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_1318715.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 { 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_1318715.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1318715.pdb" 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 1 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: 1.31, per 1000 atoms: 0.39 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: 0.31 Conformation dependent library (CDL) restraints added in 107.7 milliseconds Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 622 0.93 - 1.20: 1046 1.20 - 1.47: 791 1.47 - 1.74: 681 1.74 - 2.01: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.233 1.043 0.190 1.08e-02 8.57e+03 3.09e+02 bond pdb=" N ATYR A 67 " pdb=" CA ATYR A 67 " ideal model delta sigma weight residual 1.456 1.245 0.211 1.21e-02 6.83e+03 3.05e+02 bond pdb=" C ILE A 152 " pdb=" N ALEU A 153 " ideal model delta sigma weight residual 1.331 1.557 -0.227 1.34e-02 5.57e+03 2.87e+02 bond pdb=" C BASN A 97 " pdb=" N ARG A 98 " ideal model delta sigma weight residual 1.331 1.102 0.229 1.43e-02 4.89e+03 2.57e+02 bond pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " ideal model delta sigma weight residual 1.378 1.202 0.176 1.10e-02 8.26e+03 2.56e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 3168 4.66 - 9.33: 1865 9.33 - 13.99: 621 13.99 - 18.65: 108 18.65 - 23.31: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH1 ARG A 27 " ideal model delta sigma weight residual 121.50 140.97 -19.47 1.00e+00 1.00e+00 3.79e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.18 137.62 -14.44 1.08e+00 8.57e-01 1.79e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 131.14 -11.94 9.00e-01 1.23e+00 1.76e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.70 107.95 12.75 1.03e+00 9.43e-01 1.53e+02 angle pdb=" O GLU A 170 " pdb=" C GLU A 170 " pdb=" N ALA A 171 " ideal model delta sigma weight residual 122.09 134.96 -12.87 1.08e+00 8.57e-01 1.42e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 924 16.66 - 33.31: 136 33.31 - 49.97: 37 49.97 - 66.62: 11 66.62 - 83.28: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 106 0.225 - 0.450: 78 0.450 - 0.675: 39 0.675 - 0.900: 17 0.900 - 1.124: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 151 " pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CB LEU A 151 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.48 -1.11 2.00e-01 2.50e+01 3.06e+01 chirality pdb=" CB VAL A 169 " pdb=" CA VAL A 169 " pdb=" CG1 VAL A 169 " pdb=" CG2 VAL A 169 " both_signs ideal model delta sigma weight residual False -2.63 -3.59 0.96 2.00e-01 2.50e+01 2.32e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.110 2.00e-02 2.50e+03 6.74e-02 1.36e+02 pdb=" CG PHE A 119 " -0.090 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.131 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.050 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.078 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.048 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.096 2.00e-02 2.50e+03 6.49e-02 1.26e+02 pdb=" CG PHE A 164 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.128 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.110 2.00e-02 2.50e+03 6.12e-02 1.12e+02 pdb=" CG ATYR A 67 " 0.092 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.019 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.091 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.008 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.026 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.085 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.005 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.069 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.042 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.32: 1008 2.32 - 2.89: 8110 2.89 - 3.46: 10496 3.46 - 4.03: 15289 4.03 - 4.60: 21737 Nonbonded interactions: 56640 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.745 1.850 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.745 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.767 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.784 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.832 2.100 ... (remaining 56635 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_1318715_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= 0.2603 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787973 | | target function (ml) not normalized (work): 232254.912907 | | target function (ml) not normalized (free): 11811.889728 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3032 0.2057 7.0844 4.9424| | 2: 3.57 - 2.84 1.00 2876 122 0.2448 0.1810 4.3456 4.3452| | 3: 2.84 - 2.48 1.00 2833 165 0.2358 0.1701 4.1263 4.1635| | 4: 2.47 - 2.25 1.00 2825 136 0.2330 0.1370 3.831 3.8257| | 5: 2.25 - 2.09 1.00 2756 127 0.2477 0.1554 3.7977 3.8087| | 6: 2.09 - 1.97 1.00 2846 113 0.2532 0.1809 3.4558 3.5534| | 7: 1.97 - 1.87 1.00 2787 165 0.2522 0.1774 3.1221 3.1825| | 8: 1.87 - 1.79 1.00 2789 144 0.2459 0.1712 3.0367 3.0563| | 9: 1.79 - 1.72 1.00 2745 138 0.2398 0.1957 2.8872 2.9747| | 10: 1.72 - 1.66 1.00 2789 158 0.2423 0.1957 2.7945 2.9055| | 11: 1.66 - 1.61 1.00 2740 147 0.2505 0.1735 2.7508 2.7003| | 12: 1.61 - 1.56 1.00 2787 146 0.2485 0.2021 2.6105 2.6494| | 13: 1.56 - 1.52 1.00 2745 130 0.2541 0.1830 2.567 2.5714| | 14: 1.52 - 1.48 1.00 2803 134 0.2556 0.1987 2.5057 2.5365| | 15: 1.48 - 1.45 1.00 2738 128 