Starting phenix.refine on Sat Dec 28 21:06:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9394591.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_9394591.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9394591.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 3 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: 2.10, per 1000 atoms: 0.62 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: 0.88 Conformation dependent library (CDL) restraints added in 303.0 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: 0.65 - 0.92: 541 0.92 - 1.18: 1132 1.18 - 1.45: 732 1.45 - 1.72: 732 1.72 - 1.99: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 89 " pdb=" CA LYS A 89 " ideal model delta sigma weight residual 1.459 1.692 -0.233 1.21e-02 6.83e+03 3.70e+02 bond pdb=" N THR A 140 " pdb=" CA THR A 140 " ideal model delta sigma weight residual 1.458 1.232 0.226 1.22e-02 6.72e+03 3.42e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.463 1.662 -0.198 1.08e-02 8.57e+03 3.37e+02 bond pdb=" C BGLU A 94 " pdb=" O BGLU A 94 " ideal model delta sigma weight residual 1.236 1.027 0.209 1.15e-02 7.56e+03 3.32e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.440 -0.206 1.19e-02 7.06e+03 2.99e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 3027 4.42 - 8.84: 1845 8.84 - 13.25: 728 13.25 - 17.67: 156 17.67 - 22.09: 21 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O AGLY A 65 " pdb=" C AGLY A 65 " pdb=" N APRO A 66 " ideal model delta sigma weight residual 121.77 137.63 -15.86 1.00e+00 1.00e+00 2.52e+02 angle pdb=" O VAL A 146 " pdb=" C VAL A 146 " pdb=" N GLU A 147 " ideal model delta sigma weight residual 123.05 139.49 -16.44 1.11e+00 8.12e-01 2.19e+02 angle pdb=" O THR A 160 " pdb=" C THR A 160 " pdb=" N SER A 161 " ideal model delta sigma weight residual 122.34 140.17 -17.83 1.25e+00 6.40e-01 2.04e+02 angle pdb=" O ALA A 167 " pdb=" C ALA A 167 " pdb=" N ILE A 168 " ideal model delta sigma weight residual 122.12 137.16 -15.04 1.06e+00 8.90e-01 2.01e+02 angle pdb=" O ASN A 173 " pdb=" C ASN A 173 " pdb=" N GLY A 174 " ideal model delta sigma weight residual 122.35 139.54 -17.19 1.23e+00 6.61e-01 1.95e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 21.29: 991 21.29 - 42.57: 82 42.57 - 63.85: 33 63.85 - 85.13: 4 85.13 - 106.41: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ARG A 156 " pdb=" C ARG A 156 " pdb=" N GLY A 157 " pdb=" CA GLY A 157 " ideal model delta harmonic sigma weight residual -180.00 -156.27 -23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta harmonic sigma weight residual -180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 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 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.319: 137 0.319 - 0.631: 79 0.631 - 0.943: 21 0.943 - 1.255: 5 1.255 - 1.568: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.02 -1.57 2.00e-01 2.50e+01 6.14e+01 chirality pdb=" CA ARG A 156 " pdb=" N ARG A 156 " pdb=" C ARG A 156 " pdb=" CB ARG A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.40 1.11 2.00e-01 2.50e+01 3.06e+01 chirality pdb=" CA GLU A 143 " pdb=" N GLU A 143 " pdb=" C GLU A 143 " pdb=" CB GLU A 143 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.98e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.158 9.50e-02 1.11e+02 9.57e-02 1.46e+02 pdb=" NE ARG A 48 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.133 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.089 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.088 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " 0.065 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.081 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " 0.096 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.012 2.00e-02 2.50e+03 5.91e-02 1.05e+02 pdb=" CG TYR A 139 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.101 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.107 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.046 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.048 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.022 2.00e-02 2.50e+03 6.36e-02 9.11e+01 pdb=" CG HIS A 126 " 0.061 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.104 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.102 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.042 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.043 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.057 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 526 2.23 - 2.82: 7384 2.82 - 3.41: 10808 3.41 - 4.01: 15431 4.01 - 4.60: 22530 Nonbonded interactions: 56679 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.633 