Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5637181.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5637181.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5637181.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 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: 1.09 Conformation dependent library (CDL) restraints added in 296.0 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: 0.67 - 0.93: 646 0.93 - 1.19: 1017 1.19 - 1.45: 744 1.45 - 1.71: 729 1.71 - 1.97: 17 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.235 1.440 -0.205 9.90e-03 1.02e+04 4.27e+02 bond pdb=" N AGLU A 64 " pdb=" CA AGLU A 64 " ideal model delta sigma weight residual 1.457 1.680 -0.223 1.10e-02 8.26e+03 4.12e+02 bond pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 1.450 1.231 0.219 1.16e-02 7.43e+03 3.56e+02 bond pdb=" N GLU A 18 " pdb=" CA GLU A 18 " ideal model delta sigma weight residual 1.457 1.705 -0.248 1.32e-02 5.74e+03 3.54e+02 bond pdb=" CA AGLN A 80 " pdb=" C AGLN A 80 " ideal model delta sigma weight residual 1.524 1.759 -0.236 1.27e-02 6.20e+03 3.44e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 2872 4.14 - 8.29: 1875 8.29 - 12.43: 785 12.43 - 16.57: 219 16.57 - 20.71: 26 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 135.45 -16.25 9.00e-01 1.23e+00 3.26e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH2 ARG A 28 " ideal model delta sigma weight residual 119.20 106.11 13.09 9.00e-01 1.23e+00 2.11e+02 angle pdb=" O LEU A 112 " pdb=" C LEU A 112 " pdb=" N LEU A 113 " ideal model delta sigma weight residual 122.12 137.46 -15.34 1.06e+00 8.90e-01 2.09e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.36 137.31 -15.95 1.11e+00 8.12e-01 2.07e+02 angle pdb=" O LEU A 166 " pdb=" C LEU A 166 " pdb=" N ALA A 167 " ideal model delta sigma weight residual 122.12 107.57 14.55 1.06e+00 8.90e-01 1.88e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.51: 941 16.51 - 33.00: 112 33.00 - 49.49: 38 49.49 - 65.99: 14 65.99 - 82.48: 6 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual -180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+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 -159.72 -20.28 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.201: 100 0.201 - 0.400: 61 0.400 - 0.598: 49 0.598 - 0.797: 25 0.797 - 0.995: 8 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 -1.59 -1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" CA THR A 154 " pdb=" N THR A 154 " pdb=" C THR A 154 " pdb=" CB THR A 154 " both_signs ideal model delta sigma weight residual False 2.53 3.51 -0.99 2.00e-01 2.50e+01 2.44e+01 chirality pdb=" CB VAL A 181 " pdb=" CA VAL A 181 " pdb=" CG1 VAL A 181 " pdb=" CG2 VAL A 181 " both_signs ideal model delta sigma weight residual False -2.63 -3.54 0.91 2.00e-01 2.50e+01 2.08e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.111 2.00e-02 2.50e+03 6.02e-02 1.09e+02 pdb=" CG PHE A 164 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.117 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.061 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.099 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.073 2.00e-02 2.50e+03 5.56e-02 9.28e+01 pdb=" CG PHE A 119 " 0.096 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.116 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.042 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.061 2.00e-02 2.50e+03 5.49e-02 9.04e+01 pdb=" CG ATYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.001 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.095 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 810 2.28 - 2.86: 7854 2.86 - 3.44: 10597 3.44 - 4.02: 15300 4.02 - 4.60: 22047 Nonbonded interactions: 56608 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.702 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.723 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.800 2.450 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.834 2.450 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.842 2.450 ... (remaining 56603 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_5637181_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= 0.2609 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788953 | | target function (ml) not normalized (work): 232336.549998 | | target function (ml) not normalized (free): 11796.004970 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3016 0.2085 7.0185 4.9435| | 2: 3.57 - 2.84 1.00 2876 122 0.2446 0.1785 4.3543 4.3592| | 3: 2.84 - 2.48 1.00 