0.2581 0.2295 2.4218 2.5629| | 16: 1.45 - 1.42 1.00 2756 161 0.2679 0.2239 2.3774 2.4428| | 17: 1.42 - 1.39 1.00 2785 139 0.2694 0.2006 2.3389 2.3286| | 18: 1.39 - 1.36 1.00 2741 179 0.2622 0.2525 2.258 2.4199| | 19: 1.36 - 1.34 1.00 2807 134 0.2680 0.2265 2.2502 2.2874| | 20: 1.34 - 1.32 1.00 2696 147 0.2636 0.2189 2.1901 2.206| | 21: 1.32 - 1.30 1.00 2785 112 0.2756 0.2527 2.1675 2.2638| | 22: 1.29 - 1.27 1.00 2704 152 0.2684 0.2638 2.1238 2.2227| | 23: 1.27 - 1.26 1.00 2802 156 0.2738 0.2646 2.1092 2.2182| | 24: 1.26 - 1.24 1.00 2744 132 0.2826 0.2393 2.0887 2.1212| | 25: 1.24 - 1.22 1.00 2734 148 0.2847 0.2473 2.0509 2.0506| | 26: 1.22 - 1.21 1.00 2727 135 0.2805 0.2243 2.0001 2.0746| | 27: 1.21 - 1.19 1.00 2814 148 0.2952 0.2795 2.0083 2.0495| | 28: 1.19 - 1.18 1.00 2671 147 0.2989 0.2757 1.9873 1.9892| | 29: 1.18 - 1.16 1.00 2800 134 0.2923 0.2572 1.9553 1.9777| | 30: 1.16 - 1.15 1.00 2740 148 0.3050 0.2597 1.9389 1.8963| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.80 0.76 0.23 1475.09| | 2: 3.57 - 2.84 2876 122 0.80 26.02 1.28 0.23 1475.09| | 3: 2.84 - 2.48 2833 165 0.74 31.91 1.24 0.24 1222.85| | 4: 2.47 - 2.25 2825 136 0.81 25.49 1.26 0.25 568.25| | 5: 2.25 - 2.09 2756 127 0.77 29.21 1.28 0.25 568.25| | 6: 2.09 - 1.97 2846 113 0.84 22.52 1.29 0.25 309.86| | 7: 1.97 - 1.87 2787 165 0.90 16.55 1.28 0.25 89.49| | 8: 1.87 - 1.79 2789 144 0.86 21.07 1.25 0.25 89.49| | 9: 1.79 - 1.72 2745 138 0.88 18.22 1.23 0.25 54.06| | 10: 1.72 - 1.66 2789 158 0.87 19.95 1.22 0.25 46.97| | 11: 1.66 - 1.61 2740 147 0.86 21.05 1.24 0.25 45.30| | 12: 1.61 - 1.56 2787 146 0.89 18.13 1.23 0.25 28.41| | 13: 1.56 - 1.52 2745 130 0.87 20.02 1.24 0.25 28.41| | 14: 1.52 - 1.48 2803 134 0.87 20.33 1.23 0.25 25.69| | 15: 1.48 - 1.45 2738 128 0.87 20.34 1.23 0.25 20.72| | 16: 1.45 - 1.42 2756 161 0.85 21.86 1.24 0.25 20.72| | 17: 1.42 - 1.39 2785 139 0.86 21.06 1.24 0.25 17.90| | 18: 1.39 - 1.36 2741 179 0.86 21.38 1.23 0.25 16.27| | 19: 1.36 - 1.34 2807 134 0.85 22.17 1.22 0.25 16.27| | 20: 1.34 - 1.32 2696 147 0.86 21.25 1.21 0.25 13.54| | 21: 1.32 - 1.30 2785 112 0.85 22.56 1.21 0.25 13.34| | 22: 1.29 - 1.27 2704 152 0.85 22.72 1.21 0.24 13.00| | 23: 1.27 - 1.26 2802 156 0.86 22.26 1.21 0.24 11.24| | 24: 1.26 - 1.24 2744 132 0.85 23.03 1.21 0.24 11.24| | 25: 1.24 - 1.22 2734 148 0.84 23.68 1.20 0.24 10.46| | 26: 1.22 - 1.21 2727 135 0.85 23.30 1.19 0.23 9.60| | 27: 1.21 - 1.19 2814 148 0.84 24.19 1.20 0.23 9.60| | 28: 1.19 - 1.18 2671 147 0.84 23.92 1.19 0.23 8.56| | 29: 1.18 - 1.16 2800 134 0.84 23.79 1.16 0.23 8.18| | 30: 1.16 - 1.15 2740 148 0.83 25.29 1.15 0.23 8.18| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 8.18 max = 1475.09 mean = 213.73| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.41| |phase err.(test): min = 0.00 max = 89.51 mean = 22.23| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.261 1557 Z= 5.359 Angle : 5.264 19.467 2118 Z= 3.738 Chirality : 0.385 1.124 243 Planarity : 0.031 0.082 284 Dihedral : 13.552 83.279 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 2.48 % Allowed : 2.48 % Favored : 95.03 % Cbeta Deviations : 31.89 % 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: -2.42 (0.45), residues: 224 helix: -2.45 (0.36), residues: 108 sheet: -0.48 (0.90), residues: 28 loop : -0.50 (0.54), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.018 ARG A 98 TYR 0.107 0.039 TYR A 141 PHE 0.096 0.035 PHE A 119 HIS 0.067 0.035 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2603 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787973 | | target function (ml) not normalized (work): 232254.912907 | | target function (ml) not normalized (free): 11811.889728 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2562 0.2604 0.1935 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2562 0.2604 0.1935 n_refl.: 87602 remove outliers: r(all,work,free)=0.1976 0.1980 0.1935 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2000 0.2005 0.1947 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1636 0.1630 0.1760 n_refl.: 87594 remove outliers: r(all,work,free)=0.1636 0.1629 0.1760 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 0.3812 386.293 357.265 0.726 0.914 0.407 11.894-9.307 99.02 97 4 0.1816 613.608 594.543 1.013 0.915 0.385 9.237-7.194 100.00 213 7 0.2171 501.856 490.119 1.054 0.916 0.369 7.162-5.571 100.00 427 22 0.2204 376.615 364.246 1.015 0.916 0.302 5.546-4.326 100.00 867 58 0.1289 517.000 511.348 1.052 0.917 0.229 4.315-3.360 100.00 1859 96 0.1149 491.670 487.816 1.098 0.918 0.209 3.356-2.611 100.00 3867 181 0.1439 323.002 319.803 1.085 0.920 0.057 2.608-2.026 99.99 8198 413 0.1357 214.121 211.917 1.092 0.923 0.000 2.025-1.573 100.00 17313 902 0.1613 104.565 103.981 1.088 0.929 0.000 1.573-1.221 100.00 36679 1900 0.2055 46.369 45.122 1.068 0.937 0.000 1.221-1.150 99.97 13689 708 0.2575 29.215 27.057 1.028 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0463 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1629 r_free=0.1760 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 80 GLN A A 180 GLN Total number of N/Q/H flips: 4 r_work=0.1640 r_free=0.1765 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.230978 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2014.701198 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 0.1836 0.0118 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1558 0.1700 0.0142 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1458 0.1631 0.0174 