Starting phenix.refine on Sat Dec 28 21:06:31 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9451893.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9451893.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9451893.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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: 2.18, per 1000 atoms: 0.64 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: 0.75 Conformation dependent library (CDL) restraints added in 308.9 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 - 0.91: 494 0.91 - 1.17: 1146 1.17 - 1.43: 671 1.43 - 1.69: 816 1.69 - 1.95: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" C SER A 85 " pdb=" O SER A 85 " ideal model delta sigma weight residual 1.236 1.511 -0.275 1.24e-02 6.50e+03 4.91e+02 bond pdb=" C ARG A 5 " pdb=" O ARG A 5 " ideal model delta sigma weight residual 1.235 1.495 -0.260 1.28e-02 6.10e+03 4.13e+02 bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.241 1.054 0.188 9.80e-03 1.04e+04 3.67e+02 bond pdb=" CA ATYR A 67 " pdb=" C ATYR A 67 " ideal model delta sigma weight residual 1.523 1.289 0.234 1.24e-02 6.50e+03 3.56e+02 bond pdb=" C VAL A 70 " pdb=" O VAL A 70 " ideal model delta sigma weight residual 1.237 1.430 -0.193 1.07e-02 8.73e+03 3.26e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.80: 3262 4.80 - 9.61: 1836 9.61 - 14.41: 578 14.41 - 19.21: 94 19.21 - 24.02: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA VAL A 177 " pdb=" C VAL A 177 " pdb=" O VAL A 177 " ideal model delta sigma weight residual 120.85 105.49 15.36 1.06e+00 8.90e-01 2.10e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N BCYS A 53 " ideal model delta sigma weight residual 123.26 138.41 -15.15 1.08e+00 8.57e-01 1.97e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.91 135.44 -13.53 9.80e-01 1.04e+00 1.91e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.26 137.20 -13.94 1.08e+00 8.57e-01 1.67e+02 angle pdb=" CA ILE A 52 " pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 120.39 107.10 13.29 1.05e+00 9.07e-01 1.60e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 921 15.68 - 31.35: 121 31.35 - 47.03: 45 47.03 - 62.71: 20 62.71 - 78.38: 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 -156.92 -23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 110 0.234 - 0.469: 74 0.469 - 0.703: 40 0.703 - 0.937: 16 0.937 - 1.171: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.34 1.17 2.00e-01 2.50e+01 3.43e+01 chirality pdb=" CA ALYS A 99 " pdb=" N ALYS A 99 " pdb=" C ALYS A 99 " pdb=" CB ALYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 chirality pdb=" CA ARG A 5 " pdb=" N ARG A 5 " pdb=" C ARG A 5 " pdb=" CB ARG A 5 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.26e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.030 2.00e-02 2.50e+03 7.08e-02 1.13e+02 pdb=" CG HIS A 138 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.022 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.128 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.080 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.097 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.015 2.00e-02 2.50e+03 5.79e-02 1.01e+02 pdb=" CG BTYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.105 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.010 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.084 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.021 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.007 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.090 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.095 2.00e-02 2.50e+03 5.26e-02 8.29e+01 pdb=" CG PHE A 164 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.051 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.073 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.104 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 897 2.29 - 2.87: 7938 2.87 - 3.45: 10599 3.45 - 4.02: 15296 4.02 - 4.60: 21855 Nonbonded interactions: 56585 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.718 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.798 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.798 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.815 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.843 2.450 ... (remaining 56580 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_9451893_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= 0.2604 r_free= 0.1950 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.782134 | | target function (ml) not normalized (work): 231768.419287 | | target function (ml) not normalized (free): 11786.273580 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3033 0.2152 6.9426 4.9635| | 2: 3.57 - 2.84 1.00 2876 122 0.2431 0.1858 4.363 4.3625| | 3: 2.84 - 2.48 1.00 2833 165 0.2369 0.1720 4.1425 4.1787| | 4: 2.47 - 2.25 1.00 2825 136 0.2299 0.1465 3.8424 3.8381| | 5: 2.25 - 2.09 1.00 2756 127 0.2475 0.1537 3.811 3.8357| | 6: 2.09 - 1.97 1.00 2846 113 0.2544 0.1862 3.474 3.6029| | 7: 1.97 - 1.87 1.00 2787 165 0.2544 0.1768 3.1235 3.1816| | 8: 1.87 - 1.79 1.00 2789 144 0.2523 0.1815 3.0619 3.1334| | 9: 1.79 - 1.72 1.00 2745 138 0.2398 0.1925 2.886 2.9555| | 10: 1.72 - 1.66 1.00 2789 158 0.2363 0.2083 2.7859 2.9225| | 11: 1.66 - 1.61 1.00 2740 147 0.2507 0.1687 2.7492 2.7433| | 12: 1.61 - 1.56 1.00 2787 146 0.2528 0.1973 2.6269 2.6211| | 13: 1.56 - 1.52 1.00 2745 130 0.2560 0.1948 2.5625 2.5966| | 14: 1.52 - 1.48 1.00 2803 134 0.2574 0.1811 2.5078 2.5474| | 15: 1.48 - 1.45 1.00 2738 128 0.2584 0.2006 2.4048 2.4784| | 16: 1.45 - 1.42 1.00 2756 161 0.2635 0.2222 2.3792 2.4689| | 17: 1.42 - 1.39 1.00 2785 139 0.2687 0.2188 2.3203 2.3747| | 18: 1.39 - 1.36 1.00 2741 179 0.2663 0.2087 2.2597 2.2581| | 19: 1.36 - 1.34 1.00 2807 134 0.2650 0.2337 2.2318 2.2797| | 20: 1.34 - 1.32 1.00 2696 147 0.2671 0.2171 2.1885 2.2243| | 21: 1.32 - 1.30 1.00 2785 112 0.2688 0.2270 2.1456 2.1807| | 22: 1.29 - 1.27 1.00 2704 152 0.2749 0.2482 2.126 2.149| | 23: 1.27 - 1.26 1.00 2802 156 0.2727 0.2258 2.0902 2.1152| | 24: 1.26 - 1.24 1.00 2744 132 0.2778 0.2370 2.0744 2.1416| | 25: 1.24 - 1.22 1.00 2734 148 0.2838 0.2648 2.0383 2.0853| | 26: 1.22 - 1.21 1.00 2727 135 0.2864 0.2292 2.0098 2.0568| | 27: 1.21 - 1.19 1.00 2814 148 0.2966 0.2387 1.9916 1.9524| | 28: 1.19 - 1.18 1.00 2671 147 0.2980 0.2649 1.9779 2.0012| | 29: 1.18 - 1.16 1.00 2800 134 0.3000 0.2613 1.9665 1.9897| | 30: 1.16 - 1.15 1.00 2740 148 0.3033 0.2839 1.9289 1.9451| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.86 19.35 0.76 0.23 1544.06| | 2: 3.57 - 2.84 2876 122 0.80 26.62 1.27 0.23 1544.06| | 3: 2.84 - 2.48 2833 165 0.73 32.67 1.25 0.23 1278.95| | 4: 2.47 - 2.25 2825 136 0.81 25.86 1.25 0.25 590.96| | 5: 2.25 - 2.09 2756 127 0.77 29.67 1.28 0.25 590.96| | 6: 2.09 - 1.97 2846 113 0.83 22.71 1.29 0.25 320.49| | 7: 1.97 - 1.87 2787 165 0.90 16.42 1.29 0.26 89.80| | 8: 1.87 - 1.79 2789 144 0.86 21.04 1.25 0.26 89.80| | 9: 1.79 - 1.72 2745 138 0.88 18.62 1.23 0.25 55.02| | 10: 1.72 - 1.66 2789 158 0.86 20.33 1.22 0.25 48.05| | 11: 1.66 - 1.61 2740 147 0.86 21.37 1.24 0.25 46.35| | 12: 1.61 - 1.56 2787 146 0.89 18.28 1.24 0.25 29.11| | 13: 1.56 - 1.52 2745 130 0.87 20.36 1.25 0.25 29.11| | 14: 1.52 - 1.48 2803 134 0.86 20.68 1.24 0.25 26.08| | 15: 1.48 - 1.45 2738 128 0.87 20.23 1.24 0.25 20.53| | 16: 1.45 - 1.42 2756 161 0.86 21.59 1.23 0.25 20.53| | 17: 1.42 - 1.39 2785 139 0.87 20.66 1.24 0.25 17.33| | 18: 1.39 - 1.36 2741 179 0.86 21.08 1.23 0.24 15.47| | 19: 1.36 - 1.34 2807 134 0.85 22.07 1.22 0.24 15.47| | 20: 1.34 - 1.32 2696 147 0.87 20.68 1.21 0.24 12.73| | 21: 1.32 - 1.30 2785 112 0.86 21.71 1.20 0.24 12.53| | 22: 1.29 - 1.27 2704 152 0.86 22.14 1.21 0.24 12.24| | 23: 1.27 - 1.26 2802 156 0.86 21.81 1.21 0.24 10.74| | 24: 1.26 - 1.24 2744 132 0.85 22.44 1.21 0.24 10.74| | 25: 1.24 - 1.22 2734 148 0.85 23.18 1.20 0.24 10.18| | 26: 1.22 - 1.21 2727 135 0.84 23.56 1.21 0.23 9.55| | 27: 1.21 - 1.19 2814 148 0.83 24.47 1.21 0.23 9.55| | 28: 1.19 - 1.18 2671 147 0.83 24.79 1.19 0.23 8.82| | 29: 1.18 - 1.16 2800 134 0.83 24.72 1.17 0.23 8.55| | 30: 1.16 - 1.15 2740 148 0.82 26.04 1.15 0.23 8.55| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.55 max = 1544.06 mean = 222.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.51| |phase err.(test): min = 0.00 max = 89.83 mean = 22.35| |-----------------------------------------------------------------------------| ----------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 0.275 1557 Z= 5.352 Angle : 5.186 17.364 2118 Z= 3.623 Chirality : 0.393 1.171 243 Planarity : 0.028 0.076 284 Dihedral : 13.704 78.382 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.62 % Allowed : 2.48 % Favored : 96.89 % Cbeta Deviations : 29.73 % 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: -2.64 (0.46), residues: 224 helix: -2.29 (0.38), residues: 108 sheet: -1.39 (0.93), residues: 30 loop : -0.79 (0.56), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.097 0.018 ARG A 28 TYR 0.097 0.044 TYR A 139 PHE 0.113 0.031 PHE A 162 HIS 0.065 0.027 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2604 r_free= 0.1950 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.782134 | | target