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.816 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.819 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.839 2.450 nonbonded pdb=" O PRO A 22 " pdb=" H MET A 26 " model vdw 1.853 2.450 ... (remaining 56674 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_9394591_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= 0.2614 r_free= 0.1972 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794106 | | target function (ml) not normalized (work): 232765.799277 | | target function (ml) not normalized (free): 11827.826047 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3050 0.2123 6.9982 4.9567| | 2: 3.57 - 2.84 1.00 2876 122 0.2417 0.1753 4.3552 4.3359| | 3: 2.84 - 2.48 1.00 2833 165 0.2356 0.1821 4.1386 4.1945| | 4: 2.47 - 2.25 1.00 2825 136 0.2342 0.1565 3.8418 3.8638| | 5: 2.25 - 2.09 1.00 2756 127 0.2461 0.1639 3.8064 3.8339| | 6: 2.09 - 1.97 1.00 2846 113 0.2546 0.1663 3.4787 3.5349| | 7: 1.97 - 1.87 1.00 2787 165 0.2558 0.1826 3.1583 3.1674| | 8: 1.87 - 1.79 1.00 2789 144 0.2469 0.1919 3.0654 3.1307| | 9: 1.79 - 1.72 1.00 2745 138 0.2417 0.1951 2.8927 2.9675| | 10: 1.72 - 1.66 1.00 2789 158 0.2477 0.1994 2.8002 2.9127| | 11: 1.66 - 1.61 1.00 2740 147 0.2541 0.1779 2.7646 2.7356| | 12: 1.61 - 1.56 1.00 2787 146 0.2518 0.1966 2.625 2.6361| | 13: 1.56 - 1.52 1.00 2745 130 0.2572 0.1716 2.5723 2.5291| | 14: 1.52 - 1.48 1.00 2803 134 0.2604 0.2132 2.5123 2.5885| | 15: 1.48 - 1.45 1.00 2738 128 0.2609 0.2244 2.4373 2.5014| | 16: 1.45 - 1.42 1.00 2756 161 0.2672 0.2108 2.3957 2.4239| | 17: 1.42 - 1.39 1.00 2785 139 0.2667 0.2003 2.3443 2.3553| | 18: 1.39 - 1.36 1.00 2741 179 0.2695 0.2250 2.2924 2.3639| | 19: 1.36 - 1.34 1.00 2807 134 0.2673 0.2325 2.2477 2.3067| | 20: 1.34 - 1.32 1.00 2696 147 0.2692 0.2338 2.2016 2.235| | 21: 1.32 - 1.30 1.00 2785 112 0.2722 0.2294 2.1621 2.1829| | 22: 1.29 - 1.27 1.00 2704 152 0.2748 0.2525 2.1295 2.1689| | 23: 1.27 - 1.26 1.00 2802 156 0.2832 0.2552 2.1211 2.2196| | 24: 1.26 - 1.24 1.00 2744 132 0.2761 0.2514 2.083 2.1567| | 25: 1.24 - 1.22 1.00 2734 148 0.2854 0.2764 2.0415 2.1566| | 26: 1.22 - 1.21 1.00 2727 135 0.2924 0.2210 2.0347 2.0363| | 27: 1.21 - 1.19 1.00 2814 148 0.2965 0.2592 2.0021 1.9545| | 28: 1.19 - 1.18 1.00 2671 147 0.2961 0.2728 1.9836 2.006| | 29: 1.18 - 1.16 1.00 2800 134 0.2977 0.2682 1.9579 2.0092| | 30: 1.16 - 1.15 1.00 2740 148 0.3030 0.2838 1.9265 1.962| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 19.15 0.76 0.23 1507.46| | 2: 3.57 - 2.84 2876 122 0.80 26.37 1.27 0.23 1507.46| | 3: 2.84 - 2.48 2833 165 0.74 32.30 1.24 0.23 1250.49| | 4: 2.47 - 2.25 2825 136 0.81 25.84 1.26 0.25 583.60| | 5: 2.25 - 2.09 2756 127 0.77 29.70 1.28 0.25 583.60| | 6: 2.09 - 1.97 2846 113 0.83 23.09 1.29 0.25 319.56| | 7: 1.97 - 1.87 2787 165 0.90 16.86 1.28 0.25 94.37| | 8: 1.87 - 1.79 2789 144 0.85 21.61 1.25 0.25 94.37| | 9: 1.79 - 1.72 2745 138 0.88 19.03 1.24 0.25 56.55| | 10: 1.72 - 1.66 2789 158 0.86 20.53 1.23 0.25 48.97| | 11: 1.66 - 1.61 2740 147 0.85 21.50 1.24 0.25 47.14| | 12: 1.61 - 1.56 2787 146 0.89 18.29 1.23 0.25 28.62| | 13: 1.56 - 1.52 2745 130 0.87 20.27 1.24 0.25 28.62| | 14: 1.52 - 1.48 2803 134 0.87 20.60 1.24 0.25 25.76| | 15: 1.48 - 1.45 2738 128 0.87 20.13 1.23 0.25 20.53| | 16: 1.45 - 1.42 2756 161 0.86 21.61 1.23 0.25 20.53| | 17: 1.42 - 1.39 2785 139 0.87 20.71 1.22 0.25 17.65| | 18: 1.39 - 1.36 2741 179 0.86 21.25 1.22 0.25 15.98| | 19: 1.36 - 1.34 2807 134 0.85 22.21 1.22 0.25 15.98| | 20: 1.34 - 1.32 2696 147 0.86 21.38 1.22 0.24 13.44| | 21: 1.32 - 1.30 2785 112 0.85 22.59 1.21 0.24 13.26| | 22: 1.29 - 1.27 2704 152 0.85 23.20 1.22 0.24 12.95| | 23: 1.27 - 1.26 2802 156 0.85 22.50 1.22 0.24 11.40| | 24: 1.26 - 1.24 2744 132 0.85 22.99 1.20 0.24 11.40| | 25: 1.24 - 1.22 2734 148 0.84 24.20 1.20 0.23 10.82| | 26: 1.22 - 1.21 2727 135 0.83 24.66 1.19 0.23 10.17| | 27: 1.21 - 1.19 2814 148 0.83 25.25 1.21 0.23 10.17| | 28: 1.19 - 1.18 2671 147 0.82 25.70 1.18 0.23 9.58| | 29: 1.18 - 1.16 2800 134 0.82 26.20 1.16 0.22 9.36| | 30: 1.16 - 1.15 2740 148 0.80 27.79 1.15 0.22 9.36| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.36 max = 1507.46 mean = 218.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.92| |phase err.