2833 165 0.2373 0.1837 4.1339 4.1737| | 4: 2.47 - 2.25 1.00 2825 136 0.2362 0.1361 3.8437 3.8367| | 5: 2.25 - 2.09 1.00 2756 127 0.2489 0.1400 3.8083 3.799| | 6: 2.09 - 1.97 1.00 2846 113 0.2524 0.1821 3.469 3.572| | 7: 1.97 - 1.87 1.00 2787 165 0.2544 0.1877 3.1398 3.2458| | 8: 1.87 - 1.79 1.00 2789 144 0.2462 0.2035 3.0701 3.1957| | 9: 1.79 - 1.72 1.00 2745 138 0.2433 0.1716 2.9131 2.8922| | 10: 1.72 - 1.66 1.00 2789 158 0.2421 0.2075 2.7806 2.8685| | 11: 1.66 - 1.61 1.00 2740 147 0.2501 0.1673 2.7465 2.7088| | 12: 1.61 - 1.56 1.00 2787 146 0.2558 0.1722 2.6212 2.5251| | 13: 1.56 - 1.52 1.00 2745 130 0.2569 0.1913 2.5847 2.611| | 14: 1.52 - 1.48 1.00 2803 134 0.2586 0.2148 2.5094 2.6449| | 15: 1.48 - 1.45 1.00 2738 128 0.2534 0.1855 2.4154 2.4156| | 16: 1.45 - 1.42 1.00 2756 161 0.2649 0.2345 2.3709 2.4837| | 17: 1.42 - 1.39 1.00 2785 139 0.2693 0.1967 2.3333 2.317| | 18: 1.39 - 1.36 1.00 2741 179 0.2641 0.2254 2.2725 2.3773| | 19: 1.36 - 1.34 1.00 2807 134 0.2652 0.2393 2.255 2.3312| | 20: 1.34 - 1.32 1.00 2696 147 0.2706 0.2384 2.2192 2.2768| | 21: 1.32 - 1.30 1.00 2785 112 0.2739 0.2185 2.1638 2.1137| | 22: 1.29 - 1.27 1.00 2704 152 0.2738 0.2482 2.1313 2.1944| | 23: 1.27 - 1.26 1.00 2802 156 0.2763 0.2421 2.0892 2.1544| | 24: 1.26 - 1.24 1.00 2744 132 0.2760 0.2551 2.0674 2.1624| | 25: 1.24 - 1.22 1.00 2734 148 0.2892 0.2472 2.0492 2.0178| | 26: 1.22 - 1.21 1.00 2727 135 0.2832 0.2333 2.0016 2.0759| | 27: 1.21 - 1.19 1.00 2814 148 0.2956 0.2482 2.0116 1.9428| | 28: 1.19 - 1.18 1.00 2671 147 0.2898 0.2882 1.9663 2.0145| | 29: 1.18 - 1.16 1.00 2800 134 0.2993 0.2556 1.9562 1.9457| | 30: 1.16 - 1.15 1.00 2740 148 0.3032 0.3011 1.9181 1.9908| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.94 0.76 0.23 1498.37| | 2: 3.57 - 2.84 2876 122 0.80 26.26 1.27 0.23 1498.37| | 3: 2.84 - 2.48 2833 165 0.74 32.26 1.25 0.23 1243.65| | 4: 2.47 - 2.25 2825 136 0.81 25.84 1.26 0.25 582.61| | 5: 2.25 - 2.09 2756 127 0.77 29.57 1.28 0.25 582.61| | 6: 2.09 - 1.97 2846 113 0.83 22.91 1.28 0.25 319.88| | 7: 1.97 - 1.87 2787 165 0.89 17.09 1.28 0.26 95.81| | 8: 1.87 - 1.79 2789 144 0.85 21.70 1.25 0.26 95.81| | 9: 1.79 - 1.72 2745 138 0.88 18.56 1.23 0.26 55.40| | 10: 1.72 - 1.66 2789 158 0.86 20.26 1.23 0.25 47.30| | 11: 1.66 - 1.61 2740 147 0.86 21.03 1.24 0.25 45.53| | 12: 1.61 - 1.56 2787 146 0.89 17.78 1.24 0.25 27.57| | 13: 1.56 - 1.52 2745 130 0.87 19.64 1.23 0.25 27.57| | 14: 1.52 - 1.48 2803 134 0.87 19.98 1.23 0.25 25.00| | 15: 1.48 - 1.45 2738 128 0.87 19.71 1.23 0.25 20.30| | 16: 1.45 - 1.42 2756 161 0.86 21.47 1.25 0.25 20.30| | 17: 1.42 - 1.39 2785 139 0.86 21.00 1.24 0.25 17.67| | 18: 1.39 - 1.36 2741 179 0.86 21.49 1.22 0.25 16.15| | 19: 1.36 - 1.34 2807 134 0.85 22.24 1.22 0.25 16.15| | 20: 1.34 - 1.32 2696 147 0.87 21.09 1.21 0.25 13.49| | 21: 1.32 - 1.30 2785 112 0.85 22.51 1.21 0.25 13.31| | 22: 1.29 - 1.27 2704 152 0.85 22.87 1.21 0.24 12.95| | 23: 1.27 - 1.26 2802 156 0.86 22.15 1.22 0.24 11.13| | 24: 1.26 - 1.24 2744 132 0.85 22.74 1.20 0.24 11.13| | 25: 1.24 - 1.22 2734 148 0.84 23.71 1.22 0.24 10.49| | 26: 1.22 - 1.21 2727 135 0.84 23.78 1.20 0.23 9.78| | 27: 1.21 - 1.19 2814 148 0.84 24.39 1.19 0.23 9.78| | 28: 1.19 - 1.18 2671 147 0.83 25.15 1.18 0.23 9.23| | 29: 1.18 - 1.16 2800 134 0.82 25.93 1.17 0.22 9.03| | 30: 1.16 - 1.15 2740 148 0.80 27.41 1.16 0.22 9.03| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.03 max = 1498.37 mean = 217.81| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.94 mean = 22.65| |phase err.(test): min = 0.00 max = 89.50 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 : 0.084 0.249 1557 Z= 5.616 Angle : 5.384 16.340 2118 Z= 3.824 Chirality : 0.383 0.995 243 Planarity : 0.032 0.146 284 Dihedral : 14.086 82.483 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 39.46 % 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: -2.51 (0.48), residues: 224 helix: -2.56 (0.38), residues: 108 sheet: -0.55 (0.92), residues: 28 loop : -0.48 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.021 ARG A 98 TYR 0.141 0.047 TYR A 141 PHE 0.093 0.041 PHE A 119 HIS 0.072 0.035 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788953 | | target function (ml) not normalized (work): 232336.549998 | | target function (ml) not normalized (free): 11796.004970 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2568 0.2610 0.1940 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2568 0.2610 0.1940 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1986 0.1940 