function (ml) not normalized (work): 231768.419287 | | target function (ml) not normalized (free): 11786.273580 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2563 0.2605 0.1951 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2563 0.2605 0.1951 n_refl.: 87602 remove outliers: r(all,work,free)=0.1972 0.1975 0.1951 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.1995 0.1999 0.1962 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1632 0.1624 0.1775 n_refl.: 87594 remove outliers: r(all,work,free)=0.1631 0.1624 0.1775 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 0.3811 386.365 357.072 0.735 0.914 0.407 11.894-9.307 99.02 97 4 0.1762 613.721 594.215 1.010 0.915 0.390 9.237-7.194 100.00 213 7 0.2135 501.948 490.260 1.053 0.915 0.344 7.162-5.571 100.00 427 22 0.2168 376.684 365.208 1.028 0.916 0.330 5.546-4.326 100.00 867 58 0.1293 517.095 511.215 1.054 0.917 0.226 4.315-3.360 100.00 1859 96 0.1139 491.761 487.788 1.095 0.918 0.199 3.356-2.611 100.00 3867 181 0.1433 323.061 319.585 1.088 0.920 0.052 2.608-2.026 99.99 8198 413 0.1329 214.160 212.267 1.090 0.923 0.000 2.025-1.573 100.00 17313 902 0.1642 104.585 103.994 1.089 0.929 0.000 1.573-1.221 100.00 36679 1900 0.2040 46.377 45.152 1.065 0.939 0.000 1.221-1.150 99.97 13689 708 0.2576 29.221 26.992 1.026 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0429 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1624 r_free=0.1775 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1631 r_free=0.1788 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.900816 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2010.039321 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 0.1460 0.0249 0.007 0.9 1.3 0.5 0.0 0 11.950 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.60 2.49 3.013 19.046 2010.039 0.017 12.38 15.31 2.94 3.194 19.546 2010.039 0.016 Individual atomic B min max mean iso aniso Overall: 8.46 118.47 21.02 2.87 0 1785 Protein: 8.46 118.47 17.89 2.87 0 1519 Water: 11.06 114.56 39.21 N/A 0 258 Other: 22.67 36.24 28.92 N/A 0 8 Chain A: 8.46 118.47 21.02 N/A 0 1785 Histogram: Values Number of atoms 8.46 - 19.46 1206 19.46 - 30.46 229 30.46 - 41.46 166 41.46 - 52.46 103 52.46 - 63.46 52 63.46 - 74.47 15 74.47 - 85.47 7 85.47 - 96.47 4 96.47 - 107.47 0 107.47 - 118.47 3 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1532 r_work=0.1242 r_free=0.1535 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1242 r_free = 0.1535 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1241 r_free = 0.1539 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1241 r_free= 0.1539 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015360 | | target function (ls_wunit_k1) not normalized (work): 1279.449311 | | target function (ls_wunit_k1) not normalized (free): 112.817011 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1256 0.1241 0.1539 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1701 0.1701 0.1762 n_refl.: 87593 remove outliers: r(all,work,free)=0.1701 0.1701 0.1762 n_refl.: 87593 overall B=0.11 to atoms: r(all,work,free)=0.1721 0.1720 0.1776 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1254 0.1240 0.1531 n_refl.: 87593 remove outliers: r(all,work,free)=0.1253 0.1239 0.1531 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 95.83 87 5 0.3629 298.526 277.756 0.635 1.003 0.380 11.894-9.307 98.04 96 4 0.1512 480.163 463.897 0.908 1.003 0.380 9.237-7.194 100.00 213 7 0.1801 391.127 386.471 0.950 1.003 0.319 7.162-5.571 100.00 427 22 0.1710 293.519 288.258 0.926 1.003 0.300 5.546-4.326 100.00 867 58 0.0917 402.929 400.311 0.950 1.003 0.204 4.315-3.360 100.00 1859 96 0.0776 383.188 382.260 0.994 1.003 0.190 3.356-2.611 100.00 3867 181 0.1022 251.735 251.096 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0976 166.877 166.310 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1205 81.494 81.679 1.018 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1642 36.138 35.607 1.009 0.997 0.000 1.221-1.150 99.97 13689 708 0.2353 22.769 21.292 0.972 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0442 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1239 r_free=0.1531 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=0.1239 r_free=0.1531 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1239 r_free=0.1531 | n_water=258 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1248 r_free=0.1531 | n_water=252 | time (s): 25.510 (total time: 27.810) Filter (q & B) r_work=0.1251 r_free=0.1531 | n_water=249 | time (s): 3.350 (total time: 31.160) Compute maps r_work=0.1251 r_free=0.1531 | n_water=249 | time (s): 1.740 (total time: 32.900) Filter (map) r_work=0.1265 r_free=0.1539 | n_water=236 | time (s): 3.750 (total time: 36.650) Find peaks r_work=0.1265 r_free=0.1539 | n_water=236 | time (s): 0.690 (total time: 37.340) Add new water r_work=0.1424 r_free=0.1686 | n_water=454 | time (s): 3.640 (total time: 40.980) Refine new water occ: r_work=0.1332 r_free=0.1548 adp: r_work=0.1251 r_free=0.1509 occ: r_work=0.1265 r_free=0.1494 adp: r_work=0.1227 r_free=0.1487 occ: r_work=0.1229 r_free=0.1475 adp: r_work=0.1220 r_free=0.1476 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1476 r_work=0.1220 r_free=0.1476 | n_water=454 | time (s): 88.240 (total time: 129.220) Filter (q & B) r_work=0.1225 r_free=0.1480 | n_water=433 | time (s): 3.890 (total time: 133.110) Filter (dist only) r_work=0.1225 r_free=0.1480 | n_water=433 | time (s): 41.040 (total time: 174.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.660421 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1626.218464 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 0.1510 0.0288 0.007 0.9 2.6 0.5 0.0 0 12.830 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.22 15.10 2.88 3.788 23.222 1626.218 0.015 11.93 14.87 2.93 4.216 23.054 1626.218 0.014 Individual atomic B min max mean iso aniso Overall: 8.71 113.59 23.28 2.62 197 1763 Protein: 8.71 113.59 17.66 2.63 0 1519 Water: 11.26 72.38 42.91 N/A 197 236 Other: 24.99 36.12 29.78 N/A 0 8 Chain A: 8.71 113.59 20.38 N/A 0 1763 Chain S: 21.63 72.38 49.26 N/A 197 0 Histogram: Values Number of atoms 8.71 - 19.20 1203 19.20 - 29.69 249 29.69 - 40.18 189 40.18 - 50.66 139 50.66 - 61.15 108 61.15 - 71.64 58 71.64 - 82.13 8 82.13 - 92.61 3 92.61 - 103.10 1 103.10 - 113.59 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1487 r_work=0.1193 r_free=0.1486 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1486 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1476 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.24 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= 0.1193 r_free= 0.1476 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013660 | | target function (ls_wunit_k1) not normalized (work): 1137.797586 | | target function (ls_wunit_k1) not normalized (free): 105.162023 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1193 0.1476 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1603 0.1600 0.1695 n_refl.: 87591 remove outliers: r(all,work,free)=0.1603 0.1600 0.1695 n_refl.: 87591 overall B=0.03 to atoms: r(all,work,free)=0.1608 0.1605 0.1698 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1190 0.1470 n_refl.: 87591 remove outliers: r(all,work,free)=0.1202 0.1188 0.1470 n_refl.: 87587 ======================== 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 0.3207 291.233 272.704 0.590 1.002 0.360 11.894-9.307 98.04 96 4 0.1503 480.163 474.748 0.923 1.003 0.332 9.237-7.194 100.00 213 7 0.1649 391.127 392.043 0.981 1.003 0.270 7.162-5.571 100.00 427 22 0.1506 293.519 289.920 0.940 1.003 0.240 5.546-4.326 100.00 867 58 0.0823 402.929 399.992 0.956 1.003 0.200 4.315-3.360 100.00 1859 96 0.0702 383.188 382.179 1.000 1.003 0.190 3.356-2.611 100.00 3867 181 0.0943 251.735 250.969 1.009 1.002 0.077 2.608-2.026 99.99 8198 413 0.0952 166.877 166.511 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1179 81.494 81.694 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1604 36.138 35.642 1.020 0.996 0.000 1.221-1.150 99.97 13689 708 0.2328 22.769 21.318 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0474 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1470 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** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1190 r_free=0.1474 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1474 | n_water=433 | time (s): 2.020 (total time: 2.020) Filter (dist) r_work=0.1189 r_free=0.1474 | n_water=430 | time (s): 37.790 (total time: 39.810) Filter (q & B) r_work=0.1189 r_free=0.1474 | n_water=430 | time (s): 1.040 (total time: 40.850) Compute maps r_work=0.1189 r_free=0.1474 | n_water=430 | time (s): 1.680 (total time: 42.530) Filter (map) r_work=0.1233 r_free=0.1499 | n_water=291 | time (s): 3.350 (total time: 45.880) Find peaks r_work=0.1233 r_free=0.1499 | n_water=291 | time (s): 0.750 (total time: 46.630) Add new water r_work=0.1361 r_free=0.1645 | n_water=493 | time (s): 3.320 (total time: 49.950) Refine new water occ: r_work=0.1257 r_free=0.1549 adp: r_work=0.1259 r_free=0.1553 occ: r_work=0.1234 r_free=0.1521 adp: r_work=0.1233 r_free=0.1525 occ: r_work=0.1217 r_free=0.1496 adp: r_work=0.1211 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1211 r_free=0.1497 r_work=0.1211 r_free=0.1497 | n_water=493 | time (s): 244.010 (total time: 293.960) Filter (q & B) r_work=0.1216 r_free=0.1496 | n_water=462 | time (s): 3.400 (total time: 297.360) Filter (dist only) r_work=0.1216 r_free=0.1494 | n_water=461 | time (s): 40.160 (total time: 337.