(test): min = 0.00 max = 89.13 mean = 22.84| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.235 1557 Z= 5.484 Angle : 5.353 19.110 2118 Z= 3.755 Chirality : 0.409 1.568 243 Planarity : 0.030 0.106 284 Dihedral : 14.604 106.413 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 2.48 % Allowed : 2.48 % Favored : 95.03 % Cbeta Deviations : 31.89 % 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: -3.09 (0.46), residues: 224 helix: -2.93 (0.38), residues: 102 sheet: -0.89 (0.76), residues: 38 loop : -1.07 (0.56), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.082 0.019 ARG A 145 TYR 0.100 0.043 TYR A 139 PHE 0.112 0.044 PHE A 119 HIS 0.099 0.041 HIS A 126 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= 0.2614 r_free= 0.1972 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794106 | | target function (ml) not normalized (work): 232765.799277 | | target function (ml) not normalized (free): 11827.826047 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2573 0.2615 0.1972 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2573 0.2615 0.1972 n_refl.: 87602 remove outliers: r(all,work,free)=0.1987 0.1990 0.1972 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2013 0.2016 0.1987 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1654 0.1646 0.1803 n_refl.: 87594 remove outliers: r(all,work,free)=0.1653 0.1645 0.1803 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 0.3904 386.431 358.235 0.737 0.915 0.416 11.894-9.307 99.02 97 4 0.1834 613.826 594.828 1.011 0.916 0.403 9.237-7.194 100.00 213 7 0.2125 502.034 490.401 1.049 0.916 0.360 7.162-5.571 100.00 427 22 0.2163 376.749 364.057 1.016 0.917 0.288 5.546-4.326 100.00 867 58 0.1277 517.183 511.330 1.054 0.917 0.218 4.315-3.360 100.00 1859 96 0.1151 491.845 487.713 1.096 0.918 0.189 3.356-2.611 100.00 3867 181 0.1460 323.116 319.507 1.082 0.920 0.109 2.608-2.026 99.99 8198 413 0.1351 214.197 212.292 1.091 0.922 0.000 2.025-1.573 100.00 17313 902 0.1661 104.603 103.818 1.093 0.926 0.000 1.573-1.221 100.00 36679 1900 0.2079 46.385 45.050 1.071 0.933 0.000 1.221-1.150 99.97 13689 708 0.2584 29.226 26.936 1.031 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0490 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1645 r_free=0.1803 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1646 r_free=0.1805 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.618834 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1996.403563 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 0.1458 0.0247 0.007 0.9 1.3 0.5 0.0 0 11.809 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.58 2.47 3.013 19.073 1996.404 0.017 12.37 15.33 2.96 3.104 19.505 1996.404 0.016 Individual atomic B min max mean iso aniso Overall: 8.52 118.39 20.92 2.88 0 1785 Protein: 8.52 118.39 17.81 2.88 0 1519 Water: 11.09 114.90 38.96 N/A 0 258 Other: 22.62 35.53 28.73 N/A 0 8 Chain A: 8.52 118.39 20.92 N/A 0 1785 Histogram: Values Number of atoms 8.52 - 19.50 1211 19.50 - 30.49 227 30.49 - 41.48 169 41.48 - 52.46 97 52.46 - 63.45 52 63.45 - 74.44 18 74.44 - 85.43 4 85.43 - 96.41 4 96.41 - 107.40 0 107.40 - 118.39 3 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1533 r_work=0.1241 r_free=0.1537 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1241 r_free = 0.1537 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1242 r_free = 0.1541 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1242 r_free= 0.1541 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015460 | | target function (ls_wunit_k1) not normalized (work): 1287.798943 | | target function (ls_wunit_k1) not normalized (free): 113.607349 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1256 0.1242 0.1541 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1697 0.1695 0.1765 n_refl.: 87593 remove outliers: r(all,work,free)=0.1697 0.1695 0.1765 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1720 0.1719 0.1781 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1255 0.1241 0.1535 n_refl.: 87593 remove outliers: r(all,work,free)=0.1254 0.1240 0.1535 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 0.3600 298.736 277.939 0.635 1.001 0.380 11.894-9.307 98.04 96 4 0.1544 480.501 464.092 0.906 1.001 0.380 9.237-7.194 100.00 213 7 0.1847 391.402 385.981 0.949 1.002 0.340 7.162-5.571 100.00 427 22 0.1733 293.725 288.898 0.927 1.002 0.253 5.546-4.326 100.00 867 58 0.0920 403.212 400.854 0.951 1.002 0.204 4.315-3.360 100.00 1859 96 0.0778 383.458 382.233 0.994 1.002 0.190 3.356-2.611 100.00 3867 181 0.1025 251.912 251.312 0.996 1.002 0.120 2.608-2.026 99.99 8198 413 0.0973 166.995 166.542 1.009 1.002 0.000 2.025-1.573 100.00 17313 902 0.1203 81.551 81.796 1.016 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1642 36.163 35.619 1.002 1.003 0.000 1.221-1.150 99.97 13689 708 0.2355 22.785 21.195 0.961 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0537 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1240 r_free=0.1535 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1240 r_free=0.1535 