Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2659048.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2659048.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2659048.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } 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 =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.50, per 1000 atoms: 0.44 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: 0.32 Conformation dependent library (CDL) restraints added in 122.5 milliseconds Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 481 0.90 - 1.17: 1162 1.17 - 1.44: 717 1.44 - 1.70: 775 1.70 - 1.97: 18 Bond restraints: 3153 Sorted by residual: bond pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 1.518 1.719 -0.201 1.00e-02 1.00e+04 4.04e+02 bond pdb=" CA LYS A 122 " pdb=" C LYS A 122 " ideal model delta sigma weight residual 1.523 1.755 -0.232 1.30e-02 5.92e+03 3.19e+02 bond pdb=" CA ALA A 178 " pdb=" C ALA A 178 " ideal model delta sigma weight residual 1.523 1.292 0.231 1.30e-02 5.92e+03 3.17e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.187 0.191 1.10e-02 8.26e+03 3.02e+02 bond pdb=" N ACYS A 53 " pdb=" CA ACYS A 53 " ideal model delta sigma weight residual 1.456 1.662 -0.205 1.20e-02 6.94e+03 2.93e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.62: 3624 5.62 - 11.25: 1728 11.25 - 16.87: 393 16.87 - 22.49: 25 22.49 - 28.11: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.91 104.91 17.00 9.80e-01 1.04e+00 3.01e+02 angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH1 ARG A 48 " ideal model delta sigma weight residual 121.50 137.32 -15.82 1.00e+00 1.00e+00 2.50e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 129.38 -10.09 6.50e-01 2.37e+00 2.41e+02 angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 105.33 13.87 9.00e-01 1.23e+00 2.37e+02 angle pdb=" C GLY A 108 " pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta sigma weight residual 119.82 105.61 14.21 9.80e-01 1.04e+00 2.10e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 19.58: 973 19.58 - 39.14: 95 39.14 - 58.70: 34 58.70 - 78.26: 8 78.26 - 97.82: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ARG A 145 " pdb=" C ARG A 145 " pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+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 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -161.22 -18.78 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 104 0.208 - 0.416: 65 0.416 - 0.624: 46 0.624 - 0.832: 21 0.832 - 1.040: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 51 " pdb=" CA VAL A 51 " pdb=" CG1 VAL A 51 " pdb=" CG2 VAL A 51 " both_signs ideal model delta sigma weight residual False -2.63 -1.59 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CA ALA A 14 " pdb=" N ALA A 14 " pdb=" C ALA A 14 " pdb=" CB ALA A 14 " both_signs ideal model delta sigma weight residual False 2.48 3.51 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CB VAL A 33 " pdb=" CA VAL A 33 " pdb=" CG1 VAL A 33 " pdb=" CG2 VAL A 33 " both_signs ideal model delta sigma weight residual False -2.63 -1.66 -0.97 2.00e-01 2.50e+01 2.37e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.044 2.00e-02 2.50e+03 6.38e-02 1.22e+02 pdb=" CG PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.096 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.026 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.137 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.045 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.112 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.005 2.00e-02 2.50e+03 5.42e-02 8.81e+01 pdb=" CG BTYR A 67 " -0.097 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.037 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.107 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.039 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.032 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.020 2.00e-02 2.50e+03 4.81e-02 6.95e+01 pdb=" CG PHE A 164 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.090 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.042 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.077 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.060 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.062 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 935 2.31 - 2.88: 8022 2.88 - 3.45: 10610 3.45 - 4.03: 15159 4.03 - 4.60: 21975 Nonbonded interactions: 56701 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.733 2.100 nonbonded pdb="HH21 ARG A 145 " pdb=" OE1 GLU A 163 " model vdw 1.834 1.850 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.858 1.850 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.870 1.850 nonbonded pdb=" H LYS A 12 " pdb=" O HOH A 396 " model vdw 1.888 1.850 ... (remaining 56696 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_2659048_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= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788464 | | target function (ml) not normalized (work): 232295.810735 | | target function (ml) not normalized (free): 11788.995365 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3018 0.2132 7.0215 4.9572| | 2: 3.57 - 2.84 1.00 2876 122 0.2440 0.1730 4.3548 4.3242| | 3: 2.84 - 2.48 1.00 2833 165 0.2342 0.1622 4.1258 4.1573| | 4: 2.47 - 2.25 1.00 2825 136 0.2331 0.1478 3.8363 3.8311| | 5: 2.25 - 2.09 1.00 2756 127 0.2518 0.1712 3.8064 3.8307| | 6: 2.09 - 1.97 1.00 2846 113 0.2526 0.1774 3.4733 3.6178| | 7: 1.97 - 1.87 1.00 