Starting phenix.refine on Sat Dec 28 21:06:34 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3941866.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3941866.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3941866.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.06, per 1000 atoms: 0.61 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: 0.52 Conformation dependent library (CDL) restraints added in 342.1 milliseconds Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 577 0.92 - 1.18: 1076 1.18 - 1.43: 652 1.43 - 1.68: 822 1.68 - 1.94: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.462 1.282 0.180 9.50e-03 1.11e+04 3.59e+02 bond pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.336 1.561 -0.225 1.25e-02 6.40e+03 3.25e+02 bond pdb=" CA ILE A 91 " pdb=" CB ILE A 91 " ideal model delta sigma weight residual 1.538 1.353 0.185 1.06e-02 8.90e+03 3.05e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.496 -0.175 1.00e-02 1.00e+04 3.05e+02 bond pdb=" C THR A 110 " pdb=" N ALA A 111 " ideal model delta sigma weight residual 1.335 1.560 -0.225 1.31e-02 5.83e+03 2.94e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 3369 5.06 - 10.13: 1881 10.13 - 15.19: 452 15.19 - 20.26: 64 20.26 - 25.32: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " ideal model delta sigma weight residual 123.46 109.43 14.03 9.90e-01 1.02e+00 2.01e+02 angle pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" O ALA A 56 " ideal model delta sigma weight residual 121.10 136.58 -15.48 1.10e+00 8.26e-01 1.98e+02 angle pdb=" O GLU A 84 " pdb=" C GLU A 84 " pdb=" N SER A 85 " ideal model delta sigma weight residual 122.34 137.76 -15.42 1.25e+00 6.40e-01 1.52e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.82 108.08 12.74 1.05e+00 9.07e-01 1.47e+02 angle pdb=" O BASN A 76 " pdb=" C BASN A 76 " pdb=" N LEU A 77 " ideal model delta sigma weight residual 122.07 134.36 -12.29 1.03e+00 9.43e-01 1.42e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 15.87: 910 15.87 - 31.71: 134 31.71 - 47.55: 42 47.55 - 63.39: 22 63.39 - 79.23: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.254: 108 0.254 - 0.503: 80 0.503 - 0.753: 42 0.753 - 1.002: 10 1.002 - 1.251: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -3.88 1.25 2.00e-01 2.50e+01 3.91e+01 chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.62 -1.18 2.00e-01 2.50e+01 3.49e+01 chirality pdb=" CA MET A 133 " pdb=" N MET A 133 " pdb=" C MET A 133 " pdb=" CB MET A 133 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.71e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.039 2.00e-02 2.50e+03 5.81e-02 1.01e+02 pdb=" CG ATYR A 67 " 0.127 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.009 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.043 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.008 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.020 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.066 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.089 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.069 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.058 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.068 2.00e-02 2.50e+03 5.36e-02 8.62e+01 pdb=" CG BTYR A 67 " 0.042 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.052 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.041 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.115 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.036 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.029 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.013 2.00e-02 2.50e+03 5.28e-02 8.37e+01 pdb=" CG TYR A 139 " -0.097 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.086 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.058 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.053 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 598 2.24 - 2.83: 7500 2.83 - 3.42: 10849 3.42 - 4.01: 15322 4.01 - 4.60: 22313 Nonbonded interactions: 56582 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.652 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.749 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.794 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.811 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.827 2.100 ... (remaining 56577 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_3941866_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= 0.1917 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793292 | | target function (ml) not normalized (work): 232697.977799 | | target function (ml) not