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_7509253.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7509253.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7509253.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s 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: 2.24, per 1000 atoms: 0.66 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: 0.86 Conformation dependent library (CDL) restraints added in 354.8 milliseconds Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.91: 515 0.91 - 1.20: 1164 1.20 - 1.48: 846 1.48 - 1.77: 619 1.77 - 2.05: 9 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.556 -0.230 1.10e-02 8.26e+03 4.37e+02 bond pdb=" C GLU A 163 " pdb=" N PHE A 164 " ideal model delta sigma weight residual 1.334 1.554 -0.220 1.20e-02 6.94e+03 3.36e+02 bond pdb=" C ALYS A 132 " pdb=" O ALYS A 132 " ideal model delta sigma weight residual 1.236 1.024 0.212 1.16e-02 7.43e+03 3.34e+02 bond pdb=" C SER A 142 " pdb=" O SER A 142 " ideal model delta sigma weight residual 1.234 1.456 -0.222 1.26e-02 6.30e+03 3.10e+02 bond pdb=" CA ALA A 79 " pdb=" C ALA A 79 " ideal model delta sigma weight residual 1.523 1.288 0.235 1.35e-02 5.49e+03 3.04e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 3238 4.85 - 9.70: 1869 9.70 - 14.54: 583 14.54 - 19.39: 79 19.39 - 24.24: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ALYS A 132 " pdb=" C ALYS A 132 " pdb=" N MET A 133 " ideal model delta sigma weight residual 116.79 99.92 16.87 1.28e+00 6.10e-01 1.74e+02 angle pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" O THR A 140 " ideal model delta sigma weight residual 120.36 134.46 -14.10 1.08e+00 8.57e-01 1.70e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.43 132.88 -10.45 8.10e-01 1.52e+00 1.66e+02 angle pdb=" O AGLU A 90 " pdb=" C AGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 122.07 108.94 13.13 1.03e+00 9.43e-01 1.63e+02 angle pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 107.20 95.14 12.06 1.00e+00 1.00e+00 1.45e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.53: 912 15.53 - 31.06: 132 31.06 - 46.59: 37 46.59 - 62.12: 24 62.12 - 77.65: 6 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " pdb=" CA GLY A 118 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+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 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.198: 92 0.198 - 0.392: 83 0.392 - 0.587: 41 0.587 - 0.782: 19 0.782 - 0.977: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA SER A 161 " pdb=" N SER A 161 " pdb=" C SER A 161 " pdb=" CB SER A 161 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.38e+01 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 -1.65 -0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" CB VAL A 23 " pdb=" CA VAL A 23 " pdb=" CG1 VAL A 23 " pdb=" CG2 VAL A 23 " both_signs ideal model delta sigma weight residual False -2.63 -3.51 0.88 2.00e-01 2.50e+01 1.95e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.084 9.50e-02 1.11e+02 7.51e-02 1.10e+02 pdb=" NE ARG A 5 " -0.079 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.128 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.070 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.115 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.032 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB AASN A 97 " -0.069 2.00e-02 2.50e+03 8.55e-02 1.10e+02 pdb=" CG AASN A 97 " 0.109 2.00e-02 2.50e+03 pdb=" OD1AASN A 97 " -0.038 2.00e-02 2.50e+03 pdb=" ND2AASN A 97 " 0.126 2.00e-02 2.50e+03 pdb="HD21AASN A 97 " -0.092 2.00e-02 2.50e+03 pdb="HD22AASN A 97 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.055 2.00e-02 2.50e+03 6.88e-02 1.06e+02 pdb=" CG HIS A 115 " 0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.104 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.031 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " 0.065 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " 0.119 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " -0.078 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1340 2.37 - 2.92: 8350 2.92 - 3.48: 10476 3.48 - 4.04: 15047 4.04 - 4.60: 21459 Nonbonded interactions: 56672 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.807 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.814 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.827 2.450 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.838 2.450 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.862 2.450 ... (remaining 56667 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_7509253_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= 