2787 165 0.2548 0.1813 3.1355 3.1668| | 8: 1.87 - 1.79 1.00 2789 144 0.2510 0.1881 3.0714 3.1255| | 9: 1.79 - 1.72 1.00 2745 138 0.2414 0.1894 2.8954 2.9345| | 10: 1.72 - 1.66 1.00 2789 158 0.2377 0.1965 2.7994 2.9017| | 11: 1.66 - 1.61 1.00 2740 147 0.2526 0.1836 2.7449 2.7523| | 12: 1.61 - 1.56 1.00 2787 146 0.2500 0.1857 2.6099 2.5798| | 13: 1.56 - 1.52 1.00 2745 130 0.2527 0.2166 2.5616 2.6939| | 14: 1.52 - 1.48 1.00 2803 134 0.2616 0.1820 2.5097 2.5619| | 15: 1.48 - 1.45 1.00 2738 128 0.2612 0.2196 2.4182 2.5277| | 16: 1.45 - 1.42 1.00 2756 161 0.2720 0.2028 2.3951 2.3901| | 17: 1.42 - 1.39 1.00 2785 139 0.2649 0.1975 2.3253 2.321| | 18: 1.39 - 1.36 1.00 2741 179 0.2677 0.2059 2.2621 2.2961| | 19: 1.36 - 1.34 1.00 2807 134 0.2636 0.2499 2.2148 2.3141| | 20: 1.34 - 1.32 1.00 2696 147 0.2699 0.1988 2.1995 2.1699| | 21: 1.32 - 1.30 1.00 2785 112 0.2675 0.2282 2.1682 2.1552| | 22: 1.29 - 1.27 1.00 2704 152 0.2695 0.2590 2.1331 2.1956| | 23: 1.27 - 1.26 1.00 2802 156 0.2792 0.2377 2.0995 2.1378| | 24: 1.26 - 1.24 1.00 2744 132 0.2790 0.2445 2.0924 2.1191| | 25: 1.24 - 1.22 1.00 2734 148 0.2874 0.2580 2.0518 2.1059| | 26: 1.22 - 1.21 1.00 2727 135 0.2904 0.2170 2.0119 2.0518| | 27: 1.21 - 1.19 1.00 2814 148 0.2983 0.2701 2.0186 2.0117| | 28: 1.19 - 1.18 1.00 2671 147 0.2989 0.2923 1.9818 2.0288| | 29: 1.18 - 1.16 1.00 2800 134 0.2974 0.2680 1.9535 1.998| | 30: 1.16 - 1.15 1.00 2740 148 0.3070 0.2773 1.9283 1.9525| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.90 0.76 0.23 1490.72| | 2: 3.57 - 2.84 2876 122 0.80 26.23 1.28 0.23 1490.72| | 3: 2.84 - 2.48 2833 165 0.74 32.16 1.24 0.23 1236.63| | 4: 2.47 - 2.25 2825 136 0.81 25.65 1.26 0.25 577.23| | 5: 2.25 - 2.09 2756 127 0.77 29.41 1.28 0.25 577.23| | 6: 2.09 - 1.97 2846 113 0.83 22.75 1.29 0.25 316.11| | 7: 1.97 - 1.87 2787 165 0.90 16.78 1.28 0.26 93.42| | 8: 1.87 - 1.79 2789 144 0.86 21.35 1.25 0.26 93.42| | 9: 1.79 - 1.72 2745 138 0.88 18.63 1.23 0.26 55.82| | 10: 1.72 - 1.66 2789 158 0.86 20.24 1.22 0.26 48.29| | 11: 1.66 - 1.61 2740 147 0.86 21.28 1.25 0.26 46.51| | 12: 1.61 - 1.56 2787 146 0.89 18.14 1.23 0.25 28.50| | 13: 1.56 - 1.52 2745 130 0.87 20.25 1.23 0.25 28.50| | 14: 1.52 - 1.48 2803 134 0.86 20.63 1.24 0.25 25.62| | 15: 1.48 - 1.45 2738 128 0.87 20.06 1.24 0.25 20.35| | 16: 1.45 - 1.42 2756 161 0.86 21.53 1.25 0.25 20.35| | 17: 1.42 - 1.39 2785 139 0.87 20.32 1.23 0.25 17.06| | 18: 1.39 - 1.36 2741 179 0.86 21.13 1.23 0.25 15.15| | 19: 1.36 - 1.34 2807 134 0.86 21.78 1.22 0.25 15.15| | 20: 1.34 - 1.32 2696 147 0.87 20.57 1.21 0.24 12.70| | 21: 1.32 - 1.30 2785 112 0.86 21.52 1.19 0.24 12.52| | 22: 1.29 - 1.27 2704 152 0.86 21.85 1.20 0.24 12.24| | 23: 1.27 - 1.26 2802 156 0.86 21.86 1.22 0.24 10.77| | 24: 1.26 - 1.24 2744 132 0.86 22.10 1.20 0.24 10.77| | 25: 1.24 - 1.22 2734 148 0.84 23.44 1.20 0.24 10.29| | 26: 1.22 - 1.21 2727 135 0.84 23.83 1.21 0.23 9.75| | 27: 1.21 - 1.19 2814 148 0.84 24.21 1.20 0.23 9.75| | 28: 1.19 - 1.18 2671 147 0.83 25.27 1.18 0.23 9.14| | 29: 1.18 - 1.16 2800 134 0.83 25.47 1.17 0.22 8.91| | 30: 1.16 - 1.15 2740 148 0.81 27.04 1.16 0.22 8.91| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 8.91 max = 1490.72 mean = 216.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 22.48| |phase err.(test): min = 0.00 max = 89.91 mean = 22.29| |-----------------------------------------------------------------------------| ----------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 : 0.085 0.281 1557 Z= 5.601 Angle : 5.394 24.633 2118 Z= 3.839 Chirality : 0.390 1.040 243 Planarity : 0.031 0.098 284 Dihedral : 14.130 97.822 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.11 % Allowed : 3.73 % Favored : 93.17 % Cbeta Deviations : 30.81 % 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: -2.74 (0.46), residues: 224 helix: -2.41 (0.40), residues: 109 sheet: -1.87 (0.85), residues: 28 loop : -0.59 (0.54), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.024 ARG A 27 TYR 0.067 0.027 TYR A 139 PHE 0.111 0.037 PHE A 119 HIS 0.038 0.020 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788464 | | target function (ml) not normalized (work): 232295.810735 | | target function (ml) not normalized (free): 11788.995365 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2609 0.1942 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2609 0.1942 n_refl.: 87602 remove outliers: r(all,work,free)=0.1977 0.1981 0.1942 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2001 0.2005 0.1956 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1643 0.1637 0.1755 n_refl.: 87594 remove outliers: r(all,work,free)=0.1642 0.1637 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 98.94 88 5 0.3899 386.379 356.693 0.668 1.004 0.407 11.894-9.307 99.02 97 4 0.1864 613.745 592.226 0.925 1.004 0.390 9.237-7.194 100.00 213 7 0.2213 501.968 489.780 0.958 1.004 0.344 7.162-5.571 100.00 427 22 0.2182 376.699 364.357 0.937 1.004 0.298 5.546-4.326 100.00 867 58 0.1270 517.114 511.706 0.963 1.004 0.233 4.315-3.360 100.00 1859 96 0.1124 491.779 488.040 1.002 1.003 0.199 3.356-2.611 100.00 3867 181 0.1439 323.074 319.850 0.999 1.002 0.048 2.608-2.026 99.99 8198 413 0.1355 214.168 211.918 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1643 104.589 103.877 1.013 0.999 0.000 1.573-1.221 99.99 36678 1900 0.2067 46.378 45.037 1.004 0.995 0.000 1.221-1.150 99.97 13689 708 0.2613 29.222 26.967 0.979 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0446 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1637 