Starting phenix.refine on Fri Dec 27 17:58:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8569971.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_8569971.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8569971.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 =============================================================================== 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: 1.56, per 1000 atoms: 0.46 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: 0.55 Conformation dependent library (CDL) restraints added in 188.9 milliseconds Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.91: 530 0.91 - 1.19: 1154 1.19 - 1.47: 771 1.47 - 1.74: 684 1.74 - 2.02: 14 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 1.332 1.512 -0.180 6.60e-03 2.30e+04 7.43e+02 bond pdb=" C GLN A 180 " pdb=" N VAL A 181 " ideal model delta sigma weight residual 1.335 1.581 -0.246 1.20e-02 6.94e+03 4.22e+02 bond pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 1.230 0.984 0.246 1.22e-02 6.72e+03 4.07e+02 bond pdb=" C GLY A 37 " pdb=" O GLY A 37 " ideal model delta sigma weight residual 1.234 1.027 0.207 1.05e-02 9.07e+03 3.88e+02 bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.236 1.025 0.212 1.15e-02 7.56e+03 3.40e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.98: 3327 4.98 - 9.97: 1831 9.97 - 14.95: 525 14.95 - 19.94: 86 19.94 - 24.92: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH1 ARG A 98 " ideal model delta sigma weight residual 121.50 136.19 -14.69 1.00e+00 1.00e+00 2.16e+02 angle pdb=" CA ALYS A 132 " pdb=" C ALYS A 132 " pdb=" O ALYS A 132 " ideal model delta sigma weight residual 120.70 135.34 -14.64 1.03e+00 9.43e-01 2.02e+02 angle pdb=" CA GLY A 37 " pdb=" C GLY A 37 " pdb=" O GLY A 37 " ideal model delta sigma weight residual 120.76 132.10 -11.34 8.10e-01 1.52e+00 1.96e+02 angle pdb=" CA GLY A 37 " pdb=" C GLY A 37 " pdb=" N LEU A 38 " ideal model delta sigma weight residual 115.86 100.57 15.29 1.13e+00 7.83e-01 1.83e+02 angle pdb=" CA PHE A 164 " pdb=" C PHE A 164 " pdb=" O PHE A 164 " ideal model delta sigma weight residual 120.42 107.20 13.22 1.06e+00 8.90e-01 1.56e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 919 16.75 - 33.49: 135 33.49 - 50.24: 40 50.24 - 66.99: 16 66.99 - 83.73: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 -157.78 -22.22 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ARG A 48 " pdb=" C ARG A 48 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+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 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.207: 93 0.207 - 0.411: 73 0.411 - 0.615: 46 0.615 - 0.818: 24 0.818 - 1.022: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PHE A 164 " pdb=" N PHE A 164 " pdb=" C PHE A 164 " pdb=" CB PHE A 164 " both_signs ideal model delta sigma weight residual False 2.51 3.53 -1.02 2.00e-01 2.50e+01 2.61e+01 chirality pdb=" CA GLN A 180 " pdb=" N GLN A 180 " pdb=" C GLN A 180 " pdb=" CB GLN A 180 " both_signs ideal model delta sigma weight residual False 2.51 3.48 -0.97 2.00e-01 2.50e+01 2.36e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -1.69 -0.94 2.00e-01 2.50e+01 2.20e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.000 2.00e-02 2.50e+03 6.53e-02 1.28e+02 pdb=" CG PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.090 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.128 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " 0.040 9.50e-02 1.11e+02 6.74e-02 9.83e+01 pdb=" NE ARG A 145 " 0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.065 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " 0.147 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " 0.044 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " -0.081 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.043 2.00e-02 2.50e+03 5.45e-02 8.90e+01 pdb=" CG TYR A 139 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.106 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.048 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.063 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.062 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.059 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.035 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 951 2.31 - 2.88: 8124 2.88 - 3.46: 10582 3.46 - 4.03: 15177 4.03 - 4.60: 21855 Nonbonded interactions: 56689 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.742 2.100 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.807 2.270 nonbonded pdb="HE21 GLN A 45 " pdb=" OD1 ASP A 49 " model vdw 1.809 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.820 1.850 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.844 2.100 ... (remaining 56684 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_8569971_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795464 | | target function (ml) not normalized (work): 232878.907119 | | target function (ml) not normalized (free): 11865.045426 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3023 0.2047 7.0595 4.9394| | 2: 3.57 - 2.84 1.00 2876 122 0.2433 0.1812 4.3473 4.3473| | 3: 2.84 - 2.48 1.00 2833 165 0.2359 0.1619 4.1251 4.1765| | 4: 2.47 - 2.25 1.00 2825 136 0.2352 0.1453 3.8335 3.8238| | 5: 2.25 - 2.09 1.00 2756 127 0.2452 0.1597 3.8016 3.8184| | 6: 2.09 - 1.97 1.00 2846 113 0.2539 0.1686 3.4897 3.537| | 7: 1.97 - 1.87 1.00 2787 165 0.2572 0.1933 3.1614 3.2655| | 8: 1.87 - 1.79 1.00 2789 144 0.2476 0.1959 3.0759 3.1596| | 9: 1.79 - 1.72 1.00 2745 138 0.2428 0.1989 2.8995 3.0022| | 10: 1.72 - 1.66 1.00 2789 158 0.2396 0.1835 2.8237 2.8353| | 11: 1.66 - 1.61 1.00 2740 147 0.2491 0.2062 2.7438 2.8356| | 12: 1.61 - 1.56 1.00 2787 146 0.2572 0.1777 2.6271 2.6288| | 13: 1.56 - 1.52 1.00 2745 130 0.2572 0.2028 2.5829 2.6881| | 14: 1.52 - 1.48 1.00 2803 134 0.2587 0.2001 2.5292 2.6019| | 15: 1.48 - 1.45 1.00 2738 128 0.2588 0.2280 2.4232 2.5818| | 16: 1.45 - 1.42 1.00 2756 161 0.2681 0.2050 2.3884 2.4277| | 17: 1.42 - 1.39 1.00 2785 139 0.2743 0.2102 2.343 2.3621| | 18: 1.39 - 1.36 1.00 2741 179 0.2671 0.2166 2.2658 2.3385| | 19: 1.36 - 1.34 1.00 2807 134 0.2638 0.2343 2.2387 2.2743| | 20: 1.34 - 1.32 1.00 2696 147 0.2672 0.2299 2.1928 2.2174| | 21: 1.32 - 1.30 1.00 2785 112 0.2694 0.2255 2.1576 2.1793| | 22: 1.29 - 1.27 1.00 2704 152 0.2765 0.2346 2.1578 2.1492| | 23: 1.27 - 1.26 1.00 2802 156 0.2765 0.2465 2.0956 2.1615| | 24: 1.26 - 1.24 1.00 2744 132 0.2792 0.2536 2.0865 2.1458| | 25: 1.24 - 1.22 1.00 2734 148 0.2821 0.2524 2.0516 2.0476| | 26: 1.22 - 1.21 1.00 2727 135 0.2905 0.2265 2.0199 2.0886| | 27: 1.21 - 1.19 1.00 2814 148 0.2976 0.2738 2.0045 2.0531| | 28: 1.19 - 1.18 1.00 2671 147 0.3030 0.2867 1.9996 2.0128| | 29: 1.18 - 1.16 1.00 2800 134 0.2947 0.2851 1.9567 2.0584| | 30: 1.16 - 1.15 1.00 2740 148 0.3013 0.2818 1.9265 1.9641| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.84 0.76 0.23 1477.36| | 2: 3.57 - 2.84 2876 122 0.80 26.05 1.27 0.23 1477.36| | 3: 2.84 - 2.48 2833 165 0.74 32.08 1.24 0.24 1225.80| | 4: 2.47 - 2.25 2825 136 0.81 25.69 1.26 0.25 572.96| | 5: 2.25 - 2.09 2756 127 0.77 29.26 1.28 0.25 572.96| | 6: 2.09 - 1.97 2846 113 0.83 22.79 1.29 0.25 315.10| | 7: 1.97 - 1.87 2787 165 0.90 17.01 1.28 0.25 95.18| | 8: 1.87 - 1.79 2789 144 0.85 21.57 1.25 0.25 95.18| | 9: 1.79 - 1.72 2745 138 0.87 19.25 1.24 0.25 58.61| | 10: 1.72 - 1.66 2789 158 0.86 20.63 1.22 0.25 51.28| | 11: 1.66 - 1.61 2740 147 0.84 22.46 1.24 0.25 49.50| | 12: 1.61 - 1.56 2787 146 0.88 19.33 1.25 0.25 31.42| | 13: 1.56 - 1.52 2745 130 0.86 21.27 1.24 0.25 31.42| | 14: 1.52 - 1.48 2803 134 0.86 21.61 1.23 0.25 28.11| | 15: 1.48 - 1.45 2738 128 0.87 20.74 1.24 0.25 22.04| | 16: 1.45 - 1.42 2756 161 0.85 22.26 1.24 0.25 22.04| | 17: 1.42 - 1.39 2785 139 0.86 21.51 1.24 0.25 18.34| | 18: 1.39 - 1.36 2741 179 0.86 21.73 1.23 0.25 16.20| | 19: 1.36 - 1.34 2807 134 0.85 22.34 1.22 0.25 16.20| | 20: 1.34 - 1.32 2696 147 0.87 21.10 1.22 0.25 13.27| | 21: 1.32 - 1.30 2785 112 0.85 22.19 1.21 0.25 13.07| | 22: 1.29 - 1.27 2704 152 0.85 22.57 1.20 0.25 12.75| | 23: 1.27 - 1.26 2802 156 0.86 22.28 1.21 0.24 11.13| | 24: 1.26 - 1.24 2744 132 0.85 22.85 1.20 0.24 11.13| | 25: 1.24 - 1.22 2734 148 0.84 23.77 1.19 0.24 10.70| | 26: 1.22 - 1.21 2727 135 0.84 24.39 1.20 0.23 10.22| | 27: 1.21 - 1.19 2814 148 0.83 25.12 1.21 0.23 10.22| | 28: 1.19 - 1.18 2671 147 0.82 26.02 1.19 0.23 9.77| | 29: 1.18 - 1.16 2800 134 0.81 26.58 1.16 0.22 9.60| | 30: 1.16 - 1.15 2740 148 0.80 28.20 1.15 0.22 9.60| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.60 max = 1477.36 mean = 215.82| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 23.05| |phase err.