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.2003 0.2008 0.1953 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1648 0.1642 0.1773 n_refl.: 87594 remove outliers: r(all,work,free)=0.1648 0.1641 0.1773 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 0.3837 386.471 355.721 0.661 1.002 0.401 11.894-9.307 99.02 97 4 0.1885 613.891 593.624 0.930 1.003 0.380 9.237-7.194 100.00 213 7 0.2141 502.087 491.204 0.963 1.003 0.360 7.162-5.571 100.00 427 22 0.2221 376.788 364.696 0.932 1.003 0.330 5.546-4.326 100.00 867 58 0.1282 517.237 511.722 0.963 1.003 0.240 4.315-3.360 100.00 1859 96 0.1151 491.896 487.903 1.003 1.003 0.179 3.356-2.611 100.00 3867 181 0.1447 323.150 319.821 0.998 1.003 0.043 2.608-2.026 99.99 8198 413 0.1375 214.219 212.074 1.008 1.002 0.000 2.025-1.573 100.00 17313 902 0.1645 104.614 103.735 1.010 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2059 46.390 45.119 1.003 0.998 0.000 1.221-1.150 99.97 13689 708 0.2554 29.229 27.052 0.975 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0421 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1641 r_free=0.1773 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1641 r_free=0.1773 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.554577 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2007.740291 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 0.1464 0.0253 0.007 0.9 1.3 0.5 0.0 0 11.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.64 2.53 3.013 19.042 2007.740 0.017 12.39 15.31 2.92 3.119 19.496 2007.740 0.016 Individual atomic B min max mean iso aniso Overall: 8.55 118.13 20.93 2.88 0 1785 Protein: 8.55 118.13 17.80 2.88 0 1519 Water: 11.01 114.48 39.08 N/A 0 258 Other: 22.94 36.17 28.68 N/A 0 8 Chain A: 8.55 118.13 20.93 N/A 0 1785 Histogram: Values Number of atoms 8.55 - 19.51 1207 19.51 - 30.47 231 30.47 - 41.42 166 41.42 - 52.38 96 52.38 - 63.34 56 63.34 - 74.30 17 74.30 - 85.25 5 85.25 - 96.21 4 96.21 - 107.17 0 107.17 - 118.13 3 =========================== Idealize ADP of riding H ========================== r_work=0.1240 r_free=0.1532 r_work=0.1244 r_free=0.1536 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1244 r_free = 0.1536 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 = 0.1244 r_free = 0.1540 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 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= 0.1244 r_free= 0.1540 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015483 | | target function (ls_wunit_k1) not normalized (work): 1289.677267 | | target function (ls_wunit_k1) not normalized (free): 113.059347 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1258 0.1244 0.1540 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1697 0.1696 0.1763 n_refl.: 87593 remove outliers: r(all,work,free)=0.1697 0.1696 0.1763 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1720 0.1719 0.1779 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1255 0.1241 0.1531 n_refl.: 87593 remove outliers: r(all,work,free)=0.1255 0.1241 0.1531 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3601 299.327 277.802 0.627 1.002 0.372 11.894-9.307 99.02 97 4 0.1631 479.505 468.522 0.910 1.003 0.367 9.237-7.194 100.00 213 7 0.1819 392.176 387.466 0.951 1.003 0.319 7.162-5.571 100.00 427 22 0.1708 294.307 288.884 0.922 1.003 0.263 5.546-4.326 100.00 867 58 0.0918 404.010 401.379 0.950 1.003 0.209 4.315-3.360 100.00 1859 96 0.0778 384.216 383.267 0.994 1.002 0.190 3.356-2.611 100.00 3867 181 0.1024 252.410 251.703 0.999 1.002 0.100 2.608-2.026 99.99 8198 413 0.0973 167.325 166.748 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1201 81.713 81.883 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1648 36.235 35.695 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2363 22.830 21.329 0.968 0.997 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=0.1241 r_free=0.1531 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=0.1242 r_free=0.1534 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1242 r_free=0.1534 | n_water=258 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1252 r_free=0.1530 | n_water=252 | time (s): 25.630 (total time: 28.040) Filter (q & B) r_work=0.1255 r_free=0.1529 | n_water=249 | time (s): 3.470 (total time: 31.510) Compute maps r_work=0.1255 r_free=0.1529 | n_water=249 | time (s): 1.800 (total time: 33.310) Filter (map) r_work=0.1279 r_free=0.1541 | n_water=234 | time (s): 3.490 (total time: 36.800) Find peaks r_work=0.1279 r_free=0.1541 | n_water=234 | time (s): 0.630 (total time: 37.430) Add new water r_work=0.1430 r_free=0.1697 | n_water=451 | time (s): 3.650 (total time: 41.080) Refine new water occ: r_work=0.1328 r_free=0.1545 adp: r_work=0.1251 r_free=0.1505 occ: r_work=0.1262 r_free=0.1497 adp: r_work=0.1229 r_free=0.1487 occ: r_work=0.1233 r_free=0.1478 adp: r_work=0.1222 r_free=0.1476 ADP+occupancy (water only), MIN, final r_work=0.1222 r_free=0.1476 r_work=0.1222 r_free=0.1476 | n_water=451 | time (s): 80.160 (total time: 121.240) Filter (q & B) r_work=0.1227 r_free=0.1480 | n_water=432 | time (s): 4.000 (total time: 125.240) Filter (dist only) r_work=0.1227 r_free=0.1480 | n_water=432 | time (s): 40.910 (total time: 166.