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1406 0.1602 0.0196 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1358 0.1564 0.0206 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1353 0.1562 0.0208 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1292 0.1511 0.0219 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1268 0.1498 0.0230 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1259 0.1494 0.0236 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1249 0.1483 0.0234 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1239 0.1473 0.0234 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1238 0.1474 0.0236 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1236 0.1475 0.0239 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1232 0.1472 0.0240 0.006 0.8 3.2 0.5 0.0 0 9.000 0.1230 0.1471 0.0241 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1228 0.1473 0.0245 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1226 0.1473 0.0247 0.007 0.9 4.2 0.5 0.6 0 12.000 0.1224 0.1477 0.0253 0.007 0.9 4.2 0.5 0.6 0 13.115 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1230 0.1471 0.0241 0.006 0.9 3.8 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 14.71 2.41 3.013 19.061 2014.701 0.017 12.30 14.70 2.41 2.995 19.061 60.441 0.017 12.36 14.69 2.32 2.655 19.060 251.838 0.017 12.71 15.39 2.67 2.760 19.226 1007.351 0.017 12.57 15.54 2.97 3.198 19.542 2014.701 0.016 12.45 15.50 3.05 3.366 19.658 3022.052 0.015 12.33 15.44 3.10 3.333 19.625 4029.402 0.015 12.26 15.39 3.13 3.321 19.610 5036.753 0.015 12.15 15.29 3.14 3.306 19.610 6044.104 0.015 12.22 15.44 3.22 3.366 19.627 7051.454 0.015 12.20 15.48 3.28 3.366 19.621 8058.805 0.015 12.19 15.48 3.29 3.493 19.683 9066.155 0.015 12.19 15.53 3.34 3.531 19.689 10073.506 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: 251.838 Accepted refinement result: 12.36 14.69 2.32 2.655 19.060 251.838 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.44 20.09 3.28 0 1785 Protein: 9.06 114.86 17.00 3.29 0 1519 Water: 11.46 119.44 38.23 N/A 0 258 Other: 19.74 26.60 22.07 N/A 0 8 Chain A: 9.06 119.44 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1271 20.10 - 31.14 228 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 - 97.37 4 97.37 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1469 r_work=0.1238 r_free=0.1473 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1473 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 = 0.1463 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.26 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= 0.1463 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016875 | | target function (ls_wunit_k1) not normalized (work): 1405.602760 | | target function (ls_wunit_k1) not normalized (free): 109.356790 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1241 0.1230 0.1463 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1675 0.1677 0.1696 n_refl.: 87593 remove outliers: r(all,work,free)=0.1675 0.1677 0.1696 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1681 0.1682 0.1700 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1230 0.1455 n_refl.: 87593 remove outliers: r(all,work,free)=0.1240 0.1229 0.1455 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3565 301.332 281.021 0.644 1.002 0.373 11.894-9.307 99.02 97 4 0.1654 482.718 471.667 0.923 1.003 0.368 9.237-7.194 100.00 213 7 0.1911 394.804 388.542 0.966 1.003 0.340 7.162-5.571 100.00 427 22 0.1818 296.278 290.561 0.936 1.003 0.263 5.546-4.326 100.00 867 58 0.0994 406.717 404.022 0.964 1.003 0.209 4.315-3.360 100.00 1859 96 0.0873 386.791 385.716 1.009 1.002 0.190 3.356-2.611 100.00 3867 181 0.1178 254.101 252.991 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1025 168.446 167.708 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1117 82.260 82.442 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1451 36.478 35.979 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2252 22.983 21.470 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0489 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1455 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** A 80 GLN A A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1227 r_free=0.1453 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1453 | n_water=258 | time (s): 2.160 (total time: 2.160) Filter (dist) r_work=0.1237 r_free=0.1450 | n_water=251 | time (s): 19.710 (total time: 21.870) Filter (q & B) r_work=0.1239 r_free=0.1451 | n_water=248 | time (s): 2.890 (total time: 24.760) Compute maps r_work=0.1239 r_free=0.1451 | n_water=248 | time (s): 1.230 (total time: 25.990) Filter (map) r_work=0.1252 r_free=0.1453 | n_water=227 | time (s): 2.530 (total time: 28.520) Find peaks r_work=0.1252 r_free=0.1453 | n_water=227 | time (s): 0.450 (total time: 28.970) Add new water r_work=0.1398 r_free=0.1626 | n_water=435 | time (s): 2.460 (total time: 31.430) Refine new water occ: r_work=0.1305 r_free=0.1481 adp: r_work=0.1225 r_free=0.1430 occ: r_work=0.1235 r_free=0.1413 adp: r_work=0.1204 r_free=0.1403 occ: r_work=0.1207 r_free=0.1395 adp: r_work=0.1197 r_free=0.1393 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1393 r_work=0.1197 r_free=0.1393 | n_water=435 | time (s): 51.160 (total time: 82.590) Filter (q & B) r_work=0.1200 r_free=0.1396 | n_water=417 | time (s): 3.190 (total time: 85.780) Filter (dist only) r_work=0.1200 r_free=0.1395 | n_water=416 | time (s): 35.010 (total time: 120.