normalized (free): 11828.129705 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3038 0.2035 7.0981 4.9489| | 2: 3.57 - 2.84 1.00 2876 122 0.2441 0.1763 4.3462 4.3358| | 3: 2.84 - 2.48 1.00 2833 165 0.2346 0.1570 4.1277 4.1494| | 4: 2.47 - 2.25 1.00 2825 136 0.2328 0.1466 3.8346 3.8379| | 5: 2.25 - 2.09 1.00 2756 127 0.2468 0.1676 3.7946 3.8071| | 6: 2.09 - 1.97 1.00 2846 113 0.2524 0.1655 3.4694 3.5037| | 7: 1.97 - 1.87 1.00 2787 165 0.2547 0.1737 3.1237 3.1525| | 8: 1.87 - 1.79 1.00 2789 144 0.2447 0.1895 3.0447 3.1421| | 9: 1.79 - 1.72 1.00 2745 138 0.2370 0.1826 2.891 2.9635| | 10: 1.72 - 1.66 1.00 2789 158 0.2483 0.1985 2.8018 2.8714| | 11: 1.66 - 1.61 1.00 2740 147 0.2509 0.1879 2.7508 2.7933| | 12: 1.61 - 1.56 1.00 2787 146 0.2512 0.2166 2.6225 2.7649| | 13: 1.56 - 1.52 1.00 2745 130 0.2571 0.1967 2.5787 2.6387| | 14: 1.52 - 1.48 1.00 2803 134 0.2613 0.2028 2.5046 2.5727| | 15: 1.48 - 1.45 1.00 2738 128 0.2581 0.1963 2.4173 2.4259| | 16: 1.45 - 1.42 1.00 2756 161 0.2639 0.2085 2.3864 2.4205| | 17: 1.42 - 1.39 1.00 2785 139 0.2730 0.1929 2.3479 2.3398| | 18: 1.39 - 1.36 1.00 2741 179 0.2631 0.2255 2.2684 2.356| | 19: 1.36 - 1.34 1.00 2807 134 0.2678 0.2165 2.2603 2.2528| | 20: 1.34 - 1.32 1.00 2696 147 0.2684 0.2107 2.2114 2.2214| | 21: 1.32 - 1.30 1.00 2785 112 0.2672 0.2407 2.1621 2.2528| | 22: 1.29 - 1.27 1.00 2704 152 0.2748 0.2619 2.1384 2.1923| | 23: 1.27 - 1.26 1.00 2802 156 0.2782 0.2461 2.1232 2.1693| | 24: 1.26 - 1.24 1.00 2744 132 0.2792 0.2446 2.0933 2.0962| | 25: 1.24 - 1.22 1.00 2734 148 0.2864 0.2688 2.0445 2.1231| | 26: 1.22 - 1.21 1.00 2727 135 0.2911 0.2378 2.0143 2.0817| | 27: 1.21 - 1.19 1.00 2814 148 0.2962 0.2582 1.9938 2.0336| | 28: 1.19 - 1.18 1.00 2671 147 0.2997 0.2787 1.9894 1.9955| | 29: 1.18 - 1.16 1.00 2800 134 0.2987 0.2708 1.9724 2.0458| | 30: 1.16 - 1.15 1.00 2740 148 0.3053 0.2721 1.9298 1.9566| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.76 0.76 0.23 1479.57| | 2: 3.57 - 2.84 2876 122 0.80 25.98 1.27 0.23 1479.57| | 3: 2.84 - 2.48 2833 165 0.74 31.88 1.24 0.24 1225.64| | 4: 2.47 - 2.25 2825 136 0.81 25.35 1.25 0.25 566.65| | 5: 2.25 - 2.09 2756 127 0.77 29.17 1.28 0.25 566.65| | 6: 2.09 - 1.97 2846 113 0.84 22.39 1.29 0.25 308.32| | 7: 1.97 - 1.87 2787 165 0.90 16.37 1.29 0.26 88.01| | 8: 1.87 - 1.79 2789 144 0.86 20.61 1.25 0.26 88.01| | 9: 1.79 - 1.72 2745 138 0.88 18.56 1.23 0.25 55.15| | 10: 1.72 - 1.66 2789 158 0.86 20.51 1.23 0.25 48.57| | 11: 1.66 - 1.61 2740 147 0.85 21.52 1.24 0.25 46.95| | 12: 1.61 - 1.56 2787 146 0.88 18.78 1.24 0.25 30.48| | 13: 1.56 - 1.52 2745 130 0.86 20.68 1.24 0.25 30.48| | 14: 1.52 - 1.48 2803 134 0.86 21.22 1.24 0.25 27.09| | 15: 1.48 - 1.45 2738 128 0.87 20.29 1.24 0.25 20.88| | 16: 1.45 - 1.42 2756 161 0.86 21.54 1.23 0.25 20.88| | 17: 1.42 - 1.39 2785 139 0.86 21.05 1.24 0.25 17.61| | 18: 1.39 - 1.36 2741 179 0.86 21.30 1.22 0.25 15.71| | 19: 1.36 - 1.34 2807 134 0.86 21.89 1.22 0.25 15.71| | 20: 1.34 - 1.32 2696 147 0.87 20.78 1.21 0.25 13.03| | 21: 1.32 - 1.30 2785 112 0.86 21.74 1.20 0.25 12.84| | 22: 1.29 - 1.27 2704 152 0.85 22.52 1.21 0.25 12.56| | 23: 1.27 - 1.26 2802 156 0.86 22.05 1.20 0.24 11.16| | 24: 1.26 - 1.24 2744 132 0.85 22.38 1.20 0.24 11.16| | 25: 1.24 - 1.22 2734 148 0.84 23.88 1.20 0.24 10.67| | 26: 1.22 - 1.21 2727 135 0.84 23.92 1.21 0.24 10.13| | 27: 1.21 - 1.19 2814 148 0.83 24.94 1.21 0.24 10.13| | 28: 1.19 - 1.18 2671 147 0.83 25.36 1.19 0.23 9.59| | 29: 1.18 - 1.16 2800 134 0.82 25.62 1.16 0.23 9.38| | 30: 1.16 - 1.15 2740 148 0.80 27.42 1.16 0.23 9.38| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 9.38 max = 1479.57 mean = 214.27| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.62| |phase err.(test): min = 0.00 max = 89.97 mean = 22.49| |-----------------------------------------------------------------------------| ----------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 : 0.079 0.225 1557 Z= 5.386 Angle : 5.321 17.827 2118 Z= 3.702 Chirality : 0.409 1.251 243 Planarity : 0.032 0.116 284 Dihedral : 13.882 79.230 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 1.08 % Allowed : 5.41 % Favored : 93.51 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 35.68 % 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: -2.87 (0.49), residues: 224 helix: -3.19 (0.32), residues: 103 sheet: -1.11 (0.77), residues: 38 loop : -0.05 (0.68), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.092 0.028 ARG A 5 TYR 0.072 0.032 TYR A 141 PHE 0.058 0.025 PHE A 164 HIS 0.050 0.017 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= 0.1917 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793292 | | target function (ml) not normalized (work): 232697.977799 | | target function (ml) not normalized (free): 11828.129705 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2608 0.1917 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2608 0.1917 n_refl.: 87602 remove outliers: r(all,work,free)=0.1978 0.1983 0.1917 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.2000 0.2005 0.1930 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1647 0.1641 0.1755 n_refl.: 87594 remove outliers: r(all,work,free)=0.1646 0.1640 0.1755 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.87 87 5 0.3809 382.009 359.448 0.682 1.002 0.413 11.894-9.307 99.02 97 4 0.1829 613.617 596.249 0.933 1.003 0.400 9.237-7.194 100.00 213 7 0.2135 501.863 489.693 0.965 1.003 0.345 7.162-5.571 100.00 427 22 0.2222 376.620 364.312 0.931 1.003 0.303 5.546-4.326 100.00 867 58 0.1293 517.006 510.837 0.969 1.003 0.233 4.315-3.360 100.00 1859 96 0.1129 491.677 487.512 1.007 1.003 0.158 3.356-2.611 100.00 3867 181 0.1448 323.006 319.646 0.996 1.002 0.057 2.608-2.026 99.99 8198 413 0.1363 214.124 212.034 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1643 104.567 103.837 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2074 46.369 45.064 1.003 0.996 0.000 1.221-1.150 99.97 13689 708 0.2587 29.216 26.953 0.980 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0414 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1640 r_free=0.1755 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1640 r_free=0.1755 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.898494 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2021.335354 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 0.1209 0.1465 0.0257 0.007 0.9 1.3 0.5 0.0 0 11.949 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 14.65 2.57 3.013 19.038 2021.335 0.017 12.38 15.41 3.03 3.109 19.457 2021.335 0.016 Individual atomic B min max mean iso aniso Overall: 8.45 118.29 20.86 2.88 0 1785 Protein: 8.45 118.29 17.75 2.88 0 1519 Water: 10.89 114.88 38.92 N/A 0 258 Other: 22.73 35.85 28.74 N/A 0 8 Chain A: 8.45 118.29 20.86 N/A 0 1785 Histogram: Values Number of atoms 8.45 - 19.44 1210 19.44 - 30.42 228 30.42 - 41.40 167 41.40 - 52.39 96 52.39 - 63.37 55 63.37 - 74.36 18 74.36 - 85.34 4 85.34 - 96.33 4 96.33 - 107.31 0 107.31 - 118.29 3 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1542 r_work=0.1243 r_free=0.1547 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1243 r_free = 0.1547 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 = 0.1243 r_free = 0.1550 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= 0.1243 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015290 | | target function (ls_wunit_k1) not normalized (work): 1273.637406 | | target function (ls_wunit_k1) not normalized (free): 114.991953 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1258 0.1243 0.1550 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1690 0.1688 0.1762 n_refl.: 87592 remove outliers: r(all,work,free)=0.1690 0.1688 0.1762 n_refl.: 87592 overall B=0.19 to atoms: r(all,work,free)=0.1720 0.1719 0.1783 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1255 0.1240 0.1546 n_refl.: 87592 remove outliers: r(all,work,free)=0.1255 0.1240 0.1546 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 0.3568 299.424 280.230 0.707 0.921 0.398 11.894-9.307 99.02 97 4 0.1621 480.961 468.086 0.988 0.922 0.390 9.237-7.194 100.00 213 7 0.1803 393.367 388.548 1.031 0.922 0.340 7.162-5.571 100.00 427 22 0.1730 295.200 289.531 0.997 0.923 0.263 5.546-4.326 100.00 867 58 0.0923 405.236 402.579 1.033 0.924 0.230 4.315-3.360 100.00 1859 96 0.0776 385.383 384.475 1.075 0.926 0.179 3.356-2.611 100.00 3867 181 0.1019 253.176 252.452 1.074 0.929 0.057 2.608-2.026 99.99 8198 413 0.0968 167.833 167.278 1.080 0.934 0.000 2.025-1.573 100.00 17313 902 0.1207 81.961 82.151 1.078 0.942 0.000 1.573-1.221 100.00 36679 1900 0.1648 36.345 35.815 1.048 0.955 0.000 1.221-1.150 99.97 13689 708 0.2360 22.900 21.427 1.002 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0432 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1240 r_free=0.1546 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=0.1547 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1242 r_free=0.1547 | n_water=258 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1251 r_free=0.1545 | n_water=252 | time (s): 26.850 (total time: 29.200) Filter (q & B) r_work=0.1254 r_free=0.1543 | n_water=249 | time (s): 3.430 (total time: 32.630) Compute maps r_work=0.1254 r_free=0.1543 | n_water=249 | time (s): 1.760 (total time: 34.390) Filter (map) r_work=0.1269 r_free=0.1548 | n_water=237 | time (s): 3.660 (total time: 38.050) Find peaks r_work=0.1269 r_free=0.1548 | n_water=237 | time (s): 0.730 (total time: 38.780) Add new water r_work=0.1425 r_free=0.1684 | n_water=451 | time (s): 3.780 (total time: 42.560) Refine new water occ: r_work=0.1332 r_free=0.1569 adp: r_work=0.1250 r_free=0.1514 occ: r_work=0.1262 r_free=0.1515 adp: r_work=0.1228 r_free=0.1501 occ: r_work=0.1230 r_free=0.1491 adp: r_work=0.1220 r_free=0.1492 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1492 r_work=0.1220 r_free=0.1492 | n_water=451 | time (s): 86.830 (total time: 129.390) Filter (q & B) r_work=0.1224 r_free=0.1494 | n_water=428 | time (s): 4.120 (total time: 133.510) Filter (dist only) r_work=0.1224 r_free=0.1493 | n_water=427 | time (s): 43.400 (total time: 176.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.085203 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1530.959515 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 0.1219 0.1498 0.0279 0.007 0.9 2.2 0.5 0.0 0 13.043 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.19 14.98 2.79 3.768 23.099 1530.960 0.015 11.87 14.63 2.76 4.140 22.925 1530.960 0.014 Individual atomic B min max mean iso aniso Overall: 8.69 114.06 23.13 2.60 190 1764 Protein: 8.69 114.06 17.60 2.60 0 1519 Water: 11.06 72.83 42.69 N/A 190 237 Other: 24.21 36.06 29.24 N/A 0 8 Chain A: 8.69 114.06 20.33 N/A 0 1764 Chain S: 17.47 71.95 49.17 N/A 190 0 Histogram: Values Number of atoms 8.69 - 19.23 1207 19.23 - 29.77 251 29.77 - 40.30 175 40.30 - 50.84 148 50.84 - 61.38 113 61.38 - 71.91 48 71.91 - 82.45 6 82.45 - 92.99 3 92.99 - 103.52 1 103.52 - 114.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1464 r_work=0.1187 r_free=0.1463 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1463 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1456 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.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1188 r_free= 0.1456 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.013557 | | target function (ls_wunit_k1) not normalized (work): 1129.285268 | | target function (ls_wunit_k1) not normalized (free): 101.752541 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1188 0.1456 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1607 0.1604 0.1697 n_refl.: 87592 remove outliers: r(all,work,free)=0.1607 0.1604 0.1697 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1611 0.1608 0.1700 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1185 0.1454 n_refl.: 87592 remove outliers: r(all,work,free)=0.1198 0.1185 0.1454 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3538 296.855 276.657 0.620 1.002 0.387 11.894-9.307 99.02 97 4 0.1473 480.961 475.729 0.920 1.002 0.370 9.237-7.194 100.00 213 7 0.1610 393.367 394.748 0.981 1.003 0.271 7.162-5.571 100.00 427 22 0.1455 295.200 291.499 0.939 1.003 0.239 5.546-4.326 100.00 867 58 0.0825 405.236 402.256 0.959 1.002 0.215 4.315-3.360 100.00 1859 96 0.0706 385.383 384.479 1.003 1.002 0.210 3.356-2.611 100.00 3867 181 0.0955 253.176 252.432 1.009 1.002 0.150 2.608-2.026 99.99 8198 413 0.0950 167.833 167.432 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1164 81.961 82.159 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1596 36.345 35.859 1.018 0.999 0.000 1.221-1.150 99.97 13689 708 0.2323 22.900 21.445 0.979 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0433 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1454 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1185 r_free=0.1456 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1456 | n_water=427 | time (s): 1.950 (total time: 1.950) Filter (dist) r_work=0.1185 r_free=0.1456 | n_water=426 | time (s): 36.270 (total time: 38.220) Filter (q & B) r_work=0.1187 r_free=0.1455 | n_water=425 | time (s): 2.720 (total time: 40.940) Compute maps r_work=0.1187 r_free=0.1455 | n_water=425 | time (s): 1.620 (total time: 42.560) Filter (map) r_work=0.1233 r_free=0.1473 | n_water=287 | time (s): 3.330 (total time: 45.890) Find peaks r_work=0.1233 r_free=0.1473 | n_water=287 | time (s): 0.700 (total time: 46.590) Add new water r_work=0.1363 r_free=0.1592 | n_water=477 | time (s): 3.140 (total time: 49.730) Refine new water occ: r_work=0.1258 r_free=0.1496 adp: r_work=0.1260 r_free=0.1497 occ: r_work=0.1236 r_free=0.1478 adp: r_work=0.1233 r_free=0.1476 occ: r_work=0.1220 r_free=0.1465 adp: r_work=0.1213 r_free=0.1460 ADP+occupancy (water only), MIN, final r_work=0.1213 r_free=0.1460 r_work=0.1213 r_free=0.1460 | n_water=477 | time (s): 157.740 (total time: 207.470) Filter (q & B) r_work=0.1218 r_free=0.1462 | n_water=446 | time (s): 2.860 (total time: 210.330) Filter (dist only) r_work=0.1218 r_free=0.1462 | n_water=446 | time (s): 33.050 (total time: 243.