Starting phenix.refine on Fri Dec 27 17:58:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5239121.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.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.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5239121.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5239121.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 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== 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: 1.71, per 1000 atoms: 0.51 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: 0.53 Conformation dependent library (CDL) restraints added in 224.6 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: 0.64 - 0.89: 412 0.89 - 1.14: 1190 1.14 - 1.40: 598 1.40 - 1.65: 883 1.65 - 1.90: 70 Bond restraints: 3153 Sorted by residual: bond pdb=" N ILE A 31 " pdb=" CA ILE A 31 " ideal model delta sigma weight residual 1.459 1.193 0.266 1.24e-02 6.50e+03 4.60e+02 bond pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta sigma weight residual 1.458 1.223 0.235 1.19e-02 7.06e+03 3.89e+02 bond pdb=" C GLU A 16 " pdb=" O GLU A 16 " ideal model delta sigma weight residual 1.236 1.000 0.236 1.25e-02 6.40e+03 3.58e+02 bond pdb=" C AGLU A 96 " pdb=" O AGLU A 96 " ideal model delta sigma weight residual 1.237 1.443 -0.206 1.17e-02 7.31e+03 3.10e+02 bond pdb=" N VAL A 44 " pdb=" CA VAL A 44 " ideal model delta sigma weight residual 1.458 1.253 0.205 1.17e-02 7.31e+03 3.07e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 2745 4.15 - 8.30: 1953 8.30 - 12.44: 831 12.44 - 16.59: 224 16.59 - 20.74: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BGLY A 65 " pdb=" C BGLY A 65 " pdb=" N BPRO A 66 " ideal model delta sigma weight residual 121.77 137.73 -15.96 1.00e+00 1.00e+00 2.55e+02 angle pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" O LYS A 182 " ideal model delta sigma weight residual 121.07 137.12 -16.05 1.10e+00 8.26e-01 2.13e+02 angle pdb=" O ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 123.20 137.69 -14.49 1.06e+00 8.90e-01 1.87e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH2 ARG A 156 " ideal model delta sigma weight residual 119.20 131.37 -12.17 9.00e-01 1.23e+00 1.83e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.03 137.34 -14.31 1.11e+00 8.12e-01 1.66e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 928 15.32 - 30.63: 113 30.63 - 45.95: 45 45.95 - 61.27: 21 61.27 - 76.58: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -151.59 -28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " pdb=" CA GLY A 118 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.22e+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 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.242: 102 0.242 - 0.482: 75 0.482 - 0.721: 44 0.721 - 0.960: 18 0.960 - 1.199: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 1.24 1.20 2.00e-01 2.50e+01 3.60e+01 chirality pdb=" CA LYS A 182 " pdb=" N LYS A 182 " pdb=" C LYS A 182 " pdb=" CB LYS A 182 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.12e+01 chirality pdb=" CA ALA A 6 " pdb=" N ALA A 6 " pdb=" C ALA A 6 " pdb=" CB ALA A 6 " both_signs ideal model delta sigma weight residual False 2.48 3.47 -0.98 2.00e-01 2.50e+01 2.40e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.002 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG BTYR A 67 " 0.103 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.081 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.056 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.070 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.077 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.094 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.005 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.067 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.088 2.00e-02 2.50e+03 6.13e-02 1.13e+02 pdb=" CG TYR A 141 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.069 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.091 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.087 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.075 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 68 " -0.042 2.00e-02 2.50e+03 8.69e-02 7.54e+01 pdb=" CG ASP A 68 " 0.150 2.00e-02 2.50e+03 pdb=" OD1 ASP A 68 " -0.051 2.00e-02 2.50e+03 pdb=" OD2 ASP A 68 " -0.057 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 851 2.29 - 2.87: 7855 2.87 - 3.44: 10617 3.44 - 4.02: 15259 4.02 - 4.60: 22059 Nonbonded interactions: 56641 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.711 1.850 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.771 1.850 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.808 1.850 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.812 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.812 2.100 ... (remaining 56636 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 nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "shake_5239121_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= 0.1962 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793278 | | target function (ml) not normalized (work): 232696.817095 | | target function (ml) not normalized (free): 11852.780319 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3037 0.2100 7.0553 4.9421| | 2: 3.57 - 2.84 1.00 2876 122 0.2459 0.1799 4.3528 4.3568| | 3: 2.84 - 2.48 1.00 2833 165 0.2314 0.1704 4.1283 4.161| | 4: 2.47 - 2.25 1.00 2825 136 0.2377 0.1469 3.8378 3.8301| | 5: 2.25 - 2.09 1.00 2756 127 