(test): min = 0.00 max = 89.94 mean = 22.93| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.266 1557 Z= 5.641 Angle : 5.182 20.690 2118 Z= 3.682 Chirality : 0.386 1.022 243 Planarity : 0.032 0.094 284 Dihedral : 14.037 83.732 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.54 % Allowed : 0.54 % Favored : 98.92 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 30.27 % 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: -2.63 (0.45), residues: 224 helix: -2.81 (0.33), residues: 109 sheet: -0.30 (0.68), residues: 38 loop : -0.38 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.087 0.025 ARG A 28 TYR 0.080 0.032 TYR A 141 PHE 0.098 0.039 PHE A 119 HIS 0.026 0.012 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795464 | | target function (ml) not normalized (work): 232878.907119 | | target function (ml) not normalized (free): 11865.045426 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2568 0.2610 0.1942 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2568 0.2610 0.1942 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1985 0.1942 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2005 0.2009 0.1956 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1648 0.1642 0.1756 n_refl.: 87594 remove outliers: r(all,work,free)=0.1647 0.1642 0.1756 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 0.3819 386.300 356.639 0.669 1.003 0.401 11.894-9.307 99.02 97 4 0.1844 613.619 593.824 0.924 1.003 0.380 9.237-7.194 100.00 213 7 0.2167 501.865 490.910 0.964 1.003 0.352 7.162-5.571 100.00 427 22 0.2221 376.622 364.726 0.934 1.003 0.295 5.546-4.326 100.00 867 58 0.1277 517.008 511.095 0.962 1.003 0.224 4.315-3.360 100.00 1859 96 0.1136 491.679 487.418 1.003 1.002 0.158 3.356-2.611 100.00 3867 181 0.1419 323.007 319.810 0.999 1.002 0.057 2.608-2.026 99.99 8198 413 0.1373 214.124 211.929 1.006 1.000 0.000 2.025-1.573 100.00 17313 902 0.1653 104.567 103.917 1.014 0.998 0.000 1.573-1.221 100.00 36679 1900 0.2077 46.369 45.002 1.006 0.994 0.000 1.221-1.150 99.97 13689 708 0.2594 29.216 26.958 0.977 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0443 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1642 r_free=0.1756 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1643 r_free=0.1754 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.176576 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2018.379591 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 0.1700 0.1814 0.0114 0.001 0.4 4.2 0.0 0.0 0 0.125 0.1572 0.1709 0.0137 0.001 0.4 3.8 0.0 0.0 0 0.250 0.1455 0.1620 0.0165 0.001 0.5 3.5 0.0 0.0 0 0.500 0.1386 0.1574 0.0187 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1344 0.1547 0.0202 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1347 0.1546 0.0199 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1281 0.1494 0.0213 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1275 0.1503 0.0228 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1256 0.1488 0.0232 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1249 0.1481 0.0233 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1242 0.1478 0.0236 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1237 0.1473 0.0237 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1236 0.1473 0.0237 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1231 0.1469 0.0238 0.006 0.9 3.5 0.5 0.0 0 9.000 0.1227 0.1470 0.0243 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1228 0.1469 0.0241 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1226 0.1470 0.0244 0.007 0.9 4.2 0.5 0.6 0 12.000 0.1223 0.1470 0.0247 0.008 1.0 3.5 0.5 0.6 0 13.588 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1231 0.1469 0.0238 0.006 0.9 3.5 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 14.69 2.38 3.013 19.052 2018.380 0.017 12.31 14.69 2.38 3.013 19.052 60.551 0.017 12.38 14.66 2.28 2.666 19.052 252.297 0.017 12.74 15.35 2.61 2.837 19.300 1009.190 0.017 12.48 15.38 2.90 3.129 19.516 2018.380 0.016 12.49 15.50 3.01 3.463 19.714 3027.569 0.016 12.37 15.43 3.06 3.402 19.665 4036.759 0.015 12.31 15.45 3.14 3.418 19.666 5045.949 0.015 12.23 15.39 3.16 3.374 19.637 6055.139 0.015 12.16 15.34 3.18 3.333 19.603 7064.329 0.015 12.17 15.39 3.23 3.433 19.645 8073.518 0.015 12.14 15.39 3.25 3.406 19.616 9082.708 0.015 12.23 15.56 3.33 3.683 19.752 10091.898 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: 252.297 Accepted refinement result: 12.38 14.66 2.28 2.666 19.052 252.297 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.43 20.08 3.31 0 1785 Protein: 9.08 114.97 16.99 3.31 0 1519 Water: 11.46 119.43 38.22 N/A 0 258 Other: 19.70 26.60 22.05 N/A 0 8 Chain A: 9.08 119.43 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.15 227 31.15 - 42.19 125 42.19 - 53.22 94 53.22 - 64.26 42 64.26 - 75.29 11 75.29 - 86.33 7 86.33 - 97.36 4 97.36 - 108.40 1 108.40 - 119.