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.936901 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1481.397678 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 0.1644 0.1759 0.0115 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1524 0.1657 0.0132 0.001 0.4 7.4 0.0 0.0 0 0.250 0.1416 0.1569 0.0153 0.002 0.4 6.4 0.0 0.0 0 0.500 0.1368 0.1534 0.0166 0.001 0.4 5.4 0.0 0.0 0 0.750 0.1306 0.1476 0.0170 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1312 0.1487 0.0175 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1254 0.1451 0.0197 0.002 0.5 5.1 0.5 0.0 0 2.000 0.1227 0.1436 0.0209 0.003 0.6 5.4 0.5 0.0 0 3.000 0.1212 0.1428 0.0215 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1207 0.1428 0.0221 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1203 0.1421 0.0218 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1200 0.1420 0.0220 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1200 0.1433 0.0233 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1194 0.1419 0.0225 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1190 0.1420 0.0229 0.006 0.9 5.4 0.5 0.0 0 10.000 0.1189 0.1421 0.0232 0.007 0.9 5.4 0.5 0.0 0 11.000 0.1188 0.1420 0.0233 0.007 0.9 6.4 0.5 0.0 0 12.000 0.1185 0.1423 0.0238 0.008 0.9 5.4 0.5 0.0 0 13.968 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1419 0.0225 0.006 0.8 5.1 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 14.19 2.25 3.764 21.778 1481.398 0.016 11.94 14.19 2.25 3.764 21.778 44.442 0.016 11.94 14.19 2.25 3.764 21.778 185.175 0.016 12.17 14.62 2.46 3.616 21.785 740.699 0.016 12.11 14.87 2.76 3.551 21.846 1481.398 0.015 11.92 14.79 2.87 3.431 22.102 2222.097 0.014 11.87 14.81 2.95 3.485 21.967 2962.795 0.014 11.82 14.76 2.94 3.480 22.116 3703.494 0.014 11.81 14.89 3.07 3.504 22.221 4444.193 0.014 11.76 14.80 3.04 3.514 22.192 5184.892 0.014 11.70 14.78 3.08 3.511 22.063 5925.591 0.014 11.66 14.72 3.06 3.522 22.047 6666.290 0.014 11.73 14.95 3.22 3.611 22.285 7406.988 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: 185.175 Accepted refinement result: 11.94 14.19 2.25 3.764 21.778 185.175 0.016 Individual atomic B min max mean iso aniso Overall: 9.09 114.90 22.19 3.28 189 1754 Protein: 9.09 114.90 17.03 3.29 0 1519 Water: 11.50 76.69 41.03 N/A 189 227 Other: 19.77 26.63 22.10 N/A 0 8 Chain A: 9.09 114.90 19.48 N/A 0 1754 Chain S: 14.78 60.00 47.32 N/A 189 0 Histogram: Values Number of atoms 9.09 - 19.67 1257 19.67 - 30.26 244 30.26 - 40.84 171 40.84 - 51.42 122 51.42 - 62.00 126 62.00 - 72.58 11 72.58 - 83.16 6 83.16 - 93.74 4 93.74 - 104.32 0 104.32 - 114.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1419 r_work=0.1194 r_free=0.1419 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1419 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1416 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1195 r_free= 0.1416 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015286 | | target function (ls_wunit_k1) not normalized (work): 1273.249016 | | target function (ls_wunit_k1) not normalized (free): 106.035589 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1195 0.1416 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1590 0.1588 0.1656 n_refl.: 87592 remove outliers: r(all,work,free)=0.1590 0.1588 0.1656 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1591 0.1589 0.1657 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1192 0.1411 n_refl.: 87592 remove outliers: r(all,work,free)=0.1202 0.1191 0.1411 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 0.3332 303.336 275.430 0.601 1.003 0.360 11.894-9.307 99.02 97 4 0.1598 482.718 475.521 0.920 1.003 0.319 9.237-7.194 100.00 213 7 0.1776 394.804 393.516 0.982 1.003 0.280 7.162-5.571 100.00 427 22 0.1590 296.278 291.257 0.936 1.003 0.230 5.546-4.326 100.00 867 58 0.0901 406.717 403.258 0.962 1.003 0.220 4.315-3.360 100.00 1859 96 0.0783 386.791 385.648 1.005 1.003 0.200 3.356-2.611 100.00 3867 181 0.1095 254.101 253.042 1.009 1.002 0.130 2.608-2.026 99.99 8198 413 0.1018 168.446 167.886 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1106 82.260 82.470 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1448 36.478 36.014 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 22.983 21.504 0.988 0.995 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=0.1191 r_free=0.1411 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1411 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1411 | n_water=416 | time (s): 1.950 (total time: 1.950) Filter (dist) r_work=0.1192 r_free=0.1411 | n_water=414 | time (s): 33.230 (total time: 35.180) Filter (q & B) r_work=0.1192 r_free=0.1411 | n_water=414 | time (s): 0.900 (total time: 36.080) Compute maps r_work=0.1192 r_free=0.1411 | n_water=414 | time (s): 1.400 (total time: 37.480) Filter (map) r_work=0.1233 r_free=0.1398 | n_water=282 | time (s): 2.480 (total time: 39.960) Find peaks r_work=0.1233 r_free=0.1398 | n_water=282 | time (s): 0.540 (total time: 40.500) Add new water r_work=0.1345 r_free=0.1536 | n_water=464 | time (s): 2.940 (total time: 43.440) Refine new water occ: r_work=0.1252 r_free=0.1447 adp: r_work=0.1254 r_free=0.1449 occ: r_work=0.1231 r_free=0.1421 adp: r_work=0.1231 r_free=0.1423 occ: r_work=0.1215 r_free=0.1401 adp: r_work=0.1211 r_free=0.1399 ADP+occupancy (water only), MIN, final r_work=0.1211 r_free=0.1399 r_work=0.1211 r_free=0.1399 | n_water=464 | time (s): 158.410 (total time: 201.850) Filter (q & B) r_work=0.1218 r_free=0.1403 | n_water=427 | time (s): 2.520 (total time: 204.370) Filter (dist only) r_work=0.1218 r_free=0.1402 | n_water=426 | time (s): 35.370 (total time: 239.