0.2608 r_free= 0.1947 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794938 | | target function (ml) not normalized (work): 232835.119798 | | target function (ml) not normalized (free): 11838.361063 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3034 0.2057 7.0665 4.9502| | 2: 3.57 - 2.84 1.00 2876 122 0.2427 0.1728 4.3487 4.3309| | 3: 2.84 - 2.48 1.00 2833 165 0.2384 0.1730 4.13 4.1585| | 4: 2.47 - 2.25 1.00 2825 136 0.2362 0.1446 3.834 3.8285| | 5: 2.25 - 2.09 1.00 2756 127 0.2481 0.1680 3.7976 3.8327| | 6: 2.09 - 1.97 1.00 2846 113 0.2539 0.1836 3.4679 3.5515| | 7: 1.97 - 1.87 1.00 2787 165 0.2517 0.1723 3.148 3.1546| | 8: 1.87 - 1.79 1.00 2789 144 0.2449 0.2047 3.0712 3.1842| | 9: 1.79 - 1.72 1.00 2745 138 0.2405 0.1827 2.8884 2.9164| | 10: 1.72 - 1.66 1.00 2789 158 0.2369 0.1929 2.8042 2.8793| | 11: 1.66 - 1.61 1.00 2740 147 0.2497 0.1967 2.7636 2.8396| | 12: 1.61 - 1.56 1.00 2787 146 0.2488 0.2009 2.6239 2.6805| | 13: 1.56 - 1.52 1.00 2745 130 0.2540 0.1895 2.5702 2.6281| | 14: 1.52 - 1.48 1.00 2803 134 0.2606 0.1853 2.5105 2.5274| | 15: 1.48 - 1.45 1.00 2738 128 0.2638 0.2131 2.433 2.4933| | 16: 1.45 - 1.42 1.00 2756 161 0.2702 0.2226 2.3968 2.4226| | 17: 1.42 - 1.39 1.00 2785 139 0.2672 0.2006 2.3623 2.3378| | 18: 1.39 - 1.36 1.00 2741 179 0.2702 0.2195 2.2837 2.3442| | 19: 1.36 - 1.34 1.00 2807 134 0.2637 0.2309 2.2496 2.281| | 20: 1.34 - 1.32 1.00 2696 147 0.2684 0.2406 2.1976 2.264| | 21: 1.32 - 1.30 1.00 2785 112 0.2719 0.2524 2.1665 2.2815| | 22: 1.29 - 1.27 1.00 2704 152 0.2726 0.2588 2.1386 2.2031| | 23: 1.27 - 1.26 1.00 2802 156 0.2772 0.2224 2.1033 2.123| | 24: 1.26 - 1.24 1.00 2744 132 0.2780 0.2619 2.08 2.2039| | 25: 1.24 - 1.22 1.00 2734 148 0.2805 0.2587 2.0452 2.1129| | 26: 1.22 - 1.21 1.00 2727 135 0.2795 0.2364 2.0132 2.1153| | 27: 1.21 - 1.19 1.00 2814 148 0.2984 0.2577 2.0218 1.9528| | 28: 1.19 - 1.18 1.00 2671 147 0.2973 0.2829 1.9846 2.0206| | 29: 1.18 - 1.16 1.00 2800 134 0.3004 0.2545 1.9628 1.9723| | 30: 1.16 - 1.15 1.00 2740 148 0.3045 0.2901 1.9277 1.9579| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.84 0.76 0.23 1473.46| | 2: 3.57 - 2.84 2876 122 0.80 26.05 1.27 0.23 1473.46| | 3: 2.84 - 2.48 2833 165 0.74 31.94 1.25 0.24 1222.60| | 4: 2.47 - 2.25 2825 136 0.81 25.62 1.26 0.25 571.57| | 5: 2.25 - 2.09 2756 127 0.77 29.35 1.28 0.25 571.57| | 6: 2.09 - 1.97 2846 113 0.83 22.97 1.29 0.25 314.63| | 7: 1.97 - 1.87 2787 165 0.90 16.90 1.28 0.26 95.49| | 8: 1.87 - 1.79 2789 144 0.85 21.56 1.24 0.26 95.49| | 9: 1.79 - 1.72 2745 138 0.88 19.08 1.24 0.25 58.24| | 10: 1.72 - 1.66 2789 158 0.86 20.66 1.22 0.25 50.78| | 11: 1.66 - 1.61 2740 147 0.85 21.89 1.24 0.25 49.02| | 12: 1.61 - 1.56 2787 146 0.88 18.94 1.23 0.25 31.13| | 13: 1.56 - 1.52 2745 130 0.86 21.10 1.24 0.25 31.13| | 14: 1.52 - 1.48 2803 134 0.86 21.24 1.24 0.25 27.62| | 15: 1.48 - 1.45 2738 128 0.87 20.66 1.24 0.25 21.18| | 16: 1.45 - 1.42 2756 161 0.85 22.02 1.24 0.25 21.18| | 17: 1.42 - 1.39 2785 139 0.87 20.82 1.22 0.25 17.94| | 18: 1.39 - 1.36 2741 179 0.86 21.58 1.23 0.25 16.07| | 19: 1.36 - 1.34 2807 134 0.85 22.22 1.21 0.25 16.07| | 20: 1.34 - 1.32 2696 147 0.87 21.06 1.21 0.25 13.40| | 21: 1.32 - 1.30 2785 112 0.85 22.36 1.21 0.25 13.21| | 22: 1.29 - 1.27 2704 152 0.85 22.68 1.20 0.25 12.90| | 23: 1.27 - 1.26 2802 156 0.86 22.16 1.21 0.24 11.36| | 24: 1.26 - 1.24 2744 132 0.85 23.01 1.20 0.24 11.36| | 25: 1.24 - 1.22 2734 148 0.84 23.83 1.20 0.24 10.71| | 26: 1.22 - 1.21 2727 135 0.84 23.80 1.19 0.23 9.99| | 27: 1.21 - 1.19 2814 148 0.83 24.80 1.20 0.23 9.99| | 28: 1.19 - 1.18 2671 147 0.83 24.99 1.19 0.23 9.20| | 29: 1.18 - 1.16 2800 134 0.83 25.52 1.16 0.23 8.91| | 30: 1.16 - 1.15 2740 148 0.81 26.74 1.15 0.23 8.91| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.91 max = 1473.46 mean = 215.14| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 22.82| |phase err.(test): min = 0.00 max = 89.80 mean = 22.65| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.249 1557 Z= 5.469 Angle : 5.342 18.550 2118 Z= 3.795 Chirality : 0.368 0.977 243 Planarity : 0.032 0.115 284 Dihedral : 13.964 77.646 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 31.35 % 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: -2.44 (0.49), residues: 224 helix: -2.44 (0.39), residues: 103 sheet: -0.73 (0.80), residues: 38 loop : -0.56 (0.66), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.021 ARG A 98 TYR 0.108 0.046 TYR A 139 PHE 0.094 0.039 PHE A 164 HIS 0.035 0.016 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1947 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794938 | | target function (ml) not normalized (work): 