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1240 r_free=0.1535 | n_water=258 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1250 r_free=0.1534 | n_water=252 | time (s): 26.320 (total time: 28.700) Filter (q & B) r_work=0.1253 r_free=0.1535 | n_water=249 | time (s): 3.680 (total time: 32.380) Compute maps r_work=0.1253 r_free=0.1535 | n_water=249 | time (s): 1.850 (total time: 34.230) Filter (map) r_work=0.1269 r_free=0.1544 | n_water=236 | time (s): 3.820 (total time: 38.050) Find peaks r_work=0.1269 r_free=0.1544 | n_water=236 | time (s): 0.710 (total time: 38.760) Add new water r_work=0.1426 r_free=0.1694 | n_water=453 | time (s): 3.740 (total time: 42.500) Refine new water occ: r_work=0.1336 r_free=0.1565 adp: r_work=0.1253 r_free=0.1508 occ: r_work=0.1267 r_free=0.1508 adp: r_work=0.1230 r_free=0.1490 occ: r_work=0.1233 r_free=0.1483 adp: r_work=0.1224 r_free=0.1479 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1479 r_work=0.1224 r_free=0.1479 | n_water=453 | time (s): 110.930 (total time: 153.430) Filter (q & B) r_work=0.1232 r_free=0.1485 | n_water=430 | time (s): 3.920 (total time: 157.350) Filter (dist only) r_work=0.1232 r_free=0.1484 | n_water=429 | time (s): 43.790 (total time: 201.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.804637 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1553.086499 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 0.1530 0.0302 0.007 0.9 2.6 0.5 0.0 0 12.902 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 15.30 3.02 3.775 23.074 1553.086 0.015 11.99 14.95 2.96 4.156 22.929 1553.086 0.015 Individual atomic B min max mean iso aniso Overall: 8.75 114.07 23.11 2.61 193 1763 Protein: 8.75 114.07 17.62 2.61 0 1519 Water: 11.14 73.00 42.45 N/A 193 236 Other: 25.23 36.86 30.44 N/A 0 8 Chain A: 8.75 114.07 20.34 N/A 0 1763 Chain S: 19.33 73.00 48.50 N/A 193 0 Histogram: Values Number of atoms 8.75 - 19.28 1206 19.28 - 29.82 251 29.82 - 40.35 191 40.35 - 50.88 141 50.88 - 61.41 99 61.41 - 71.94 54 71.94 - 82.48 8 82.48 - 93.01 3 93.01 - 103.54 1 103.54 - 114.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1495 r_work=0.1199 r_free=0.1495 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1495 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1494 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.14 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= 0.1201 r_free= 0.1494 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.013968 | | target function (ls_wunit_k1) not normalized (work): 1163.442272 | | target function (ls_wunit_k1) not normalized (free): 109.178100 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1201 0.1494 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1607 0.1602 0.1739 n_refl.: 87591 remove outliers: r(all,work,free)=0.1607 0.1602 0.1739 n_refl.: 87591 overall B=0.03 to atoms: r(all,work,free)=0.1611 0.1606 0.1741 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1197 0.1490 n_refl.: 87591 remove outliers: r(all,work,free)=0.1210 0.1195 0.1490 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3441 294.677 270.956 0.630 0.940 0.370 11.894-9.307 98.04 96 4 0.1400 480.501 479.534 0.986 0.941 0.363 9.237-7.194 100.00 213 7 0.1718 391.402 390.994 1.041 0.941 0.290 7.162-5.571 100.00 427 22 0.1485 293.725 290.845 1.003 0.941 0.229 5.546-4.326 100.00 867 58 0.0828 403.212 400.359 1.019 0.941 0.210 4.315-3.360 100.00 1859 96 0.0711 383.458 382.409 1.067 0.941 0.200 3.356-2.611 100.00 3867 181 0.0966 251.912 251.249 1.072 0.942 0.150 2.608-2.026 99.99 8198 413 0.0969 166.995 166.616 1.082 0.943 0.000 2.025-1.573 100.00 17313 902 0.1173 81.551 81.750 1.089 0.944 0.000 1.573-1.221 100.00 36679 1900 0.1600 36.163 35.669 1.075 0.946 0.000 1.221-1.150 99.97 13689 708 0.2336 22.785 21.349 1.031 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0393 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1490 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1195 r_free=0.1490 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1490 | n_water=429 | time (s): 2.070 (total time: 2.070) Filter (dist) r_work=0.1196 r_free=0.1486 | n_water=426 | time (s): 41.870 (total time: 43.940) Filter (q & B) r_work=0.1196 r_free=0.1486 | n_water=426 | time (s): 0.890 (total time: 44.830) Compute maps r_work=0.1196 r_free=0.1486 | n_water=426 | time (s): 1.530 (total time: 46.360) Filter (map) r_work=0.1234 r_free=0.1480 | n_water=293 | time (s): 3.710 (total time: 50.070) Find peaks r_work=0.1234 r_free=0.1480 | n_water=293 | time (s): 0.480 (total time: 50.550) Add new water r_work=0.1364 r_free=0.1589 | n_water=487 | time (s): 2.450 (total time: 53.000) Refine new water occ: r_work=0.1263 r_free=0.1509 adp: r_work=0.1265 r_free=0.1510 occ: r_work=0.1242 r_free=0.1490 adp: r_work=0.1240 r_free=0.1489 occ: r_work=0.1227 r_free=0.1478 adp: r_work=0.1220 r_free=0.1473 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1473 r_work=0.1220 r_free=0.1473 | n_water=487 | time (s): 259.820 (total time: 312.820) Filter (q & B) r_work=0.1223 r_free=0.1476 | n_water=454 | time (s): 3.630 (total time: 316.450) Filter (dist only) r_work=0.1222 r_free=0.1474 | n_water=453 | time (s): 39.310 (total time: 355.