 2.84 - 2.48 2833 165 0.74 32.28 1.24 0.23 1237.96| | 4: 2.47 - 2.25 2825 136 0.81 25.61 1.26 0.25 574.64| | 5: 2.25 - 2.09 2756 127 0.77 29.44 1.28 0.25 574.64| | 6: 2.09 - 1.97 2846 113 0.83 22.87 1.29 0.25 313.43| | 7: 1.97 - 1.87 2787 165 0.90 16.43 1.28 0.25 90.65| | 8: 1.87 - 1.79 2789 144 0.86 21.19 1.26 0.25 90.65| | 9: 1.79 - 1.72 2745 138 0.88 18.52 1.24 0.25 55.02| | 10: 1.72 - 1.66 2789 158 0.87 20.19 1.23 0.25 47.88| | 11: 1.66 - 1.61 2740 147 0.86 21.42 1.25 0.25 46.29| | 12: 1.61 - 1.56 2787 146 0.88 18.79 1.23 0.25 30.14| | 13: 1.56 - 1.52 2745 130 0.86 20.89 1.24 0.25 30.14| | 14: 1.52 - 1.48 2803 134 0.86 21.19 1.23 0.25 27.14| | 15: 1.48 - 1.45 2738 128 0.86 20.68 1.23 0.25 21.63| | 16: 1.45 - 1.42 2756 161 0.85 22.33 1.23 0.25 21.63| | 17: 1.42 - 1.39 2785 139 0.86 21.10 1.22 0.25 18.37| | 18: 1.39 - 1.36 2741 179 0.86 21.89 1.22 0.25 16.48| | 19: 1.36 - 1.34 2807 134 0.85 22.47 1.21 0.25 16.48| | 20: 1.34 - 1.32 2696 147 0.86 21.50 1.21 0.24 13.59| | 21: 1.32 - 1.30 2785 112 0.85 22.46 1.20 0.24 13.39| | 22: 1.29 - 1.27 2704 152 0.85 22.93 1.21 0.24 13.05| | 23: 1.27 - 1.26 2802 156 0.86 22.06 1.21 0.24 11.31| | 24: 1.26 - 1.24 2744 132 0.85 23.22 1.20 0.24 11.31| | 25: 1.24 - 1.22 2734 148 0.84 23.85 1.20 0.24 10.70| | 26: 1.22 - 1.21 2727 135 0.84 23.88 1.19 0.23 10.02| | 27: 1.21 - 1.19 2814 148 0.83 25.09 1.20 0.23 10.02| | 28: 1.19 - 1.18 2671 147 0.83 24.94 1.17 0.23 9.23| | 29: 1.18 - 1.16 2800 134 0.83 25.08 1.16 0.23 8.93| | 30: 1.16 - 1.15 2740 148 0.81 26.89 1.15 0.23 8.93| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 8.93 max = 1493.56 mean = 216.63| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 22.82| |phase err.(test): min = 0.00 max = 89.83 mean = 22.74| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.239 1557 Z= 5.520 Angle : 5.413 19.796 2118 Z= 3.892 Chirality : 0.397 0.996 243 Planarity : 0.032 0.090 284 Dihedral : 14.027 82.534 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 2.48 % Allowed : 1.24 % Favored : 96.27 % Cbeta Deviations : 34.59 % 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: -2.69 (0.51), residues: 224 helix: -3.09 (0.37), residues: 108 sheet: -0.73 (0.78), residues: 38 loop : 0.17 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.089 0.020 ARG A 98 TYR 0.087 0.038 TYR A 139 PHE 0.138 0.046 PHE A 164 HIS 0.088 0.044 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2613 r_free= 0.1952 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794678 | | target function (ml) not normalized (work): 232813.404500 | | target function (ml) not normalized (free): 11845.770782 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2572 0.2614 0.1952 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2572 0.2614 0.1952 n_refl.: 87602 remove outliers: r(all,work,free)=0.1988 0.1992 0.1952 n_refl.: 87594 overall B=0.23 to atoms: r(all,work,free)=0.2016 0.2021 0.1969 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1651 0.1645 0.1778 n_refl.: 87594 remove outliers: r(all,work,free)=0.1650 0.1644 0.1778 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.87 87 5 0.3801 382.013 356.138 0.722 0.911 0.401 11.894-9.307 99.02 97 4 0.1884 613.622 592.086 1.016 0.911 0.380 9.237-7.194 100.00 213 7 0.2154 501.868 492.028 1.055 0.911 0.344 7.162-5.571 100.00 427 22 0.2229 376.624 364.999 1.022 0.912 0.282 5.546-4.326 100.00 867 58 0.1299 517.011 511.609 1.060 0.913 0.221 4.315-3.360 100.00 1859 96 0.1147 491.681 488.133 1.099 0.914 0.203 3.356-2.611 100.00 3867 181 0.1467 323.009 319.144 1.088 0.916 0.029 2.608-2.026 99.99 8198 413 0.1337 214.126 211.946 1.095 0.920 0.000 2.025-1.573 100.00 17313 902 0.1661 104.568 103.787 1.093 0.926 0.000 1.573-1.221 100.00 36679 1900 0.2071 46.370 45.012 1.067 0.936 0.000 1.221-1.150 