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.015890 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.236593 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 0.1462 0.0233 0.006 0.9 1.9 0.5 0.0 0 1.008 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.62 2.33 3.623 22.117 50.237 3.724 12.18 14.17 1.99 4.127 21.935 50.237 3.654 Individual atomic B min max mean iso aniso Overall: 9.22 109.06 21.70 2.32 226 1762 Protein: 9.22 109.06 17.21 2.33 0 1519 Water: 11.62 70.94 36.42 N/A 226 235 Other: 20.25 31.68 25.92 N/A 0 8 Chain A: 9.22 109.06 19.92 N/A 0 1762 Chain S: 16.47 65.15 35.58 N/A 226 0 Histogram: Values Number of atoms 9.22 - 19.21 1234 19.21 - 29.19 282 29.19 - 39.17 232 39.17 - 49.16 129 49.16 - 59.14 74 59.14 - 69.13 23 69.13 - 79.11 8 79.11 - 89.10 3 89.10 - 99.08 1 99.08 - 109.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1218 r_free=0.1417 r_work=0.1219 r_free=0.1418 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1219 r_free = 0.1418 target_work(ml) = 3.654 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1211 r_free = 0.1411 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1211 r_free= 0.1411 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.650713 | | target function (ml) not normalized (work): 304071.502544 | | target function (ml) not normalized (free): 16069.052841 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1211 0.1411 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1537 0.1537 0.1580 n_refl.: 87587 remove outliers: r(all,work,free)=0.1537 0.1537 0.1580 n_refl.: 87587 overall B=-0.01 to atoms: r(all,work,free)=0.1535 0.1534 0.1579 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1201 0.1385 n_refl.: 87587 remove outliers: r(all,work,free)=0.1207 0.1198 0.1385 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3893 287.876 264.420 0.456 1.000 0.282 11.894-9.307 95.10 93 4 0.2364 473.583 453.204 0.858 1.001 0.263 9.237-7.194 98.64 210 7 0.2349 386.754 384.839 0.946 1.001 0.160 7.162-5.571 100.00 427 22 0.2123 293.519 283.466 0.912 1.001 0.160 5.546-4.326 100.00 867 58 0.1101 402.929 397.793 0.952 1.001 0.160 4.315-3.360 100.00 1859 96 0.0926 383.188 380.460 0.993 1.002 0.160 3.356-2.611 100.00 3867 181 0.1152 251.735 249.985 0.999 1.002 0.160 2.608-2.026 99.99 8198 413 0.1053 166.877 165.977 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1011 81.494 81.693 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1286 36.138 35.731 1.019 1.001 0.000 1.221-1.150 99.97 13689 708 0.2132 22.769 21.338 0.974 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0395 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1385 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1385 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1385 | n_water=461 | time (s): 2.270 (total time: 2.270) Filter (dist) r_work=0.1197 r_free=0.1387 | n_water=460 | time (s): 42.670 (total time: 44.940) Filter (q & B) r_work=0.1198 r_free=0.1386 | n_water=458 | time (s): 2.620 (total time: 47.560) Compute maps r_work=0.1198 r_free=0.1386 | n_water=458 | time (s): 1.580 (total time: 49.140) Filter (map) r_work=0.1223 r_free=0.1385 | n_water=318 | time (s): 3.060 (total time: 52.200) Find peaks r_work=0.1223 r_free=0.1385 | n_water=318 | time (s): 0.560 (total time: 52.760) Add new water r_work=0.1287 r_free=0.1440 | n_water=479 | time (s): 3.640 (total time: 56.400) Refine new water occ: r_work=0.1216 r_free=0.1372 adp: r_work=0.1216 r_free=0.1374 occ: r_work=0.1201 r_free=0.1362 adp: r_work=0.1200 r_free=0.1362 occ: r_work=0.1191 r_free=0.1354 adp: r_work=0.1187 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1353 r_work=0.1187 r_free=0.1353 | n_water=479 | time (s): 186.040 (total time: 242.440) Filter (q & B) r_work=0.1192 r_free=0.1354 | n_water=453 | time (s): 3.120 (total time: 245.560) Filter (dist only) r_work=0.1192 r_free=0.1354 | n_water=452 | time (s): 39.390 (total time: 284.