r_free=0.1755 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.1638 r_free=0.1751 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.526138 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2029.624931 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 0.1731 0.1847 0.0116 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1555 0.1694 0.0139 0.001 0.4 4.8 0.0 0.0 0 0.250 0.1462 0.1627 0.0165 0.002 0.4 4.2 0.0 0.0 0 0.500 0.1382 0.1566 0.0184 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1353 0.1556 0.0203 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1346 0.1544 0.0198 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1294 0.1510 0.0216 0.002 0.6 3.8 0.5 0.0 0 2.000 0.1271 0.1497 0.0226 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1259 0.1485 0.0226 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1248 0.1483 0.0235 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1243 0.1475 0.0232 0.004 0.8 4.2 0.5 0.0 0 6.000 0.1242 0.1477 0.0235 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1237 0.1473 0.0236 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1232 0.1467 0.0235 0.006 0.8 4.5 0.5 0.0 0 9.000 0.1230 0.1470 0.0240 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1228 0.1471 0.0243 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1225 0.1469 0.0244 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1225 0.1473 0.0249 0.008 1.0 4.2 0.5 0.6 0 13.763 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1232 0.1467 0.0235 0.006 0.8 4.5 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.67 2.35 3.013 19.053 2029.625 0.017 12.32 14.67 2.35 3.005 19.053 60.889 0.017 12.38 14.64 2.26 2.666 19.053 253.703 0.017 12.70 15.29 2.58 2.741 19.222 1014.812 0.017 12.60 15.49 2.90 3.398 19.675 2029.625 0.016 12.44 15.44 3.01 3.333 19.638 3044.437 0.015 12.35 15.43 3.08 3.376 19.656 4059.250 0.015 12.33 15.44 3.11 3.397 19.647 5074.062 0.015 12.25 15.44 3.19 3.434 19.667 6088.875 0.015 12.23 15.46 3.23 3.477 19.680 7103.687 0.015 12.15 15.37 3.21 3.347 19.600 8118.500 0.015 12.21 15.50 3.29 3.585 19.717 9133.312 0.015 12.22 15.55 3.33 3.564 19.697 10148.125 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: 253.703 Accepted refinement result: 12.38 14.64 2.26 2.666 19.053 253.703 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.44 20.08 3.31 0 1785 Protein: 9.07 114.97 16.99 3.31 0 1519 Water: 11.44 119.44 38.22 N/A 0 258 Other: 19.71 26.60 22.05 N/A 0 8 Chain A: 9.07 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.10 1272 20.10 - 31.14 227 31.14 - 42.18 125 42.18 - 53.21 94 53.21 - 64.25 42 64.25 - 75.29 11 75.29 - 86.33 7 86.33 - 97.36 4 97.36 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1464 r_work=0.1239 r_free=0.1467 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1467 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 = 0.1231 r_free = 0.1459 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 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= 0.1231 r_free= 0.1459 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016885 | | target function (ls_wunit_k1) not normalized (work): 1406.412455 | | target function (ls_wunit_k1) not normalized (free): 109.315336 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1242 0.1231 0.1459 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1672 0.1674 0.1689 n_refl.: 87592 remove outliers: r(all,work,free)=0.1672 0.1674 0.1689 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1679 0.1680 0.1694 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1230 0.1451 n_refl.: 87592 remove outliers: r(all,work,free)=0.1240 0.1229 0.1451 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3543 301.585 281.651 0.650 1.003 0.380 11.894-9.307 99.02 97 4 0.1676 483.122 470.717 0.920 1.003 0.371 9.237-7.194 100.00 213 7 0.1887 395.135 389.338 0.965 1.003 0.350 7.162-5.571 100.00 427 22 0.1828 296.527 290.692 0.939 1.003 0.264 5.546-4.326 100.00 867 58 0.0999 407.058 404.032 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0874 387.115 386.071 1.007 1.002 0.180 3.356-2.611 100.00 3867 181 0.1178 254.314 253.104 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1024 168.587 167.846 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1115 82.329 82.518 1.026 0.999 0.000 1.573-1.221 99.99 36678 1900 0.1451 36.507 36.012 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 23.003 21.484 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0538 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1451 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=0.1229 r_free=0.1451 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1229 r_free=0.1451 | n_water=258 | time (s): 1.630 (total time: 1.630) Filter (dist) r_work=0.1239 r_free=0.1450 | n_water=251 | time (s): 20.530 (total time: 22.160) Filter (q & B) r_work=0.1241 r_free=0.1450 | n_water=248 | time (s): 2.780 (total time: 24.940) Compute maps r_work=0.1241 r_free=0.1450 | n_water=248 | time (s): 1.670 (total time: 26.610) Filter (map) r_work=0.1252 r_free=0.1461 | n_water=229 | time (s): 3.060 (total time: 29.670) Find peaks r_work=0.1252 r_free=0.1461 | n_water=229 | time (s): 0.710 (total time: 30.380) Add new water r_work=0.1393 r_free=0.1627 | n_water=435 | time (s): 2.940 (total time: 33.320) Refine new water occ: r_work=0.1301 r_free=0.1485 adp: r_work=0.1223 r_free=0.1427 occ: r_work=0.1234 r_free=0.1408 adp: r_work=0.1202 r_free=0.1395 occ: r_work=0.1204 r_free=0.1384 adp: r_work=0.1195 r_free=0.1383 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1383 r_work=0.1195 r_free=0.1383 | n_water=435 | time (s): 47.390 (total time: 80.710) Filter (q & B) r_work=0.1201 r_free=0.1385 | n_water=415 | time (s): 2.450 (total time: 83.160) Filter (dist only) r_work=0.1201 r_free=0.1384 | n_water=414 | time (s): 34.780 (total time: 117.