99.97 13689 708 0.2578 29.216 26.965 1.027 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0531 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1644 r_free=0.1778 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=0.1649 r_free=0.1782 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.684085 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1970.540816 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 0.1211 0.1461 0.0250 0.007 1.0 1.3 0.5 0.0 0 12.842 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.61 2.50 3.013 19.090 1970.541 0.017 12.47 15.37 2.90 3.341 19.652 1970.541 0.016 Individual atomic B min max mean iso aniso Overall: 8.61 118.92 21.18 2.89 0 1785 Protein: 8.61 118.92 18.02 2.89 0 1519 Water: 11.12 114.53 39.50 N/A 0 258 Other: 23.40 37.39 29.83 N/A 0 8 Chain A: 8.61 118.92 21.18 N/A 0 1785 Histogram: Values Number of atoms 8.61 - 19.64 1208 19.64 - 30.67 227 30.67 - 41.70 162 41.70 - 52.73 103 52.73 - 63.77 52 63.77 - 74.80 17 74.80 - 85.83 9 85.83 - 96.86 3 96.86 - 107.89 1 107.89 - 118.92 3 =========================== Idealize ADP of riding H ========================== r_work=0.1248 r_free=0.1538 r_work=0.1251 r_free=0.1541 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1251 r_free = 0.1541 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 = 0.1250 r_free = 0.1543 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1250 r_free= 0.1543 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015383 | | target function (ls_wunit_k1) not normalized (work): 1281.360980 | | target function (ls_wunit_k1) not normalized (free): 113.105443 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1265 0.1250 0.1543 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1714 0.1713 0.1775 n_refl.: 87592 remove outliers: r(all,work,free)=0.1714 0.1713 0.1775 n_refl.: 87592 overall B=0.11 to atoms: r(all,work,free)=0.1732 0.1731 0.1788 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1263 0.1249 0.1537 n_refl.: 87592 remove outliers: r(all,work,free)=0.1263 0.1249 0.1537 n_refl.: 87591 ======================== 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 94.79 86 5 0.3611 294.200 275.362 0.623 1.003 0.380 11.894-9.307 99.02 97 4 0.1625 476.734 464.559 0.904 1.003 0.380 9.237-7.194 100.00 213 7 0.1806 389.910 384.372 0.948 1.003 0.340 7.162-5.571 100.00 427 22 0.1721 292.606 287.200 0.922 1.003 0.253 5.546-4.326 100.00 867 58 0.0911 401.675 399.149 0.949 1.003 0.204 4.315-3.360 100.00 1859 96 0.0771 381.996 381.042 0.995 1.003 0.190 3.356-2.611 100.00 3867 181 0.1022 250.951 250.228 0.999 1.002 0.048 2.608-2.026 99.99 8198 413 0.0985 166.358 165.726 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1220 81.241 81.401 1.017 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1663 36.025 35.480 1.006 1.000 0.000 1.221-1.150 99.97 13689 708 0.2366 22.699 21.216 0.970 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0421 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1249 r_free=0.1537 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=0.1249 r_free=0.1537 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1249 r_free=0.1537 | n_water=258 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1259 r_free=0.1537 | n_water=251 | time (s): 25.350 (total time: 27.610) Filter (q & B) r_work=0.1262 r_free=0.1536 | n_water=248 | time (s): 3.640 (total time: 31.250) Compute maps r_work=0.1262 r_free=0.1536 | n_water=248 | time (s): 1.840 (total time: 33.090) Filter (map) r_work=0.1272 r_free=0.1545 | n_water=238 | time (s): 3.750 (total time: 36.840) Find peaks r_work=0.1272 r_free=0.1545 | n_water=238 | time (s): 0.710 (total time: 37.550) Add new water r_work=0.1422 r_free=0.1693 | n_water=451 | time (s): 3.720 (total time: 41.270) Refine new water occ: r_work=0.1332 r_free=0.1558 adp: r_work=0.1255 r_free=0.1509 occ: r_work=0.1267 r_free=0.1504 adp: r_work=0.1234 r_free=0.1489 occ: r_work=0.1237 r_free=0.1483 adp: r_work=0.1228 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1482 r_work=0.1228 r_free=0.1482 | n_water=451 | time (s): 87.810 (total time: 129.080) Filter (q & B) r_work=0.1234 r_free=0.1487 | n_water=427 | time (s): 3.690 (total time: 132.770) Filter (dist only) r_work=0.1234 r_free=0.1487 | n_water=427 | time (s): 39.910 (total time: 172.