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.298918 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.572296 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1378 0.0189 0.006 1.0 4.5 0.5 0.0 0 1.149 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.78 1.89 3.422 21.534 37.572 3.635 11.84 13.75 1.91 3.654 21.459 37.572 3.627 Individual atomic B min max mean iso aniso Overall: 9.26 105.41 21.41 2.14 219 1760 Protein: 9.26 105.41 17.04 2.14 0 1519 Water: 11.51 70.29 36.02 N/A 219 233 Other: 19.90 29.15 24.97 N/A 0 8 Chain A: 9.26 105.41 19.68 N/A 0 1760 Chain S: 16.07 65.31 35.27 N/A 219 0 Histogram: Values Number of atoms 9.26 - 18.88 1229 18.88 - 28.49 283 28.49 - 38.11 207 38.11 - 47.72 143 47.72 - 57.34 73 57.34 - 66.95 30 66.95 - 76.56 9 76.56 - 86.18 2 86.18 - 95.79 1 95.79 - 105.41 2 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1375 r_work=0.1185 r_free=0.1375 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1185 r_free = 0.1375 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1181 r_free = 0.1372 target_work(ml) = 3.626 | | 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.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1181 r_free= 0.1372 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.626194 | | target function (ml) not normalized (work): 302000.290968 | | target function (ml) not normalized (free): 15965.708109 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1190 0.1181 0.1372 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1500 0.1498 0.1562 n_refl.: 87579 remove outliers: r(all,work,free)=0.1500 0.1498 0.1562 n_refl.: 87579 overall B=-0.02 to atoms: r(all,work,free)=0.1497 0.1495 0.1560 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1189 0.1180 0.1373 n_refl.: 87579 remove outliers: r(all,work,free)=0.1187 0.1178 0.1373 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 0.4168 283.174 249.215 0.439 1.000 0.304 11.894-9.307 94.12 92 4 0.2091 477.515 458.881 0.849 1.002 0.300 9.237-7.194 97.73 208 7 0.2352 383.756 380.350 0.927 1.002 0.160 7.162-5.571 100.00 427 22 0.2144 293.519 283.201 0.905 1.002 0.133 5.546-4.326 100.00 867 58 0.1123 402.929 398.001 0.952 1.002 0.130 4.315-3.360 100.00 1859 96 0.0936 383.188 380.358 0.993 1.002 0.130 3.356-2.611 100.00 3867 181 0.1147 251.735 249.933 1.000 1.002 0.110 2.608-2.026 99.99 8198 413 0.1025 166.877 165.976 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0980 81.494 81.755 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.138 35.752 1.024 0.996 0.000 1.221-1.150 99.97 13689 708 0.2124 22.769 21.394 0.983 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0435 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1178 r_free=0.1373 After: r_work=0.1179 r_free=0.1373 ================================== NQH flips ================================== r_work=0.1179 r_free=0.1373 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1179 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1179 r_free=0.1373 | n_water=452 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1179 r_free=0.1373 | n_water=452 | time (s): 35.920 (total time: 38.220) Filter (q & B) r_work=0.1179 r_free=0.1373 | n_water=450 | time (s): 3.260 (total time: 41.480) Compute maps r_work=0.1179 r_free=0.1373 | n_water=450 | time (s): 1.240 (total time: 42.720) Filter (map) r_work=0.1203 r_free=0.1395 | n_water=337 | time (s): 2.880 (total time: 45.600) Find peaks r_work=0.1203 r_free=0.1395 | n_water=337 | time (s): 0.470 (total time: 46.070) Add new water r_work=0.1253 r_free=0.1452 | n_water=482 | time (s): 2.670 (total time: 48.740) Refine new water occ: r_work=0.1195 r_free=0.1386 adp: r_work=0.1195 r_free=0.1389 occ: r_work=0.1183 r_free=0.1371 adp: r_work=0.1182 r_free=0.1373 occ: r_work=0.1174 r_free=0.1358 adp: r_work=0.1171 r_free=0.1360 ADP+occupancy (water only), MIN, final r_work=0.1171 r_free=0.1360 r_work=0.1171 r_free=0.1360 | n_water=482 | time (s): 178.300 (total time: 227.040) Filter (q & B) r_work=0.1179 r_free=0.1361 | n_water=446 | time (s): 2.690 (total time: 229.730) Filter (dist only) r_work=0.1179 r_free=0.1361 | n_water=445 | time (s): 39.020 (total time: 268.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.980349 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.611787 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1379 0.0181 0.006 1.0 2.6 0.5 0.0 0 0.990 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.79 1.81 3.307 21.269 38.612 3.632 11.99 13.80 1.80 3.629 21.156 38.612 3.625 Individual atomic B min max mean iso aniso Overall: 9.27 101.22 21.07 2.02 212 1760 Protein: 9.27 101.22 16.78 2.02 0 1519 Water: 11.31 69.43 35.64 N/A 212 233 Other: 19.59 27.57 23.87 N/A 0 8 Chain A: 9.27 101.22 19.41 N/A 0 1760 Chain S: 15.72 65.55 34.82 N/A 212 0 Histogram: Values Number of atoms 9.27 - 18.46 1223 18.46 - 27.66 283 27.66 - 36.85 200 36.85 - 46.05 138 46.05 - 55.24 85 55.24 - 64.44 25 64.44 - 73.63 13 73.63 - 82.83 2 82.83 - 92.02 1 92.02 - 101.