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.182315 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1436.434003 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 0.1718 0.1813 0.0095 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1556 0.1676 0.0119 0.001 0.4 7.0 0.0 0.0 0 0.250 0.1393 0.1545 0.0152 0.001 0.4 6.1 0.0 0.0 0 0.500 0.1354 0.1515 0.0161 0.002 0.5 4.8 0.0 0.0 0 0.750 0.1313 0.1485 0.0172 0.002 0.5 4.2 0.0 0.0 0 1.000 0.1330 0.1500 0.0170 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1254 0.1454 0.0199 0.002 0.5 3.8 0.5 0.0 0 2.000 0.1229 0.1426 0.0197 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1210 0.1424 0.0214 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1207 0.1421 0.0213 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1204 0.1418 0.0214 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1196 0.1413 0.0217 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1193 0.1413 0.0219 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1192 0.1411 0.0220 0.006 0.8 4.5 0.5 0.0 0 9.000 0.1190 0.1408 0.0218 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1188 0.1412 0.0224 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1186 0.1408 0.0222 0.007 0.9 5.4 0.5 0.0 0 12.000 0.1185 0.1414 0.0229 0.007 0.9 5.1 0.5 0.0 0 13.000 0.1184 0.1417 0.0233 0.008 0.9 5.1 0.5 0.0 0 14.091 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1408 0.0218 0.006 0.9 4.8 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 14.08 2.18 3.773 21.757 1436.434 0.016 11.90 14.08 2.18 3.773 21.757 43.093 0.016 11.90 14.08 2.18 3.773 21.757 179.554 0.016 12.05 14.47 2.41 3.632 21.761 718.217 0.015 12.08 14.76 2.68 3.456 21.959 1436.434 0.015 11.98 14.81 2.83 3.458 21.993 2154.651 0.015 11.86 14.76 2.90 3.482 21.941 2872.868 0.014 11.77 14.69 2.93 3.478 21.970 3591.085 0.014 11.70 14.69 2.98 3.518 21.922 4309.302 0.014 11.73 14.69 2.95 3.501 22.129 5027.519 0.014 11.71 14.73 3.02 3.528 22.147 5745.736 0.014 11.71 14.78 3.07 3.540 22.160 6463.953 0.014 11.70 14.83 3.13 3.567 22.187 7182.170 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: 43.093 Accepted refinement result: 11.90 14.08 2.18 3.773 21.757 43.093 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.00 22.15 3.31 185 1756 Protein: 9.10 115.00 17.02 3.31 0 1519 Water: 11.47 76.68 40.97 N/A 185 229 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.10 115.00 19.52 N/A 0 1756 Chain S: 17.85 60.00 47.15 N/A 185 0 Histogram: Values Number of atoms 9.10 - 19.69 1260 19.69 - 30.28 240 30.28 - 40.87 163 40.87 - 51.46 139 51.46 - 62.05 116 62.05 - 72.64 12 72.64 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1408 r_work=0.1190 r_free=0.1408 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1408 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1410 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 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= 0.1188 r_free= 0.1410 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015130 | | target function (ls_wunit_k1) not normalized (work): 1260.214950 | | target function (ls_wunit_k1) not normalized (free): 99.262862 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1188 0.1410 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1579 0.1577 0.1649 n_refl.: 87591 remove outliers: r(all,work,free)=0.1579 0.1577 0.1649 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1581 0.1579 0.1650 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1185 0.1402 n_refl.: 87591 remove outliers: r(all,work,free)=0.1194 0.1184 0.1402 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3375 297.487 275.760 0.595 1.003 0.350 11.894-9.307 99.02 97 4 0.1636 483.122 476.381 0.923 1.003 0.312 9.237-7.194 100.00 213 7 0.1710 395.135 394.865 0.983 1.003 0.276 7.162-5.571 100.00 427 22 0.1591 296.527 290.935 0.936 1.003 0.230 5.546-4.326 100.00 867 58 0.0879 407.058 403.613 0.961 1.003 0.210 4.315-3.360 100.00 1859 96 0.0791 387.115 386.286 1.005 1.002 0.200 3.356-2.611 100.00 3867 181 0.1075 254.314 253.492 1.011 1.002 0.100 2.608-2.026 99.99 8198 413 0.1004 168.587 168.050 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1102 82.329 82.577 1.030 0.999 0.000 1.573-1.221 99.99 36678 1900 0.1446 36.507 36.044 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 23.003 21.520 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0158 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1184 r_free=0.1402 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1184 r_free=0.1402 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1402 | n_water=414 | time (s): 1.780 (total time: 1.780) Filter (dist) r_work=0.1184 r_free=0.1403 | n_water=410 | time (s): 34.020 (total time: 35.800) Filter (q & B) r_work=0.1184 r_free=0.1403 | n_water=410 | time (s): 0.920 (total time: 36.720) Compute maps r_work=0.1184 r_free=0.1403 | n_water=410 | time (s): 1.190 (total time: 37.910) Filter (map) r_work=0.1235 r_free=0.1392 | n_water=280 | time (s): 2.490 (total time: 40.400) Find peaks r_work=0.1235 r_free=0.1392 | n_water=280 | time (s): 0.660 (total time: 41.060) Add new water r_work=0.1356 r_free=0.1521 | n_water=470 | time (s): 3.050 (total time: 44.110) Refine new water occ: r_work=0.1256 r_free=0.1432 adp: r_work=0.1257 r_free=0.1431 occ: r_work=0.1233 r_free=0.1413 adp: r_work=0.1233 r_free=0.1410 occ: r_work=0.1213 r_free=0.1394 adp: r_work=0.1209 r_free=0.1389 ADP+occupancy (water only), MIN, final r_work=0.1209 r_free=0.1389 r_work=0.1209 r_free=0.1389 | n_water=470 | time (s): 187.190 (total time: 231.300) Filter (q & B) r_work=0.1213 r_free=0.1392 | n_water=440 | time (s): 3.730 (total time: 235.030) Filter (dist only) r_work=0.1213 r_free=0.1392 | n_water=439 | time (s): 36.500 (total time: 271.