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.029745 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1531.326362 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 0.1228 0.1514 0.0286 0.007 0.9 1.3 0.5 0.0 0 13.015 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 15.14 2.86 3.820 23.296 1531.326 0.015 11.95 14.88 2.93 4.241 23.106 1531.326 0.014 Individual atomic B min max mean iso aniso Overall: 8.86 114.65 23.26 2.62 189 1765 Protein: 8.86 114.65 17.79 2.62 0 1519 Water: 11.00 72.83 42.62 N/A 189 238 Other: 21.54 33.71 26.80 N/A 0 8 Chain A: 8.86 114.65 20.52 N/A 0 1765 Chain S: 15.97 71.16 48.82 N/A 189 0 Histogram: Values Number of atoms 8.86 - 19.44 1208 19.44 - 30.02 248 30.02 - 40.60 180 40.60 - 51.18 149 51.18 - 61.75 106 61.75 - 72.33 50 72.33 - 82.91 7 82.91 - 93.49 3 93.49 - 104.07 1 104.07 - 114.65 2 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1488 r_work=0.1195 r_free=0.1488 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1488 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1485 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1195 r_free= 0.1485 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013714 | | target function (ls_wunit_k1) not normalized (work): 1142.311706 | | target function (ls_wunit_k1) not normalized (free): 103.044924 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1195 0.1485 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1612 0.1608 0.1718 n_refl.: 87591 remove outliers: r(all,work,free)=0.1612 0.1608 0.1718 n_refl.: 87591 overall B=0.02 to atoms: r(all,work,free)=0.1616 0.1612 0.1721 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1192 0.1482 n_refl.: 87591 remove outliers: r(all,work,free)=0.1206 0.1192 0.1482 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3453 296.164 267.733 0.585 1.001 0.364 11.894-9.307 99.02 97 4 0.1522 476.734 475.936 0.918 1.002 0.360 9.237-7.194 100.00 213 7 0.1644 389.910 390.672 0.979 1.002 0.290 7.162-5.571 100.00 427 22 0.1506 292.606 288.131 0.936 1.002 0.229 5.546-4.326 100.00 867 58 0.0814 401.675 399.508 0.958 1.002 0.215 4.315-3.360 100.00 1859 96 0.0703 381.996 380.953 1.002 1.002 0.210 3.356-2.611 100.00 3867 181 0.0951 250.951 250.183 1.010 1.002 0.140 2.608-2.026 99.99 8198 413 0.0949 166.358 165.926 1.019 1.002 0.000 2.025-1.573 100.00 17313 902 0.1177 81.241 81.453 1.028 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1615 36.025 35.529 1.018 0.999 0.000 1.221-1.150 99.97 13689 708 0.2336 22.699 21.250 0.979 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0384 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1482 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1482 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1482 | n_water=427 | time (s): 1.560 (total time: 1.560) Filter (dist) r_work=0.1192 r_free=0.1483 | n_water=425 | time (s): 37.340 (total time: 38.900) Filter (q & B) r_work=0.1192 r_free=0.1483 | n_water=425 | time (s): 1.120 (total time: 40.020) Compute maps r_work=0.1192 r_free=0.1483 | n_water=425 | time (s): 1.500 (total time: 41.520) Filter (map) r_work=0.1237 r_free=0.1478 | n_water=292 | time (s): 3.520 (total time: 45.040) Find peaks r_work=0.1237 r_free=0.1478 | n_water=292 | time (s): 