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.042851 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1610.377132 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 0.1498 0.0270 0.007 0.9 1.9 0.5 0.0 0 13.021 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.98 2.70 3.773 23.091 1610.377 0.015 12.00 14.84 2.84 4.117 22.927 1610.377 0.015 Individual atomic B min max mean iso aniso Overall: 8.67 113.26 23.15 2.62 198 1761 Protein: 8.67 113.26 17.65 2.62 0 1519 Water: 10.95 72.33 42.37 N/A 198 234 Other: 25.69 36.93 30.64 N/A 0 8 Chain A: 8.67 113.26 20.36 N/A 0 1761 Chain S: 15.62 69.79 47.99 N/A 198 0 Histogram: Values Number of atoms 8.67 - 19.13 1204 19.13 - 29.59 249 29.59 - 40.05 192 40.05 - 50.51 137 50.51 - 60.97 116 60.97 - 71.43 50 71.43 - 81.89 5 81.89 - 92.35 3 92.35 - 102.81 1 102.81 - 113.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1484 r_work=0.1200 r_free=0.1484 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1484 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1473 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1200 r_free= 0.1473 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013908 | | target function (ls_wunit_k1) not normalized (work): 1158.469737 | | target function (ls_wunit_k1) not normalized (free): 99.336788 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1200 0.1473 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1613 0.1610 0.1717 n_refl.: 87592 remove outliers: r(all,work,free)=0.1613 0.1610 0.1717 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1618 0.1615 0.1721 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1197 0.1468 n_refl.: 87592 remove outliers: r(all,work,free)=0.1208 0.1195 0.1468 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3250 292.015 271.187 0.608 0.938 0.340 11.894-9.307 99.02 97 4 0.1527 479.505 476.825 0.979 0.938 0.333 9.237-7.194 100.00 213 7 0.1660 392.176 393.360 1.045 0.938 0.290 7.162-5.571 100.00 427 22 0.1468 294.307 290.438 1.005 0.938 0.229 5.546-4.326 100.00 867 58 0.0824 404.010 401.655 1.023 0.939 0.210 4.315-3.360 100.00 1859 96 0.0723 384.216 383.056 1.069 0.939 0.200 3.356-2.611 100.00 3867 181 0.0963 252.410 251.708 1.075 0.940 0.170 2.608-2.026 99.99 8198 413 0.0957 167.325 166.853 1.084 0.941 0.000 2.025-1.573 100.00 17313 902 0.1176 81.713 81.911 1.090 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1611 36.235 35.745 1.074 0.947 0.000 1.221-1.150 99.97 13689 708 0.2338 22.830 21.390 1.028 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0475 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1468 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=0.1468 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1468 | n_water=432 | time (s): 2.000 (total time: 2.000) Filter (dist) r_work=0.1197 r_free=0.1469 | n_water=430 | time (s): 39.330 (total time: 41.330) Filter (q & B) r_work=0.1197 r_free=0.1469 | n_water=430 | time (s): 1.190 (total time: 42.520) Compute maps r_work=0.1197 r_free=0.1469 | n_water=430 | time (s): 1.630 (total time: 44.150) Filter (map) r_work=0.1239 r_free=0.1483 | n_water=292 | time (s): 2.650 (total time: 46.800) Find peaks r_work=0.1239 r_free=0.1483 | n_water=292 | time (s): 0.510 (total time: 47.310) Add new water r_work=0.1361 r_free=0.1593 | n_water=479 | time (s): 2.880 (total time: 50.190) Refine new water occ: r_work=0.1261 r_free=0.1512 adp: r_work=0.1262 r_free=0.1512 occ: r_work=0.1240 r_free=0.1493 adp: r_work=0.1237 r_free=0.1492 occ: r_work=0.1225 r_free=0.1478 adp: r_work=0.1218 r_free=0.1476 ADP+occupancy (water only), MIN, final r_work=0.1218 r_free=0.1476 r_work=0.1218 r_free=0.1476 | n_water=479 | time (s): 224.900 (total time: 275.090) Filter (q & B) r_work=0.1222 r_free=0.1474 | n_water=444 | time (s): 2.750 (total time: 277.840) Filter (dist only) r_work=0.1222 r_free=0.1474 | n_water=444 | time (s): 34.330 (total time: 312.