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.779617 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.794784 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 0.1240 0.1374 0.0134 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1197 0.1341 0.0144 0.003 0.7 3.8 0.5 0.0 0 0.267 0.1179 0.1331 0.0152 0.004 0.8 3.5 0.5 0.0 0 0.534 0.1173 0.1328 0.0155 0.005 0.9 3.2 0.5 0.0 0 0.801 0.1169 0.1329 0.0160 0.006 1.0 3.5 0.5 0.0 0 1.068 0.1166 0.1326 0.0160 0.007 1.0 3.5 0.5 0.0 0 1.335 0.1164 0.1327 0.0163 0.007 1.1 4.5 0.5 0.0 0 1.602 0.1162 0.1327 0.0165 0.008 1.1 4.8 0.5 0.0 0 1.869 0.1170 0.1328 0.0159 0.005 0.9 3.2 0.5 0.0 0 0.890 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1166 0.1326 0.0160 0.007 1.0 3.5 0.5 0.0 0 1.335 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.66 13.26 1.60 3.767 21.200 48.795 3.624 11.66 13.26 1.60 3.767 21.200 1.464 3.624 11.66 13.26 1.60 3.752 21.200 6.099 3.624 11.67 13.33 1.66 3.712 21.194 24.397 3.617 11.69 13.42 1.72 3.735 21.153 48.795 3.616 11.65 13.41 1.76 3.750 21.138 73.192 3.611 11.61 13.40 1.79 3.765 21.133 97.590 3.607 11.57 13.39 1.83 3.781 21.123 121.987 3.604 11.55 13.40 1.86 3.798 21.113 146.384 3.603 11.53 13.38 1.85 3.808 21.107 170.782 3.600 11.53 13.40 1.87 3.821 21.102 195.179 3.600 11.50 13.36 1.86 3.822 21.107 219.577 3.598 11.49 13.34 1.85 3.833 21.099 243.974 3.597 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.464 Accepted refinement result: 11.66 13.26 1.60 3.767 21.200 1.464 3.624 Individual atomic B min max mean iso aniso Overall: 9.10 114.90 21.12 3.28 205 1748 Protein: 9.10 114.90 17.04 3.29 0 1519 Water: 11.50 76.70 35.68 N/A 205 221 Other: 19.78 26.64 22.11 N/A 0 8 Chain A: 9.10 114.90 19.39 N/A 0 1748 Chain S: 14.79 60.01 35.90 N/A 205 0 Histogram: Values Number of atoms 9.10 - 19.68 1262 19.68 - 30.26 286 30.26 - 40.84 208 40.84 - 51.42 122 51.42 - 62.00 52 62.00 - 72.58 11 72.58 - 83.16 6 83.16 - 93.74 4 93.74 - 104.32 0 104.32 - 114.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1166 r_free=0.1326 r_work=0.1166 r_free=0.1326 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1166 r_free = 0.1326 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1158 r_free = 0.1323 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1158 r_free= 0.1323 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.617675 | | target function (ml) not normalized (work): 301334.245683 | | target function (ml) not normalized (free): 15857.361336 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1166 0.1158 0.1323 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1502 0.1502 0.1543 n_refl.: 87591 remove outliers: r(all,work,free)=0.1502 0.1502 0.1543 n_refl.: 87591 overall B=-0.01 to atoms: r(all,work,free)=0.1501 0.1501 0.1542 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1161 0.1153 0.1314 n_refl.: 87591 remove outliers: r(all,work,free)=0.1159 0.1151 0.1314 n_refl.: 87585 ======================== 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 0.3929 297.238 275.486 0.501 1.000 0.302 11.894-9.307 97.06 95 4 0.2362 482.942 464.033 0.877 1.002 0.290 9.237-7.194 99.09 211 7 0.2390 389.302 386.352 0.953 1.002 0.200 7.162-5.571 100.00 427 22 0.2114 296.278 285.796 0.923 1.002 0.185 5.546-4.326 100.00 867 58 0.1128 406.717 401.930 0.964 1.002 0.170 4.315-3.360 100.00 1859 96 0.0946 386.791 384.347 1.005 1.002 0.160 3.356-2.611 100.00 3867 181 0.1140 254.101 252.040 1.008 1.002 0.034 2.608-2.026 99.99 8198 413 0.0937 168.446 167.657 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0903 82.260 82.570 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1260 36.478 36.069 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2167 22.983 21.528 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0152 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1151 r_free=0.1314 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=0.1155 r_free=0.1316 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1155 r_free=0.1316 | n_water=426 | time (s): 2.290 (total time: 2.290) Filter (dist) r_work=0.1155 r_free=0.1317 | n_water=424 | time (s): 46.240 (total time: 48.530) Filter (q & B) r_work=0.1156 r_free=0.1317 | n_water=422 | time (s): 3.760 (total time: 52.290) Compute maps r_work=0.1156 r_free=0.1317 | n_water=422 | time (s): 1.800 (total time: 54.090) Filter (map) r_work=0.1184 r_free=0.1305 | n_water=312 | time (s): 3.760 (total time: 57.850) Find peaks r_work=0.1184 r_free=0.1305 | n_water=312 | time (s): 0.730 (total time: 58.580) Add new water r_work=0.1259 r_free=0.1386 | n_water=489 | time (s): 3.690 (total time: 62.270) Refine new water occ: r_work=0.1179 r_free=0.1327 adp: r_work=0.1180 r_free=0.1328 occ: r_work=0.1162 r_free=0.1307 adp: r_work=0.1162 r_free=0.1307 occ: r_work=0.1150 r_free=0.1294 adp: r_work=0.1146 r_free=0.1293 ADP+occupancy (water only), MIN, final r_work=0.1146 r_free=0.1293 r_work=0.1146 r_free=0.1293 | n_water=489 | time (s): 226.140 (total time: 288.410) Filter (q & B) r_work=0.1155 r_free=0.1300 | n_water=444 | time (s): 4.090 (total time: 292.500) Filter (dist only) r_work=0.1155 r_free=0.1300 | n_water=442 | time (s): 47.900 (total time: 340.