0.550 (total time: 45.590) Add new water r_work=0.1370 r_free=0.1585 | n_water=476 | time (s): 3.300 (total time: 48.890) Refine new water occ: r_work=0.1267 r_free=0.1505 adp: r_work=0.1268 r_free=0.1506 occ: r_work=0.1242 r_free=0.1485 adp: r_work=0.1239 r_free=0.1483 occ: r_work=0.1226 r_free=0.1476 adp: r_work=0.1216 r_free=0.1469 ADP+occupancy (water only), MIN, final r_work=0.1216 r_free=0.1469 r_work=0.1216 r_free=0.1469 | n_water=476 | time (s): 162.330 (total time: 211.220) Filter (q & B) r_work=0.1219 r_free=0.1469 | n_water=449 | time (s): 3.600 (total time: 214.820) Filter (dist only) r_work=0.1219 r_free=0.1469 | n_water=449 | time (s): 35.920 (total time: 250.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.029983 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.012448 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 0.1222 0.1449 0.0227 0.006 0.9 1.6 0.5 0.0 0 1.015 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.22 14.49 2.27 3.646 22.304 49.012 3.722 12.11 14.01 1.90 4.181 22.093 49.012 3.649 Individual atomic B min max mean iso aniso Overall: 9.25 109.67 21.87 2.35 214 1762 Protein: 9.25 109.67 17.30 2.35 0 1519 Water: 11.58 71.69 37.29 N/A 214 235 Other: 18.68 30.34 24.59 N/A 0 8 Chain A: 9.25 109.67 20.00 N/A 0 1762 Chain S: 15.73 65.92 37.29 N/A 214 0 Histogram: Values Number of atoms 9.25 - 19.30 1235 19.30 - 29.34 265 29.34 - 39.38 221 39.38 - 49.42 136 49.42 - 59.46 83 59.46 - 69.51 23 69.51 - 79.55 7 79.55 - 89.59 3 89.59 - 99.63 1 99.63 - 109.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1401 r_work=0.1212 r_free=0.1402 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1212 r_free = 0.1402 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1399 target_work(ml) = 3.647 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1207 r_free= 0.1399 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.646829 | | target function (ml) not normalized (work): 303758.960034 | | target function (ml) not normalized (free): 16051.426755 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1207 0.1399 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1542 0.1540 0.1610 n_refl.: 87590 remove outliers: r(all,work,free)=0.1542 0.1540 0.1610 n_refl.: 87590 overall B=-0.02 to atoms: r(all,work,free)=0.1539 0.1537 0.1608 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1197 0.1375 n_refl.: 87590 remove outliers: r(all,work,free)=0.1203 0.1194 0.1375 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3912 290.318 262.863 0.479 1.000 0.314 11.894-9.307 98.04 96 4 0.2406 476.857 459.914 0.854 1.001 0.310 9.237-7.194 98.64 210 7 0.2298 382.486 383.379 0.946 1.002 0.200 7.162-5.571 100.00 427 22 0.2004 292.606 283.628 0.914 1.002 0.175 5.546-4.326 100.00 867 58 0.1077 401.675 397.638 0.953 1.002 0.170 4.315-3.360 100.00 1859 96 0.0910 381.996 379.285 0.993 1.002 0.170 3.356-2.611 100.00 3867 181 0.1152 250.951 249.027 0.999 1.002 0.072 2.608-2.026 99.99 8198 413 0.1049 166.358 165.313 1.012 1.002 0.000 2.025-1.573 100.00 17313 902 0.1019 81.241 81.407 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1291 36.025 35.599 1.021 1.000 0.000 1.221-1.150 99.97 13689 708 0.2125 22.699 21.324 0.980 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0453 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1375 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1375 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1375 | n_water=449 | time (s): 1.610 (total time: 1.610) Filter (dist) r_work=0.1194 r_free=0.1375 | n_water=449 | time (s): 37.170 (total time: 38.780) Filter (q & B) r_work=0.1194 r_free=0.1375 | n_water=449 | time (s): 1.280 (total time: 40.060) Compute maps r_work=0.1194 r_free=0.1375 | n_water=449 | time (s): 1.550 (total time: 