232835.119798 | | target function (ml) not normalized (free): 11838.361063 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2608 0.1948 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2608 0.1948 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1985 0.1948 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2005 0.2010 0.1963 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1647 0.1641 0.1767 n_refl.: 87594 remove outliers: r(all,work,free)=0.1646 0.1640 0.1767 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3787 386.167 359.553 0.668 1.002 0.401 11.894-9.307 98.04 96 4 0.1696 615.897 590.567 0.934 1.003 0.380 9.237-7.194 100.00 213 7 0.2163 501.692 492.185 0.955 1.003 0.359 7.162-5.571 100.00 427 22 0.2229 376.492 364.974 0.926 1.003 0.282 5.546-4.326 100.00 867 58 0.1273 516.831 511.684 0.962 1.003 0.219 4.315-3.360 100.00 1859 96 0.1146 491.510 487.780 1.009 1.003 0.209 3.356-2.611 100.00 3867 181 0.1421 322.896 319.922 0.998 1.002 0.043 2.608-2.026 99.99 8198 413 0.1370 214.051 211.765 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1644 104.531 103.868 1.009 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2078 46.353 45.046 1.005 0.996 0.000 1.221-1.150 99.97 13689 708 0.2597 29.206 26.944 0.975 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0472 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1640 r_free=0.1767 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=0.1640 r_free=0.1767 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.314225 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2012.982750 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 0.1462 0.0252 0.008 1.0 1.0 0.5 0.0 0 13.157 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.62 2.52 3.013 19.064 2012.983 0.017 12.40 15.36 2.95 3.161 19.519 2012.983 0.015 Individual atomic B min max mean iso aniso Overall: 8.49 118.56 20.95 2.87 0 1785 Protein: 8.49 118.56 17.83 2.87 0 1519 Water: 11.07 114.59 39.12 N/A 0 258 Other: 22.92 35.81 28.88 N/A 0 8 Chain A: 8.49 118.56 20.95 N/A 0 1785 Histogram: Values Number of atoms 8.49 - 19.50 1206 19.50 - 30.51 231 30.51 - 41.51 164 41.51 - 52.52 100 52.52 - 63.53 55 63.53 - 74.53 17 74.53 - 85.54 5 85.54 - 96.55 4 96.55 - 107.56 0 107.56 - 118.56 3 =========================== Idealize ADP of riding H ========================== r_work=0.1241 r_free=0.1536 r_work=0.1245 r_free=0.1541 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1245 r_free = 0.1541 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1244 r_free = 0.1542 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1244 r_free= 0.1542 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015175 | | target function (ls_wunit_k1) not normalized (work): 1264.040418 | | target function (ls_wunit_k1) not normalized (free): 113.812026 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1258 0.1244 0.1542 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1694 0.1692 0.1764 n_refl.: 87592 remove outliers: r(all,work,free)=0.1694 0.1692 0.1764 n_refl.: 87592 overall B=0.18 to atoms: r(all,work,free)=0.1723 0.1722 0.1785 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1257 0.1243 0.1538 n_refl.: 87592 remove outliers: r(all,work,free)=0.1257 0.1242 0.1538 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 0.3578 299.400 279.249 0.633 1.003 0.380 11.894-9.307 98.04 96 4 0.1499 481.568 470.617 0.917 1.003 0.380 9.237-7.194 100.00 213 7 0.1812 392.272 387.300 0.946 1.003 0.340 7.162-5.571 100.00 427 22 0.1742 294.378 288.728 0.916 1.003 0.253 5.546-4.326 100.00 867 58 0.0919 404.108 401.498 0.945 1.003 0.204 4.315-3.360 100.00 1859 96 0.0774 384.310 383.338 0.993 1.003 0.189 3.356-2.611 100.00 3867 181 0.1017 252.472 251.750 0.996 1.002 0.052 2.608-2.026 99.99 8198 413 0.0969 167.366 166.821 1.009 1.001 0.000 2.025-1.573 100.00 17313 902 0.1211 81.733 81.913 1.015 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1657 36.244 35.704 1.005 0.998 0.000 1.221-1.150 99.97 13689 708 0.2367 22.836 21.338 0.969 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0406 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1242 r_free=0.1538 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1244 r_free=0.1539 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1244 r_free=0.1539 | n_water=258 | time (s): 2.650 (total time: 2.650) Filter (dist) r_work=0.1253 r_free=0.1539 | n_water=252 | time (s): 27.170 (total time: 29.820) Filter (q & B) r_work=0.1256 r_free=0.1538 | n_water=249 | time (s): 3.950 (total time: 33.770) Compute maps r_work=0.1256 r_free=0.1538 | n_water=249 | time (s): 1.920 (total time: 35.690) Filter (map) r_work=0.1268 r_free=0.1546 | n_water=237 | time (s): 4.030 (total time: 39.720) Find peaks r_work=0.1268 r_free=0.1546 | n_water=237 | time (s): 0.740 (total time: 40.460) Add new water r_work=0.1421 r_free=0.1704 | n_water=459 | time (s): 3.880 (total time: 44.340) Refine new water occ: r_work=0.1328 r_free=0.1566 adp: r_work=0.1252 r_free=0.1522 occ: r_work=0.1266 r_free=0.1510 adp: r_work=0.1232 r_free=0.1500 occ: r_work=0.1235 r_free=0.1487 adp: r_work=0.1225 r_free=0.1488 ADP+occupancy (water only), MIN, final r_work=0.1225 r_free=0.1488 r_work=0.1225 r_free=0.1488 | n_water=459 | time (s): 148.520 (total time: 192.860) Filter (q & B) r_work=0.1230 r_free=0.1490 | n_water=437 | time (s): 3.960 (total time: 196.820) Filter (dist only) r_work=0.1231 r_free=0.1490 | n_water=435 | time (s): 45.900 (total time: 242.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.959246 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1539.913571 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 0.1510 0.0281 0.007 0.9 1.9 0.5 0.0 0 12.480 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 15.10 2.81 3.779 23.170 1539.914 0.015 12.00 14.77 2.77 4.227 22.977 1539.914 0.015 Individual atomic B min max mean iso aniso Overall: 8.73 114.01 23.17 2.60 198 1764 Protein: 8.73 114.01 17.61 2.61 0 1519 Water: 10.96 75.91 42.47 N/A 198 237 Other: 25.46 35.68 29.87 N/A 0 8 Chain A: 8.73 114.01 20.36 N/A 0 1764 Chain S: 14.48 75.91 48.22 N/A 198 0 Histogram: Values Number of atoms 8.73 - 19.26 1210 19.26 - 29.79 253 29.79 - 40.32 186 40.32 - 50.84 138 50.84 - 61.37 109 61.37 - 71.90 51 71.90 - 82.43 9 82.43 - 92.95 3 92.95 - 103.48 1 103.48 - 114.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1477 r_work=0.1200 r_free=0.1476 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1476 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1469 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 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= 0.1205 r_free= 0.1469 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014115 | | target function (ls_wunit_k1) not normalized (work): 1175.685886 | | target function (ls_wunit_k1) not normalized (free): 104.614131 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1205 0.1469 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1615 0.1612 0.1702 n_refl.: 87591 remove outliers: r(all,work,free)=0.1615 0.1612 0.1702 n_refl.: 87591 overall B=0.03 to atoms: r(all,work,free)=0.1620 0.1617 0.1705 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1203 0.1467 n_refl.: 87591 remove outliers: r(all,work,free)=0.1214 0.1201 0.1467 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 0.3243 292.086 270.976 0.569 1.003 0.340 11.894-9.307 98.04 96 4 0.1417 481.568 478.987 0.925 1.003 0.333 9.237-7.194 100.00 213 7 0.1725 392.272 392.719 0.974 1.003 0.300 7.162-5.571 100.00 427 22 0.1561 294.378 291.960 0.935 1.003 0.233 5.546-4.326 100.00 867 58 0.0851 404.108 401.351 0.957 1.003 0.212 4.315-3.360 100.00 1859 96 0.0722 384.310 383.169 1.002 1.002 0.200 3.356-2.611 100.00 3867 181 0.0966 252.472 251.703 1.009 1.002 0.062 2.608-2.026 99.99 8198 413 0.0963 167.366 166.980 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1181 81.733 81.908 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1608 36.244 35.734 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2337 22.836 21.366 0.979 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0521 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1467 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=0.1201 r_free=0.1467 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1467 | n_water=435 | time (s): 2.010 (total time: 2.010) Filter (dist) r_work=0.1202 r_free=0.1467 | n_water=432 | time (s): 38.330 (total time: 40.340) Filter (q & B) r_work=0.1202 r_free=0.1467 | n_water=432 | time (s): 0.920 (total time: 41.260) Compute maps r_work=0.1202 r_free=0.1467 | n_water=432 | time (s): 1.820 (total time: 43.080) Filter (map) r_work=0.1239 r_free=0.1477 | n_water=296 | time (s): 3.610 (total time: 46.690) Find peaks r_work=0.1239 r_free=0.1477 | n_water=296 | time (s): 0.570 (total time: 47.260) Add new water r_work=0.1366 r_free=0.1593 | n_water=482 | time (s): 2.850 (total time: 50.110) Refine new water occ: r_work=0.1268 r_free=0.1522 adp: r_work=0.1269 r_free=0.1521 occ: r_work=0.1247 r_free=0.1503 adp: r_work=0.1244 r_free=0.1501 occ: r_work=0.1233 r_free=0.1492 adp: r_work=0.1225 r_free=0.1486 ADP+occupancy (water only), MIN, final r_work=0.1225 r_free=0.1486 r_work=0.1225 r_free=0.1486 | n_water=482 | time (s): 127.500 (total time: 177.610) Filter (q & B) r_work=0.1230 r_free=0.1494 | n_water=446 | time (s): 3.350 (total time: 180.960) Filter (dist only) r_work=0.1229 r_free=0.1493 | n_water=445 | time (s): 37.350 (total time: 218.