0.2460 0.1542 3.8 3.8142| | 6: 2.09 - 1.97 1.00 2846 113 0.2512 0.1716 3.4717 3.5244| | 7: 1.97 - 1.87 1.00 2787 165 0.2604 0.1992 3.1566 3.2302| | 8: 1.87 - 1.79 1.00 2789 144 0.2508 0.1887 3.0732 3.1316| | 9: 1.79 - 1.72 1.00 2745 138 0.2408 0.1941 2.9019 2.9936| | 10: 1.72 - 1.66 1.00 2789 158 0.2425 0.1941 2.8117 2.8981| | 11: 1.66 - 1.61 1.00 2740 147 0.2473 0.1745 2.7368 2.7794| | 12: 1.61 - 1.56 1.00 2787 146 0.2546 0.1965 2.6422 2.6186| | 13: 1.56 - 1.52 1.00 2745 130 0.2536 0.1887 2.5791 2.5885| | 14: 1.52 - 1.48 1.00 2803 134 0.2549 0.2204 2.51 2.6211| | 15: 1.48 - 1.45 1.00 2738 128 0.2625 0.2114 2.4329 2.5215| | 16: 1.45 - 1.42 1.00 2756 161 0.2637 0.2314 2.3797 2.4761| | 17: 1.42 - 1.39 1.00 2785 139 0.2654 0.2190 2.3217 2.4275| | 18: 1.39 - 1.36 1.00 2741 179 0.2674 0.2202 2.2717 2.3363| | 19: 1.36 - 1.34 1.00 2807 134 0.2636 0.2461 2.2416 2.3365| | 20: 1.34 - 1.32 1.00 2696 147 0.2665 0.1984 2.2046 2.1226| | 21: 1.32 - 1.30 1.00 2785 112 0.2664 0.2487 2.1659 2.2516| | 22: 1.29 - 1.27 1.00 2704 152 0.2722 0.2674 2.1398 2.1889| | 23: 1.27 - 1.26 1.00 2802 156 0.2788 0.2353 2.1115 2.1513| | 24: 1.26 - 1.24 1.00 2744 132 0.2823 0.2470 2.0879 2.1742| | 25: 1.24 - 1.22 1.00 2734 148 0.2845 0.2537 2.0562 2.0834| | 26: 1.22 - 1.21 1.00 2727 135 0.2837 0.2520 1.9959 2.1479| | 27: 1.21 - 1.19 1.00 2814 148 0.2957 0.2575 2.0027 1.9854| | 28: 1.19 - 1.18 1.00 2671 147 0.2954 0.2860 1.9825 1.9973| | 29: 1.18 - 1.16 1.00 2800 134 0.2968 0.2598 1.9563 1.9853| | 30: 1.16 - 1.15 1.00 2740 148 0.3048 0.2878 1.9341 1.9666| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.92 0.76 0.23 1492.87| | 2: 3.57 - 2.84 2876 122 0.80 26.13 1.27 0.23 1492.87| | 3: 2.84 - 2.48 2833 165 0.74 32.00 1.24 0.24 1238.65| | 4: 2.47 - 2.25 2825 136 0.81 25.82 1.26 0.25 578.90| | 5: 2.25 - 2.09 2756 127 0.77 29.52 1.28 0.25 578.90| | 6: 2.09 - 1.97 2846 113 0.83 22.87 1.29 0.25 317.99| | 7: 1.97 - 1.87 2787 165 0.90 17.05 1.29 0.26 95.47| | 8: 1.87 - 1.79 2789 144 0.85 21.61 1.25 0.26 95.47| | 9: 1.79 - 1.72 2745 138 0.88 18.83 1.23 0.26 57.21| | 10: 1.72 - 1.66 2789 158 0.86 20.45 1.22 0.25 49.55| | 11: 1.66 - 1.61 2740 147 0.85 21.69 1.24 0.25 47.83| | 12: 1.61 - 1.56 2787 146 0.88 18.77 1.24 0.25 30.46| | 13: 1.56 - 1.52 2745 130 0.86 20.83 1.23 0.25 30.46| | 14: 1.52 - 1.48 2803 134 0.86 21.16 1.23 0.25 27.36| | 15: 1.48 - 1.45 2738 128 0.87 20.67 1.23 0.25 21.69| | 16: 1.45 - 1.42 2756 161 0.85 22.17 1.24 0.25 21.69| | 17: 1.42 - 1.39 2785 139 0.86 21.49 1.23 0.25 18.56| | 18: 1.39 - 1.36 2741 179 0.85 22.01 1.23 0.25 16.75| | 19: 1.36 - 1.34 2807 134 0.85 22.85 1.22 0.25 16.75| | 20: 1.34 - 1.32 2696 147 0.86 21.42 1.21 0.25 13.71| | 21: 1.32 - 1.30 2785 112 0.85 22.29 1.20 0.25 13.50| | 22: 1.29 - 1.27 2704 152 0.85 22.79 1.21 0.25 13.15| | 23: 1.27 - 1.26 2802 156 0.85 22.52 1.21 0.24 11.39| | 24: 1.26 - 1.24 2744 132 0.84 23.26 1.21 0.24 11.39| | 25: 1.24 - 1.22 2734 148 0.84 23.70 1.20 0.24 10.76| | 26: 1.22 - 1.21 2727 135 0.84 24.19 1.21 0.23 10.05| | 27: 1.21 - 1.19 2814 148 0.83 24.98 1.20 0.23 10.05| | 28: 1.19 - 1.18 2671 147 0.83 25.05 1.18 0.23 9.29| | 29: 1.18 - 1.16 2800 134 0.82 25.61 1.16 0.23 9.01| | 30: 1.16 - 1.15 2740 148 0.81 26.92 1.15 0.23 9.01| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.01 max = 1492.87 mean = 217.63| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.92| |phase err.(test): min = 0.00 max = 89.79 mean = 22.94| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.266 1557 Z= 5.538 Angle : 5.610 17.491 2118 Z= 3.877 Chirality : 0.426 1.199 243 Planarity : 0.033 0.128 284 Dihedral : 13.512 76.582 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 32.43 % 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: -2.34 (0.51), residues: 224 helix: -3.09 (0.35), residues: 102 sheet: -0.83 (0.90), residues: 30 loop : 0.48 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.013 ARG A 156 TYR 0.100 0.040 TYR A 141 PHE 0.087 0.036 PHE A 164 HIS 0.054 0.018 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= 0.2609 r_free= 0.1962 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793278 | | target function (ml) not normalized (work): 232696.817095 | | target function (ml) not normalized (free): 11852.780319 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2569 0.2610 0.1962 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2569 0.2610 0.1962 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1984 0.1962 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2006 0.2010 0.1976 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1642 0.1635 0.1784 n_refl.: 87594 remove outliers: r(all,work,free)=0.1642 0.1634 0.1784 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 386.166 358.071 0.663 1.003 0.401 11.894-9.307 99.02 97 4 0.1786 613.406 596.063 0.923 1.004 0.380 9.237-7.194 100.00 213 7 0.2132 501.690 491.186 0.956 1.004 0.349 7.162-5.571 100.00 427 22 0.2233 376.491 364.699 0.931 1.004 0.282 5.546-4.326 100.00 867 58 0.1267 516.829 511.417 0.964 1.004 0.235 4.315-3.360 100.00 1859 96 0.1146 491.508 487.478 1.005 1.003 0.231 3.356-2.611 100.00 3867 181 0.1424 322.895 319.924 0.996 1.003 0.067 2.608-2.026 99.99 8198 413 0.1358 214.050 211.658 1.005 1.001 0.000 2.025-1.573 100.00 17313 902 0.1649 104.531 103.826 1.014 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2061 46.353 44.991 1.003 0.996 0.000 1.221-1.150 99.97 13689 708 0.2568 29.206 26.903 0.977 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0488 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1634 