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.044961 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 34.890364 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 0.1231 0.1455 0.0225 0.006 0.9 1.9 0.5 0.0 0 1.022 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 14.55 2.25 3.613 22.080 34.890 3.723 12.31 14.20 1.89 3.965 21.940 34.890 3.664 Individual atomic B min max mean iso aniso Overall: 9.24 110.04 21.75 2.28 220 1760 Protein: 9.24 110.04 17.29 2.28 0 1519 Water: 11.61 71.68 36.58 N/A 220 233 Other: 21.23 33.07 27.93 N/A 0 8 Chain A: 9.24 110.04 19.97 N/A 0 1760 Chain S: 16.31 66.26 36.02 N/A 220 0 Histogram: Values Number of atoms 9.24 - 19.32 1229 19.32 - 29.40 286 29.40 - 39.48 225 39.48 - 49.56 127 49.56 - 59.64 80 59.64 - 69.72 21 69.72 - 79.80 6 79.80 - 89.88 3 89.88 - 99.96 1 99.96 - 110.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1420 r_work=0.1232 r_free=0.1420 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1420 target_work(ml) = 3.664 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1422 target_work(ml) = 3.663 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1227 r_free= 0.1422 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.662594 | | target function (ml) not normalized (work): 305064.818504 | | target function (ml) not normalized (free): 16097.433694 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1236 0.1227 0.1422 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1547 0.1546 0.1597 n_refl.: 87588 remove outliers: r(all,work,free)=0.1547 0.1546 0.1597 n_refl.: 87588 overall B=-0.02 to atoms: r(all,work,free)=0.1544 0.1543 0.1595 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1224 0.1216 0.1390 n_refl.: 87588 remove outliers: r(all,work,free)=0.1222 0.1213 0.1390 n_refl.: 87582 ======================== 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 0.3849 299.514 257.405 0.474 1.001 0.328 11.894-9.307 97.06 95 4 0.2453 480.645 460.989 0.851 1.002 0.320 9.237-7.194 98.64 210 7 0.2437 384.963 384.835 0.940 1.002 0.160 7.162-5.571 100.00 427 22 0.2097 293.725 283.162 0.909 1.002 0.150 5.546-4.326 100.00 867 58 0.1100 403.212 398.839 0.951 1.002 0.146 4.315-3.360 100.00 1859 96 0.0925 383.458 381.065 0.994 1.002 0.143 3.356-2.611 100.00 3867 181 0.1167 251.912 249.919 1.000 1.002 0.130 2.608-2.026 99.99 8198 413 0.1062 166.995 166.061 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.1035 81.551 81.760 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1310 36.163 35.740 1.021 0.999 0.000 1.221-1.150 99.97 13689 708 0.2135 22.785 21.398 0.982 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0491 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1213 r_free=0.1390 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1213 r_free=0.1390 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1213 r_free=0.1390 | n_water=453 | time (s): 2.010 (total time: 2.010) Filter (dist) r_work=0.1213 r_free=0.1390 | n_water=452 | time (s): 41.660 (total time: 43.670) Filter (q & B) r_work=0.1213 r_free=0.1390 | n_water=451 | time (s): 3.670 (total time: 47.340) Compute maps r_work=0.1213 r_free=0.1390 | n_water=451 | time (s): 1.830 (total time: 49.170) Filter (map) r_work=0.1235 r_free=0.1388 | n_water=316 | time (s): 2.780 (total time: 51.950) Find peaks r_work=0.1235 r_free=0.1388 | n_water=316 | time (s): 0.530 (total time: 52.480) Add new water r_work=0.1296 r_free=0.1439 | n_water=475 | time (s): 3.500 (total time: 55.980) Refine new water occ: r_work=0.1224 r_free=0.1380 adp: r_work=0.1224 r_free=0.1382 occ: r_work=0.1210 r_free=0.1371 adp: r_work=0.1208 r_free=0.1371 occ: r_work=0.1201 r_free=0.1368 adp: r_work=0.1197 r_free=0.1364 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1364 r_work=0.1197 r_free=0.1364 | n_water=475 | time (s): 226.370 (total time: 282.350) Filter (q & B) r_work=0.1203 r_free=0.1364 | n_water=441 | time (s): 2.560 (total time: 284.910) Filter (dist only) r_work=0.1203 r_free=0.1364 | n_water=441 | time (s): 34.600 (total time: 319.