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1380 r_work=0.1200 r_free=0.1380 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1380 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1377 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1197 r_free= 0.1377 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.624137 | | target function (ml) not normalized (work): 301814.479274 | | target function (ml) not normalized (free): 15957.692681 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1415 0.1428 5.6717 5.6699| | 2: 3.57 - 2.84 1.00 2888 124 0.1107 0.1450 5.2047 5.2603| | 3: 2.83 - 2.48 1.00 2820 163 0.1213 0.1282 5.0142 5.04| | 4: 2.47 - 2.25 1.00 2825 136 0.1035 0.1171 4.717 4.7762| | 5: 2.25 - 2.09 1.00 2756 127 0.0998 0.1127 4.6602 4.7289| | 6: 2.09 - 1.97 1.00 2846 113 0.0984 0.1223 4.3614 4.4949| | 7: 1.97 - 1.87 1.00 2787 165 0.0994 0.1165 4.0783 4.1632| | 8: 1.87 - 1.79 1.00 2789 144 0.1035 0.1301 3.9988 4.1051| | 9: 1.79 - 1.72 1.00 2745 138 0.0963 0.1310 3.7199 3.8927| | 10: 1.72 - 1.66 1.00 2831 160 0.1009 0.1253 3.6382 3.7633| | 11: 1.66 - 1.61 1.00 2712 147 0.0964 0.1073 3.5734 3.6121| | 12: 1.61 - 1.56 1.00 2773 144 0.0918 0.1195 3.3472 3.4901| | 13: 1.56 - 1.52 1.00 2745 130 0.0982 0.1069 3.3413 3.4341| | 14: 1.52 - 1.48 1.00 2803 134 0.0990 0.1126 3.2616 3.3361| | 15: 1.48 - 1.45 1.00 2738 128 0.1022 0.1371 3.1729 3.3477| | 16: 1.45 - 1.42 1.00 2756 161 0.1079 0.1248 3.1572 3.2396| | 17: 1.42 - 1.39 1.00 2785 139 0.1127 0.1325 3.1179 3.24| | 18: 1.39 - 1.36 1.00 2741 179 0.1152 0.1397 3.0883 3.2686| | 19: 1.36 - 1.34 1.00 2807 134 0.1216 0.1611 3.0935 3.2793| | 20: 1.34 - 1.32 1.00 2696 147 0.1327 0.1501 3.0925 3.1439| | 21: 1.32 - 1.30 1.00 2785 112 0.1412 0.1622 3.0871 3.1641| | 22: 1.29 - 1.27 1.00 2704 152 0.1479 0.1902 3.0868 3.2841| | 23: 1.27 - 1.26 1.00 2802 156 0.1567 0.1879 3.1016 3.2123| | 24: 1.26 - 1.24 1.00 2744 132 0.1624 0.1780 3.0954 3.1945| | 25: 1.24 - 1.22 1.00 2733 148 0.1795 0.2331 3.1102 3.2897| | 26: 1.22 - 1.21 1.00 2727 135 0.1866 0.1793 3.1239 3.2017| | 27: 1.21 - 1.19 1.00 2814 148 0.2012 0.2081 3.138 3.1488| | 28: 1.19 - 1.18 1.00 2671 147 0.2143 0.2315 3.1374 3.1608| | 29: 1.18 - 1.16 1.00 2800 134 0.2223 0.2341 3.1269 3.2152| | 30: 1.16 - 1.15 1.00 2739 148 0.2374 0.2479 3.1142 3.1608| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.27 1.00 0.97 6478.25| | 2: 3.57 - 2.84 2888 124 0.92 13.61 1.01 0.97 6478.25| | 3: 2.83 - 2.48 2820 163 0.88 17.83 0.99 0.97 5428.71| | 4: 2.47 - 2.25 2825 136 0.91 14.88 1.00 0.98 2722.28| | 5: 2.25 - 2.09 2756 127 0.89 17.16 1.01 0.98 2722.28| | 6: 2.09 - 1.97 2846 113 0.91 13.81 1.02 0.97 1596.37| | 7: 1.97 - 1.87 2787 165 0.94 10.97 1.02 0.97 636.12| | 8: 1.87 - 1.79 2789 144 0.91 14.51 0.99 0.97 636.12| | 9: 1.79 - 1.72 2745 138 0.93 11.56 0.98 0.97 344.06| | 10: 1.72 - 1.66 2831 160 0.93 12.40 0.98 0.97 285.57| | 11: 1.66 - 1.61 2712 147 0.93 13.01 0.98 0.97 272.49| | 12: 1.61 - 1.56 2773 144 0.95 9.63 0.99 0.97 149.12| | 13: 1.56 - 1.52 2745 130 0.94 11.18 1.02 0.97 149.12| | 14: 1.52 - 1.48 2803 134 0.94 11.37 1.02 0.97 133.22| | 15: 1.48 - 1.45 2738 128 0.95 10.52 1.01 0.98 104.11| | 16: 1.45 - 1.42 2756 161 0.94 11.67 1.02 0.98 104.11| | 17: 1.42 - 1.39 2785 139 0.94 11.52 1.01 0.98 94.09| | 18: 1.39 - 1.36 2741 179 0.94 11.83 1.01 0.98 88.29| | 19: 1.36 - 1.34 2807 134 0.94 12.44 1.00 0.98 88.29| | 20: 1.34 - 1.32 2696 147 0.94 12.57 0.99 0.97 83.22| | 21: 1.32 - 1.30 2785 112 0.93 13.48 0.99 0.97 82.87| | 22: 1.29 - 1.27 2704 152 0.93 14.01 0.99 0.96 82.96| | 23: 1.27 - 1.26 2802 156 0.92 14.89 0.98 0.95 83.42| | 24: 1.26 - 1.24 2744 132 0.92 15.04 0.97 0.95 83.42| | 25: 1.24 - 1.22 2733 148 0.91 16.42 0.96 0.94 84.69| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.03 0.94 86.11| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.02 0.94 86.11| | 28: 1.19 - 1.18 2671 147 0.88 20.17 1.01 0.93 88.83| | 29: 1.18 - 1.16 2800 134 0.88 20.48 0.99 0.93 89.86| | 30: 1.16 - 1.15 2739 148 0.86 21.83 0.98 0.93 89.86| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.87 max = 6478.25 mean = 1006.21| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.15| |phase err.