r_free=0.1784 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=0.1634 r_free=0.1784 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.905513 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2002.648625 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 0.1613 0.1737 0.0124 0.002 0.5 4.8 0.0 0.0 0 0.125 0.1554 0.1689 0.0135 0.002 0.5 4.8 0.0 0.0 0 0.250 0.1431 0.1592 0.0160 0.002 0.5 4.2 0.0 0.0 0 0.500 0.1369 0.1549 0.0180 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1353 0.1543 0.0190 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1351 0.1542 0.0191 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1294 0.1504 0.0210 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1268 0.1488 0.0220 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1255 0.1483 0.0228 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1252 0.1487 0.0235 0.004 0.7 2.9 0.5 0.0 0 5.000 0.1243 0.1482 0.0239 0.005 0.8 3.5 0.5 0.0 0 6.000 0.1242 0.1482 0.0240 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1236 0.1474 0.0238 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1234 0.1477 0.0243 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1233 0.1476 0.0244 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1227 0.1471 0.0245 0.007 0.9 3.2 0.5 0.0 0 11.000 0.1228 0.1475 0.0247 0.007 0.9 3.2 0.5 0.0 0 12.000 0.1224 0.1474 0.0250 0.008 1.0 4.2 0.5 0.6 0 13.953 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1227 0.1471 0.0245 0.007 0.9 3.2 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.71 2.45 3.013 19.072 2002.649 0.017 12.27 14.71 2.45 3.013 19.072 60.079 0.017 12.34 14.67 2.32 2.669 19.070 250.331 0.017 12.69 15.31 2.62 2.747 19.228 1001.324 0.016 12.55 15.47 2.92 3.290 19.607 2002.649 0.016 12.45 15.51 3.07 3.361 19.647 3003.973 0.015 12.42 15.57 3.15 3.471 19.695 4005.297 0.015 12.25 15.38 3.13 3.252 19.568 5006.622 0.015 12.28 15.49 3.21 3.380 19.639 6007.946 0.015 12.25 15.42 3.17 3.363 19.620 7009.270 0.015 12.17 15.36 3.19 3.267 19.547 8010.595 0.015 12.17 15.41 3.24 3.308 19.557 9011.919 0.015 12.19 15.46 3.27 3.408 19.605 10013.243 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 250.331 Accepted refinement result: 12.34 14.67 2.32 2.669 19.070 250.331 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.45 20.10 3.31 0 1785 Protein: 9.08 115.01 17.00 3.32 0 1519 Water: 11.49 119.45 38.24 N/A 0 258 Other: 19.70 26.61 22.06 N/A 0 8 Chain A: 9.08 119.45 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.15 227 31.15 - 42.19 125 42.19 - 53.23 94 53.23 - 64.27 42 64.27 - 75.30 11 75.30 - 86.34 7 86.34 - 97.38 4 97.38 - 108.42 1 108.42 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1467 r_work=0.1236 r_free=0.1470 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1470 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1464 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 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= 0.1230 r_free= 0.1464 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016912 | | target function (ls_wunit_k1) not normalized (work): 1408.699101 | | target function (ls_wunit_k1) not normalized (free): 111.010843 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1241 0.1230 0.1464 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1676 0.1677 0.1694 n_refl.: 87593 remove outliers: r(all,work,free)=0.1676 0.1677 0.1694 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1681 0.1682 0.1698 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1227 0.1457 n_refl.: 87593 remove outliers: r(all,work,free)=0.1237 0.1226 0.1457 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 0.3566 297.640 281.270 0.639 1.002 0.374 11.894-9.307 99.02 97 4 0.1693 482.308 469.129 0.920 1.003 0.370 9.237-7.194 100.00 213 7 0.1900 394.469 387.920 0.962 1.003 0.350 7.162-5.571 100.00 427 22 0.1847 296.027 289.864 0.938 1.003 0.254 5.546-4.326 100.00 867 58 0.1013 406.372 403.228 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0866 386.463 385.274 1.009 1.003 0.190 3.356-2.611 100.00 3867 181 0.1170 253.886 252.747 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1019 168.303 167.576 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1112 82.190 82.383 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1450 36.447 35.952 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 22.964 21.450 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0459 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1457 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=0.1228 r_free=0.1457 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1228 r_free=0.1457 | n_water=258 | time (s): 1.730 (total time: 1.730) Filter (dist) r_work=0.1235 r_free=0.1455 | n_water=251 | time (s): 22.580 (total time: 24.310) Filter (q & B) r_work=0.1237 r_free=0.1455 | n_water=248 | time (s): 2.450 (total time: 26.760) Compute maps r_work=0.1237 r_free=0.1455 | n_water=248 | time (s): 1.140 (total time: 27.900) Filter (map) r_work=0.1254 r_free=0.1460 | n_water=229 | time (s): 3.080 (total time: 30.980) Find peaks r_work=0.1254 r_free=0.1460 | n_water=229 | time (s): 0.690 (total time: 31.670) Add new water r_work=0.1393 r_free=0.1626 | n_water=437 | time (s): 2.450 (total time: 34.120) Refine new water occ: r_work=0.1296 r_free=0.1479 adp: r_work=0.1225 r_free=0.1431 occ: r_work=0.1237 r_free=0.1416 adp: r_work=0.1208 r_free=0.1406 occ: r_work=0.1211 r_free=0.1397 adp: r_work=0.1201 r_free=0.1398 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1398 r_work=0.1201 r_free=0.1398 | n_water=437 | time (s): 54.660 (total time: 88.780) Filter (q & B) r_work=0.1206 r_free=0.1407 | n_water=417 | time (s): 2.710 (total time: 91.490) Filter (dist only) r_work=0.1206 r_free=0.1405 | n_water=416 | time (s): 36.820 (total time: 128.