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.055285 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.592855 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 0.1226 0.1431 0.0204 0.006 0.9 3.5 0.5 0.0 0 1.028 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.31 2.04 3.620 22.101 48.593 3.722 12.10 13.88 1.78 4.098 21.920 48.593 3.651 Individual atomic B min max mean iso aniso Overall: 9.19 108.29 21.68 2.32 213 1758 Protein: 9.19 108.29 17.23 2.33 0 1519 Water: 11.55 71.24 36.80 N/A 213 231 Other: 21.26 32.84 27.28 N/A 0 8 Chain A: 9.19 108.29 19.89 N/A 0 1758 Chain S: 15.18 65.96 36.47 N/A 213 0 Histogram: Values Number of atoms 9.19 - 19.10 1227 19.10 - 29.01 271 29.01 - 38.92 221 38.92 - 48.83 137 48.83 - 58.74 78 58.74 - 68.65 24 68.65 - 78.56 7 78.56 - 88.47 3 88.47 - 98.38 1 98.38 - 108.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1388 r_work=0.1211 r_free=0.1389 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1211 r_free = 0.1389 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1384 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1204 r_free= 0.1384 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.648555 | | target function (ml) not normalized (work): 303895.448761 | | target function (ml) not normalized (free): 16041.897228 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1204 0.1384 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1541 0.1540 0.1586 n_refl.: 87588 remove outliers: r(all,work,free)=0.1541 0.1540 0.1586 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1539 0.1538 0.1584 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1199 0.1366 n_refl.: 87588 remove outliers: r(all,work,free)=0.1203 0.1195 0.1366 n_refl.: 87578 ======================== 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 0.3814 286.519 258.383 0.467 1.000 0.302 11.894-9.307 97.06 95 4 0.2306 472.885 461.632 0.857 1.001 0.289 9.237-7.194 98.18 209 7 0.2262 383.709 386.363 0.948 1.002 0.204 7.162-5.571 100.00 427 22 0.1941 294.307 286.122 0.917 1.002 0.190 5.546-4.326 100.00 867 58 0.1089 404.010 399.474 0.953 1.002 0.190 4.315-3.360 100.00 1859 96 0.0941 384.216 381.483 0.994 1.002 0.190 3.356-2.611 100.00 3867 181 0.1159 252.410 250.371 0.999 1.002 0.077 2.608-2.026 99.99 8198 413 0.1045 167.325 166.256 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1012 81.713 81.854 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1296 36.235 35.802 1.021 0.999 0.000 1.221-1.150 99.97 13689 708 0.2134 22.830 21.437 0.979 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0354 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1195 r_free=0.1370 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1370 | n_water=444 | time (s): 1.960 (total time: 1.960) Filter (dist) r_work=0.1195 r_free=0.1369 | n_water=442 | time (s): 41.680 (total time: 43.640) Filter (q & B) r_work=0.1195 r_free=0.1368 | n_water=441 | time (s): 3.390 (total time: 47.030) Compute maps r_work=0.1195 r_free=0.1368 | n_water=441 | time (s): 1.650 (total time: 48.680) Filter (map) r_work=0.1213 r_free=0.1376 | n_water=317 | time (s): 3.320 (total time: 52.000) Find peaks r_work=0.1213 r_free=0.1376 | n_water=317 | time (s): 0.480 (total time: 52.480) Add new water r_work=0.1285 r_free=0.1451 | n_water=481 | time (s): 3.070 (total time: 55.550) Refine new water occ: r_work=0.1210 r_free=0.1382 adp: r_work=0.1210 r_free=0.1383 occ: r_work=0.1194 r_free=0.1368 adp: r_work=0.1193 r_free=0.1369 occ: r_work=0.1183 r_free=0.1358 adp: r_work=0.1179 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1356 r_work=0.1179 r_free=0.1356 | n_water=481 | time (s): 247.550 (total time: 303.100) Filter (q & B) r_work=0.1186 r_free=0.1357 | n_water=445 | time (s): 3.140 (total time: 306.240) Filter (dist only) r_work=0.1186 r_free=0.1356 | n_water=444 | time (s): 36.070 (total time: 342.