(test): min = 0.00 max = 88.60 mean = 14.31| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1197 0.1377 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1519 0.1519 0.1562 n_refl.: 87575 remove outliers: r(all,work,free)=0.1519 0.1519 0.1562 n_refl.: 87575 overall B=-0.02 to atoms: r(all,work,free)=0.1516 0.1516 0.1560 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1197 0.1380 n_refl.: 87575 remove outliers: r(all,work,free)=0.1205 0.1196 0.1380 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4172 283.174 247.557 0.429 1.001 0.300 11.894-9.307 93.14 91 4 0.2320 471.282 456.087 0.855 1.002 0.207 9.237-7.194 97.73 208 7 0.2509 383.756 376.655 0.910 1.003 0.120 7.162-5.571 100.00 427 22 0.2248 293.519 282.231 0.896 1.003 0.119 5.546-4.326 100.00 867 58 0.1195 402.929 397.775 0.953 1.003 0.117 4.315-3.360 100.00 1859 96 0.0984 383.188 380.418 0.993 1.002 0.117 3.356-2.611 100.00 3867 181 0.1174 251.735 249.789 1.001 1.002 0.100 2.608-2.026 99.99 8198 413 0.1046 166.877 165.942 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0983 81.494 81.736 1.029 0.998 0.000 1.573-1.221 100.00 36679 1900 0.1230 36.138 35.758 1.026 0.995 0.000 1.221-1.150 99.97 13689 708 0.2118 22.769 21.392 0.985 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0467 ================= 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 : 0.2604 0.1950 0.081 5.186 8.8 119.3 19.9 258 0.000 1_bss: 0.1624 0.1775 0.081 5.186 9.0 119.5 20.1 258 0.000 1_settarget: 0.1624 0.1775 0.081 5.186 9.0 119.5 20.1 258 0.000 1_nqh: 0.1631 0.1788 0.081 5.186 9.0 119.5 20.1 258 0.007 1_weight: 0.1631 0.1788 0.081 5.186 9.0 119.5 20.1 258 0.007 1_xyzrec: 0.1211 0.1460 0.007 0.931 9.0 119.5 20.1 258 0.131 1_adp: 0.1238 0.1532 0.007 0.931 8.5 118.5 21.0 258 0.131 1_regHadp: 0.1242 0.1535 0.007 0.931 8.5 118.5 21.0 258 0.131 1_occ: 0.1241 0.1539 0.007 0.931 8.5 118.5 21.0 258 0.131 2_bss: 0.1239 0.1531 0.007 0.931 8.6 118.6 21.1 258 0.131 2_settarget: 0.1239 0.1531 0.007 0.931 8.6 118.6 21.1 258 0.131 2_updatecdl: 0.1239 0.1531 0.007 0.936 8.6 118.6 21.1 258 0.131 2_nqh: 0.1239 0.1531 0.007 0.936 8.6 118.6 21.1 258 0.131 2_sol: 0.1225 0.1480 0.007 0.936 8.6 118.6 23.6 433 n/a 2_weight: 0.1225 0.1480 0.007 0.936 8.6 118.6 23.6 433 n/a 2_xyzrec: 0.1222 0.1510 0.007 0.877 8.6 118.6 23.6 433 n/a 2_adp: 0.1193 0.1487 0.007 0.877 8.7 113.6 23.3 433 n/a 2_regHadp: 0.1193 0.1486 0.007 0.877 8.7 113.6 23.3 433 n/a 2_occ: 0.1193 0.1476 0.007 0.877 8.7 113.6 23.3 433 n/a 3_bss: 0.1188 0.1470 0.007 0.877 8.7 113.6 23.3 433 n/a 3_settarget: 0.1188 0.1470 0.007 0.877 8.7 113.6 23.3 433 n/a 3_updatecdl: 0.1188 0.1470 0.007 0.878 8.7 113.6 23.3 433 n/a 3_nqh: 0.1190 0.1474 0.007 0.878 8.7 113.6 23.3 433 n/a 3_sol: 0.1216 0.1494 0.007 0.878 8.7 113.6 22.0 461 n/a 3_weight: 0.1216 0.1494 0.007 0.878 8.7 113.6 22.0 461 n/a 3_xyzrec: 0.1229 0.1462 0.006 0.908 8.7 113.6 22.0 461 n/a 3_adp: 0.1218 0.1417 0.006 0.908 9.2 109.1 21.7 461 n/a 3_regHadp: 0.1219 0.1418 0.006 0.908 9.2 109.1 21.7 461 n/a 3_occ: 0.1211 0.1411 0.006 0.908 9.2 109.1 21.7 461 n/a 4_bss: 0.1198 0.1385 0.006 0.908 9.2 109.0 21.7 461 n/a 4_settarget: 0.1198 0.1385 0.006 0.908 9.2 109.0 21.7 461 n/a 4_updatecdl: 0.1198 0.1385 0.006 0.907 9.2 109.0 21.7 461 n/a 4_nqh: 0.1198 0.1385 0.006 0.907 9.2 109.0 21.7 461 n/a 4_sol: 0.1192 0.1354 0.006 0.907 9.2 109.0 21.5 452 n/a 4_weight: 0.1192 0.1354 0.006 0.907 9.2 109.0 21.5 452 n/a 4_xyzrec: 0.1189 0.1378 0.006 0.977 9.2 109.0 21.5 452 n/a 4_adp: 0.1184 0.1375 0.006 0.977 9.3 105.4 21.4 452 n/a 4_regHadp: 0.1185 0.1375 0.006 0.977 9.3 105.4 21.4 452 n/a 4_occ: 0.1181 0.1372 0.006 0.977 9.3 105.4 21.4 452 n/a 5_bss: 0.1178 0.1373 0.006 0.977 9.2 105.4 21.4 452 n/a 5_settarget: 0.1178 0.1373 0.006 0.977 9.2 105.4 21.4 452 n/a 5_updatecdl: 0.1178 0.1373 0.006 0.978 9.2 105.4 21.4 452 n/a 5_setrh: 0.1179 0.1373 0.006 0.978 9.2 105.4 21.4 452 n/a 5_nqh: 0.1179 0.1373 0.006 0.978 9.2 105.4 21.4 452 n/a 5_sol: 0.1179 0.1361 0.006 0.978 9.2 105.4 21.3 445 n/a 5_weight: 0.1179 0.1361 0.006 0.978 9.2 105.4 21.3 445 n/a 5_xyzrec: 0.1198 0.1379 0.006 1.046 9.2 105.4 21.3 445 n/a 5_adp: 0.1199 0.1380 0.006 1.046 9.3 101.2 21.1 445 n/a 5_regHadp: 0.1200 0.1380 0.006 1.046 9.3 101.2 21.1 445 n/a 5_occ: 0.1197 0.1377 0.006 1.046 9.3 101.2 21.1 445 n/a end: 0.1196 0.1380 0.006 1.046 9.3 101.2 21.1 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_9451893_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_9451893_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7200 Refinement macro-cycles (run) : 3492.1800 Write final files (write_after_run_outputs) : 65.2200 Total : 3562.1200 Total CPU time: 59.95 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:22 PST -0800 (1735452682.15 s) Start R-work = 0.1624, R-free = 0.1775 Final R-work = 0.1196, R-free = 0.1380 =============================================================================== Job complete usr+sys time: 3694.61 seconds wall clock time: 66 minutes 33.39 seconds (3993.39 seconds total)