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.776697 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.006153 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 0.1212 0.1343 0.0130 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1174 0.1314 0.0139 0.003 0.7 3.5 0.5 0.0 0 0.267 0.1160 0.1305 0.0144 0.004 0.9 3.8 0.5 0.0 0 0.533 0.1154 0.1301 0.0146 0.006 0.9 3.5 0.5 0.0 0 0.800 0.1150 0.1299 0.0149 0.006 1.0 3.8 0.5 0.0 0 1.066 0.1147 0.1299 0.0151 0.007 1.1 3.8 0.5 0.0 0 1.333 0.1145 0.1297 0.0152 0.008 1.1 4.2 0.5 0.0 0 1.599 0.1144 0.1294 0.0150 0.009 1.1 4.5 0.5 0.0 0 1.866 0.1153 0.1300 0.0147 0.006 1.0 3.5 0.5 0.0 0 0.888 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1144 0.1294 0.0150 0.009 1.1 4.5 0.5 0.0 0 1.866 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.44 12.94 1.50 3.768 21.203 45.006 3.608 11.44 12.94 1.50 3.768 21.203 1.350 3.608 11.44 12.94 1.50 3.768 21.203 5.626 3.608 11.48 13.00 1.52 3.705 21.192 22.503 3.603 11.54 13.11 1.57 3.728 21.159 45.006 3.605 11.48 13.07 1.59 3.746 21.148 67.509 3.599 11.40 13.00 1.60 3.766 21.148 90.012 3.594 11.37 12.97 1.61 3.773 21.148 112.515 3.591 11.36 12.99 1.63 3.789 21.138 135.018 3.590 11.36 13.03 1.67 3.808 21.127 157.522 3.590 11.34 13.01 1.67 3.817 21.123 180.025 3.588 11.32 12.99 1.67 3.824 21.121 202.528 3.587 11.30 12.97 1.67 3.825 21.124 225.031 3.586 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.350 Accepted refinement result: 11.44 12.94 1.50 3.768 21.203 1.350 3.608 Individual atomic B min max mean iso aniso Overall: 9.10 114.90 21.13 3.28 223 1746 Protein: 9.10 114.90 17.03 3.29 0 1519 Water: 11.50 76.70 35.21 N/A 223 219 Other: 19.77 26.64 22.11 N/A 0 8 Chain A: 9.10 114.90 19.36 N/A 0 1746 Chain S: 14.79 60.00 34.98 N/A 223 0 Histogram: Values Number of atoms 9.10 - 19.68 1263 19.68 - 30.26 294 30.26 - 40.84 219 40.84 - 51.42 119 51.42 - 62.00 51 62.00 - 72.58 11 72.58 - 83.16 6 83.16 - 93.74 4 93.74 - 104.32 0 104.32 - 114.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1144 r_free=0.1294 r_work=0.1144 r_free=0.1294 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1144 r_free = 0.1294 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1137 r_free = 0.1292 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87585 (all), 4.90 % free)------------| | | | r_work= 0.1137 r_free= 0.1292 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605161 | | target function (ml) not normalized (work): 300270.247872 | | target function (ml) not normalized (free): 15812.783676 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1145 0.1137 0.1292 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1466 0.1465 0.1511 n_refl.: 87585 remove outliers: r(all,work,free)=0.1466 0.1465 0.1511 n_refl.: 87585 overall B=-0.01 to atoms: r(all,work,free)=0.1465 0.1464 0.1510 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1144 0.1136 0.1295 n_refl.: 87585 remove outliers: r(all,work,free)=0.1140 0.1132 0.1295 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 0.3858 293.209 258.453 0.451 0.999 0.292 11.894-9.307 95.10 93 4 0.2374 479.992 469.517 0.866 1.001 0.280 9.237-7.194 97.73 208 7 0.2401 385.800 382.839 0.933 1.001 0.190 7.162-5.571 100.00 427 22 0.2167 296.278 285.569 0.915 1.002 0.167 5.546-4.326 100.00 867 58 0.1123 406.717 402.069 0.964 1.002 0.124 4.315-3.360 100.00 1859 96 0.0919 386.791 384.669 1.004 1.002 0.103 3.356-2.611 100.00 3867 181 0.1112 254.101 252.258 1.010 1.002 0.029 2.608-2.026 99.99 8198 413 0.0912 168.446 167.743 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.260 82.581 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.478 36.074 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2169 22.983 21.523 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0145 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1132 r_free=0.1295 After: r_work=0.1134 r_free=0.1295 ================================== NQH flips ================================== r_work=0.1134 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=0.1134 r_free=0.1295 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1134 r_free=0.1295 | n_water=442 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1134 r_free=0.1295 | n_water=442 | time (s): 45.820 (total time: 48.170) Filter (q & B) r_work=0.1134 r_free=0.1295 | n_water=441 | time (s): 3.960 (total time: 52.130) Compute maps r_work=0.1134 r_free=0.1295 | n_water=441 | time (s): 1.820 (total time: 53.950) Filter (map) r_work=0.1160 r_free=0.1304 | n_water=340 | time (s): 3.970 (total time: 57.920) Find peaks r_work=0.1160 r_free=0.1304 | n_water=340 | time (s): 0.700 (total time: 58.620) Add new water r_work=0.1210 r_free=0.1350 | n_water=479 | time (s): 3.690 (total time: 62.310) Refine new water occ: r_work=0.1153 r_free=0.1291 adp: r_work=0.1153 r_free=0.1293 occ: r_work=0.1142 r_free=0.1276 adp: r_work=0.1141 r_free=0.1280 occ: r_work=0.1133 r_free=0.1264 adp: r_work=0.1130 r_free=0.1266 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1266 r_work=0.1130 r_free=0.1266 | n_water=479 | time (s): 224.610 (total time: 286.920) Filter (q & B) r_work=0.1136 r_free=0.1277 | n_water=449 | time (s): 3.940 (total time: 290.860) Filter (dist only) r_work=0.1136 r_free=0.1277 | n_water=447 | time (s): 47.750 (total time: 338.