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.044008 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1474.904147 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 0.1639 0.1758 0.0119 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1544 0.1670 0.0126 0.001 0.4 7.0 0.0 0.0 0 0.250 0.1403 0.1556 0.0153 0.001 0.4 6.4 0.0 0.0 0 0.500 0.1350 0.1512 0.0162 0.001 0.5 5.4 0.0 0.0 0 0.750 0.1312 0.1485 0.0173 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1308 0.1481 0.0173 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1261 0.1448 0.0187 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1233 0.1432 0.0199 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1219 0.1426 0.0207 0.003 0.7 5.1 0.5 0.0 0 4.000 0.1211 0.1420 0.0209 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1206 0.1414 0.0208 0.004 0.7 5.1 0.5 0.0 0 6.000 0.1206 0.1412 0.0206 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1203 0.1415 0.0211 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1200 0.1415 0.0216 0.006 0.8 4.5 0.5 0.0 0 9.000 0.1198 0.1415 0.0216 0.006 0.8 5.1 0.5 0.0 0 10.000 0.1197 0.1412 0.0215 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1196 0.1418 0.0222 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1195 0.1412 0.0217 0.007 0.9 4.5 0.5 0.0 0 13.000 0.1195 0.1417 0.0222 0.008 0.9 4.5 0.5 0.0 0 14.022 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1206 0.1412 0.0206 0.005 0.8 4.8 0.5 0.0 0 7.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 14.12 2.06 3.777 21.736 1474.904 0.017 12.06 14.12 2.06 3.777 21.736 44.247 0.017 12.06 14.12 2.06 3.777 21.736 184.363 0.017 12.36 14.75 2.39 3.595 21.765 737.452 0.016 12.25 14.94 2.69 3.472 22.037 1474.904 0.015 12.09 14.91 2.83 3.484 21.914 2212.356 0.015 11.99 14.80 2.82 3.478 22.084 2949.808 0.015 11.94 14.83 2.89 3.494 22.085 3687.260 0.015 11.93 14.90 2.97 3.527 22.117 4424.712 0.015 11.86 14.84 2.98 3.533 22.116 5162.165 0.014 11.81 14.79 2.98 3.545 22.122 5899.617 0.014 11.83 14.91 3.09 3.562 22.039 6637.069 0.014 11.82 14.88 3.06 3.574 22.113 7374.521 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.247 Accepted refinement result: 12.06 14.12 2.06 3.777 21.736 44.247 0.017 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 22.10 3.31 187 1756 Protein: 9.11 115.04 17.03 3.32 0 1519 Water: 11.16 76.70 40.61 N/A 187 229 Other: 19.73 26.64 22.09 N/A 0 8 Chain A: 9.11 115.04 19.53 N/A 0 1756 Chain S: 11.16 60.00 46.25 N/A 187 0 Histogram: Values Number of atoms 9.11 - 19.70 1259 19.70 - 30.29 242 30.29 - 40.89 175 40.89 - 51.48 125 51.48 - 62.08 118 62.08 - 72.67 13 72.67 - 83.26 5 83.26 - 93.86 4 93.86 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1412 r_work=0.1206 r_free=0.1412 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1412 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1413 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1206 r_free= 0.1413 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015817 | | target function (ls_wunit_k1) not normalized (work): 1317.445068 | | target function (ls_wunit_k1) not normalized (free): 100.285253 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1206 0.1413 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1599 0.1597 0.1660 n_refl.: 87591 remove outliers: r(all,work,free)=0.1599 0.1597 0.1660 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1600 0.1598 0.1661 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1203 0.1409 n_refl.: 87591 remove outliers: r(all,work,free)=0.1212 0.1202 0.1409 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3396 296.986 270.022 0.579 1.003 0.350 11.894-9.307 99.02 97 4 0.1728 482.308 471.733 0.911 1.003 0.350 9.237-7.194 100.00 213 7 0.1761 394.469 392.120 0.980 1.003 0.290 7.162-5.571 100.00 427 22 0.1693 296.027 290.715 0.931 1.003 0.234 5.546-4.326 100.00 867 58 0.0917 406.372 403.155 0.960 1.003 0.215 4.315-3.360 100.00 1859 96 0.0824 386.463 385.242 1.005 1.003 0.210 3.356-2.611 100.00 3867 181 0.1099 253.886 252.833 1.011 1.002 0.080 2.608-2.026 99.99 8198 413 0.1014 168.303 167.803 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1114 82.190 82.362 1.031 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1453 36.447 35.973 1.025 0.996 0.000 1.221-1.150 99.97 13689 708 0.2259 22.964 21.472 0.988 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0126 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1202 r_free=0.1409 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1202 r_free=0.1409 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1202 r_free=0.1409 | n_water=416 | time (s): 1.580 (total time: 1.580) Filter (dist) r_work=0.1203 r_free=0.1414 | n_water=414 | time (s): 33.540 (total time: 35.120) Filter (q & B) r_work=0.1204 r_free=0.1417 | n_water=413 | time (s): 2.530 (total time: 37.650) Compute maps r_work=0.1204 r_free=0.1417 | n_water=413 | time (s): 1.330 (total time: 38.980) Filter (map) r_work=0.1237 r_free=0.1393 | n_water=285 | time (s): 2.380 (total time: 41.360) Find peaks r_work=0.1237 r_free=0.1393 | n_water=285 | time (s): 0.620 (total time: 41.980) Add new water r_work=0.1354 r_free=0.1515 | n_water=468 | time (s): 2.780 (total time: 44.760) Refine new water occ: r_work=0.1259 r_free=0.1435 adp: r_work=0.1261 r_free=0.1436 occ: r_work=0.1237 r_free=0.1412 adp: r_work=0.1236 r_free=0.1411 occ: r_work=0.1220 r_free=0.1391 adp: r_work=0.1215 r_free=0.1388 ADP+occupancy (water only), MIN, final r_work=0.1215 r_free=0.1388 r_work=0.1215 r_free=0.1388 | n_water=468 | time (s): 197.830 (total time: 242.590) Filter (q & B) r_work=0.1222 r_free=0.1396 | n_water=430 | time (s): 3.610 (total time: 246.200) Filter (dist only) r_work=0.1222 r_free=0.1395 | n_water=429 | time (s): 35.280 (total time: 281.