41.610) Filter (map) r_work=0.1214 r_free=0.1381 | n_water=316 | time (s): 2.380 (total time: 43.990) Find peaks r_work=0.1214 r_free=0.1381 | n_water=316 | time (s): 0.440 (total time: 44.430) Add new water r_work=0.1283 r_free=0.1433 | n_water=482 | time (s): 2.630 (total time: 47.060) Refine new water occ: r_work=0.1212 r_free=0.1374 adp: r_work=0.1212 r_free=0.1375 occ: r_work=0.1197 r_free=0.1361 adp: r_work=0.1195 r_free=0.1360 occ: r_work=0.1186 r_free=0.1352 adp: r_work=0.1182 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1349 r_work=0.1182 r_free=0.1349 | n_water=482 | time (s): 178.160 (total time: 225.220) Filter (q & B) r_work=0.1188 r_free=0.1350 | n_water=446 | time (s): 3.220 (total time: 228.440) Filter (dist only) r_work=0.1189 r_free=0.1349 | n_water=445 | time (s): 38.800 (total time: 267.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.992318 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.512861 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 0.1196 0.1365 0.0169 0.006 1.0 1.6 0.5 0.0 0 0.996 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.65 1.69 3.447 21.629 51.513 3.634 11.76 13.57 1.82 3.815 21.519 51.513 3.617 Individual atomic B min max mean iso aniso Overall: 9.33 105.51 21.43 2.20 212 1760 Protein: 9.33 105.51 17.03 2.21 0 1519 Water: 11.52 70.30 36.42 N/A 212 233 Other: 18.79 27.23 22.83 N/A 0 8 Chain A: 9.33 105.51 19.65 N/A 0 1760 Chain S: 15.23 60.01 36.19 N/A 212 0 Histogram: Values Number of atoms 9.33 - 18.95 1230 18.95 - 28.57 282 28.57 - 38.19 201 38.19 - 47.80 136 47.80 - 57.42 84 57.42 - 67.04 25 67.04 - 76.66 9 76.66 - 86.28 2 86.28 - 95.89 1 95.89 - 105.51 2 =========================== Idealize ADP of riding H ========================== r_work=0.1176 r_free=0.1357 r_work=0.1176 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1176 r_free = 0.1358 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1171 r_free = 0.1353 target_work(ml) = 3.616 | | 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.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1171 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.615514 | | target function (ml) not normalized (work): 301125.342311 | | target function (ml) not normalized (free): 15913.345661 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1180 0.1171 0.1353 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1501 0.1501 0.1541 n_refl.: 87583 remove outliers: r(all,work,free)=0.1501 0.1501 0.1541 n_refl.: 87583 overall B=-0.02 to atoms: r(all,work,free)=0.1497 0.1497 0.1539 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1179 0.1170 0.1351 n_refl.: 87583 remove outliers: r(all,work,free)=0.1176 0.1167 0.1351 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 0.3922 282.293 258.257 0.451 1.000 0.291 11.894-9.307 93.14 91 4 0.2358 465.731 452.059 0.845 1.002 0.270 9.237-7.194 98.18 209 7 0.2403 381.492 377.408 0.920 1.002 0.170 7.162-5.571 100.00 427 22 0.2141 292.606 282.238 0.904 1.002 0.144 5.546-4.326 100.00 867 58 0.1126 401.675 397.683 0.953 1.002 0.141 4.315-3.360 100.00 1859 96 0.0924 381.996 379.464 0.994 1.002 0.129 3.356-2.611 100.00 3867 181 0.1134 250.951 249.191 1.000 1.002 0.053 2.608-2.026 99.99 8198 413 0.1008 166.358 165.477 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0964 81.241 81.504 1.028 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1239 36.025 35.656 1.023 0.999 0.000 1.221-1.150 99.97 13689 708 0.2123 22.699 21.338 0.982 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0549 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1167 r_free=0.1351 After: r_work=0.1168 r_free=0.1351 ================================== NQH flips ================================== r_work=0.1168 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1168 