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.994906 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.815127 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 0.1367 0.0175 0.006 1.0 3.2 0.5 0.0 0 0.997 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.67 1.75 3.424 21.482 46.815 3.639 11.81 13.65 1.84 3.790 21.376 46.815 3.625 Individual atomic B min max mean iso aniso Overall: 9.28 104.41 21.23 2.17 214 1757 Protein: 9.28 104.41 16.96 2.17 0 1519 Water: 11.47 70.07 35.76 N/A 214 230 Other: 20.50 29.72 25.34 N/A 0 8 Chain A: 9.28 104.41 19.56 N/A 0 1757 Chain S: 15.28 60.54 34.97 N/A 214 0 Histogram: Values Number of atoms 9.28 - 18.79 1222 18.79 - 28.30 279 28.30 - 37.82 225 37.82 - 47.33 129 47.33 - 56.84 73 56.84 - 66.36 29 66.36 - 75.87 9 75.87 - 85.38 2 85.38 - 94.90 1 94.90 - 104.41 2 =========================== Idealize ADP of riding H ========================== r_work=0.1181 r_free=0.1365 r_work=0.1182 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1182 r_free = 0.1365 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1178 r_free = 0.1364 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1178 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.624073 | | target function (ml) not normalized (work): 301820.037900 | | target function (ml) not normalized (free): 15959.063110 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1187 0.1178 0.1364 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1505 0.1504 0.1559 n_refl.: 87578 remove outliers: r(all,work,free)=0.1505 0.1504 0.1559 n_refl.: 87578 overall B=-0.02 to atoms: r(all,work,free)=0.1502 0.1501 0.1557 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1185 0.1176 0.1363 n_refl.: 87578 remove outliers: r(all,work,free)=0.1185 0.1175 0.1363 n_refl.: 87577 ======================== 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 0.3878 286.519 257.318 0.442 1.001 0.282 11.894-9.307 96.08 94 4 0.2465 473.421 459.750 0.832 1.002 0.261 9.237-7.194 98.18 209 7 0.2453 383.709 378.343 0.923 1.002 0.152 7.162-5.571 100.00 427 22 0.2096 294.307 284.546 0.904 1.002 0.150 5.546-4.326 100.00 867 58 0.1144 404.010 399.571 0.953 1.002 0.139 4.315-3.360 100.00 1859 96 0.0939 384.216 381.902 0.995 1.002 0.138 3.356-2.611 100.00 3867 181 0.1143 252.410 250.568 1.001 1.002 0.110 2.608-2.026 99.99 8198 413 0.1020 167.325 166.417 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0965 81.713 81.961 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1243 36.235 35.858 1.023 0.998 0.000 1.221-1.150 99.97 13689 708 0.2125 22.830 21.456 0.983 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0532 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1175 r_free=0.1363 After: r_work=0.1176 r_free=0.1364 ================================== NQH flips ================================== r_work=0.1176 r_free=0.1364 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1176 r_free=0.1364 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1176 r_free=0.1364 | n_water=444 | time (s): 1.780 (total time: 1.780) Filter (dist) r_work=0.1176 r_free=0.1364 | n_water=444 | time (s): 33.840 (total time: 35.620) Filter (q & B) r_work=0.1176 r_free=0.1364 | n_water=442 | time (s): 2.750 (total time: 38.370) Compute maps r_work=0.1176 r_free=0.1364 | n_water=442 | time (s): 1.370 (total time: 39.740) Filter (map) r_work=0.1200 r_free=0.1375 | n_water=335 | time (s): 3.320 (total time: 43.060) Find peaks r_work=0.1200 r_free=0.1375 | n_water=335 | time (s): 0.530 (total time: 43.590) Add new water r_work=0.1252 r_free=0.1422 | n_water=490 | time (s): 2.390 (total time: 45.980) Refine new water occ: r_work=0.1188 r_free=0.1359 adp: r_work=0.1188 r_free=0.1361 occ: r_work=0.1176 r_free=0.1345 adp: r_work=0.1174 r_free=0.1348 occ: r_work=0.1168 r_free=0.1335 adp: r_work=0.1164 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1164 r_free=0.1338 r_work=0.1164 r_free=0.1338 | n_water=490 | time (s): 202.560 (total time: 248.540) Filter (q & B) r_work=0.1171 r_free=0.1346 | n_water=452 | time (s): 3.420 (total time: 251.960) Filter (dist only) r_work=0.1172 r_free=0.1345 | n_water=451 | time (s): 39.070 (total time: 291.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.064008 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.779552 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 0.1195 0.1366 0.0171 0.007 1.0 4.8 0.5 0.0 0 1.032 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.66 1.71 3.296 21.198 42.780 3.631 11.97 13.67 1.70 3.442 21.150 42.780 3.625 Individual atomic B min max mean iso aniso Overall: 9.20 101.12 21.14 2.05 221 1757 Protein: 9.20 101.12 16.81 2.05 0 1519 Water: 11.49 69.61 35.65 N/A 221 230 Other: 20.39 29.08 25.01 N/A 0 8 Chain A: 9.20 101.12 19.41 N/A 0 1757 Chain S: 14.80 60.38 34.93 N/A 221 0 Histogram: Values Number of atoms 9.20 - 18.40 1214 18.40 - 27.59 283 27.59 - 36.78 207 36.78 - 45.97 141 45.97 - 55.16 87 55.16 - 64.35 29 64.35 - 73.54 12 73.54 - 82.73 2 82.73 - 91.92 1 91.92 - 101.