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.797976 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.134282 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 0.1235 0.1362 0.0127 0.002 0.6 4.8 0.5 0.0 0 0.090 0.1193 0.1329 0.0136 0.003 0.7 4.5 0.5 0.0 0 0.270 0.1176 0.1316 0.0139 0.004 0.8 3.5 0.5 0.0 0 0.539 0.1169 0.1311 0.0142 0.005 0.9 3.8 0.5 0.0 0 0.809 0.1166 0.1311 0.0145 0.006 1.0 3.8 0.5 0.0 0 1.079 0.1163 0.1311 0.0148 0.007 1.0 3.8 0.5 0.0 0 1.348 0.1161 0.1311 0.0150 0.007 1.0 3.8 0.5 0.0 0 1.618 0.1160 0.1307 0.0147 0.008 1.1 3.8 0.5 0.0 0 1.888 0.1168 0.1311 0.0142 0.005 0.9 3.8 0.5 0.0 0 0.899 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1160 0.1307 0.0147 0.008 1.1 3.8 0.5 0.0 0 1.888 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.60 13.07 1.47 3.780 21.218 51.134 3.619 11.60 13.07 1.47 3.780 21.218 1.534 3.619 11.60 13.07 1.46 3.770 21.218 6.392 3.619 11.67 13.16 1.50 3.717 21.199 25.567 3.614 11.65 13.24 1.59 3.743 21.167 51.134 3.612 11.56 13.20 1.64 3.768 21.161 76.701 3.606 11.54 13.18 1.64 3.777 21.152 102.269 3.602 11.50 13.17 1.67 3.794 21.145 127.836 3.600 11.49 13.18 1.69 3.811 21.131 153.403 3.598 11.48 13.17 1.69 3.825 21.124 178.970 3.597 11.47 13.17 1.70 3.834 21.120 204.537 3.596 11.46 13.15 1.69 3.839 21.115 230.104 3.594 11.45 13.15 1.70 3.848 21.117 255.671 3.594 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.534 Accepted refinement result: 11.60 13.07 1.47 3.780 21.218 1.534 3.619 Individual atomic B min max mean iso aniso Overall: 9.12 115.05 21.15 3.31 203 1753 Protein: 9.12 115.05 17.04 3.32 0 1519 Water: 11.53 76.70 35.67 N/A 203 226 Other: 19.74 26.65 22.10 N/A 0 8 Chain A: 9.12 115.05 19.49 N/A 0 1753 Chain S: 16.27 60.01 35.48 N/A 203 0 Histogram: Values Number of atoms 9.12 - 19.71 1262 19.71 - 30.30 286 30.30 - 40.90 212 40.90 - 51.49 124 51.49 - 62.08 48 62.08 - 72.68 13 72.68 - 83.27 5 83.27 - 93.86 4 93.86 - 104.46 0 104.46 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1307 r_work=0.1160 r_free=0.1307 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1160 r_free = 0.1307 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1151 r_free = 0.1305 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1151 r_free= 0.1305 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.611726 | | target function (ml) not normalized (work): 300831.491689 | | target function (ml) not normalized (free): 15831.652314 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1159 0.1151 0.1305 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1501 0.1499 0.1553 n_refl.: 87589 remove outliers: r(all,work,free)=0.1501 0.1499 0.1553 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1499 0.1498 0.1552 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1154 0.1147 0.1295 n_refl.: 87589 remove outliers: r(all,work,free)=0.1151 0.1144 0.1295 n_refl.: 87582 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3917 288.178 265.912 0.479 1.000 0.300 11.894-9.307 97.06 95 4 0.2310 482.532 461.903 0.860 1.001 0.287 9.237-7.194 98.64 210 7 0.2329 386.958 385.793 0.941 1.002 0.200 7.162-5.571 100.00 427 22 0.2121 296.027 284.723 0.909 1.002 0.174 5.546-4.326 100.00 867 58 0.1119 406.372 402.016 0.955 1.002 0.160 4.315-3.360 100.00 1859 96 0.0943 386.463 384.009 0.994 1.002 0.160 3.356-2.611 100.00 3867 181 0.1126 253.886 251.872 0.998 1.002 0.038 2.608-2.026 99.99 8198 413 0.0937 168.303 167.536 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0897 82.190 82.485 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.447 36.030 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.964 21.503 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0200 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1144 r_free=0.1295 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=0.1144 r_free=0.1295 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1144 r_free=0.1295 | n_water=429 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1150 r_free=0.1291 | n_water=427 | time (s): 44.600 (total time: 47.060) Filter (q & B) r_work=0.1151 r_free=0.1291 | n_water=426 | time (s): 3.840 (total time: 50.900) Compute maps r_work=0.1151 r_free=0.1291 | n_water=426 | time (s): 1.880 (total time: 52.780) Filter (map) r_work=0.1168 r_free=0.1292 | n_water=326 | time (s): 3.900 (total time: 56.680) Find peaks r_work=0.1168 r_free=0.1292 | n_water=326 | time (s): 0.680 (total time: 57.360) Add new water r_work=0.1237 r_free=0.1354 | n_water=493 | time (s): 3.690 (total time: 61.050) Refine new water occ: r_work=0.1171 r_free=0.1299 adp: r_work=0.1171 r_free=0.1301 occ: r_work=0.1156 r_free=0.1288 adp: r_work=0.1155 r_free=0.1289 occ: r_work=0.1145 r_free=0.1277 adp: r_work=0.1140 r_free=0.1276 ADP+occupancy (water only), MIN, final r_work=0.1140 r_free=0.1276 r_work=0.1140 r_free=0.1276 | n_water=493 | time (s): 222.380 (total time: 283.430) Filter (q & B) r_work=0.1145 r_free=0.1276 | n_water=459 | time (s): 4.040 (total time: 287.470) Filter (dist only) r_work=0.1146 r_free=0.1275 | n_water=457 | time (s): 46.880 (total time: 334.