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1168 r_free=0.1351 | n_water=445 | time (s): 1.730 (total time: 1.730) Filter (dist) r_work=0.1168 r_free=0.1350 | n_water=444 | time (s): 38.580 (total time: 40.310) Filter (q & B) r_work=0.1168 r_free=0.1351 | n_water=442 | time (s): 2.370 (total time: 42.680) Compute maps r_work=0.1168 r_free=0.1351 | n_water=442 | time (s): 1.280 (total time: 43.960) Filter (map) r_work=0.1191 r_free=0.1364 | n_water=335 | time (s): 3.230 (total time: 47.190) Find peaks r_work=0.1191 r_free=0.1364 | n_water=335 | time (s): 0.610 (total time: 47.800) Add new water r_work=0.1247 r_free=0.1406 | n_water=501 | time (s): 2.660 (total time: 50.460) Refine new water occ: r_work=0.1182 r_free=0.1338 adp: r_work=0.1182 r_free=0.1341 occ: r_work=0.1168 r_free=0.1329 adp: r_work=0.1166 r_free=0.1330 occ: r_work=0.1158 r_free=0.1324 adp: r_work=0.1154 r_free=0.1323 ADP+occupancy (water only), MIN, final r_work=0.1154 r_free=0.1323 r_work=0.1154 r_free=0.1323 | n_water=501 | time (s): 204.720 (total time: 255.180) Filter (q & B) r_work=0.1163 r_free=0.1331 | n_water=458 | time (s): 2.930 (total time: 258.110) Filter (dist only) r_work=0.1163 r_free=0.1327 | n_water=456 | time (s): 40.420 (total time: 298.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.944891 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.843394 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 0.1187 0.1355 0.0169 0.007 1.0 2.6 0.5 0.0 0 0.972 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.87 13.55 1.69 3.325 21.354 36.843 3.620 11.90 13.52 1.61 3.364 21.333 36.843 3.617 Individual atomic B min max mean iso aniso Overall: 9.27 104.15 21.41 2.13 225 1758 Protein: 9.27 104.15 16.96 2.13 0 1519 Water: 11.38 70.13 36.20 N/A 225 231 Other: 19.08 26.84 22.88 N/A 0 8 Chain A: 9.27 104.15 19.54 N/A 0 1758 Chain S: 14.97 60.01 36.02 N/A 225 0 Histogram: Values Number of atoms 9.27 - 18.76 1227 18.76 - 28.25 286 28.25 - 37.73 199 37.73 - 47.22 153 47.22 - 56.71 75 56.71 - 66.20 28 66.20 - 75.68 10 75.68 - 85.17 2 85.17 - 94.66 1 94.66 - 104.15 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1352 r_work=0.1190 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1352 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1351 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1187 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.615645 | | target function (ml) not normalized (work): 301107.281214 | | target function (ml) not normalized (free): 15896.884559 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1383 0.1366 5.6604 5.5858| | 2: 3.57 - 2.84 1.00 2888 124 0.1086 0.1451 5.1634 5.2545| | 3: 2.83 - 2.48 1.00 2820 163 0.1198 0.1280 4.9762 5.0085| | 4: 2.47 - 2.25 1.00 2825 136 0.1015 0.1099 4.6816 4.7282| | 5: 2.25 - 2.09 1.00 2756 127 0.0994 0.1076 4.6218 4.6897| | 6: 2.09 - 1.97 1.00 2846 113 0.0972 0.1206 4.3382 4.4666| | 7: 1.97 - 1.87 1.00 2787 165 0.0994 0.1188 4.0728 4.1553| | 8: 1.87 - 1.79 1.00 2789 144 0.1029 0.1254 3.9893 4.0841| | 9: 1.79 - 1.72 1.00 2745 138 0.0957 0.1263 3.7135 3.8791| | 10: 1.72 - 1.66 1.00 2831 160 0.1013 0.1279 3.6356 3.7682| | 11: 1.66 - 1.61 1.00 2712 147 0.0973 0.1107 3.5674 3.6065| | 12: 1.61 - 1.56 1.00 2773 144 0.0929 0.1161 3.3497 3.465| | 13: 1.56 - 1.52 1.00 2745 130 0.0992 0.1047 3.3382 3.4224| | 14: 1.52 - 1.48 1.00 2803 134 0.0996 0.1088 3.2601 3.3309| | 15: 1.48 - 1.45 1.00 2738 128 0.1026 0.1329 3.1679 3.3094| | 16: 1.45 - 1.42 1.00 2756 161 0.1069 0.1263 3.147 3.2526| | 17: 1.42 - 1.39 1.00 2785 139 0.1125 0.1284 3.1138 3.2256| | 18: 1.39 - 1.36 1.00 2741 179 0.1170 0.1377 3.088 3.2641| | 19: 1.36 - 1.34 1.00 2807 134 0.1228 0.1562 3.0933 3.2656| | 20: 1.34 - 1.32 1.00 2696 147 0.1328 0.1423 3.0854 3.1187| | 21: 