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.324455 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 52.568981 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 0.1446 0.0217 0.006 0.9 3.5 0.5 0.0 0 1.162 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.46 2.17 3.609 22.059 52.569 3.724 12.15 14.06 1.91 4.071 21.878 52.569 3.654 Individual atomic B min max mean iso aniso Overall: 9.20 109.93 21.67 2.33 211 1761 Protein: 9.20 109.93 17.20 2.33 0 1519 Water: 11.54 71.79 36.83 N/A 211 234 Other: 21.36 31.77 26.93 N/A 0 8 Chain A: 9.20 109.93 19.88 N/A 0 1761 Chain S: 15.35 62.55 36.54 N/A 211 0 Histogram: Values Number of atoms 9.20 - 19.28 1237 19.28 - 29.35 274 29.35 - 39.42 220 39.42 - 49.49 131 49.49 - 59.57 73 59.57 - 69.64 24 69.64 - 79.71 7 79.71 - 89.78 3 89.78 - 99.85 1 99.85 - 109.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.1215 r_free=0.1406 r_work=0.1216 r_free=0.1408 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1216 r_free = 0.1408 target_work(ml) = 3.654 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1407 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.20 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= 0.1210 r_free= 0.1407 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.652123 | | target function (ml) not normalized (work): 304188.992975 | | target function (ml) not normalized (free): 16075.589935 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1210 0.1407 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1540 0.1540 0.1570 n_refl.: 87587 remove outliers: r(all,work,free)=0.1540 0.1540 0.1570 n_refl.: 87587 overall B=-0.01 to atoms: r(all,work,free)=0.1537 0.1538 0.1569 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1201 0.1378 n_refl.: 87587 remove outliers: r(all,work,free)=0.1205 0.1196 0.1378 n_refl.: 87576 ======================== 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 0.3790 291.329 257.372 0.459 1.001 0.301 11.894-9.307 94.12 92 4 0.2269 473.726 457.060 0.851 1.002 0.280 9.237-7.194 98.18 209 7 0.2386 386.899 385.698 0.944 1.002 0.166 7.162-5.571 100.00 427 22 0.2012 294.378 285.720 0.913 1.002 0.162 5.546-4.326 100.00 867 58 0.1111 404.108 399.260 0.951 1.002 0.157 4.315-3.360 100.00 1859 96 0.0947 384.310 381.492 0.992 1.002 0.153 3.356-2.611 100.00 3867 181 0.1160 252.472 250.506 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1044 167.366 166.397 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1010 81.733 81.898 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1284 36.244 35.828 1.020 0.999 0.000 1.221-1.150 99.97 13689 708 0.2124 22.836 21.457 0.979 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0365 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1378 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1378 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1378 | n_water=445 | time (s): 1.780 (total time: 1.780) Filter (dist) r_work=0.1196 r_free=0.1379 | n_water=444 | time (s): 37.900 (total time: 39.680) Filter (q & B) r_work=0.1196 r_free=0.1380 | n_water=443 | time (s): 3.290 (total time: 42.970) Compute maps r_work=0.1196 r_free=0.1380 | n_water=443 | time (s): 1.590 (total time: 44.560) Filter (map) r_work=0.1221 r_free=0.1383 | n_water=315 | time (s): 3.450 (total time: 48.010) Find peaks r_work=0.1221 r_free=0.1383 | n_water=315 | time (s): 0.550 (total time: 48.560) Add new water r_work=0.1286 r_free=0.1436 | n_water=475 | time (s): 3.410 (total time: 51.970) Refine new water occ: r_work=0.1212 r_free=0.1369 adp: r_work=0.1212 r_free=0.1371 occ: r_work=0.1197 r_free=0.1357 adp: r_work=0.1195 r_free=0.1358 occ: r_work=0.1186 r_free=0.1351 adp: r_work=0.1182 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1351 r_work=0.1182 r_free=0.1351 | n_water=475 | time (s): 269.890 (total time: 321.860) Filter (q & B) r_work=0.1189 r_free=0.1353 | n_water=439 | time (s): 2.800 (total time: 324.660) Filter (dist only) r_work=0.1189 r_free=0.1352 | n_water=438 | time (s): 35.460 (total time: 360.