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.857802 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.857528 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1210 0.1387 0.0177 0.006 0.9 2.2 0.5 0.0 0 0.929 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 13.87 1.77 3.425 21.573 49.858 3.648 11.89 13.73 1.84 4.027 21.387 49.858 3.625 Individual atomic B min max mean iso aniso Overall: 9.33 105.06 21.17 2.19 210 1758 Protein: 9.33 105.06 16.84 2.19 0 1519 Water: 11.69 69.92 36.03 N/A 210 231 Other: 19.47 29.28 24.39 N/A 0 8 Chain A: 9.33 105.06 19.44 N/A 0 1758 Chain S: 16.34 59.86 35.70 N/A 210 0 Histogram: Values Number of atoms 9.33 - 18.90 1232 18.90 - 28.47 282 28.47 - 38.05 208 38.05 - 47.62 129 47.62 - 57.19 76 57.19 - 66.77 29 66.77 - 76.34 7 76.34 - 85.91 2 85.91 - 95.49 1 95.49 - 105.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1373 r_work=0.1189 r_free=0.1374 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1374 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1185 r_free = 0.1369 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1185 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.622983 | | target function (ml) not normalized (work): 301743.728857 | | target function (ml) not normalized (free): 15958.645955 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1185 0.1369 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1507 0.1506 0.1564 n_refl.: 87582 remove outliers: r(all,work,free)=0.1507 0.1506 0.1564 n_refl.: 87582 overall B=-0.02 to atoms: r(all,work,free)=0.1504 0.1503 0.1561 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1185 0.1372 n_refl.: 87582 remove outliers: r(all,work,free)=0.1191 0.1182 0.1372 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 87.50 79 5 0.3803 285.953 270.804 0.462 0.998 0.279 11.894-9.307 94.12 92 4 0.2254 482.262 461.422 0.849 1.000 0.257 9.237-7.194 97.73 208 7 0.2483 384.026 376.581 0.913 1.001 0.165 7.162-5.571 100.00 427 22 0.2229 293.725 282.984 0.903 1.001 0.133 5.546-4.326 100.00 867 58 0.1136 403.212 398.645 0.951 1.001 0.130 4.315-3.360 100.00 1859 96 0.0954 383.458 380.757 0.994 1.001 0.130 3.356-2.611 100.00 3867 181 0.1163 251.912 250.024 1.001 1.001 0.100 2.608-2.026 99.99 8198 413 0.1033 166.995 166.110 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0966 81.551 81.827 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1236 36.163 35.786 1.021 1.001 0.000 1.221-1.150 99.97 13689 708 0.2119 22.785 21.379 0.976 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0449 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1182 r_free=0.1372 After: r_work=0.1183 r_free=0.1371 ================================== NQH flips ================================== r_work=0.1183 r_free=0.1371 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1183 r_free=0.1371 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1371 | n_water=441 | time (s): 1.820 (total time: 1.820) Filter (dist) r_work=0.1183 r_free=0.1370 | n_water=439 | time (s): 35.810 (total time: 37.630) Filter (q & B) r_work=0.1183 r_free=0.1371 | n_water=438 | time (s): 2.800 (total time: 40.430) Compute maps r_work=0.1183 r_free=0.1371 | n_water=438 | time (s): 1.430 (total time: 41.860) Filter (map) r_work=0.1206 r_free=0.1382 | n_water=330 | time (s): 3.500 (total time: 45.360) Find peaks r_work=0.1206 r_free=0.1382 | n_water=330 | time (s): 0.640 (total time: 46.000) Add new water r_work=0.1258 r_free=0.1422 | n_water=492 | time (s): 3.630 (total time: 49.630) Refine new water occ: r_work=0.1193 r_free=0.1365 adp: r_work=0.1193 r_free=0.1367 occ: r_work=0.1180 r_free=0.1355 adp: r_work=0.1179 r_free=0.1356 occ: r_work=0.1171 r_free=0.1350 adp: r_work=0.1168 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1168 r_free=0.1350 r_work=0.1168 r_free=0.1350 | n_water=492 | time (s): 174.310 (total time: 223.940) Filter (q & B) r_work=0.1174 r_free=0.1350 | n_water=451 | time (s): 3.560 (total time: 227.500) Filter (dist only) r_work=0.1174 r_free=0.1349 | n_water=450 | time (s): 41.580 (total time: 269.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.003288 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 55.228554 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 0.1379 0.0167 0.006 1.0 4.5 0.5 0.0 0 1.002 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 13.79 1.67 3.284 21.085 55.229 3.633 12.06 13.75 1.69 3.380 21.061 55.229 3.623 Individual atomic B min max mean iso aniso Overall: 9.28 101.72 21.10 2.05 219 1758 Protein: 9.28 101.72 16.74 2.06 0 1519 Water: 11.80 69.29 35.74 N/A 219 231 Other: 20.04 28.61 24.57 N/A 0 8 Chain A: 9.28 101.72 19.34 N/A 0 1758 Chain S: 15.34 58.88 35.25 N/A 219 0 Histogram: Values Number of atoms 9.28 - 18.52 1218 18.52 - 27.77 287 27.77 - 37.01 211 37.01 - 46.25 139 46.25 - 55.50 80 55.50 - 64.74 26 64.74 - 73.98 12 73.98 - 83.23 1 83.23 - 92.47 1 92.47 - 101.