1.32 - 1.30 1.00 2785 112 0.1420 0.1641 3.0848 3.1724| | 22: 1.29 - 1.27 1.00 2704 152 0.1485 0.1946 3.0839 3.2833| | 23: 1.27 - 1.26 1.00 2802 156 0.1590 0.1818 3.1048 3.1948| | 24: 1.26 - 1.24 1.00 2744 132 0.1635 0.1806 3.0938 3.204| | 25: 1.24 - 1.22 1.00 2733 148 0.1805 0.2326 3.1087 3.2886| | 26: 1.22 - 1.21 1.00 2727 135 0.1868 0.1773 3.123 3.1884| | 27: 1.21 - 1.19 1.00 2814 148 0.2022 0.2087 3.1403 3.1398| | 28: 1.19 - 1.18 1.00 2671 147 0.2143 0.2319 3.137 3.1587| | 29: 1.18 - 1.16 1.00 2800 134 0.2225 0.2386 3.1256 3.2193| | 30: 1.16 - 1.15 1.00 2739 148 0.2381 0.2511 3.1142 3.1684| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2917 171 0.95 8.58 1.00 0.97 5758.79| | 2: 3.57 - 2.84 2888 124 0.92 12.75 1.01 0.97 5758.79| | 3: 2.83 - 2.48 2820 163 0.89 16.80 0.99 0.97 4839.61| | 4: 2.47 - 2.25 2825 136 0.91 14.09 1.00 0.98 2469.32| | 5: 2.25 - 2.09 2756 127 0.90 16.33 1.01 0.98 2469.32| | 6: 2.09 - 1.97 2846 113 0.92 13.33 1.02 0.97 1472.22| | 7: 1.97 - 1.87 2787 165 0.94 10.78 1.02 0.97 621.82| | 8: 1.87 - 1.79 2789 144 0.91 14.38 1.00 0.97 621.82| | 9: 1.79 - 1.72 2745 138 0.93 11.40 0.98 0.97 336.73| | 10: 1.72 - 1.66 2831 160 0.93 12.28 0.98 0.97 279.63| | 11: 1.66 - 1.61 2712 147 0.93 12.86 0.98 0.97 266.85| | 12: 1.61 - 1.56 2773 144 0.95 9.50 0.99 0.97 146.25| | 13: 1.56 - 1.52 2745 130 0.94 11.09 1.02 0.97 146.25| | 14: 1.52 - 1.48 2803 134 0.94 11.22 1.02 0.97 130.49| | 15: 1.48 - 1.45 2738 128 0.95 10.35 1.01 0.98 101.63| | 16: 1.45 - 1.42 2756 161 0.94 11.54 1.02 0.98 101.63| | 17: 1.42 - 1.39 2785 139 0.94 11.39 1.01 0.98 91.94| | 18: 1.39 - 1.36 2741 179 0.94 11.73 1.01 0.98 86.33| | 19: 1.36 - 1.34 2807 134 0.94 12.27 1.00 0.98 86.33| | 20: 1.34 - 1.32 2696 147 0.94 12.39 0.99 0.96 81.42| | 21: 1.32 - 1.30 2785 112 0.94 13.30 0.98 0.96 81.07| | 22: 1.29 - 1.27 2704 152 0.93 13.84 0.98 0.96 81.26| | 23: 1.27 - 1.26 2802 156 0.92 14.90 0.98 0.94 82.18| | 24: 1.26 - 1.24 2744 132 0.92 14.98 0.97 0.94 82.18| | 25: 1.24 - 1.22 2733 148 0.91 16.39 0.96 0.94 83.74| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.02 0.93 85.47| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 85.47| | 28: 1.19 - 1.18 2671 147 0.88 20.21 1.01 0.93 88.87| | 29: 1.18 - 1.16 2800 134 0.88 20.57 0.99 0.92 90.15| | 30: 1.16 - 1.15 2739 148 0.86 22.00 0.98 0.92 90.15| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.07 max = 5758.79 mean = 912.38| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.92| |phase err.(test): min = 0.00 max = 89.34 mean = 13.99| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1187 0.1351 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1510 0.1509 0.1559 n_refl.: 87575 remove outliers: r(all,work,free)=0.1510 0.1509 0.1559 n_refl.: 87575 overall B=-0.02 to atoms: r(all,work,free)=0.1507 0.1506 0.1557 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1188 0.1352 n_refl.: 87575 remove outliers: r(all,work,free)=0.1194 0.1186 0.1352 n_refl.: 87571 ======================== 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 86.46 78 5 0.3930 282.326 247.864 0.434 1.002 0.314 11.894-9.307 92.16 90 4 0.2450 469.666 445.652 0.840 1.002 0.310 9.237-7.194 97.73 208 7 0.2457 381.017 375.731 0.910 1.002 0.150 7.162-5.571 100.00 427 22 0.2193 292.606 282.312 0.899 1.002 0.124 5.546-4.326 100.00 867 58 0.1154 401.675 397.833 0.954 1.002 0.118 4.315-3.360 100.00 1859 96 0.0952 381.996 379.601 0.995 1.002 0.113 3.356-2.611 100.00 3867 181 0.1161 250.951 249.035 1.001 1.002 0.048 2.608-2.026 99.99 8198 413 0.1032 166.358 165.434 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0982 81.241 81.532 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1238 36.025 35.661 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2123 22.699 21.329 0.981 