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1367 r_work=0.1197 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1367 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1366 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1194 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623912 | | target function (ml) not normalized (work): 301803.007206 | | target function (ml) not normalized (free): 15950.656337 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1416 0.1404 5.7038 5.616| | 2: 3.57 - 2.84 1.00 2888 124 0.1092 0.1433 5.1834 5.252| | 3: 2.83 - 2.48 1.00 2820 163 0.1226 0.1271 4.9956 5.0126| | 4: 2.47 - 2.25 1.00 2825 136 0.1027 0.1162 4.7009 4.7711| | 5: 2.25 - 2.09 1.00 2756 127 0.1000 0.1091 4.6406 4.7056| | 6: 2.09 - 1.97 1.00 2846 113 0.0971 0.1188 4.3436 4.4822| | 7: 1.97 - 1.87 1.00 2787 165 0.0983 0.1232 4.0697 4.1847| | 8: 1.87 - 1.79 1.00 2789 144 0.1019 0.1230 3.9898 4.0658| | 9: 1.79 - 1.72 1.00 2745 138 0.0956 0.1301 3.7167 3.9087| | 10: 1.72 - 1.66 1.00 2831 160 0.0998 0.1242 3.6324 3.7556| | 11: 1.66 - 1.61 1.00 2712 147 0.0963 0.1101 3.5707 3.6161| | 12: 1.61 - 1.56 1.00 2773 144 0.0922 0.1198 3.3553 3.4946| | 13: 1.56 - 1.52 1.00 2745 130 0.0986 0.1088 3.3396 3.4422| | 14: 1.52 - 1.48 1.00 2803 134 0.0998 0.1120 3.2659 3.3532| | 15: 1.48 - 1.45 1.00 2738 128 0.1026 0.1368 3.1795 3.3269| | 16: 1.45 - 1.42 1.00 2756 161 0.1068 0.1288 3.157 3.2563| | 17: 1.42 - 1.39 1.00 2785 139 0.1126 0.1306 3.1224 3.2534| | 18: 1.39 - 1.36 1.00 2741 179 0.1164 0.1385 3.096 3.2777| | 19: 1.36 - 1.34 1.00 2807 134 0.1224 0.1627 3.1015 3.2867| | 20: 1.34 - 1.32 1.00 2696 147 0.1324 0.1483 3.0944 3.1454| | 21: 1.32 - 1.30 1.00 2785 112 0.1418 0.1627 3.0935 3.1663| | 22: 1.29 - 1.27 1.00 2704 152 0.1483 0.1916 3.0934 3.2904| | 23: 1.27 - 1.26 1.00 2802 156 0.1577 0.1861 3.107 3.2125| | 24: 1.26 - 1.24 1.00 2744 132 0.1626 0.1783 3.0969 3.2065| | 25: 1.24 - 1.22 1.00 2733 148 0.1799 0.2305 3.1134 3.2902| | 26: 1.22 - 1.21 1.00 2727 135 0.1863 0.1755 3.1267 3.1923| | 27: 1.21 - 1.19 1.00 2814 148 0.2015 0.2088 3.1439 3.1506| | 28: 1.19 - 1.18 1.00 2671 147 0.2142 0.2300 3.1414 3.1634| | 29: 1.18 - 1.16 1.00 2800 134 0.2222 0.2370 3.1297 3.2245| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2500 3.1191 3.1683| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2919 171 0.95 8.75 1.00 0.97 6048.54| | 2: 3.57 - 2.84 2888 124 0.92 13.01 1.01 0.97 6048.54| | 3: 2.83 - 2.48 2820 163 0.89 17.18 0.99 0.97 5075.94| | 4: 2.47 - 2.25 2825 136 0.91 14.35 1.00 0.98 2567.94| | 5: 2.25 - 2.09 2756 127 0.90 16.58 1.01 0.98 2567.94| | 6: 2.09 - 1.97 2846 113 0.92 13.43 1.02 0.98 1519.09| | 7: 1.97 - 1.87 2787 165 0.94 10.73 1.02 0.98 624.57| | 8: 1.87 - 1.79 2789 144 0.91 14.34 1.00 0.98 624.57| | 9: 1.79 - 1.72 2745 138 0.93 11.38 0.98 0.97 338.88| | 10: 1.72 - 1.66 2831 160 0.93 12.22 0.98 0.97 281.67| | 11: 1.66 - 1.61 2712 147 0.93 12.82 0.98 0.97 268.99| | 12: 1.61 - 1.56 2773 144 0.95 9.56 0.99 0.97 149.42| | 13: 1.56 - 1.52 2745 130 0.94 11.22 1.02 0.97 149.42| | 14: 1.52 - 1.48 2803 134 0.94 11.36 1.02 0.98 133.85| | 15: 1.48 - 1.45 2738 128 0.95 10.56 1.01 0.98 105.33| | 16: 1.45 - 1.42 2756 161 0.94 11.74 1.02 0.98 105.33| | 17: 1.42 - 1.39 2785 139 0.94 11.57 1.01 0.99 95.38| | 18: 1.39 - 1.36 2741 179 0.94 11.96 1.01 0.99 89.62| | 19: 1.36 - 1.34 2807 134 0.94 12.53 1.00 0.99 89.62| | 20: 1.34 - 1.32 2696 147 0.94 12.61 0.99 0.97 84.23| | 21: 1.32 - 1.30 2785 112 0.93 13.52 0.99 0.97 83.86| | 22: 1.29 - 1.27 2704 152 0.93 13.98 0.98 0.96 83.90| | 23: 1.27 - 1.26 2802 156 0.92 14.97 0.98 0.95 84.10| | 24: 1.26 - 1.24 2744 132 0.92 15.07 0.97 0.95 84.10| | 25: 1.24 - 1.22 2733 148 0.91 16.46 0.96 0.94 85.43| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.94 86.90| | 27: 1.21 - 1.19 2814 148 0.89 18.81 1.02 0.94 86.90| | 28: 1.19 - 1.18 2671 147 0.88 20.26 1.01 0.93 90.03| | 29: 1.18 - 1.16 2800 134 0.88 20.61 0.99 0.93 91.21| | 30: 1.16 - 1.15 2739 148 0.86 22.01 0.98 0.93 91.21| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 83.86 max = 6048.54 mean = 950.86| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.04| |phase err.