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.764233 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.942817 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 0.1218 0.1331 0.0113 0.003 0.7 6.1 0.0 0.0 0 0.088 0.1167 0.1296 0.0129 0.004 0.8 5.8 0.0 0.0 0 0.265 0.1151 0.1286 0.0135 0.005 0.9 5.4 0.5 0.0 0 0.529 0.1143 0.1281 0.0138 0.006 1.0 5.1 0.5 0.0 0 0.794 0.1140 0.1279 0.0139 0.007 1.1 5.1 0.5 0.0 0 1.059 0.1138 0.1278 0.0140 0.008 1.1 5.4 0.5 0.0 0 1.323 0.1136 0.1277 0.0141 0.008 1.1 5.4 0.5 0.0 0 1.588 0.1136 0.1277 0.0141 0.009 1.1 5.4 0.5 0.0 0 1.852 0.1142 0.1280 0.0138 0.006 1.0 5.1 0.5 0.0 0 0.882 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1136 0.1277 0.0141 0.008 1.1 5.4 0.5 0.0 0 1.588 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.36 12.77 1.41 3.767 21.197 38.943 3.604 11.36 12.77 1.41 3.767 21.197 1.168 3.604 11.36 12.77 1.41 3.767 21.197 4.868 3.604 11.39 12.81 1.42 3.703 21.190 19.471 3.599 11.49 12.98 1.49 3.717 21.159 38.943 3.604 11.36 12.89 1.53 3.747 21.152 58.414 3.595 11.34 12.89 1.54 3.759 21.145 77.886 3.592 11.33 12.88 1.56 3.767 21.142 97.357 3.590 11.30 12.87 1.57 3.781 21.137 116.828 3.588 11.29 12.90 1.61 3.797 21.128 136.300 3.587 11.28 12.90 1.62 3.808 21.122 155.771 3.586 11.25 12.87 1.62 3.814 21.124 175.243 3.584 11.24 12.85 1.61 3.821 21.123 194.714 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.168 Accepted refinement result: 11.36 12.77 1.41 3.767 21.197 1.168 3.604 Individual atomic B min max mean iso aniso Overall: 9.09 114.89 21.13 3.28 228 1746 Protein: 9.09 114.89 17.02 3.29 0 1519 Water: 11.49 76.69 35.05 N/A 228 219 Other: 19.77 26.63 22.10 N/A 0 8 Chain A: 9.09 114.89 19.36 N/A 0 1746 Chain S: 14.78 60.00 34.68 N/A 228 0 Histogram: Values Number of atoms 9.09 - 19.67 1262 19.67 - 30.25 294 30.25 - 40.83 227 40.83 - 51.41 124 51.41 - 61.99 44 61.99 - 72.57 11 72.57 - 83.15 6 83.15 - 93.73 4 93.73 - 104.31 0 104.31 - 114.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1136 r_free=0.1277 r_work=0.1136 r_free=0.1277 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1136 r_free = 0.1277 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1133 r_free = 0.1274 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1133 r_free= 0.1274 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.602316 | | target function (ml) not normalized (work): 300000.866423 | | target function (ml) not normalized (free): 15794.160657 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1344 0.1316 5.6583 5.5926| | 2: 3.57 - 2.84 1.00 2888 124 0.1059 0.1353 5.1553 5.2185| | 3: 2.83 - 2.48 1.00 2820 163 0.1104 0.1189 4.9384 4.9687| | 4: 2.47 - 2.25 1.00 2825 136 0.0888 0.0987 4.6156 4.6488| | 5: 2.25 - 2.09 1.00 2756 127 0.0861 0.0924 4.5641 4.606| | 6: 2.09 - 1.97 1.00 2846 113 0.0853 0.1002 4.2628 4.3631| | 7: 1.97 - 1.87 1.00 2787 165 0.0884 0.1129 3.9747 4.0889| | 8: 1.87 - 1.79 1.00 2789 144 0.0911 0.1059 3.8818 3.9737| | 9: 1.79 - 1.72 1.00 2745 138 0.0873 0.1164 3.6407 3.8112| | 10: 1.72 - 1.66 1.00 2831 160 0.0919 0.1178 3.5583 3.696| | 11: 1.66 - 1.61 1.00 2712 147 0.0874 0.1034 3.4912 3.5702| | 12: 1.61 - 1.56 1.00 2773 144 0.0907 0.1146 3.3275 3.4635| | 13: 1.56 - 1.52 1.00 2745 130 0.0951 0.1059 3.3072 3.408| | 14: 1.52 - 1.48 1.00 2803 134 0.0983 0.1059 3.2391 3.3173| | 15: 1.48 - 1.45 1.00 2738 128 0.1008 0.1238 3.1543 3.2735| | 16: 1.45 - 1.42 1.00 2756 161 0.1054 0.1235 3.1356 3.2319| | 17: 1.42 - 1.39 1.00 2785 139 0.1139 0.1304 3.1183 3.2301| | 18: 1.39 - 1.36 1.00 2741 179 0.1201 0.1319 3.1073 3.2336| | 19: 1.36 - 1.34 1.00 2807 134 0.1266 0.1564 3.1144 3.2712| | 20: 1.34 - 1.32 1.00 2696 147 0.1372 0.1465 3.1145 3.1518| | 21: 1.32 - 1.30 1.00 2785 112 0.1471 0.1517 3.1143 3.1114| | 22: 1.29 - 1.27 1.00 2704 152 0.1566 0.1972 3.1251 3.2921| | 23: 1.27 - 1.26 1.00 2802 156 0.1651 0.1788 3.135 3.2021| | 24: 1.26 - 1.24 1.00 2744 132 0.1708 0.1840 3.1272 3.2268| | 25: 1.24 - 1.22 1.00 2733 148 0.1885 0.2151 3.1438 3.2592| | 26: 1.22 - 1.21 1.00 2727 135 0.1911 0.1774 3.1496 3.2052| | 27: 1.21 - 1.19 1.00 2814 148 0.2077 0.2176 3.1726 3.1657| | 28: 1.19 - 1.18 1.00 2671 147 0.2205 0.2296 3.1668 3.1729| | 29: 1.18 - 1.16 1.00 2800 134 0.2267 0.2396 3.1488 3.2337| | 30: 1.16 - 1.15 1.00 2739 148 0.2449 0.2449 3.1437 3.168| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2918 171 0.95 8.30 1.00 0.97 5568.96| | 2: 3.57 - 2.84 2888 124 0.93 12.28 1.01 0.97 5568.96| | 3: 2.83 - 2.48 2820 163 0.90 16.25 0.99 0.97 4653.48| | 4: 2.47 - 2.25 2825 136 0.92 13.28 1.00 0.98 2292.75| | 5: 2.25 - 2.09 2756 127 0.90 15.40 1.01 0.98 2292.75| | 6: 2.09 - 1.97 2846 113 0.93 12.18 1.02 0.98 1326.32| | 7: 1.97 - 1.87 2787 165 0.95 9.17 1.02 0.97 502.09| | 8: 1.87 - 1.79 2789 144 0.93 12.53 1.00 0.97 502.09| | 9: 1.79 - 1.72 2745 138 0.95 9.92 0.98 0.97 284.29| | 10: 1.72 - 1.66 2831 160 0.94 11.01 0.98 0.97 240.67| | 11: 1.66 - 1.61 2712 147 0.94 11.60 0.98 0.97 230.70| | 12: 1.61 - 1.56 2773 144 0.96 8.85 0.99 0.97 136.60| | 13: 1.56 - 1.52 2745 130 0.95 10.36 1.03 0.97 136.60| | 14: 1.52 - 1.48 2803 134 0.94 10.70 1.02 0.98 122.80| | 15: 1.48 - 1.45 2738 128 0.95 9.89 1.02 0.98 97.52| | 16: 1.45 - 1.42 2756 161 0.94 11.04 1.02 0.98 97.52| | 17: 1.42 - 1.39 2785 139 0.95 10.90 1.01 0.98 88.96| | 18: 1.39 - 1.36 2741 179 0.94 11.53 1.01 0.98 84.01| | 19: 1.36 - 1.34 2807 134 0.94 11.84 1.00 0.98 84.01| | 20: 1.34 - 1.32 2696 147 0.94 12.14 0.98 0.96 80.17| | 21: 1.32 - 1.30 2785 112 0.94 13.11 0.98 0.96 79.90| | 22: 1.29 - 1.27 2704 152 0.93 13.66 0.98 0.96 80.31| | 23: 1.27 - 1.26 2802 156 0.92 14.87 0.97 0.94 82.43| | 24: 1.26 - 1.24 2744 132 0.92 14.88 0.96 0.94 82.43| | 25: 1.24 - 1.22 2733 148 0.91 16.39 0.96 0.94 84.47| | 26: 1.22 - 1.21 2727 135 0.90 18.15 1.02 0.93 86.73| | 27: 1.21 - 1.19 2814 148 0.89 18.81 1.02 0.93 86.73| | 28: 1.19 - 1.18 2671 147 0.88 20.45 1.01 0.93 90.43| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.92 91.83| | 30: 1.16 - 1.15 2739 148 0.86 22.10 0.98 0.92 91.83| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.90 max = 5568.96 mean = 862.58| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.96 mean = 13.39| |phase err.