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0418 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2613 0.1952 0.082 5.413 8.8 119.3 19.9 258 0.000 1_bss: 0.1644 0.1778 0.082 5.413 9.1 119.5 20.1 258 0.000 1_settarget: 0.1644 0.1778 0.082 5.413 9.1 119.5 20.1 258 0.000 1_nqh: 0.1649 0.1782 0.082 5.413 9.1 119.5 20.1 258 0.003 1_weight: 0.1649 0.1782 0.082 5.413 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1211 0.1461 0.007 0.958 9.1 119.5 20.1 258 0.127 1_adp: 0.1248 0.1538 0.007 0.958 8.6 118.9 21.2 258 0.127 1_regHadp: 0.1251 0.1541 0.007 0.958 8.6 118.9 21.2 258 0.127 1_occ: 0.1250 0.1543 0.007 0.958 8.6 118.9 21.2 258 0.127 2_bss: 0.1249 0.1537 0.007 0.958 8.7 119.0 21.3 258 0.127 2_settarget: 0.1249 0.1537 0.007 0.958 8.7 119.0 21.3 258 0.127 2_updatecdl: 0.1249 0.1537 0.007 0.963 8.7 119.0 21.3 258 0.127 2_nqh: 0.1249 0.1537 0.007 0.963 8.7 119.0 21.3 258 0.127 2_sol: 0.1234 0.1487 0.007 0.963 8.7 119.0 23.6 427 n/a 2_weight: 0.1234 0.1487 0.007 0.963 8.7 119.0 23.6 427 n/a 2_xyzrec: 0.1228 0.1514 0.007 0.880 8.7 119.0 23.6 427 n/a 2_adp: 0.1195 0.1488 0.007 0.880 8.9 114.6 23.3 427 n/a 2_regHadp: 0.1195 0.1488 0.007 0.880 8.9 114.6 23.3 427 n/a 2_occ: 0.1195 0.1485 0.007 0.880 8.9 114.6 23.3 427 n/a 3_bss: 0.1192 0.1482 0.007 0.880 8.9 114.7 23.3 427 n/a 3_settarget: 0.1192 0.1482 0.007 0.880 8.9 114.7 23.3 427 n/a 3_updatecdl: 0.1192 0.1482 0.007 0.880 8.9 114.7 23.3 427 n/a 3_nqh: 0.1192 0.1482 0.007 0.880 8.9 114.7 23.3 427 n/a 3_sol: 0.1219 0.1469 0.007 0.880 8.9 114.7 22.3 449 n/a 3_weight: 0.1219 0.1469 0.007 0.880 8.9 114.7 22.3 449 n/a 3_xyzrec: 0.1222 0.1449 0.006 0.920 8.9 114.7 22.3 449 n/a 3_adp: 0.1211 0.1401 0.006 0.920 9.3 109.7 21.9 449 n/a 3_regHadp: 0.1212 0.1402 0.006 0.920 9.3 109.7 21.9 449 n/a 3_occ: 0.1207 0.1399 0.006 0.920 9.3 109.7 21.9 449 n/a 4_bss: 0.1194 0.1375 0.006 0.920 9.2 109.7 21.9 449 n/a 4_settarget: 0.1194 0.1375 0.006 0.920 9.2 109.7 21.9 449 n/a 4_updatecdl: 0.1194 0.1375 0.006 0.919 9.2 109.7 21.9 449 n/a 4_nqh: 0.1194 0.1375 0.006 0.919 9.2 109.7 21.9 449 n/a 4_sol: 0.1189 0.1349 0.006 0.919 9.2 109.7 21.6 445 n/a 4_weight: 0.1189 0.1349 0.006 0.919 9.2 109.7 21.6 445 n/a 4_xyzrec: 0.1196 0.1365 0.006 0.962 9.2 109.7 21.6 445 n/a 4_adp: 0.1176 0.1357 0.006 0.962 9.3 105.5 21.4 445 n/a 4_regHadp: 0.1176 0.1358 0.006 0.962 9.3 105.5 21.4 445 n/a 4_occ: 0.1171 0.1353 0.006 0.962 9.3 105.5 21.4 445 n/a 5_bss: 0.1167 0.1351 0.006 0.962 9.3 105.5 21.4 445 n/a 5_settarget: 0.1167 0.1351 0.006 0.962 9.3 105.5 21.4 445 n/a 5_updatecdl: 0.1167 0.1351 0.006 0.961 9.3 105.5 21.4 445 n/a 5_setrh: 0.1168 0.1351 0.006 0.961 9.3 105.5 21.4 445 n/a 5_nqh: 0.1168 0.1351 0.006 0.961 9.3 105.5 21.4 445 n/a 5_sol: 0.1163 0.1327 0.006 0.961 9.3 105.5 21.4 456 n/a 5_weight: 0.1163 0.1327 0.006 0.961 9.3 105.5 21.4 456 n/a 5_xyzrec: 0.1187 0.1355 0.007 1.035 9.3 105.5 21.4 456 n/a 5_adp: 0.1190 0.1352 0.007 1.035 9.3 104.1 21.4 456 n/a 5_regHadp: 0.1190 0.1352 0.007 1.035 9.3 104.1 21.4 456 n/a 5_occ: 0.1187 0.1351 0.007 1.035 9.3 104.1 21.4 456 n/a end: 0.1186 0.1352 0.007 1.035 9.3 104.1 21.4 456 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1541177_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1541177_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7300 Refinement macro-cycles (run) : 3349.9200 Write final files (write_after_run_outputs) : 73.9800 Total : 3428.6300 Total CPU time: 57.75 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:09:18 PST -0800 (1735452558.08 s) Start R-work = 0.1644, R-free = 0.1778 Final R-work = 0.1186, R-free = 0.1352 =============================================================================== Job complete usr+sys time: 3581.76 seconds wall clock time: 64 minutes 47.62 seconds (3887.62 seconds total)