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.968479 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.713470 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 0.1225 0.1440 0.0215 0.005 0.9 1.6 0.5 0.0 0 0.984 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 14.40 2.15 3.607 22.050 47.713 3.726 12.18 14.05 1.88 4.058 21.865 47.713 3.659 Individual atomic B min max mean iso aniso Overall: 9.16 109.73 21.63 2.32 213 1760 Protein: 9.16 109.73 17.20 2.32 0 1519 Water: 11.54 71.91 36.64 N/A 213 233 Other: 20.39 32.16 26.60 N/A 0 8 Chain A: 9.16 109.73 19.84 N/A 0 1760 Chain S: 15.68 67.08 36.39 N/A 213 0 Histogram: Values Number of atoms 9.16 - 19.22 1233 19.22 - 29.27 274 29.27 - 39.33 224 39.33 - 49.39 134 49.39 - 59.44 76 59.44 - 69.50 20 69.50 - 79.56 6 79.56 - 89.61 3 89.61 - 99.67 1 99.67 - 109.73 2 =========================== Idealize ADP of riding H ========================== r_work=0.1218 r_free=0.1406 r_work=0.1219 r_free=0.1406 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1219 r_free = 0.1406 target_work(ml) = 3.659 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1213 r_free = 0.1407 target_work(ml) = 3.657 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1213 r_free= 0.1407 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.656707 | | target function (ml) not normalized (work): 304585.423436 | | target function (ml) not normalized (free): 16092.299725 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1223 0.1213 0.1407 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1587 0.1591 0.1560 n_refl.: 87591 remove outliers: r(all,work,free)=0.1587 0.1591 0.1560 n_refl.: 87591 overall B=-0.02 to atoms: r(all,work,free)=0.1584 0.1588 0.1559 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1202 0.1375 n_refl.: 87591 remove outliers: r(all,work,free)=0.1207 0.1198 0.1375 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.4186 290.727 255.059 0.462 1.001 0.320 11.894-9.307 97.06 95 4 0.2380 474.320 459.162 0.854 1.002 0.269 9.237-7.194 98.64 210 7 0.2357 385.877 385.258 0.939 1.002 0.203 7.162-5.571 100.00 427 22 0.2102 295.200 285.349 0.908 1.003 0.176 5.546-4.326 100.00 867 58 0.1121 405.236 400.511 0.952 1.003 0.161 4.315-3.360 100.00 1859 96 0.0926 385.383 382.891 0.994 1.003 0.156 3.356-2.611 100.00 3867 181 0.1156 253.176 251.132 0.999 1.002 0.057 2.608-2.026 99.99 8198 413 0.1046 167.833 166.786 1.011 1.002 0.000 2.025-1.573 100.00 17313 902 0.1008 81.961 82.133 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1287 36.345 35.921 1.020 1.000 0.000 1.221-1.150 99.97 13689 708 0.2125 22.900 21.519 0.978 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0402 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1375 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=0.1198 r_free=0.1375 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1375 | n_water=446 | time (s): 2.160 (total time: 2.160) Filter (dist) r_work=0.1198 r_free=0.1375 | n_water=446 | time (s): 36.210 (total time: 38.370) Filter (q & B) r_work=0.1197 r_free=0.1374 | n_water=445 | time (s): 3.180 (total time: 41.550) Compute maps r_work=0.1197 r_free=0.1374 | n_water=445 | time (s): 1.180 (total time: 42.730) Filter (map) r_work=0.1217 r_free=0.1384 | n_water=317 | time (s): 2.840 (total time: 45.570) Find peaks r_work=0.1217 r_free=0.1384 | n_water=317 | time (s): 0.530 (total time: 46.100) Add new water r_work=0.1284 r_free=0.1446 | n_water=488 | time (s): 3.070 (total time: 49.170) Refine new water occ: r_work=0.1210 r_free=0.1379 adp: r_work=0.1211 r_free=0.1382 occ: r_work=0.1195 r_free=0.1366 adp: r_work=0.1194 r_free=0.1366 occ: r_work=0.1184 r_free=0.1357 adp: r_work=0.1180 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1354 r_work=0.1180 r_free=0.1354 | n_water=488 | time (s): 149.180 (total time: 198.350) Filter (q & B) r_work=0.1188 r_free=0.1356 | n_water=450 | time (s): 2.990 (total time: 201.340) Filter (dist only) r_work=0.1188 r_free=0.1355 | n_water=449 | time (s): 36.340 (total time: 237.