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.954443 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.686365 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 0.1192 0.1359 0.0167 0.006 1.0 1.9 0.5 0.0 0 0.977 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.59 1.67 3.425 21.463 43.686 3.635 11.83 13.57 1.74 3.666 21.382 43.686 3.625 Individual atomic B min max mean iso aniso Overall: 9.28 106.13 21.27 2.17 206 1759 Protein: 9.28 106.13 17.01 2.17 0 1519 Water: 11.36 70.96 35.96 N/A 206 232 Other: 21.29 30.51 26.17 N/A 0 8 Chain A: 9.28 106.13 19.63 N/A 0 1759 Chain S: 15.95 62.91 35.30 N/A 206 0 Histogram: Values Number of atoms 9.28 - 18.97 1232 18.97 - 28.65 280 28.65 - 38.34 202 38.34 - 48.02 141 48.02 - 57.71 72 57.71 - 67.39 24 67.39 - 77.08 9 77.08 - 86.76 2 86.76 - 96.45 1 96.45 - 106.13 2 =========================== Idealize ADP of riding H ========================== r_work=0.1183 r_free=0.1357 r_work=0.1183 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1183 r_free = 0.1357 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1178 r_free = 0.1354 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1178 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 3.623371 | | target function (ml) not normalized (work): 301754.363862 | | target function (ml) not normalized (free): 15942.150461 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1187 0.1178 0.1354 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1503 0.1503 0.1538 n_refl.: 87576 remove outliers: r(all,work,free)=0.1503 0.1503 0.1538 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1500 0.1500 0.1536 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1187 0.1178 0.1355 n_refl.: 87576 remove outliers: r(all,work,free)=0.1184 0.1175 0.1355 n_refl.: 87569 ======================== 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 0.3906 286.589 259.151 0.445 1.001 0.281 11.894-9.307 90.20 88 4 0.2161 474.535 454.764 0.844 1.002 0.260 9.237-7.194 97.27 207 7 0.2411 384.405 380.403 0.922 1.002 0.140 7.162-5.571 100.00 427 22 0.2135 294.378 284.635 0.907 1.002 0.133 5.546-4.326 100.00 867 58 0.1139 404.108 399.752 0.953 1.002 0.130 4.315-3.360 100.00 1859 96 0.0937 384.310 381.732 0.993 1.002 0.120 3.356-2.611 100.00 3867 181 0.1149 252.472 250.499 1.001 1.001 0.090 2.608-2.026 99.99 8198 413 0.1015 167.366 166.439 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0977 81.733 81.996 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.244 35.865 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2123 22.836 21.462 0.979 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0357 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1176 r_free=0.1355 After: r_work=0.1176 r_free=0.1354 ================================== NQH flips ================================== r_work=0.1176 r_free=0.1354 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=0.1176 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1176 r_free=0.1354 | n_water=438 | time (s): 1.650 (total time: 1.650) Filter (dist) r_work=0.1176 r_free=0.1354 | n_water=438 | time (s): 34.030 (total time: 35.680) Filter (q & B) r_work=0.1177 r_free=0.1354 | n_water=436 | time (s): 3.270 (total time: 38.950) Compute maps r_work=0.1177 r_free=0.1354 | n_water=436 | time (s): 1.520 (total time: 40.470) Filter (map) r_work=0.1200 r_free=0.1367 | n_water=341 | time (s): 2.790 (total time: 43.260) Find peaks r_work=0.1200 r_free=0.1367 | n_water=341 | time (s): 0.570 (total time: 43.830) Add new water r_work=0.1248 r_free=0.1402 | n_water=495 | time (s): 2.910 (total time: 46.740) Refine new water occ: r_work=0.1187 r_free=0.1354 adp: r_work=0.1187 r_free=0.1354 occ: r_work=0.1174 r_free=0.1347 adp: r_work=0.1173 r_free=0.1346 occ: r_work=0.1165 r_free=0.1343 adp: r_work=0.1161 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1161 r_free=0.1341 r_work=0.1161 r_free=0.1341 | n_water=495 | time (s): 163.460 (total time: 210.200) Filter (q & B) r_work=0.1168 r_free=0.1345 | n_water=463 | time (s): 2.780 (total time: 212.980) Filter (dist only) r_work=0.1169 r_free=0.1344 | n_water=462 | time (s): 43.060 (total time: 256.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.288345 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.560890 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 0.1199 0.1373 0.0174 0.007 1.1 5.4 0.5 0.0 0 1.144 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.73 1.74 3.317 21.314 49.561 3.631 11.98 13.72 1.74 3.694 21.197 49.561 3.622 Individual atomic B min max mean iso aniso Overall: 9.23 101.70 21.15 2.05 231 1758 Protein: 9.23 101.70 16.71 2.05 0 1519 Water: 11.52 69.71 35.68 N/A 231 231 Other: 20.61 28.88 24.95 N/A 0 8 Chain A: 9.23 101.70 19.30 N/A 0 1758 Chain S: 14.43 63.55 35.25 N/A 231 0 Histogram: Values Number of atoms 9.23 - 18.47 1223 18.47 - 27.72 272 27.72 - 36.97 224 36.97 - 46.22 148 46.22 - 55.46 82 55.46 - 64.71 24 64.71 - 73.96 11 73.96 - 83.21 2 83.21 - 92.45 1 92.45 - 101.70 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1372 