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.783734 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.555530 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 0.1204 0.1318 0.0114 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1171 0.1296 0.0125 0.003 0.8 3.5 0.5 0.0 0 0.268 0.1156 0.1286 0.0130 0.005 0.9 4.2 0.5 0.0 0 0.535 0.1150 0.1281 0.0132 0.006 1.0 4.5 0.5 0.0 0 0.803 0.1146 0.1281 0.0135 0.007 1.0 3.8 0.5 0.0 0 1.070 0.1144 0.1280 0.0137 0.007 1.1 4.2 0.5 0.0 0 1.338 0.1142 0.1281 0.0139 0.008 1.1 4.2 0.5 0.0 0 1.605 0.1141 0.1278 0.0137 0.009 1.1 4.5 0.5 0.0 0 1.873 0.1148 0.1281 0.0133 0.006 1.0 4.5 0.5 0.0 0 0.892 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1141 0.1278 0.0137 0.009 1.1 4.5 0.5 0.0 0 1.873 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.41 12.78 1.37 3.781 21.302 36.556 3.606 11.41 12.78 1.37 3.781 21.302 1.097 3.606 11.41 12.78 1.37 3.781 21.302 4.569 3.606 11.45 12.82 1.38 3.711 21.296 18.278 3.601 11.56 13.05 1.49 3.716 21.269 36.556 3.608 11.47 13.00 1.53 3.749 21.257 54.833 3.602 11.42 12.97 1.55 3.760 21.251 73.111 3.597 11.37 12.92 1.55 3.772 21.251 91.389 3.594 11.35 12.90 1.56 3.779 21.248 109.667 3.591 11.32 12.88 1.56 3.787 21.248 127.944 3.589 11.32 12.92 1.60 3.800 21.239 146.222 3.590 11.31 12.92 1.61 3.809 21.233 164.500 3.588 11.29 12.91 1.61 3.816 21.231 182.778 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.097 Accepted refinement result: 11.41 12.78 1.37 3.781 21.302 1.097 3.606 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.31 3.31 232 1752 Protein: 9.11 115.04 17.03 3.32 0 1519 Water: 11.52 76.70 35.49 N/A 232 225 Other: 19.73 26.64 22.09 N/A 0 8 Chain A: 9.11 115.04 19.48 N/A 0 1752 Chain S: 16.27 60.00 35.11 N/A 232 0 Histogram: Values Number of atoms 9.11 - 19.70 1262 19.70 - 30.30 297 30.30 - 40.89 220 40.89 - 51.48 131 51.48 - 62.08 50 62.08 - 72.67 13 72.67 - 83.26 5 83.26 - 93.86 4 93.86 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1141 r_free=0.1278 r_work=0.1141 r_free=0.1278 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1141 r_free = 0.1278 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1134 r_free = 0.1276 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1134 r_free= 0.1276 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.602871 | | target function (ml) not normalized (work): 300068.695191 | | target function (ml) not normalized (free): 15797.960955 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1141 0.1134 0.1276 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1464 0.1464 0.1489 n_refl.: 87582 remove outliers: r(all,work,free)=0.1464 0.1464 0.1489 n_refl.: 87582 overall B=-0.01 to atoms: r(all,work,free)=0.1463 0.1463 0.1489 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1141 0.1134 0.1277 n_refl.: 87582 remove outliers: r(all,work,free)=0.1138 0.1131 0.1277 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 0.3874 288.194 248.367 0.446 1.000 0.304 11.894-9.307 94.12 92 4 0.2341 481.586 468.094 0.862 1.002 0.300 9.237-7.194 98.18 209 7 0.2286 385.952 382.381 0.935 1.002 0.180 7.162-5.571 100.00 427 22 0.2078 296.027 285.688 0.911 1.003 0.160 5.546-4.326 100.00 867 58 0.1119 406.372 401.777 0.965 1.003 0.121 4.315-3.360 100.00 1859 96 0.0928 386.463 384.270 1.003 1.002 0.107 3.356-2.611 100.00 3867 181 0.1111 253.886 251.998 1.010 1.002 0.034 2.608-2.026 99.99 8198 413 0.0913 168.303 167.702 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0890 82.190 82.541 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.447 36.055 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.964 21.516 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0172 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1131 r_free=0.1277 After: r_work=0.1132 r_free=0.1277 ================================== NQH flips ================================== r_work=0.1132 r_free=0.1277 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=0.1132 r_free=0.1277 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1132 r_free=0.1277 | n_water=457 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1132 r_free=0.1276 | n_water=456 | time (s): 50.190 (total time: 52.660) Filter (q & B) r_work=0.1132 r_free=0.1276 | n_water=456 | time (s): 1.330 (total time: 53.990) Compute maps r_work=0.1132 r_free=0.1276 | n_water=456 | time (s): 1.850 (total time: 55.840) Filter (map) r_work=0.1154 r_free=0.1285 | n_water=362 | time (s): 3.820 (total time: 59.660) Find peaks r_work=0.1154 r_free=0.1285 | n_water=362 | time (s): 0.690 (total time: 60.350) Add new water r_work=0.1205 r_free=0.1324 | n_water=500 | time (s): 3.680 (total time: 64.030) Refine new water occ: r_work=0.1144 r_free=0.1280 adp: r_work=0.1144 r_free=0.1281 occ: r_work=0.1132 r_free=0.1274 adp: r_work=0.1131 r_free=0.1273 occ: r_work=0.1123 r_free=0.1273 adp: r_work=0.1119 r_free=0.1269 ADP+occupancy (water only), MIN, final r_work=0.1119 r_free=0.1269 r_work=0.1119 r_free=0.1269 | n_water=500 | time (s): 240.750 (total time: 304.780) Filter (q & B) r_work=0.1125 r_free=0.1279 | n_water=468 | time (s): 3.910 (total time: 308.690) Filter (dist only) r_work=0.1126 r_free=0.1278 | n_water=467 | time (s): 48.130 (total time: 356.