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.731411 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.698755 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 0.1238 0.1365 0.0127 0.002 0.6 4.8 0.5 0.0 0 0.087 0.1194 0.1328 0.0134 0.003 0.7 3.8 0.5 0.0 0 0.260 0.1177 0.1315 0.0138 0.004 0.8 3.2 0.5 0.0 0 0.519 0.1169 0.1312 0.0142 0.005 0.9 3.5 0.5 0.0 0 0.779 0.1165 0.1311 0.0146 0.006 1.0 3.2 0.5 0.0 0 1.039 0.1163 0.1313 0.0150 0.007 1.0 3.2 0.5 0.0 0 1.299 0.1161 0.1314 0.0153 0.007 1.0 3.5 0.5 0.0 0 1.558 0.1159 0.1309 0.0151 0.008 1.1 3.5 0.5 0.0 0 1.818 0.1168 0.1313 0.0145 0.005 0.9 3.5 0.5 0.0 0 0.866 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1159 0.1309 0.0151 0.008 1.1 3.5 0.5 0.0 0 1.818 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 13.09 1.51 3.776 21.210 48.699 3.620 11.59 13.09 1.51 3.776 21.210 1.461 3.620 11.59 13.10 1.50 3.761 21.210 6.087 3.620 11.65 13.22 1.57 3.713 21.193 24.349 3.615 11.66 13.35 1.68 3.731 21.159 48.699 3.615 11.58 13.30 1.72 3.762 21.147 73.048 3.608 11.53 13.27 1.74 3.779 21.141 97.398 3.604 11.49 13.24 1.75 3.792 21.137 121.747 3.601 11.49 13.26 1.77 3.809 21.126 146.096 3.600 11.46 13.22 1.76 3.821 21.117 170.446 3.598 11.44 13.22 1.77 3.830 21.117 194.795 3.597 11.46 13.24 1.78 3.845 21.109 219.144 3.597 11.42 13.18 1.76 3.846 21.109 243.494 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: 1.461 Accepted refinement result: 11.59 13.09 1.51 3.776 21.210 1.461 3.620 Individual atomic B min max mean iso aniso Overall: 9.11 115.01 21.14 3.31 217 1749 Protein: 9.11 115.01 17.03 3.31 0 1519 Water: 11.48 76.69 35.34 N/A 217 222 Other: 19.75 26.65 22.10 N/A 0 8 Chain A: 9.11 115.01 19.40 N/A 0 1749 Chain S: 16.17 60.01 35.22 N/A 217 0 Histogram: Values Number of atoms 9.11 - 19.70 1265 19.70 - 30.29 290 30.29 - 40.88 215 40.88 - 51.47 123 51.47 - 62.06 50 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1159 r_free=0.1309 r_work=0.1159 r_free=0.1309 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1159 r_free = 0.1309 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1308 target_work(ml) = 3.613 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1150 r_free= 0.1308 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.612966 | | target function (ml) not normalized (work): 300931.173304 | | target function (ml) not normalized (free): 15846.477643 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1158 0.1150 0.1308 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1496 0.1495 0.1538 n_refl.: 87588 remove outliers: r(all,work,free)=0.1496 0.1495 0.1538 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1495 0.1494 0.1537 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1154 0.1147 0.1299 n_refl.: 87588 remove outliers: r(all,work,free)=0.1151 0.1143 0.1299 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 90.62 82 5 0.3873 288.664 269.706 0.495 1.000 0.303 11.894-9.307 97.06 95 4 0.2262 476.452 464.258 0.871 1.001 0.284 9.237-7.194 97.73 208 7 0.2153 386.123 389.609 0.949 1.001 0.211 7.162-5.571 100.00 427 22 0.2103 296.527 285.789 0.911 1.002 0.183 5.546-4.326 100.00 867 58 0.1095 407.058 401.684 0.957 1.002 0.161 4.315-3.360 100.00 1859 96 0.0933 387.115 384.552 0.994 1.001 0.143 3.356-2.611 100.00 3867 181 0.1137 254.314 252.130 0.999 1.001 0.043 2.608-2.026 99.99 8198 413 0.0948 168.587 167.720 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0899 82.329 82.611 1.025 1.000 0.000 1.573-1.221 99.99 36678 1900 0.1255 36.507 36.086 1.018 0.998 0.000 1.221-1.150 99.97 13689 708 0.2164 23.003 21.542 0.980 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0214 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 r_free=0.1299 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=0.1147 r_free=0.1300 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1147 r_free=0.1300 | n_water=439 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1147 r_free=0.1300 | n_water=436 | time (s): 48.110 (total time: 50.590) Filter (q & B) r_work=0.1148 r_free=0.1303 | n_water=433 | time (s): 3.750 (total time: 54.340) Compute maps r_work=0.1148 r_free=0.1303 | n_water=433 | time (s): 1.860 (total time: 56.200) Filter (map) r_work=0.1168 r_free=0.1309 | n_water=325 | time (s): 3.950 (total time: 60.150) Find peaks r_work=0.1168 r_free=0.1309 | n_water=325 | time (s): 0.730 (total time: 60.880) Add new water r_work=0.1246 r_free=0.1395 | n_water=504 | time (s): 3.900 (total time: 64.780) Refine new water occ: r_work=0.1171 r_free=0.1335 adp: r_work=0.1172 r_free=0.1335 occ: r_work=0.1154 r_free=0.1320 adp: r_work=0.1153 r_free=0.1319 occ: r_work=0.1140 r_free=0.1304 adp: r_work=0.1137 r_free=0.1303 ADP+occupancy (water only), MIN, final r_work=0.1137 r_free=0.1303 r_work=0.1137 r_free=0.1303 | n_water=504 | time (s): 199.390 (total time: 264.170) Filter (q & B) r_work=0.1146 r_free=0.1311 | n_water=459 | time (s): 3.880 (total time: 268.050) Filter (dist only) r_work=0.1146 r_free=0.1309 | n_water=458 | time (s): 48.040 (total time: 316.