(test): min = 0.00 max = 87.18 mean = 13.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1140 0.1133 0.1274 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1452 0.1452 0.1487 n_refl.: 87576 remove outliers: r(all,work,free)=0.1452 0.1452 0.1487 n_refl.: 87576 overall B=-0.00 to atoms: r(all,work,free)=0.1452 0.1451 0.1487 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1140 0.1133 0.1276 n_refl.: 87576 remove outliers: r(all,work,free)=0.1139 0.1132 0.1276 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4090 293.209 253.393 0.448 1.000 0.310 11.894-9.307 93.14 91 4 0.2258 484.050 461.830 0.850 1.002 0.310 9.237-7.194 97.73 208 7 0.2426 385.800 381.463 0.922 1.002 0.162 7.162-5.571 100.00 427 22 0.2170 296.278 285.398 0.907 1.003 0.120 5.546-4.326 100.00 867 58 0.1129 406.717 402.266 0.962 1.003 0.110 4.315-3.360 100.00 1859 96 0.0916 386.791 384.670 1.003 1.002 0.110 3.356-2.611 100.00 3867 181 0.1106 254.101 252.269 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0905 168.446 167.851 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0888 82.260 82.633 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.478 36.085 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2171 22.983 21.527 0.989 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0087 ================= 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 : 0.2603 0.1934 0.081 5.264 8.8 119.3 19.9 258 0.000 1_bss: 0.1629 0.1760 0.081 5.264 9.0 119.5 20.1 258 0.000 1_settarget: 0.1629 0.1760 0.081 5.264 9.0 119.5 20.1 258 0.000 1_nqh: 0.1640 0.1765 0.081 5.264 9.0 119.5 20.1 258 0.013 1_weight: 0.1640 0.1765 0.081 5.264 9.0 119.5 20.1 258 0.013 1_xyzrec: 0.1230 0.1471 0.006 0.870 9.0 119.5 20.1 258 0.145 1_adp: 0.1236 0.1469 0.006 0.870 9.1 119.4 20.1 258 0.145 1_regHadp: 0.1238 0.1473 0.006 0.870 9.1 119.4 20.1 258 0.145 1_occ: 0.1230 0.1463 0.006 0.870 9.1 119.4 20.1 258 0.145 2_bss: 0.1229 0.1455 0.006 0.870 9.1 119.5 20.1 258 0.145 2_settarget: 0.1229 0.1455 0.006 0.870 9.1 119.5 20.1 258 0.145 2_updatecdl: 0.1229 0.1455 0.006 0.893 9.1 119.5 20.1 258 0.145 2_nqh: 0.1227 0.1453 0.006 0.893 9.1 119.5 20.1 258 0.140 2_sol: 0.1200 0.1395 0.006 0.893 9.1 114.9 22.2 416 n/a 2_weight: 0.1200 0.1395 0.006 0.893 9.1 114.9 22.2 416 n/a 2_xyzrec: 0.1194 0.1419 0.006 0.828 9.1 114.9 22.2 416 n/a 2_adp: 0.1194 0.1419 0.006 0.828 9.1 114.9 22.2 416 n/a 2_regHadp: 0.1194 0.1419 0.006 0.828 9.1 114.9 22.2 416 n/a 2_occ: 0.1195 0.1416 0.006 0.828 9.1 114.9 22.2 416 n/a 3_bss: 0.1191 0.1411 0.006 0.828 9.1 114.9 22.2 416 n/a 3_settarget: 0.1191 0.1411 0.006 0.828 9.1 114.9 22.2 416 n/a 3_updatecdl: 0.1191 0.1411 0.006 0.827 9.1 114.9 22.2 416 n/a 3_nqh: 0.1191 0.1411 0.006 0.827 9.1 114.9 22.2 416 n/a 3_sol: 0.1218 0.1402 0.006 0.827 9.1 114.9 21.1 426 n/a 3_weight: 0.1218 0.1402 0.006 0.827 9.1 114.9 21.1 426 n/a 3_xyzrec: 0.1166 0.1326 0.007 1.013 9.1 114.9 21.1 426 n/a 3_adp: 0.1166 0.1326 0.007 1.013 9.1 114.9 21.1 426 n/a 3_regHadp: 0.1166 0.1326 0.007 1.013 9.1 114.9 21.1 426 n/a 3_occ: 0.1158 0.1323 0.007 1.013 9.1 114.9 21.1 426 n/a 4_bss: 0.1151 0.1314 0.007 1.013 9.1 114.9 21.1 426 n/a 4_settarget: 0.1151 0.1314 0.007 1.013 9.1 114.9 21.1 426 n/a 4_updatecdl: 0.1151 0.1314 0.007 1.014 9.1 114.9 21.1 426 n/a 4_nqh: 0.1155 0.1316 0.007 1.014 9.1 114.9 21.1 426 n/a 4_sol: 0.1155 0.1300 0.007 1.014 9.1 114.9 21.1 442 n/a 4_weight: 0.1155 0.1300 0.007 1.014 9.1 114.9 21.1 442 n/a 4_xyzrec: 0.1144 0.1294 0.009 1.124 9.1 114.9 21.1 442 n/a 4_adp: 0.1144 0.1294 0.009 1.124 9.1 114.9 21.1 442 n/a 4_regHadp: 0.1144 0.1294 0.009 1.124 9.1 114.9 21.1 442 n/a 4_occ: 0.1137 0.1292 0.009 1.124 9.1 114.9 21.1 442 n/a 5_bss: 0.1132 0.1295 0.009 1.124 9.1 114.9 21.1 442 n/a 5_settarget: 0.1132 0.1295 0.009 1.124 9.1 114.9 21.1 442 n/a 5_updatecdl: 0.1132 0.1295 0.009 1.124 9.1 114.9 21.1 442 n/a 5_setrh: 0.1134 0.1295 0.009 1.124 9.1 114.9 21.1 442 n/a 5_nqh: 0.1134 0.1295 0.009 1.124 9.1 114.9 21.1 442 n/a 5_sol: 0.1136 0.1277 0.009 1.124 9.1 114.9 21.1 447 n/a 5_weight: 0.1136 0.1277 0.009 1.124 9.1 114.9 21.1 447 n/a 5_xyzrec: 0.1136 0.1277 0.008 1.123 9.1 114.9 21.1 447 n/a 5_adp: 0.1136 0.1277 0.008 1.123 9.1 114.9 21.1 447 n/a 5_regHadp: 0.1136 0.1277 0.008 1.123 9.1 114.9 21.1 447 n/a 5_occ: 0.1133 0.1274 0.008 1.123 9.1 114.9 21.1 447 n/a end: 0.1132 0.1276 0.008 1.123 9.1 114.9 21.1 447 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1318715_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1318715_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1600 Refinement macro-cycles (run) : 12774.3900 Write final files (write_after_run_outputs) : 92.1300 Total : 12869.6800 Total CPU time: 3.58 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 21:54:18 PST -0800 (1735365258.75 s) Start R-work = 0.1629, R-free = 0.1760 Final R-work = 0.1132, R-free = 0.1276 =============================================================================== Job complete usr+sys time: 13045.16 seconds wall clock time: 238 minutes 50.82 seconds (14330.82 seconds total)