r_work=0.1198 r_free=0.1372 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1372 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1371 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87569 (all), 4.91 % free)------------| | | | r_work= 0.1194 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 3.620737 | | target function (ml) not normalized (work): 301509.623871 | | target function (ml) not normalized (free): 15948.363814 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2911 171 0.1398 0.1419 5.6566 5.6394| | 2: 3.57 - 2.84 1.00 2888 124 0.1128 0.1448 5.2025 5.2611| | 3: 2.83 - 2.48 1.00 2820 163 0.1228 0.1287 5.0047 5.0228| | 4: 2.47 - 2.25 1.00 2825 136 0.1032 0.1108 4.7105 4.7568| | 5: 2.25 - 2.09 1.00 2756 127 0.0992 0.1137 4.6491 4.7233| | 6: 2.09 - 1.97 1.00 2846 113 0.0988 0.1253 4.3615 4.4992| | 7: 1.97 - 1.87 1.00 2787 165 0.0993 0.1215 4.0836 4.1836| | 8: 1.87 - 1.79 1.00 2789 144 0.1031 0.1264 4.004 4.0978| | 9: 1.79 - 1.72 1.00 2745 138 0.0945 0.1310 3.7143 3.9018| | 10: 1.72 - 1.66 1.00 2831 160 0.0998 0.1221 3.6338 3.7534| | 11: 1.66 - 1.61 1.00 2712 147 0.0960 0.1081 3.5708 3.612| | 12: 1.61 - 1.56 1.00 2773 144 0.0911 0.1158 3.3454 3.4819| | 13: 1.56 - 1.52 1.00 2745 130 0.0973 0.1080 3.338 3.4479| | 14: 1.52 - 1.48 1.00 2803 134 0.0977 0.1122 3.2554 3.3481| | 15: 1.48 - 1.45 1.00 2738 128 0.1005 0.1323 3.1632 3.3168| | 16: 1.45 - 1.42 1.00 2756 161 0.1061 0.1206 3.1495 3.219| | 17: 1.42 - 1.39 1.00 2785 139 0.1115 0.1312 3.1138 3.2355| | 18: 1.39 - 1.36 1.00 2741 179 0.1139 0.1388 3.0801 3.2632| | 19: 1.36 - 1.34 1.00 2807 134 0.1205 0.1615 3.0899 3.2699| | 20: 1.34 - 1.32 1.00 2696 147 0.1321 0.1457 3.0886 3.1311| | 21: 1.32 - 1.30 1.00 2785 112 0.1408 0.1625 3.0845 3.1655| | 22: 1.29 - 1.27 1.00 2704 152 0.1460 0.1897 3.0801 3.2832| | 23: 1.27 - 1.26 1.00 2802 156 0.1566 0.1845 3.1005 3.2133| | 24: 1.26 - 1.24 1.00 2744 132 0.1624 0.1772 3.0954 3.1912| | 25: 1.24 - 1.22 1.00 2733 148 0.1785 0.2325 3.1083 3.3001| | 26: 1.22 - 1.21 1.00 2727 135 0.1855 0.1804 3.1246 3.2127| | 27: 1.21 - 1.19 1.00 2814 148 0.1995 0.2137 3.1401 3.1644| | 28: 1.19 - 1.18 1.00 2671 147 0.2139 0.2313 3.1406 3.1699| | 29: 1.18 - 1.16 1.00 2800 134 0.2214 0.2390 3.1278 3.2291| | 30: 1.16 - 1.15 1.00 2739 148 0.2375 0.2491 3.1174 3.1677| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2911 171 0.95 9.00 1.00 0.97 6210.72| | 2: 3.57 - 2.84 2888 124 0.92 13.27 1.01 0.97 6210.72| | 3: 2.83 - 2.48 2820 163 0.89 17.45 0.99 0.97 5213.14| | 4: 2.47 - 2.25 2825 136 0.91 14.57 1.00 0.98 2640.72| | 5: 2.25 - 2.09 2756 127 0.89 16.80 1.01 0.98 2640.72| | 6: 2.09 - 1.97 2846 113 0.92 13.74 1.02 0.98 1562.75| | 7: 1.97 - 1.87 2787 165 0.94 10.95 1.02 0.97 643.39| | 8: 1.87 - 1.79 2789 144 0.91 14.64 0.99 0.97 643.39| | 9: 1.79 - 1.72 2745 138 0.93 11.50 0.98 0.97 343.86| | 10: 1.72 - 1.66 2831 160 0.93 12.25 0.98 0.97 283.87| | 11: 1.66 - 1.61 2712 147 0.93 12.89 0.98 0.97 270.87| | 12: 1.61 - 1.56 2773 144 0.95 9.60 0.99 0.97 148.20| | 13: 1.56 - 1.52 2745 130 0.94 11.09 1.02 0.97 148.20| | 14: 1.52 - 1.48 2803 134 0.94 11.28 1.02 0.98 132.29| | 15: 1.48 - 1.45 2738 128 0.95 10.39 1.01 0.98 103.17| | 16: 1.45 - 1.42 2756 161 0.94 11.54 1.02 0.98 103.17| | 17: 1.42 - 1.39 2785 139 0.94 11.40 1.01 0.98 93.00| | 18: 1.39 - 1.36 2741 179 0.94 11.67 1.01 0.98 87.11| | 19: 1.36 - 1.34 2807 134 0.94 12.20 1.00 0.98 87.11| | 20: 1.34 - 1.32 2696 147 0.94 12.40 0.99 0.97 82.31| | 21: 1.32 - 1.30 2785 112 0.94 13.30 0.98 0.96 81.97| | 22: 1.29 - 1.27 2704 152 0.93 13.84 0.98 0.96 82.19| | 23: 1.27 - 1.26 2802 156 0.93 14.74 0.97 0.95 83.34| | 24: 1.26 - 1.24 2744 132 0.92 14.97 0.96 0.95 83.34| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.94 85.18| | 26: 1.22 - 1.21 2727 135 0.90 18.16 1.02 0.93 87.21| | 27: 1.21 - 1.19 2814 148 0.89 18.81 1.02 0.93 87.21| | 28: 1.19 - 1.18 2671 147 0.88 20.35 1.01 0.93 90.71| | 29: 1.18 - 1.16 2800 134 0.88 20.67 0.99 0.92 92.02| | 30: 1.16 - 1.15 2739 148 0.86 22.11 0.98 0.92 92.02| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.97 max = 6210.72 mean = 973.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.05| |phase err.