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.741924 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.832006 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 0.1207 0.1342 0.0135 0.002 0.6 4.2 0.5 0.0 0 0.087 0.1172 0.1318 0.0145 0.003 0.7 3.5 0.5 0.0 0 0.261 0.1156 0.1311 0.0155 0.005 0.9 3.5 0.5 0.0 0 0.523 0.1149 0.1308 0.0159 0.006 0.9 3.5 0.5 0.0 0 0.784 0.1145 0.1308 0.0163 0.006 1.0 3.2 0.5 0.0 0 1.045 0.1143 0.1309 0.0166 0.007 1.0 3.5 0.5 0.0 0 1.306 0.1141 0.1308 0.0167 0.008 1.1 3.2 0.5 0.0 0 1.568 0.1140 0.1308 0.0169 0.008 1.1 3.5 0.5 0.0 0 1.829 0.1148 0.1310 0.0161 0.006 1.0 3.5 0.5 0.0 0 0.871 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1141 0.1308 0.0167 0.008 1.1 3.2 0.5 0.0 0 1.568 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.41 13.08 1.67 3.777 21.237 35.832 3.611 11.41 13.08 1.67 3.777 21.237 1.075 3.611 11.41 13.08 1.67 3.777 21.237 4.479 3.611 11.45 13.13 1.68 3.707 21.230 17.916 3.607 11.47 13.20 1.73 3.729 21.213 35.832 3.608 11.44 13.22 1.79 3.749 21.192 53.748 3.604 11.41 13.23 1.83 3.763 21.187 71.664 3.601 11.38 13.24 1.86 3.772 21.183 89.580 3.599 11.34 13.20 1.86 3.783 21.182 107.496 3.596 11.31 13.17 1.86 3.789 21.183 125.412 3.594 11.31 13.20 1.89 3.802 21.173 143.328 3.594 11.31 13.22 1.90 3.815 21.169 161.244 3.594 11.31 13.23 1.92 3.827 21.162 179.160 3.593 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.075 Accepted refinement result: 11.41 13.08 1.67 3.777 21.237 1.075 3.611 Individual atomic B min max mean iso aniso Overall: 9.10 115.00 21.20 3.31 237 1748 Protein: 9.10 115.00 17.02 3.31 0 1519 Water: 11.47 76.68 35.02 N/A 237 221 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.10 115.00 19.38 N/A 0 1748 Chain S: 16.16 60.00 34.58 N/A 237 0 Histogram: Values Number of atoms 9.10 - 19.69 1266 19.69 - 30.28 297 30.28 - 40.87 230 40.87 - 51.46 121 51.46 - 62.05 48 62.05 - 72.64 12 72.64 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1141 r_free=0.1308 r_work=0.1141 r_free=0.1308 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1141 r_free = 0.1308 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1136 r_free = 0.1306 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1136 r_free= 0.1306 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.608600 | | target function (ml) not normalized (work): 300535.034956 | | target function (ml) not normalized (free): 15839.974613 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1144 0.1136 0.1306 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1469 0.1467 0.1521 n_refl.: 87579 remove outliers: r(all,work,free)=0.1469 0.1467 0.1521 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1468 0.1467 0.1521 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1143 0.1135 0.1311 n_refl.: 87579 remove outliers: r(all,work,free)=0.1142 0.1134 0.1311 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4056 290.825 246.387 0.436 1.000 0.310 11.894-9.307 96.08 94 4 0.2470 476.483 459.068 0.849 1.001 0.238 9.237-7.194 97.73 208 7 0.2301 386.123 381.411 0.927 1.001 0.154 7.162-5.571 100.00 427 22 0.2133 296.527 286.466 0.910 1.001 0.135 5.546-4.326 100.00 867 58 0.1123 407.058 402.072 0.966 1.002 0.130 4.315-3.360 100.00 1859 96 0.0903 387.115 385.207 1.003 1.002 0.130 3.356-2.611 100.00 3867 181 0.1117 254.314 252.550 1.010 1.002 0.070 2.608-2.026 99.99 8198 413 0.0920 168.587 168.014 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0886 82.329 82.708 1.034 1.001 0.000 1.573-1.221 99.99 36678 1900 0.1254 36.507 36.103 1.024 1.001 0.000 1.221-1.150 99.97 13689 708 0.2169 23.003 21.470 0.980 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0025 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1134 r_free=0.1311 After: r_work=0.1135 r_free=0.1310 ================================== NQH flips ================================== r_work=0.1135 r_free=0.1310 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=0.1135 r_free=0.1310 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1135 r_free=0.1310 | n_water=458 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1135 r_free=0.1309 | n_water=457 | time (s): 48.090 (total time: 50.430) Filter (q & B) r_work=0.1135 r_free=0.1309 | n_water=456 | time (s): 3.790 (total time: 54.220) Compute maps r_work=0.1135 r_free=0.1309 | n_water=456 | time (s): 1.790 (total time: 56.010) Filter (map) r_work=0.1159 r_free=0.1309 | n_water=358 | time (s): 3.820 (total time: 59.830) Find peaks r_work=0.1159 r_free=0.1309 | n_water=358 | time (s): 0.690 (total time: 60.520) Add new water r_work=0.1199 r_free=0.1352 | n_water=479 | time (s): 3.700 (total time: 64.220) Refine new water occ: r_work=0.1150 r_free=0.1315 adp: r_work=0.1150 r_free=0.1317 occ: r_work=0.1140 r_free=0.1304 adp: r_work=0.1139 r_free=0.1306 occ: r_work=0.1133 r_free=0.1295 adp: r_work=0.1130 r_free=0.1295 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1295 r_work=0.1130 r_free=0.1295 | n_water=479 | time (s): 153.720 (total time: 217.940) Filter (q & B) r_work=0.1135 r_free=0.1303 | n_water=453 | time (s): 3.930 (total time: 221.870) Filter (dist only) r_work=0.1135 r_free=0.1304 | n_water=451 | time (s): 47.660 (total time: 269.