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.816297 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.010858 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1210 0.1336 0.0125 0.004 0.7 6.4 0.0 0.0 0 0.091 0.1164 0.1303 0.0139 0.004 0.8 6.1 0.0 0.0 0 0.272 0.1146 0.1291 0.0145 0.005 0.9 6.1 0.5 0.0 0 0.545 0.1137 0.1284 0.0147 0.006 1.0 6.1 0.5 0.0 0 0.817 0.1132 0.1280 0.0148 0.006 1.1 5.8 0.5 0.0 0 1.090 0.1128 0.1278 0.0150 0.008 1.1 5.4 0.5 0.0 0 1.362 0.1126 0.1278 0.0152 0.008 1.1 5.4 0.5 0.0 0 1.635 0.1125 0.1277 0.0152 0.009 1.1 5.4 0.5 0.0 0 1.907 0.1135 0.1282 0.0147 0.006 1.0 5.8 0.5 0.0 0 0.908 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1125 0.1277 0.0152 0.009 1.1 5.4 0.5 0.0 0 1.907 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.25 12.77 1.52 3.780 21.307 40.011 3.600 11.25 12.77 1.52 3.780 21.307 1.200 3.600 11.25 12.77 1.52 3.780 21.307 5.001 3.600 11.28 12.83 1.55 3.713 21.300 20.005 3.595 11.35 12.98 1.64 3.735 21.274 40.011 3.600 11.29 12.98 1.68 3.753 21.260 60.016 3.594 11.22 12.92 1.70 3.767 21.260 80.022 3.589 11.22 12.91 1.69 3.775 21.256 100.027 3.587 11.18 12.87 1.70 3.785 21.254 120.033 3.584 11.16 12.87 1.71 3.794 21.252 140.038 3.583 11.17 12.91 1.74 3.811 21.239 160.043 3.583 11.15 12.89 1.74 3.816 21.240 180.049 3.582 11.14 12.88 1.74 3.827 21.237 200.054 3.581 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.001 Accepted refinement result: 11.25 12.77 1.52 3.780 21.307 5.001 3.600 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 21.32 3.31 244 1750 Protein: 9.10 115.04 17.03 3.32 0 1519 Water: 11.52 76.69 35.26 N/A 244 223 Other: 19.73 26.64 22.09 N/A 0 8 Chain A: 9.10 115.04 19.44 N/A 0 1750 Chain S: 16.17 59.99 34.82 N/A 244 0 Histogram: Values Number of atoms 9.10 - 19.70 1264 19.70 - 30.29 300 30.29 - 40.88 224 40.88 - 51.48 132 51.48 - 62.07 50 62.07 - 72.66 13 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1125 r_free=0.1277 r_work=0.1125 r_free=0.1277 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1125 r_free = 0.1277 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1122 r_free = 0.1278 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1122 r_free= 0.1278 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.598556 | | target function (ml) not normalized (work): 299684.155205 | | target function (ml) not normalized (free): 15788.924294 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1309 0.1322 5.6263 5.5784| | 2: 3.57 - 2.84 1.00 2888 124 0.1042 0.1387 5.1361 5.2093| | 3: 2.83 - 2.48 1.00 2820 163 0.1087 0.1141 4.9272 4.9481| | 4: 2.47 - 2.25 1.00 2825 136 0.0890 0.1012 4.6117 4.6591| | 5: 2.25 - 2.09 1.00 2756 127 0.0856 0.0946 4.5602 4.6057| | 6: 2.09 - 1.97 1.00 2846 113 0.0856 0.1039 4.2591 4.368| | 7: 1.97 - 1.87 1.00 2787 165 0.0883 0.1100 3.9781 4.0792| | 8: 1.87 - 1.79 1.00 2789 144 0.0910 0.1117 3.8866 4.0092| | 9: 1.79 - 1.72 1.00 2745 138 0.0871 0.1162 3.6416 3.8059| | 10: 1.72 - 1.66 1.00 2831 160 0.0913 0.1196 3.56 3.7128| | 11: 1.66 - 1.61 1.00 2712 147 0.0874 0.1025 3.4953 3.5738| | 12: 1.61 - 1.56 1.00 2773 144 0.0902 0.1164 3.3262 3.4639| | 13: 1.56 - 1.52 1.00 2745 130 0.0940 0.1011 3.303 3.3811| | 14: 1.52 - 1.48 1.00 2803 134 0.0976 0.1053 3.2344 3.32| | 15: 1.48 - 1.45 1.00 2738 128 0.1000 0.1237 3.1488 3.2691| | 16: 1.45 - 1.42 1.00 2756 161 0.1055 0.1232 3.1335 3.2385| | 17: 1.42 - 1.39 1.00 2785 139 0.1140 0.1291 3.1174 3.2234| | 18: 1.39 - 1.36 1.00 2741 179 0.1201 0.1294 3.1045 3.2288| | 19: 1.36 - 1.34 1.00 2807 134 0.1263 0.1562 3.1114 3.2714| | 20: 1.34 - 1.32 1.00 2696 147 0.1366 0.1468 3.1107 3.1545| | 21: 1.32 - 1.30 1.00 2785 112 0.1471 0.1507 3.1125 3.1042| | 22: 1.29 - 1.27 1.00 2704 152 0.1562 0.1994 3.1218 3.2982| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1785 3.1331 3.202| | 24: 1.26 - 1.24 1.00 2744 132 0.1710 0.1844 3.1258 3.2284| | 25: 1.24 - 1.22 1.00 2733 148 0.1883 0.2160 3.1419 3.2626| | 26: 1.22 - 1.21 1.00 2727 135 0.1908 0.1772 3.1471 3.2005| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2173 3.1694 3.1621| | 28: 1.19 - 1.18 1.00 2671 147 0.2202 0.2296 3.1652 3.1694| | 29: 1.18 - 1.16 1.00 2800 134 0.2262 0.2385 3.1461 3.2268| | 30: 1.16 - 1.15 1.00 2739 148 0.2444 0.2442 3.1415 3.1644| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2917 171 0.95 8.09 1.00 0.97 5461.45| | 2: 3.57 - 2.84 2888 124 0.93 12.18 1.01 0.97 5461.45| | 3: 2.83 - 2.48 2820 163 0.90 16.10 0.99 0.97 4569.06| | 4: 2.47 - 2.25 2825 136 0.92 13.16 1.00 0.98 2267.87| | 5: 2.25 - 2.09 2756 127 0.91 15.22 1.01 0.98 2267.87| | 6: 2.09 - 1.97 2846 113 0.93 12.22 1.02 0.98 1321.36| | 7: 1.97 - 1.87 2787 165 0.95 9.32 1.02 0.97 514.12| | 8: 1.87 - 1.79 2789 144 0.93 12.69 1.00 0.97 514.12| | 9: 1.79 - 1.72 2745 138 0.94 10.04 0.98 0.97 289.82| | 10: 1.72 - 1.66 2831 160 0.94 11.18 0.98 0.97 244.90| | 11: 1.66 - 1.61 2712 147 0.93 11.81 0.98 0.97 234.59| | 12: 1.61 - 1.56 2773 144 0.96 8.87 0.99 0.97 137.32| | 13: 1.56 - 1.52 2745 130 0.95 10.41 1.03 0.97 137.32| | 14: 1.52 - 1.48 2803 134 0.94 10.78 1.02 0.98 123.08| | 15: 1.48 - 1.45 2738 128 0.95 9.89 1.02 0.98 97.01| | 16: 1.45 - 1.42 2756 161 0.94 11.05 1.02 0.98 97.01| | 17: 1.42 - 1.39 2785 139 0.95 10.89 1.01 0.98 88.55| | 18: 1.39 - 1.36 2741 179 0.94 11.53 1.01 0.98 83.65| | 19: 1.36 - 1.34 2807 134 0.94 11.87 0.99 0.98 83.65| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.96 79.96| | 21: 1.32 - 1.30 2785 112 0.94 13.12 0.98 0.96 79.70| | 22: 1.29 - 1.27 2704 152 0.93 13.67 0.98 0.96 80.12| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.97 0.94 82.28| | 24: 1.26 - 1.24 2744 132 0.92 14.89 0.96 0.94 82.28| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.94 84.12| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.02 0.93 86.17| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 86.17| | 28: 1.19 - 1.18 2671 147 0.88 20.33 1.01 0.93 89.43| | 29: 1.18 - 1.16 2800 134 0.88 20.41 0.99 0.92 90.66| | 30: 1.16 - 1.15 2739 148 0.86 21.92 0.98 0.92 90.66| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.70 max = 5461.45 mean = 851.39| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.38| |phase err.