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.935342 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 54.701481 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1377 0.0182 0.006 0.9 1.6 0.5 0.0 0 0.968 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.77 1.82 3.420 21.499 54.701 3.641 11.78 13.74 1.96 3.836 21.371 54.701 3.624 Individual atomic B min max mean iso aniso Overall: 9.22 105.31 21.25 2.20 217 1759 Protein: 9.22 105.31 16.89 2.20 0 1519 Water: 11.44 70.29 35.92 N/A 217 232 Other: 21.26 29.82 25.33 N/A 0 8 Chain A: 9.22 105.31 19.48 N/A 0 1759 Chain S: 15.89 67.49 35.57 N/A 217 0 Histogram: Values Number of atoms 9.22 - 18.83 1230 18.83 - 28.44 283 28.44 - 38.05 216 38.05 - 47.66 125 47.66 - 57.27 83 57.27 - 66.88 26 66.88 - 76.48 8 76.48 - 86.09 2 86.09 - 95.70 1 95.70 - 105.31 2 =========================== Idealize ADP of riding H ========================== r_work=0.1178 r_free=0.1374 r_work=0.1179 r_free=0.1374 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1179 r_free = 0.1374 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1171 r_free = 0.1367 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1171 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621623 | | target function (ml) not normalized (work): 301634.083359 | | target function (ml) not normalized (free): 15949.922063 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1181 0.1171 0.1367 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1506 0.1506 0.1550 n_refl.: 87583 remove outliers: r(all,work,free)=0.1506 0.1506 0.1550 n_refl.: 87583 overall B=-0.01 to atoms: r(all,work,free)=0.1503 0.1503 0.1548 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1180 0.1171 0.1367 n_refl.: 87583 remove outliers: r(all,work,free)=0.1179 0.1169 0.1367 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4204 288.258 247.615 0.431 1.001 0.297 11.894-9.307 96.08 94 4 0.2386 478.174 456.981 0.844 1.002 0.280 9.237-7.194 98.18 209 7 0.2463 384.874 380.055 0.910 1.002 0.137 7.162-5.571 100.00 427 22 0.2221 295.200 283.272 0.898 1.002 0.129 5.546-4.326 100.00 867 58 0.1147 405.236 400.866 0.952 1.002 0.121 4.315-3.360 100.00 1859 96 0.0927 385.383 383.023 0.994 1.002 0.117 3.356-2.611 100.00 3867 181 0.1139 253.176 251.208 1.001 1.002 0.090 2.608-2.026 99.99 8198 413 0.1008 167.833 167.038 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0948 81.961 82.259 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1232 36.345 35.989 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2124 22.900 21.532 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=-0.0381 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1169 r_free=0.1367 After: r_work=0.1169 r_free=0.1367 ================================== NQH flips ================================== r_work=0.1169 r_free=0.1367 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=0.1169 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1169 r_free=0.1367 | n_water=449 | time (s): 1.710 (total time: 1.710) Filter (dist) r_work=0.1171 r_free=0.1368 | n_water=448 | time (s): 36.710 (total time: 38.420) Filter (q & B) r_work=0.1171 r_free=0.1368 | n_water=447 | time (s): 2.600 (total time: 41.020) Compute maps r_work=0.1171 r_free=0.1368 | n_water=447 | time (s): 1.170 (total time: 42.190) Filter (map) r_work=0.1200 r_free=0.1385 | n_water=329 | time (s): 2.560 (total time: 44.750) Find peaks r_work=0.1200 r_free=0.1385 | n_water=329 | time (s): 0.590 (total time: 45.340) Add new water r_work=0.1247 r_free=0.1430 | n_water=483 | time (s): 2.380 (total time: 47.720) Refine new water occ: r_work=0.1185 r_free=0.1365 adp: r_work=0.1186 r_free=0.1369 occ: r_work=0.1174 r_free=0.1350 adp: r_work=0.1173 r_free=0.1354 occ: r_work=0.1165 r_free=0.1339 adp: r_work=0.1162 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1162 r_free=0.1341 r_work=0.1162 r_free=0.1341 | n_water=483 | time (s): 133.890 (total time: 181.610) Filter (q & B) r_work=0.1170 r_free=0.1352 | n_water=439 | time (s): 2.480 (total time: 184.090) Filter (dist only) r_work=0.1170 r_free=0.1350 | n_water=437 | time (s): 37.710 (total time: 221.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.880362 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.433819 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 0.1376 0.0185 0.007 1.0 2.6 0.5 0.0 0 0.940 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.76 1.85 3.297 21.095 49.434 3.630 11.97 13.76 1.79 3.409 21.045 49.434 3.625 Individual atomic B min max mean iso aniso Overall: 9.28 102.42 21.01 2.08 208 1756 Protein: 9.28 102.42 16.77 2.08 0 1519 Water: 11.52 69.77 35.67 N/A 208 229 Other: 20.89 29.04 24.99 N/A 0 8 Chain A: 9.28 102.42 19.30 N/A 0 1756 Chain S: 15.73 60.05 35.49 N/A 208 0 Histogram: Values Number of atoms 9.28 - 18.59 1225 18.59 - 27.91 276 27.91 - 37.22 207 37.22 - 46.54 139 46.54 - 55.85 76 55.85 - 65.17 25 65.17 - 74.48 12 74.48 - 83.79 1 83.79 - 93.11 1 93.11 - 102.