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.765721 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.204459 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 0.1356 0.0131 0.004 0.7 5.1 0.0 0.0 0 0.088 0.1171 0.1323 0.0152 0.004 0.8 4.2 0.0 0.0 0 0.265 0.1154 0.1313 0.0159 0.005 0.9 3.5 0.5 0.0 0 0.530 0.1145 0.1307 0.0162 0.006 1.0 3.5 0.5 0.0 0 0.795 0.1138 0.1304 0.0166 0.007 1.1 3.2 0.5 0.0 0 1.059 0.1136 0.1303 0.0167 0.007 1.1 3.2 0.5 0.0 0 1.324 0.1135 0.1304 0.0168 0.008 1.1 3.2 0.5 0.0 0 1.589 0.1135 0.1303 0.0169 0.008 1.1 3.2 0.5 0.0 0 1.854 0.1143 0.1306 0.0163 0.006 1.0 3.2 0.5 0.0 0 0.883 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1136 0.1303 0.0167 0.007 1.1 3.2 0.5 0.0 0 1.324 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.36 13.03 1.67 3.776 21.178 47.204 3.610 11.36 13.03 1.67 3.776 21.178 1.416 3.610 11.37 13.03 1.66 3.766 21.179 5.901 3.610 11.42 13.12 1.70 3.711 21.165 23.602 3.606 11.42 13.22 1.79 3.738 21.139 47.204 3.605 11.36 13.21 1.85 3.760 21.130 70.807 3.600 11.33 13.20 1.86 3.773 21.127 94.409 3.598 11.29 13.16 1.87 3.786 21.124 118.011 3.594 11.29 13.20 1.91 3.806 21.112 141.613 3.594 11.26 13.18 1.92 3.815 21.112 165.216 3.592 11.25 13.18 1.93 3.827 21.109 188.818 3.591 11.23 13.16 1.92 3.832 21.110 212.420 3.590 11.23 13.17 1.94 3.844 21.108 236.022 3.589 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.901 Accepted refinement result: 11.37 13.03 1.66 3.766 21.179 5.901 3.610 Individual atomic B min max mean iso aniso Overall: 9.11 114.88 21.09 3.27 231 1747 Protein: 9.11 114.88 17.02 3.28 0 1519 Water: 11.48 76.68 34.78 N/A 231 220 Other: 19.73 26.61 22.09 N/A 0 8 Chain A: 9.11 114.88 19.36 N/A 0 1747 Chain S: 16.16 60.00 34.17 N/A 231 0 Histogram: Values Number of atoms 9.11 - 19.69 1266 19.69 - 30.27 299 30.27 - 40.84 221 40.84 - 51.42 124 51.42 - 62.00 45 62.00 - 72.58 11 72.58 - 83.15 6 83.15 - 93.73 4 93.73 - 104.31 0 104.31 - 114.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1137 r_free=0.1303 r_work=0.1137 r_free=0.1303 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1137 r_free = 0.1303 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1132 r_free = 0.1299 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1132 r_free= 0.1299 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607849 | | target function (ml) not normalized (work): 300465.233023 | | target function (ml) not normalized (free): 15827.758101 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1317 0.1365 5.6256 5.6278| | 2: 3.57 - 2.84 1.00 2888 124 0.1063 0.1356 5.1647 5.221| | 3: 2.83 - 2.48 1.00 2820 163 0.1096 0.1287 4.9515 5.0051| | 4: 2.47 - 2.25 1.00 2825 136 0.0910 0.0968 4.6402 4.6675| | 5: 2.25 - 2.09 1.00 2756 127 0.0867 0.0983 4.5862 4.6386| | 6: 2.09 - 1.97 1.00 2846 113 0.0856 0.1047 4.2778 4.3853| | 7: 1.97 - 1.87 1.00 2787 165 0.0890 0.1125 3.995 4.1011| | 8: 1.87 - 1.79 1.00 2789 144 0.0918 0.1111 3.9022 4.0077| | 9: 1.79 - 1.72 1.00 2745 138 0.0875 0.1185 3.6517 3.83| | 10: 1.72 - 1.66 1.00 2831 160 0.0926 0.1193 3.5705 3.708| | 11: 1.66 - 1.61 1.00 2712 147 0.0878 0.1043 3.5026 3.5831| | 12: 1.61 - 1.56 1.00 2773 144 0.0917 0.1143 3.3376 3.468| | 13: 1.56 - 1.52 1.00 2745 130 0.0949 0.1039 3.3138 3.4078| | 14: 1.52 - 1.48 1.00 2803 134 0.0988 0.1039 3.2455 3.3239| | 15: 1.48 - 1.45 1.00 2738 128 0.1008 0.1242 3.1575 3.2727| | 16: 1.45 - 1.42 1.00 2756 161 0.1060 0.1230 3.1386 3.2366| | 17: 1.42 - 1.39 1.00 2785 139 0.1144 0.1287 3.1204 3.2148| | 18: 1.39 - 1.36 1.00 2740 179 0.1200 0.1306 3.1052 3.229| | 19: 1.36 - 1.34 1.00 2807 134 0.1264 0.1545 3.112 3.2635| | 20: 1.34 - 1.32 1.00 2696 147 0.1374 0.1459 3.1157 3.1519| | 21: 1.32 - 1.30 1.00 2785 112 0.1472 0.1531 3.1159 3.1111| | 22: 1.29 - 1.27 1.00 2704 152 0.1565 0.1974 3.1253 3.2915| | 23: 1.27 - 1.26 1.00 2802 156 0.1651 0.1782 3.1339 3.1973| | 24: 1.26 - 1.24 1.00 2744 132 0.1713 0.1830 3.1285 3.2297| | 25: 1.24 - 1.22 1.00 2733 148 0.1884 0.2149 3.1443 3.263| | 26: 1.22 - 1.21 1.00 2727 135 0.1915 0.1783 3.1521 3.2084| | 27: 1.21 - 1.19 1.00 2814 148 0.2083 0.2168 3.1748 3.163| | 28: 1.19 - 1.18 1.00 2671 147 0.2204 0.2293 3.1679 3.1732| | 29: 1.18 - 1.16 1.00 2800 134 0.2264 0.2394 3.1492 3.233| | 30: 1.16 - 1.15 1.00 2739 148 0.2448 0.2465 3.145 3.1717| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2920 171 0.95 8.63 1.00 0.97 5860.61| | 2: 3.57 - 2.84 2888 124 0.92 12.72 1.01 0.97 5860.61| | 3: 2.83 - 2.48 2820 163 0.89 16.72 0.99 0.97 4898.85| | 4: 2.47 - 2.25 2825 136 0.92 13.66 1.00 0.98 2418.77| | 5: 2.25 - 2.09 2756 127 0.90 15.84 1.01 0.98 2418.77| | 6: 2.09 - 1.97 2846 113 0.92 12.57 1.02 0.98 1401.15| | 7: 1.97 - 1.87 2787 165 0.95 9.56 1.02 0.97 533.25| | 8: 1.87 - 1.79 2789 144 0.92 12.96 0.99 0.97 533.25| | 9: 1.79 - 1.72 2745 138 0.94 10.24 0.98 0.97 297.76| | 10: 1.72 - 1.66 2831 160 0.94 11.32 0.98 0.97 250.60| | 11: 1.66 - 1.61 2712 147 0.93 11.90 0.98 0.97 239.94| | 12: 1.61 - 1.56 2773 144 0.95 8.96 0.99 0.97 139.39| | 13: 1.56 - 1.52 2745 130 0.95 10.52 1.03 0.97 139.39| | 14: 1.52 - 1.48 2803 134 0.94 10.82 1.02 0.98 124.67| | 15: 1.48 - 1.45 2738 128 0.95 9.90 1.02 0.99 97.73| | 16: 1.45 - 1.42 2756 161 0.94 11.05 1.02 0.99 97.73| | 17: 1.42 - 1.39 2785 139 0.95 10.86 1.01 0.99 88.63| | 18: 1.39 - 1.36 2740 179 0.94 11.44 1.01 0.99 83.37| | 19: 1.36 - 1.34 2807 134 0.94 11.79 0.99 0.99 83.37| | 20: 1.34 - 1.32 2696 147 0.94 12.08 0.98 0.97 79.54| | 21: 1.32 - 1.30 2785 112 0.94 12.99 0.98 0.97 79.27| | 22: 1.29 - 1.27 2704 152 0.93 13.57 0.97 0.96 79.72| | 23: 1.27 - 1.26 2802 156 0.92 14.78 0.97 0.95 82.04| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.95 82.04| | 25: 1.24 - 1.22 2733 148 0.91 16.31 0.96 0.94 84.26| | 26: 1.22 - 1.21 2727 135 0.90 18.16 1.03 0.93 86.72| | 27: 1.21 - 1.19 2814 148 0.89 18.81 1.03 0.93 86.72| | 28: 1.19 - 1.18 2671 147 0.88 20.46 1.01 0.93 90.64| | 29: 1.18 - 1.16 2800 134 0.88 20.58 0.99 0.93 92.11| | 30: 1.16 - 1.15 2739 148 0.86 22.11 0.98 0.93 92.11| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.27 max = 5860.61 mean = 905.66| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 13.52| |phase err.