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1375 r_work=0.1206 r_free=0.1375 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1375 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1378 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1203 r_free= 0.1378 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.622871 | | target function (ml) not normalized (work): 301705.419720 | | target function (ml) not normalized (free): 15958.987925 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1416 0.1410 5.6824 5.6198| | 2: 3.57 - 2.84 1.00 2888 124 0.1142 0.1467 5.2041 5.2667| | 3: 2.83 - 2.48 1.00 2820 163 0.1243 0.1262 5.0065 5.0147| | 4: 2.47 - 2.25 1.00 2825 136 0.1039 0.1176 4.7075 4.7729| | 5: 2.25 - 2.09 1.00 2756 127 0.1004 0.1143 4.6476 4.7211| | 6: 2.09 - 1.97 1.00 2846 113 0.0999 0.1164 4.3625 4.4806| | 7: 1.97 - 1.87 1.00 2787 165 0.1004 0.1255 4.0886 4.2054| | 8: 1.87 - 1.79 1.00 2789 144 0.1022 0.1259 3.9971 4.0951| | 9: 1.79 - 1.72 1.00 2745 138 0.0958 0.1337 3.7247 3.9237| | 10: 1.72 - 1.66 1.00 2831 160 0.1002 0.1289 3.6448 3.7792| | 11: 1.66 - 1.61 1.00 2712 147 0.0964 0.1104 3.5783 3.627| | 12: 1.61 - 1.56 1.00 2773 144 0.0917 0.1227 3.3534 3.5012| | 13: 1.56 - 1.52 1.00 2745 130 0.0977 0.1100 3.3453 3.4471| | 14: 1.52 - 1.48 1.00 2803 134 0.0996 0.1126 3.268 3.365| | 15: 1.48 - 1.45 1.00 2738 128 0.1008 0.1356 3.1716 3.3354| | 16: 1.45 - 1.42 1.00 2756 161 0.1064 0.1293 3.1534 3.2576| | 17: 1.42 - 1.39 1.00 2785 139 0.1114 0.1242 3.1155 3.2035| | 18: 1.39 - 1.36 1.00 2741 179 0.1140 0.1370 3.0812 3.266| | 19: 1.36 - 1.34 1.00 2807 134 0.1202 0.1591 3.0881 3.2759| | 20: 1.34 - 1.32 1.00 2696 147 0.1304 0.1492 3.0807 3.1429| | 21: 1.32 - 1.30 1.00 2785 112 0.1407 0.1616 3.0831 3.1567| | 22: 1.29 - 1.27 1.00 2704 152 0.1471 0.1939 3.0818 3.2868| | 23: 1.27 - 1.26 1.00 2802 156 0.1562 0.1858 3.0973 3.2108| | 24: 1.26 - 1.24 1.00 2744 132 0.1613 0.1772 3.0877 3.1929| | 25: 1.24 - 1.22 1.00 2733 148 0.1786 0.2318 3.1052 3.2873| | 26: 1.22 - 1.21 1.00 2727 135 0.1857 0.1805 3.1213 3.1996| | 27: 1.21 - 1.19 1.00 2814 148 0.2009 0.2096 3.1387 3.1475| | 28: 1.19 - 1.18 1.00 2671 147 0.2142 0.2333 3.1373 3.1633| | 29: 1.18 - 1.16 1.00 2800 134 0.2214 0.2356 3.1242 3.2198| | 30: 1.16 - 1.15 1.00 2739 148 0.2374 0.2484 3.1153 3.1616| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2916 171 0.95 8.92 1.00 0.97 6171.25| | 2: 3.57 - 2.84 2888 124 0.92 13.24 1.01 0.97 6171.25| | 3: 2.83 - 2.48 2820 163 0.89 17.39 0.99 0.97 5179.80| | 4: 2.47 - 2.25 2825 136 0.91 14.53 1.00 0.98 2623.18| | 5: 2.25 - 2.09 2756 127 0.89 16.78 1.01 0.98 2623.18| | 6: 2.09 - 1.97 2846 113 0.92 13.70 1.02 0.97 1553.73| | 7: 1.97 - 1.87 2787 165 0.94 11.03 1.02 0.97 641.64| | 8: 1.87 - 1.79 2789 144 0.91 14.60 1.00 0.97 641.64| | 9: 1.79 - 1.72 2745 138 0.93 11.76 0.98 0.97 350.67| | 10: 1.72 - 1.66 2831 160 0.93 12.53 0.98 0.97 292.40| | 11: 1.66 - 1.61 2712 147 0.92 13.20 0.98 0.97 279.05| | 12: 1.61 - 1.56 2773 144 0.95 9.87 0.99 0.97 153.14| | 13: 1.56 - 1.52 2745 130 0.94 11.45 1.02 0.97 153.14| | 14: 1.52 - 1.48 2803 134 0.94 11.59 1.02 0.97 136.36| | 15: 1.48 - 1.45 2738 128 0.95 10.63 1.01 0.98 105.62| | 16: 1.45 - 1.42 2756 161 0.94 11.81 1.02 0.98 105.62| | 17: 1.42 - 1.39 2785 139 0.94 11.53 1.01 0.98 94.57| | 18: 1.39 - 1.36 2741 179 0.94 11.81 1.01 0.98 88.17| | 19: 1.36 - 1.34 2807 134 0.94 12.38 1.00 0.98 88.17| | 20: 1.34 - 1.32 2696 147 0.94 12.47 0.99 0.96 82.36| | 21: 1.32 - 1.30 2785 112 0.94 13.37 0.98 0.96 81.95| | 22: 1.29 - 1.27 2704 152 0.93 13.88 0.98 0.96 82.07| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.98 0.95 82.69| | 24: 1.26 - 1.24 2744 132 0.92 14.94 0.97 0.95 82.69| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.94 84.16| | 26: 1.22 - 1.21 2727 135 0.90 18.08 1.02 0.93 85.79| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.02 0.93 85.79| | 28: 1.19 - 1.18 2671 147 0.88 20.17 1.01 0.93 88.96| | 29: 1.18 - 1.16 2800 134 0.88 20.47 0.99 0.93 90.15| | 30: 1.16 - 1.15 2739 148 0.86 21.83 0.98 0.93 90.15| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 81.95 max = 6171.25 mean = 969.58| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 14.11| |phase err.