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1376 r_work=0.1197 r_free=0.1376 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1376 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1374 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1195 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.624689 | | target function (ml) not normalized (work): 301874.995438 | | target function (ml) not normalized (free): 15963.322659 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1421 0.1458 5.6959 5.6531| | 2: 3.57 - 2.84 1.00 2888 124 0.1133 0.1444 5.2114 5.2784| | 3: 2.83 - 2.48 1.00 2820 163 0.1221 0.1286 5.0158 5.0502| | 4: 2.47 - 2.25 1.00 2825 136 0.1024 0.1120 4.7146 4.7616| | 5: 2.25 - 2.09 1.00 2756 127 0.0982 0.1086 4.6558 4.7252| | 6: 2.09 - 1.97 1.00 2846 113 0.0971 0.1172 4.3616 4.4684| | 7: 1.97 - 1.87 1.00 2787 165 0.0986 0.1252 4.0806 4.208| | 8: 1.87 - 1.79 1.00 2789 144 0.1011 0.1269 3.9944 4.0932| | 9: 1.79 - 1.72 1.00 2745 138 0.0947 0.1306 3.7146 3.8986| | 10: 1.72 - 1.66 1.00 2831 160 0.0993 0.1247 3.6327 3.7484| | 11: 1.66 - 1.61 1.00 2712 147 0.0949 0.1088 3.5633 3.6061| | 12: 1.61 - 1.56 1.00 2773 144 0.0905 0.1134 3.3436 3.4673| | 13: 1.56 - 1.52 1.00 2745 130 0.0967 0.1060 3.3325 3.428| | 14: 1.52 - 1.48 1.00 2803 134 0.0978 0.1095 3.2564 3.3435| | 15: 1.48 - 1.45 1.00 2738 128 0.1007 0.1372 3.1693 3.3416| | 16: 1.45 - 1.42 1.00 2756 161 0.1066 0.1273 3.1531 3.2607| | 17: 1.42 - 1.39 1.00 2785 139 0.1123 0.1292 3.1213 3.2404| | 18: 1.39 - 1.36 1.00 2741 179 0.1143 0.1391 3.0868 3.2803| | 19: 1.36 - 1.34 1.00 2807 134 0.1210 0.1624 3.0955 3.2824| | 20: 1.34 - 1.32 1.00 2696 147 0.1315 0.1455 3.0895 3.134| | 21: 1.32 - 1.30 1.00 2785 112 0.1408 0.1611 3.0873 3.1661| | 22: 1.29 - 1.27 1.00 2704 152 0.1458 0.1936 3.0837 3.2903| | 23: 1.27 - 1.26 1.00 2802 156 0.1568 0.1852 3.1043 3.2073| | 24: 1.26 - 1.24 1.00 2744 132 0.1618 0.1749 3.0966 3.192| | 25: 1.24 - 1.22 1.00 2733 148 0.1792 0.2322 3.1138 3.2932| | 26: 1.22 - 1.21 1.00 2727 135 0.1861 0.1755 3.1278 3.1999| | 27: 1.21 - 1.19 1.00 2814 148 0.2012 0.2119 3.1448 3.1634| | 28: 1.19 - 1.18 1.00 2671 147 0.2146 0.2295 3.1432 3.1655| | 29: 1.18 - 1.16 1.00 2800 134 0.2217 0.2346 3.132 3.2259| | 30: 1.16 - 1.15 1.00 2739 148 0.2378 0.2509 3.1213 3.1714| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2921 171 0.95 9.12 1.00 0.98 6423.91| | 2: 3.57 - 2.84 2888 124 0.92 13.56 1.01 0.98 6423.91| | 3: 2.83 - 2.48 2820 163 0.88 17.63 0.99 0.98 5384.48| | 4: 2.47 - 2.25 2825 136 0.91 14.70 1.00 0.98 2704.13| | 5: 2.25 - 2.09 2756 127 0.89 16.97 1.01 0.98 2704.13| | 6: 2.09 - 1.97 2846 113 0.92 13.71 1.02 0.98 1587.38| | 7: 1.97 - 1.87 2787 165 0.94 10.87 1.02 0.98 634.94| | 8: 1.87 - 1.79 2789 144 0.91 14.44 1.00 0.98 634.94| | 9: 1.79 - 1.72 2745 138 0.93 11.40 0.98 0.98 340.42| | 10: 1.72 - 1.66 2831 160 0.93 12.20 0.98 0.97 281.43| | 11: 1.66 - 1.61 2712 147 0.93 12.81 0.98 0.97 268.63| | 12: 1.61 - 1.56 2773 144 0.95 9.45 0.99 0.98 147.87| | 13: 1.56 - 1.52 2745 130 0.94 11.07 1.02 0.98 147.87| | 14: 1.52 - 1.48 2803 134 0.94 11.20 1.02 0.98 132.39| | 15: 1.48 - 1.45 2738 128 0.95 10.38 1.01 0.99 104.04| | 16: 1.45 - 1.42 2756 161 0.94 11.56 1.02 0.99 104.04| | 17: 1.42 - 1.39 2785 139 0.94 11.43 1.01 0.99 94.29| | 18: 1.39 - 1.36 2741 179 0.94 11.77 1.01 0.99 88.64| | 19: 1.36 - 1.34 2807 134 0.94 12.38 1.00 0.99 88.64| | 20: 1.34 - 1.32 2696 147 0.94 12.43 0.99 0.97 83.20| | 21: 1.32 - 1.30 2785 112 0.94 13.38 0.99 0.97 82.82| | 22: 1.29 - 1.27 2704 152 0.93 13.83 0.98 0.97 82.93| | 23: 1.27 - 1.26 2802 156 0.92 14.79 0.98 0.95 83.50| | 24: 1.26 - 1.24 2744 132 0.93 14.92 0.97 0.95 83.50| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.95 84.96| | 26: 1.22 - 1.21 2727 135 0.90 18.01 1.02 0.94 86.57| | 27: 1.21 - 1.19 2814 148 0.89 18.68 1.02 0.94 86.57| | 28: 1.19 - 1.18 2671 147 0.88 20.16 1.01 0.93 89.87| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.99 0.93 91.11| | 30: 1.16 - 1.15 2739 148 0.86 21.84 0.98 0.93 91.11| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 82.82 max = 6423.91 mean = 999.27| |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 = 89.02 mean = 14.12| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1195 0.1374 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1517 0.1517 0.1545 n_refl.: 87579 remove outliers: r(all,work,free)=0.1517 0.1517 0.1545 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1515 0.1515 0.1543 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1195 0.1379 n_refl.: 87579 remove outliers: r(all,work,free)=0.1202 0.1193 0.1379 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4129 290.861 249.026 0.435 0.999 0.298 11.894-9.307 92.16 90 4 0.2305 470.123 450.292 0.838 1.001 0.207 9.237-7.194 98.18 209 7 0.2543 384.874 378.277 0.903 1.001 0.130 7.162-5.571 100.00 427 22 0.2261 295.200 283.636 0.890 1.001 0.120 5.546-4.326 100.00 867 58 0.1198 405.236 400.617 0.951 1.002 0.120 4.315-3.360 100.00 1859 96 0.0991 385.383 382.756 0.995 1.002 0.120 3.356-2.611 100.00 3867 181 0.1189 253.176 251.037 1.002 1.002 0.053 2.608-2.026 99.99 8198 413 0.1033 167.833 166.916 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0969 81.961 82.252 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1222 36.345 36.000 1.019 1.000 0.000 1.221-1.150 99.97 13689 708 0.2119 22.900 21.506 0.974 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0319 ================= 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 0.1917 0.079 5.321 8.8 119.3 19.9 258 0.000 1_bss: 0.1640 0.1755 0.079 5.321 9.0 119.5 20.1 258 0.000 1_settarget: 0.1640 0.1755 0.079 5.321 9.0 119.5 20.1 258 0.000 1_nqh: 0.1640 0.1755 0.079 5.321 9.0 119.5 20.1 258 0.000 1_weight: 0.1640 0.1755 0.079 5.321 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1209 0.1465 0.007 0.938 9.0 119.5 20.1 258 0.126 1_adp: 0.1238 0.1542 0.007 0.938 8.5 118.3 20.9 258 0.126 1_regHadp: 0.1243 0.1547 0.007 0.938 8.5 118.3 20.9 258 0.126 1_occ: 0.1243 0.1550 0.007 0.938 8.5 118.3 20.9 258 0.126 2_bss: 0.1240 0.1546 0.007 0.938 8.6 118.5 21.0 258 0.126 2_settarget: 0.1240 0.1546 0.007 0.938 8.6 118.5 21.0 258 0.126 2_updatecdl: 0.1240 0.1546 0.007 0.950 8.6 118.5 21.0 258 0.126 2_nqh: 0.1242 0.1547 0.007 0.950 8.6 118.5 21.0 258 0.129 2_sol: 0.1224 0.1493 0.007 0.950 8.6 118.5 23.5 427 n/a 2_weight: 0.1224 0.1493 0.007 0.950 8.6 118.5 23.5 427 n/a 2_xyzrec: 0.1219 0.1498 0.007 0.883 8.6 118.5 23.5 427 n/a 2_adp: 0.1187 0.1464 0.007 0.883 8.7 114.1 23.1 427 n/a 2_regHadp: 0.1187 0.1463 0.007 0.883 8.7 114.1 23.1 427 n/a 2_occ: 0.1188 0.1456 0.007 0.883 8.7 114.1 23.1 427 n/a 3_bss: 0.1185 0.1454 0.007 0.883 8.7 114.1 23.2 427 n/a 3_settarget: 0.1185 0.1454 0.007 0.883 8.7 114.1 23.2 427 n/a 3_updatecdl: 0.1185 0.1454 0.007 0.886 8.7 114.1 23.2 427 n/a 3_nqh: 0.1185 0.1456 0.007 0.886 8.7 114.1 23.2 427 n/a 3_sol: 0.1218 0.1462 0.007 0.886 8.7 114.1 22.0 446 n/a 3_weight: 0.1218 0.1462 0.007 0.886 8.7 114.1 22.0 446 n/a 3_xyzrec: 0.1225 0.1440 0.005 0.920 8.7 114.1 22.0 446 n/a 3_adp: 0.1218 0.1406 0.005 0.920 9.2 109.7 21.6 446 n/a 3_regHadp: 0.1219 0.1406 0.005 0.920 9.2 109.7 21.6 446 n/a 3_occ: 0.1213 0.1407 0.005 0.920 9.2 109.7 21.6 446 n/a 4_bss: 0.1198 0.1375 0.005 0.920 9.1 109.7 21.6 446 n/a 4_settarget: 0.1198 0.1375 0.005 0.920 9.1 109.7 21.6 446 n/a 4_updatecdl: 0.1198 0.1375 0.005 0.916 9.1 109.7 21.6 446 n/a 4_nqh: 0.1198 0.1375 0.005 0.916 9.1 109.7 21.6 446 n/a 4_sol: 0.1188 0.1355 0.005 0.916 9.1 109.7 21.5 449 n/a 4_weight: 0.1188 0.1355 0.005 0.916 9.1 109.7 21.5 449 n/a 4_xyzrec: 0.1196 0.1377 0.006 0.949 9.1 109.7 21.5 449 n/a 4_adp: 0.1178 0.1374 0.006 0.949 9.2 105.3 21.3 449 n/a 4_regHadp: 0.1179 0.1374 0.006 0.949 9.2 105.3 21.3 449 n/a 4_occ: 0.1171 0.1367 0.006 0.949 9.2 105.3 21.3 449 n/a 5_bss: 0.1169 0.1367 0.006 0.949 9.2 105.3 21.2 449 n/a 5_settarget: 0.1169 0.1367 0.006 0.949 9.2 105.3 21.2 449 n/a 5_updatecdl: 0.1169 0.1367 0.006 0.951 9.2 105.3 21.2 449 n/a 5_setrh: 0.1169 0.1367 0.006 0.951 9.2 105.3 21.2 449 n/a 5_nqh: 0.1169 0.1367 0.006 0.951 9.2 105.3 21.2 449 n/a 5_sol: 0.1170 0.1350 0.006 0.951 9.2 105.3 21.1 437 n/a 5_weight: 0.1170 0.1350 0.006 0.951 9.2 105.3 21.1 437 n/a 5_xyzrec: 0.1192 0.1376 0.007 1.037 9.2 105.3 21.1 437 n/a 5_adp: 0.1197 0.1376 0.007 1.037 9.3 102.4 21.0 437 n/a 5_regHadp: 0.1197 0.1376 0.007 1.037 9.3 102.4 21.0 437 n/a 5_occ: 0.1195 0.1374 0.007 1.037 9.3 102.4 21.0 437 n/a end: 0.1193 0.1379 0.007 1.037 9.3 102.4 21.0 437 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3941866_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3941866_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8200 Refinement macro-cycles (run) : 3274.9600 Write final files (write_after_run_outputs) : 72.1600 Total : 3351.9400 Total CPU time: 56.47 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:07:28 PST -0800 (1735452448.14 s) Start R-work = 0.1640, R-free = 0.1755 Final R-work = 0.1193, R-free = 0.1379 =============================================================================== Job complete usr+sys time: 3510.47 seconds wall clock time: 63 minutes 2.01 seconds (3782.01 seconds total)