(test): min = 0.00 max = 89.76 mean = 13.50| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1140 0.1132 0.1299 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1452 0.1452 0.1492 n_refl.: 87577 remove outliers: r(all,work,free)=0.1452 0.1452 0.1492 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1451 0.1451 0.1492 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1139 0.1131 0.1299 n_refl.: 87577 remove outliers: r(all,work,free)=0.1138 0.1130 0.1299 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3927 293.455 255.260 0.462 1.000 0.314 11.894-9.307 96.08 94 4 0.2341 476.483 464.911 0.854 1.002 0.310 9.237-7.194 97.73 208 7 0.2307 386.123 380.695 0.926 1.002 0.155 7.162-5.571 100.00 427 22 0.2110 296.527 286.798 0.911 1.002 0.140 5.546-4.326 100.00 867 58 0.1113 407.058 402.039 0.967 1.002 0.125 4.315-3.360 100.00 1859 96 0.0915 387.115 385.058 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1103 254.314 252.349 1.011 1.002 0.024 2.608-2.026 99.99 8198 413 0.0913 168.587 167.978 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0891 82.329 82.666 1.035 1.000 0.000 1.573-1.221 99.99 36678 1900 0.1253 36.507 36.117 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 23.003 21.556 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=-0.0167 ================= 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 0.1941 0.085 5.394 8.8 119.3 19.9 258 0.000 1_bss: 0.1637 0.1755 0.085 5.394 9.0 119.5 20.1 258 0.000 1_settarget: 0.1637 0.1755 0.085 5.394 9.0 119.5 20.1 258 0.000 1_nqh: 0.1638 0.1751 0.085 5.394 9.0 119.5 20.1 258 0.006 1_weight: 0.1638 0.1751 0.085 5.394 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1232 0.1467 0.006 0.848 9.0 119.5 20.1 258 0.137 1_adp: 0.1238 0.1464 0.006 0.848 9.1 119.4 20.1 258 0.137 1_regHadp: 0.1239 0.1467 0.006 0.848 9.1 119.4 20.1 258 0.137 1_occ: 0.1231 0.1459 0.006 0.848 9.1 119.4 20.1 258 0.137 2_bss: 0.1229 0.1451 0.006 0.848 9.1 119.5 20.1 258 0.137 2_settarget: 0.1229 0.1451 0.006 0.848 9.1 119.5 20.1 258 0.137 2_updatecdl: 0.1229 0.1451 0.006 0.866 9.1 119.5 20.1 258 0.137 2_nqh: 0.1229 0.1451 0.006 0.866 9.1 119.5 20.1 258 0.137 2_sol: 0.1201 0.1384 0.006 0.866 9.1 115.0 22.2 414 n/a 2_weight: 0.1201 0.1384 0.006 0.866 9.1 115.0 22.2 414 n/a 2_xyzrec: 0.1190 0.1408 0.006 0.850 9.1 115.0 22.2 414 n/a 2_adp: 0.1190 0.1408 0.006 0.850 9.1 115.0 22.2 414 n/a 2_regHadp: 0.1190 0.1408 0.006 0.850 9.1 115.0 22.2 414 n/a 2_occ: 0.1188 0.1410 0.006 0.850 9.1 115.0 22.2 414 n/a 3_bss: 0.1184 0.1402 0.006 0.850 9.1 115.0 22.2 414 n/a 3_settarget: 0.1184 0.1402 0.006 0.850 9.1 115.0 22.2 414 n/a 3_updatecdl: 0.1184 0.1402 0.006 0.849 9.1 115.0 22.2 414 n/a 3_nqh: 0.1184 0.1402 0.006 0.849 9.1 115.0 22.2 414 n/a 3_sol: 0.1213 0.1392 0.006 0.849 9.1 115.0 21.1 439 n/a 3_weight: 0.1213 0.1392 0.006 0.849 9.1 115.0 21.1 439 n/a 3_xyzrec: 0.1159 0.1309 0.008 1.079 9.1 115.0 21.1 439 n/a 3_adp: 0.1159 0.1309 0.008 1.079 9.1 115.0 21.1 439 n/a 3_regHadp: 0.1159 0.1309 0.008 1.079 9.1 115.0 21.1 439 n/a 3_occ: 0.1150 0.1308 0.008 1.079 9.1 115.0 21.1 439 n/a 4_bss: 0.1143 0.1299 0.008 1.079 9.1 115.0 21.1 439 n/a 4_settarget: 0.1143 0.1299 0.008 1.079 9.1 115.0 21.1 439 n/a 4_updatecdl: 0.1143 0.1299 0.008 1.082 9.1 115.0 21.1 439 n/a 4_nqh: 0.1147 0.1300 0.008 1.082 9.1 115.0 21.1 439 n/a 4_sol: 0.1146 0.1309 0.008 1.082 9.1 115.0 21.2 458 n/a 4_weight: 0.1146 0.1309 0.008 1.082 9.1 115.0 21.2 458 n/a 4_xyzrec: 0.1141 0.1308 0.008 1.086 9.1 115.0 21.2 458 n/a 4_adp: 0.1141 0.1308 0.008 1.086 9.1 115.0 21.2 458 n/a 4_regHadp: 0.1141 0.1308 0.008 1.086 9.1 115.0 21.2 458 n/a 4_occ: 0.1136 0.1306 0.008 1.086 9.1 115.0 21.2 458 n/a 5_bss: 0.1134 0.1311 0.008 1.086 9.1 115.0 21.2 458 n/a 5_settarget: 0.1134 0.1311 0.008 1.086 9.1 115.0 21.2 458 n/a 5_updatecdl: 0.1134 0.1311 0.008 1.087 9.1 115.0 21.2 458 n/a 5_setrh: 0.1135 0.1310 0.008 1.087 9.1 115.0 21.2 458 n/a 5_nqh: 0.1135 0.1310 0.008 1.087 9.1 115.0 21.2 458 n/a 5_sol: 0.1135 0.1304 0.008 1.087 9.1 115.0 21.1 451 n/a 5_weight: 0.1135 0.1304 0.008 1.087 9.1 115.0 21.1 451 n/a 5_xyzrec: 0.1136 0.1303 0.007 1.088 9.1 115.0 21.1 451 n/a 5_adp: 0.1137 0.1303 0.007 1.088 9.1 114.9 21.1 451 n/a 5_regHadp: 0.1137 0.1303 0.007 1.088 9.1 114.9 21.1 451 n/a 5_occ: 0.1132 0.1299 0.007 1.088 9.1 114.9 21.1 451 n/a end: 0.1130 0.1299 0.007 1.088 9.1 114.9 21.1 451 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2659048_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2659048_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.8300 Refinement macro-cycles (run) : 13531.2100 Write final files (write_after_run_outputs) : 95.2800 Total : 13629.3200 Total CPU time: 3.79 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:06:23 PST -0800 (1735365983.78 s) Start R-work = 0.1637, R-free = 0.1755 Final R-work = 0.1130, R-free = 0.1299 =============================================================================== Job complete usr+sys time: 13816.98 seconds wall clock time: 250 minutes 46.02 seconds (15046.02 seconds total)