(test): min = 0.00 max = 89.30 mean = 14.15| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1194 0.1366 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1511 0.1510 0.1563 n_refl.: 87577 remove outliers: r(all,work,free)=0.1511 0.1510 0.1563 n_refl.: 87577 overall B=-0.02 to atoms: r(all,work,free)=0.1508 0.1507 0.1561 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1195 0.1367 n_refl.: 87577 remove outliers: r(all,work,free)=0.1203 0.1194 0.1367 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.4072 286.519 251.188 0.431 1.001 0.298 11.894-9.307 94.12 92 4 0.2579 471.109 456.104 0.834 1.002 0.239 9.237-7.194 98.18 209 7 0.2525 383.709 377.323 0.914 1.002 0.157 7.162-5.571 100.00 427 22 0.2221 294.307 283.303 0.897 1.002 0.127 5.546-4.326 100.00 867 58 0.1197 404.010 398.995 0.952 1.002 0.120 4.315-3.360 100.00 1859 96 0.0973 384.216 381.482 0.995 1.002 0.113 3.356-2.611 100.00 3867 181 0.1167 252.410 250.445 1.000 1.002 0.053 2.608-2.026 99.99 8198 413 0.1044 167.325 166.321 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0974 81.713 81.957 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1234 36.235 35.855 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2119 22.830 21.449 0.983 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0474 ================= 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 : 0.2609 0.1940 0.084 5.384 8.8 119.3 19.9 258 0.000 1_bss: 0.1641 0.1773 0.084 5.384 9.0 119.5 20.1 258 0.000 1_settarget: 0.1641 0.1773 0.084 5.384 9.0 119.5 20.1 258 0.000 1_nqh: 0.1641 0.1773 0.084 5.384 9.0 119.5 20.1 258 0.000 1_weight: 0.1641 0.1773 0.084 5.384 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1211 0.1464 0.007 0.940 9.0 119.5 20.1 258 0.124 1_adp: 0.1240 0.1532 0.007 0.940 8.6 118.1 20.9 258 0.124 1_regHadp: 0.1244 0.1536 0.007 0.940 8.6 118.1 20.9 258 0.124 1_occ: 0.1244 0.1540 0.007 0.940 8.6 118.1 20.9 258 0.124 2_bss: 0.1241 0.1531 0.007 0.940 8.7 118.3 21.1 258 0.124 2_settarget: 0.1241 0.1531 0.007 0.940 8.7 118.3 21.1 258 0.124 2_updatecdl: 0.1241 0.1531 0.007 0.948 8.7 118.3 21.1 258 0.124 2_nqh: 0.1242 0.1534 0.007 0.948 8.7 118.3 21.1 258 0.126 2_sol: 0.1227 0.1480 0.007 0.948 8.7 118.3 23.4 432 n/a 2_weight: 0.1227 0.1480 0.007 0.948 8.7 118.3 23.4 432 n/a 2_xyzrec: 0.1228 0.1498 0.007 0.887 8.7 118.3 23.4 432 n/a 2_adp: 0.1200 0.1484 0.007 0.887 8.7 113.3 23.2 432 n/a 2_regHadp: 0.1200 0.1484 0.007 0.887 8.7 113.3 23.2 432 n/a 2_occ: 0.1200 0.1473 0.007 0.887 8.7 113.3 23.2 432 n/a 3_bss: 0.1195 0.1468 0.007 0.887 8.7 113.3 23.2 432 n/a 3_settarget: 0.1195 0.1468 0.007 0.887 8.7 113.3 23.2 432 n/a 3_updatecdl: 0.1195 0.1468 0.007 0.888 8.7 113.3 23.2 432 n/a 3_nqh: 0.1195 0.1468 0.007 0.888 8.7 113.3 23.2 432 n/a 3_sol: 0.1222 0.1474 0.007 0.888 8.7 113.3 22.0 444 n/a 3_weight: 0.1222 0.1474 0.007 0.888 8.7 113.3 22.0 444 n/a 3_xyzrec: 0.1226 0.1431 0.006 0.923 8.7 113.3 22.0 444 n/a 3_adp: 0.1210 0.1388 0.006 0.923 9.2 108.3 21.7 444 n/a 3_regHadp: 0.1211 0.1389 0.006 0.923 9.2 108.3 21.7 444 n/a 3_occ: 0.1204 0.1384 0.006 0.923 9.2 108.3 21.7 444 n/a 4_bss: 0.1195 0.1366 0.006 0.923 9.2 108.3 21.7 444 n/a 4_settarget: 0.1195 0.1366 0.006 0.923 9.2 108.3 21.7 444 n/a 4_updatecdl: 0.1195 0.1366 0.006 0.923 9.2 108.3 21.7 444 n/a 4_nqh: 0.1195 0.1370 0.006 0.923 9.2 108.3 21.7 444 n/a 4_sol: 0.1186 0.1356 0.006 0.923 9.2 108.3 21.4 444 n/a 4_weight: 0.1186 0.1356 0.006 0.923 9.2 108.3 21.4 444 n/a 4_xyzrec: 0.1192 0.1367 0.006 0.952 9.2 108.3 21.4 444 n/a 4_adp: 0.1181 0.1365 0.006 0.952 9.3 104.4 21.2 444 n/a 4_regHadp: 0.1182 0.1365 0.006 0.952 9.3 104.4 21.2 444 n/a 4_occ: 0.1178 0.1364 0.006 0.952 9.3 104.4 21.2 444 n/a 5_bss: 0.1175 0.1363 0.006 0.952 9.3 104.4 21.2 444 n/a 5_settarget: 0.1175 0.1363 0.006 0.952 9.3 104.4 21.2 444 n/a 5_updatecdl: 0.1175 0.1363 0.006 0.952 9.3 104.4 21.2 444 n/a 5_setrh: 0.1176 0.1364 0.006 0.952 9.3 104.4 21.2 444 n/a 5_nqh: 0.1176 0.1364 0.006 0.952 9.3 104.4 21.2 444 n/a 5_sol: 0.1172 0.1345 0.006 0.952 9.3 104.4 21.2 451 n/a 5_weight: 0.1172 0.1345 0.006 0.952 9.3 104.4 21.2 451 n/a 5_xyzrec: 0.1195 0.1366 0.007 1.025 9.3 104.4 21.2 451 n/a 5_adp: 0.1197 0.1367 0.007 1.025 9.2 101.1 21.1 451 n/a 5_regHadp: 0.1197 0.1367 0.007 1.025 9.2 101.1 21.1 451 n/a 5_occ: 0.1194 0.1366 0.007 1.025 9.2 101.1 21.1 451 n/a end: 0.1194 0.1367 0.007 1.025 9.2 101.1 21.1 451 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5637181_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5637181_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8000 Refinement macro-cycles (run) : 3507.6900 Write final files (write_after_run_outputs) : 69.4000 Total : 3581.8900 Total CPU time: 60.31 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:24 PST -0800 (1735452684.91 s) Start R-work = 0.1641, R-free = 0.1773 Final R-work = 0.1194, R-free = 0.1367 =============================================================================== Job complete usr+sys time: 3719.25 seconds wall clock time: 66 minutes 37.77 seconds (3997.77 seconds total)