(test): min = 0.00 max = 88.20 mean = 13.38| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1130 0.1122 0.1278 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1441 0.1439 0.1494 n_refl.: 87575 remove outliers: r(all,work,free)=0.1441 0.1439 0.1494 n_refl.: 87575 overall B=-0.00 to atoms: r(all,work,free)=0.1440 0.1439 0.1493 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1130 0.1122 0.1280 n_refl.: 87575 remove outliers: r(all,work,free)=0.1129 0.1121 0.1280 n_refl.: 87573 ======================== 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 0.3956 288.194 252.716 0.451 0.999 0.303 11.894-9.307 93.14 91 4 0.2324 482.828 466.832 0.869 1.002 0.247 9.237-7.194 97.73 208 7 0.2230 387.673 379.561 0.926 1.002 0.168 7.162-5.571 100.00 427 22 0.2088 296.027 285.183 0.907 1.002 0.140 5.546-4.326 100.00 867 58 0.1123 406.372 402.356 0.965 1.003 0.120 4.315-3.360 100.00 1859 96 0.0899 386.463 384.465 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1090 253.886 252.120 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0902 168.303 167.780 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0885 82.190 82.555 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.447 36.065 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.964 21.527 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0141 ================= 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 0.1962 0.083 5.610 8.8 119.3 19.9 258 0.000 1_bss: 0.1634 0.1784 0.083 5.610 9.1 119.5 20.1 258 0.000 1_settarget: 0.1634 0.1784 0.083 5.610 9.1 119.5 20.1 258 0.000 1_nqh: 0.1634 0.1784 0.083 5.610 9.1 119.5 20.1 258 0.000 1_weight: 0.1634 0.1784 0.083 5.610 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1227 0.1471 0.007 0.911 9.1 119.5 20.1 258 0.127 1_adp: 0.1234 0.1467 0.007 0.911 9.1 119.5 20.1 258 0.127 1_regHadp: 0.1236 0.1470 0.007 0.911 9.1 119.5 20.1 258 0.127 1_occ: 0.1230 0.1464 0.007 0.911 9.1 119.5 20.1 258 0.127 2_bss: 0.1226 0.1457 0.007 0.911 9.1 119.5 20.1 258 0.127 2_settarget: 0.1226 0.1457 0.007 0.911 9.1 119.5 20.1 258 0.127 2_updatecdl: 0.1226 0.1457 0.007 0.923 9.1 119.5 20.1 258 0.127 2_nqh: 0.1228 0.1457 0.007 0.923 9.1 119.5 20.1 258 0.130 2_sol: 0.1206 0.1405 0.007 0.923 9.1 115.0 22.1 416 n/a 2_weight: 0.1206 0.1405 0.007 0.923 9.1 115.0 22.1 416 n/a 2_xyzrec: 0.1206 0.1412 0.005 0.766 9.1 115.0 22.1 416 n/a 2_adp: 0.1206 0.1412 0.005 0.766 9.1 115.0 22.1 416 n/a 2_regHadp: 0.1206 0.1412 0.005 0.766 9.1 115.0 22.1 416 n/a 2_occ: 0.1206 0.1413 0.005 0.766 9.1 115.0 22.1 416 n/a 3_bss: 0.1202 0.1409 0.005 0.766 9.1 115.1 22.1 416 n/a 3_settarget: 0.1202 0.1409 0.005 0.766 9.1 115.1 22.1 416 n/a 3_updatecdl: 0.1202 0.1409 0.005 0.767 9.1 115.1 22.1 416 n/a 3_nqh: 0.1202 0.1409 0.005 0.767 9.1 115.1 22.1 416 n/a 3_sol: 0.1222 0.1395 0.005 0.767 9.1 115.1 21.1 429 n/a 3_weight: 0.1222 0.1395 0.005 0.767 9.1 115.1 21.1 429 n/a 3_xyzrec: 0.1160 0.1307 0.008 1.085 9.1 115.1 21.1 429 n/a 3_adp: 0.1160 0.1307 0.008 1.085 9.1 115.1 21.1 429 n/a 3_regHadp: 0.1160 0.1307 0.008 1.085 9.1 115.1 21.1 429 n/a 3_occ: 0.1151 0.1305 0.008 1.085 9.1 115.1 21.1 429 n/a 4_bss: 0.1144 0.1295 0.008 1.085 9.1 115.0 21.1 429 n/a 4_settarget: 0.1144 0.1295 0.008 1.085 9.1 115.0 21.1 429 n/a 4_updatecdl: 0.1144 0.1295 0.008 1.088 9.1 115.0 21.1 429 n/a 4_nqh: 0.1144 0.1295 0.008 1.088 9.1 115.0 21.1 429 n/a 4_sol: 0.1146 0.1275 0.008 1.088 9.1 115.0 21.3 457 n/a 4_weight: 0.1146 0.1275 0.008 1.088 9.1 115.0 21.3 457 n/a 4_xyzrec: 0.1141 0.1278 0.009 1.130 9.1 115.0 21.3 457 n/a 4_adp: 0.1141 0.1278 0.009 1.130 9.1 115.0 21.3 457 n/a 4_regHadp: 0.1141 0.1278 0.009 1.130 9.1 115.0 21.3 457 n/a 4_occ: 0.1134 0.1276 0.009 1.130 9.1 115.0 21.3 457 n/a 5_bss: 0.1131 0.1277 0.009 1.130 9.1 115.0 21.3 457 n/a 5_settarget: 0.1131 0.1277 0.009 1.130 9.1 115.0 21.3 457 n/a 5_updatecdl: 0.1131 0.1277 0.009 1.131 9.1 115.0 21.3 457 n/a 5_setrh: 0.1132 0.1277 0.009 1.131 9.1 115.0 21.3 457 n/a 5_nqh: 0.1132 0.1277 0.009 1.131 9.1 115.0 21.3 457 n/a 5_sol: 0.1126 0.1278 0.009 1.131 9.1 115.0 21.3 467 n/a 5_weight: 0.1126 0.1278 0.009 1.131 9.1 115.0 21.3 467 n/a 5_xyzrec: 0.1125 0.1277 0.009 1.139 9.1 115.0 21.3 467 n/a 5_adp: 0.1125 0.1277 0.009 1.139 9.1 115.0 21.3 467 n/a 5_regHadp: 0.1125 0.1277 0.009 1.139 9.1 115.0 21.3 467 n/a 5_occ: 0.1122 0.1278 0.009 1.139 9.1 115.0 21.3 467 n/a end: 0.1121 0.1280 0.009 1.139 9.1 115.0 21.3 467 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5239121_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5239121_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.3300 Refinement macro-cycles (run) : 13750.5800 Write final files (write_after_run_outputs) : 90.6300 Total : 13845.5400 Total CPU time: 3.85 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:11:16 PST -0800 (1735366276.18 s) Start R-work = 0.1634, R-free = 0.1784 Final R-work = 0.1121, R-free = 0.1280 =============================================================================== Job complete usr+sys time: 14035.29 seconds wall clock time: 255 minutes 33.91 seconds (15333.91 seconds total)