(test): min = 0.00 max = 89.57 mean = 14.16| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1194 0.1371 n_refl.: 87569 re-set all scales: r(all,work,free)=0.1497 0.1496 0.1550 n_refl.: 87569 remove outliers: r(all,work,free)=0.1497 0.1496 0.1550 n_refl.: 87569 overall B=-0.01 to atoms: r(all,work,free)=0.1496 0.1495 0.1549 n_refl.: 87569 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1194 0.1372 n_refl.: 87569 remove outliers: r(all,work,free)=0.1202 0.1194 0.1372 n_refl.: 87569 ======================== 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 0.4036 286.589 251.844 0.417 1.002 0.292 11.894-9.307 90.20 88 4 0.2128 474.535 459.669 0.830 1.002 0.280 9.237-7.194 97.27 207 7 0.2444 384.405 379.372 0.882 1.002 0.119 7.162-5.571 100.00 427 22 0.2176 294.378 284.392 0.876 1.002 0.119 5.546-4.326 100.00 867 58 0.1209 404.108 399.648 0.924 1.002 0.116 4.315-3.360 100.00 1859 96 0.1008 384.310 381.295 0.963 1.002 0.111 3.356-2.611 100.00 3867 181 0.1191 252.472 250.397 0.969 1.001 0.038 2.608-2.026 99.99 8198 413 0.1040 167.366 166.421 0.983 1.000 0.000 2.025-1.573 100.00 17313 902 0.0978 81.733 81.964 0.996 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1219 36.244 35.879 0.991 0.996 0.000 1.221-1.150 99.97 13689 708 0.2110 22.836 21.469 0.949 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9743 b_overall=-0.0216 ================= 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 : 0.2608 0.1947 0.082 5.342 8.8 119.3 19.9 258 0.000 1_bss: 0.1640 0.1767 0.082 5.342 9.1 119.5 20.1 258 0.000 1_settarget: 0.1640 0.1767 0.082 5.342 9.1 119.5 20.1 258 0.000 1_nqh: 0.1640 0.1767 0.082 5.342 9.1 119.5 20.1 258 0.000 1_weight: 0.1640 0.1767 0.082 5.342 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1211 0.1462 0.008 0.965 9.1 119.5 20.1 258 0.122 1_adp: 0.1241 0.1536 0.008 0.965 8.5 118.6 21.0 258 0.122 1_regHadp: 0.1245 0.1541 0.008 0.965 8.5 118.6 21.0 258 0.122 1_occ: 0.1244 0.1542 0.008 0.965 8.5 118.6 21.0 258 0.122 2_bss: 0.1242 0.1538 0.008 0.965 8.7 118.7 21.1 258 0.122 2_settarget: 0.1242 0.1538 0.008 0.965 8.7 118.7 21.1 258 0.122 2_updatecdl: 0.1242 0.1538 0.008 0.969 8.7 118.7 21.1 258 0.122 2_nqh: 0.1244 0.1539 0.008 0.969 8.7 118.7 21.1 258 0.125 2_sol: 0.1231 0.1490 0.008 0.969 8.7 118.7 23.5 435 n/a 2_weight: 0.1231 0.1490 0.008 0.969 8.7 118.7 23.5 435 n/a 2_xyzrec: 0.1229 0.1510 0.007 0.875 8.7 118.7 23.5 435 n/a 2_adp: 0.1200 0.1477 0.007 0.875 8.7 114.0 23.2 435 n/a 2_regHadp: 0.1200 0.1476 0.007 0.875 8.7 114.0 23.2 435 n/a 2_occ: 0.1205 0.1469 0.007 0.875 8.7 114.0 23.2 435 n/a 3_bss: 0.1201 0.1467 0.007 0.875 8.8 114.0 23.2 435 n/a 3_settarget: 0.1201 0.1467 0.007 0.875 8.8 114.0 23.2 435 n/a 3_updatecdl: 0.1201 0.1467 0.007 0.877 8.8 114.0 23.2 435 n/a 3_nqh: 0.1201 0.1467 0.007 0.877 8.8 114.0 23.2 435 n/a 3_sol: 0.1229 0.1493 0.007 0.877 8.8 114.0 22.0 445 n/a 3_weight: 0.1229 0.1493 0.007 0.877 8.8 114.0 22.0 445 n/a 3_xyzrec: 0.1229 0.1446 0.006 0.940 8.8 114.0 22.0 445 n/a 3_adp: 0.1215 0.1406 0.006 0.940 9.2 109.9 21.7 445 n/a 3_regHadp: 0.1216 0.1408 0.006 0.940 9.2 109.9 21.7 445 n/a 3_occ: 0.1210 0.1407 0.006 0.940 9.2 109.9 21.7 445 n/a 4_bss: 0.1196 0.1378 0.006 0.940 9.2 109.9 21.7 445 n/a 4_settarget: 0.1196 0.1378 0.006 0.940 9.2 109.9 21.7 445 n/a 4_updatecdl: 0.1196 0.1378 0.006 0.940 9.2 109.9 21.7 445 n/a 4_nqh: 0.1196 0.1378 0.006 0.940 9.2 109.9 21.7 445 n/a 4_sol: 0.1189 0.1352 0.006 0.940 9.2 109.9 21.4 438 n/a 4_weight: 0.1189 0.1352 0.006 0.940 9.2 109.9 21.4 438 n/a 4_xyzrec: 0.1192 0.1359 0.006 0.959 9.2 109.9 21.4 438 n/a 4_adp: 0.1183 0.1357 0.006 0.959 9.3 106.1 21.3 438 n/a 4_regHadp: 0.1183 0.1357 0.006 0.959 9.3 106.1 21.3 438 n/a 4_occ: 0.1178 0.1354 0.006 0.959 9.3 106.1 21.3 438 n/a 5_bss: 0.1176 0.1355 0.006 0.959 9.3 106.1 21.3 438 n/a 5_settarget: 0.1176 0.1355 0.006 0.959 9.3 106.1 21.3 438 n/a 5_updatecdl: 0.1176 0.1355 0.006 0.957 9.3 106.1 21.3 438 n/a 5_setrh: 0.1176 0.1354 0.006 0.957 9.3 106.1 21.3 438 n/a 5_nqh: 0.1176 0.1354 0.006 0.957 9.3 106.1 21.3 438 n/a 5_sol: 0.1169 0.1344 0.006 0.957 9.3 106.1 21.4 462 n/a 5_weight: 0.1169 0.1344 0.006 0.957 9.3 106.1 21.4 462 n/a 5_xyzrec: 0.1199 0.1373 0.007 1.130 9.3 106.1 21.4 462 n/a 5_adp: 0.1198 0.1372 0.007 1.130 9.2 101.7 21.2 462 n/a 5_regHadp: 0.1198 0.1372 0.007 1.130 9.2 101.7 21.2 462 n/a 5_occ: 0.1194 0.1371 0.007 1.130 9.2 101.7 21.2 462 n/a end: 0.1194 0.1372 0.007 1.130 9.2 101.7 21.1 462 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7509253_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7509253_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7900 Refinement macro-cycles (run) : 3447.0300 Write final files (write_after_run_outputs) : 69.2600 Total : 3521.0800 Total CPU time: 59.28 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:04 PST -0800 (1735452664.01 s) Start R-work = 0.1640, R-free = 0.1767 Final R-work = 0.1194, R-free = 0.1372 =============================================================================== Job complete usr+sys time: 3655.61 seconds wall clock time: 66 minutes 14.26 seconds (3974.26 seconds total)