(test): min = 0.00 max = 89.51 mean = 14.24| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1203 0.1378 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1518 0.1516 0.1580 n_refl.: 87574 remove outliers: r(all,work,free)=0.1518 0.1516 0.1580 n_refl.: 87574 overall B=-0.01 to atoms: r(all,work,free)=0.1515 0.1513 0.1578 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1204 0.1380 n_refl.: 87574 remove outliers: r(all,work,free)=0.1211 0.1203 0.1380 n_refl.: 87572 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3866 285.953 260.939 0.447 0.998 0.279 11.894-9.307 93.14 91 4 0.2394 475.285 457.532 0.854 1.000 0.229 9.237-7.194 97.27 207 7 0.2493 383.553 376.742 0.908 1.001 0.165 7.162-5.571 100.00 427 22 0.2244 293.725 283.062 0.900 1.001 0.130 5.546-4.326 100.00 867 58 0.1196 403.212 398.529 0.951 1.001 0.118 4.315-3.360 100.00 1859 96 0.1006 383.458 380.710 0.995 1.001 0.107 3.356-2.611 100.00 3867 181 0.1208 251.912 249.711 1.001 1.001 0.038 2.608-2.026 99.99 8198 413 0.1055 166.995 165.924 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0982 81.551 81.803 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1221 36.163 35.808 1.021 0.999 0.000 1.221-1.150 99.97 13689 708 0.2112 22.785 21.406 0.977 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0407 ================= 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 : 0.2614 0.1972 0.083 5.353 8.8 119.3 19.9 258 0.000 1_bss: 0.1645 0.1803 0.083 5.353 9.1 119.5 20.1 258 0.000 1_settarget: 0.1645 0.1803 0.083 5.353 9.1 119.5 20.1 258 0.000 1_nqh: 0.1646 0.1805 0.083 5.353 9.1 119.5 20.1 258 0.006 1_weight: 0.1646 0.1805 0.083 5.353 9.1 119.5 20.1 258 0.006 1_xyzrec: 0.1211 0.1458 0.007 0.926 9.1 119.5 20.1 258 0.131 1_adp: 0.1237 0.1533 0.007 0.926 8.5 118.4 20.9 258 0.131 1_regHadp: 0.1241 0.1537 0.007 0.926 8.5 118.4 20.9 258 0.131 1_occ: 0.1242 0.1541 0.007 0.926 8.5 118.4 20.9 258 0.131 2_bss: 0.1240 0.1535 0.007 0.926 8.7 118.5 21.1 258 0.131 2_settarget: 0.1240 0.1535 0.007 0.926 8.7 118.5 21.1 258 0.131 2_updatecdl: 0.1240 0.1535 0.007 0.933 8.7 118.5 21.1 258 0.131 2_nqh: 0.1240 0.1535 0.007 0.933 8.7 118.5 21.1 258 0.131 2_sol: 0.1232 0.1484 0.007 0.933 8.7 118.5 23.4 429 n/a 2_weight: 0.1232 0.1484 0.007 0.933 8.7 118.5 23.4 429 n/a 2_xyzrec: 0.1228 0.1530 0.007 0.882 8.7 118.5 23.4 429 n/a 2_adp: 0.1199 0.1495 0.007 0.882 8.8 114.1 23.1 429 n/a 2_regHadp: 0.1199 0.1495 0.007 0.882 8.8 114.1 23.1 429 n/a 2_occ: 0.1201 0.1494 0.007 0.882 8.8 114.1 23.1 429 n/a 3_bss: 0.1195 0.1490 0.007 0.882 8.8 114.1 23.1 429 n/a 3_settarget: 0.1195 0.1490 0.007 0.882 8.8 114.1 23.1 429 n/a 3_updatecdl: 0.1195 0.1490 0.007 0.883 8.8 114.1 23.1 429 n/a 3_nqh: 0.1195 0.1490 0.007 0.883 8.8 114.1 23.1 429 n/a 3_sol: 0.1222 0.1474 0.007 0.883 8.8 114.1 22.0 453 n/a 3_weight: 0.1222 0.1474 0.007 0.883 8.8 114.1 22.0 453 n/a 3_xyzrec: 0.1231 0.1455 0.006 0.918 8.8 114.1 22.0 453 n/a 3_adp: 0.1231 0.1420 0.006 0.918 9.2 110.0 21.8 453 n/a 3_regHadp: 0.1232 0.1420 0.006 0.918 9.2 110.0 21.8 453 n/a 3_occ: 0.1227 0.1422 0.006 0.918 9.2 110.0 21.8 453 n/a 4_bss: 0.1213 0.1390 0.006 0.918 9.2 110.0 21.7 453 n/a 4_settarget: 0.1213 0.1390 0.006 0.918 9.2 110.0 21.7 453 n/a 4_updatecdl: 0.1213 0.1390 0.006 0.915 9.2 110.0 21.7 453 n/a 4_nqh: 0.1213 0.1390 0.006 0.915 9.2 110.0 21.7 453 n/a 4_sol: 0.1203 0.1364 0.006 0.915 9.2 110.0 21.5 441 n/a 4_weight: 0.1203 0.1364 0.006 0.915 9.2 110.0 21.5 441 n/a 4_xyzrec: 0.1210 0.1387 0.006 0.935 9.2 110.0 21.5 441 n/a 4_adp: 0.1189 0.1373 0.006 0.935 9.3 105.1 21.2 441 n/a 4_regHadp: 0.1189 0.1374 0.006 0.935 9.3 105.1 21.2 441 n/a 4_occ: 0.1185 0.1369 0.006 0.935 9.3 105.1 21.2 441 n/a 5_bss: 0.1182 0.1372 0.006 0.935 9.3 105.0 21.2 441 n/a 5_settarget: 0.1182 0.1372 0.006 0.935 9.3 105.0 21.2 441 n/a 5_updatecdl: 0.1182 0.1372 0.006 0.938 9.3 105.0 21.2 441 n/a 5_setrh: 0.1183 0.1371 0.006 0.938 9.3 105.0 21.2 441 n/a 5_nqh: 0.1183 0.1371 0.006 0.938 9.3 105.0 21.2 441 n/a 5_sol: 0.1174 0.1349 0.006 0.938 9.3 105.0 21.1 450 n/a 5_weight: 0.1174 0.1349 0.006 0.938 9.3 105.0 21.1 450 n/a 5_xyzrec: 0.1211 0.1379 0.006 1.034 9.3 105.0 21.1 450 n/a 5_adp: 0.1206 0.1375 0.006 1.034 9.3 101.7 21.1 450 n/a 5_regHadp: 0.1206 0.1375 0.006 1.034 9.3 101.7 21.1 450 n/a 5_occ: 0.1203 0.1378 0.006 1.034 9.3 101.7 21.1 450 n/a end: 0.1203 0.1380 0.006 1.034 9.3 101.7 21.1 450 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_9394591_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_9394591_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.1000 Refinement macro-cycles (run) : 3634.8100 Write final files (write_after_run_outputs) : 56.8700 Total : 3696.7800 Total CPU time: 62.22 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:13:27 PST -0800 (1735452807.56 s) Start R-work = 0.1645, R-free = 0.1803 Final R-work = 0.1203, R-free = 0.1380 =============================================================================== Job complete usr+sys time: 3826.88 seconds wall clock time: 68 minutes 33.38 seconds (4113.38 seconds total)