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1466 r_work=0.1239 r_free=0.1469 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1469 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 = 0.1462 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= 0.1231 r_free= 0.1462 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016859 | | target function (ls_wunit_k1) not normalized (work): 1404.338447 | | target function (ls_wunit_k1) not normalized (free): 108.958629 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1242 0.1231 0.1462 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1674 0.1675 0.1695 n_refl.: 87593 remove outliers: r(all,work,free)=0.1674 0.1675 0.1695 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1680 0.1682 0.1699 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)=0.1241 0.1230 0.1455 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 96.88 88 5 0.3548 304.043 283.846 0.670 1.003 0.396 11.894-9.307 99.02 97 4 0.1649 482.958 469.743 0.925 1.003 0.386 9.237-7.194 100.00 213 7 0.1883 395.000 390.650 0.966 1.003 0.324 7.162-5.571 100.00 427 22 0.1798 296.426 290.894 0.937 1.003 0.269 5.546-4.326 100.00 867 58 0.1001 406.919 404.012 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0878 386.983 385.846 1.008 1.002 0.180 3.356-2.611 100.00 3867 181 0.1181 254.228 253.051 1.010 1.002 0.053 2.608-2.026 99.99 8198 413 0.1024 168.530 167.793 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1114 82.301 82.488 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1454 36.496 36.001 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 22.995 21.480 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0526 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1230 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** Total number of N/Q/H flips: 0 r_work=0.1230 r_free=0.1455 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1455 | n_water=258 | time (s): 1.480 (total time: 1.480) Filter (dist) r_work=0.1237 r_free=0.1454 | n_water=251 | time (s): 23.740 (total time: 25.220) Filter (q & B) r_work=0.1240 r_free=0.1453 | n_water=248 | time (s): 2.890 (total time: 28.110) Compute maps r_work=0.1240 r_free=0.1453 | n_water=248 | time (s): 1.080 (total time: 29.190) Filter (map) r_work=0.1267 r_free=0.1459 | n_water=222 | time (s): 2.660 (total time: 31.850) Find peaks r_work=0.1267 r_free=0.1459 | n_water=222 | time (s): 0.540 (total time: 32.390) Add new water r_work=0.1420 r_free=0.1631 | n_water=430 | time (s): 2.510 (total time: 34.900) Refine new water occ: r_work=0.1320 r_free=0.1496 adp: r_work=0.1234 r_free=0.1437 occ: r_work=0.1246 r_free=0.1430 adp: r_work=0.1211 r_free=0.1415 occ: r_work=0.1213 r_free=0.1407 adp: r_work=0.1204 r_free=0.1405 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1405 r_work=0.1204 r_free=0.1405 | n_water=430 | time (s): 60.080 (total time: 94.980) Filter (q & B) r_work=0.1207 r_free=0.1407 | n_water=418 | time (s): 2.650 (total time: 97.630) Filter (dist only) r_work=0.1207 r_free=0.1404 | n_water=417 | time (s): 34.930 (total time: 132.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.936686 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1496.666354 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 0.1638 0.1756 0.0118 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1552 0.1682 0.0129 0.001 0.4 8.0 0.0 0.0 0 0.250 0.1433 0.1585 0.0153 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1371 0.1536 0.0166 0.001 0.4 5.4 0.0 0.0 0 0.750 0.1316 0.1493 0.0177 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1321 0.1504 0.0182 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1256 0.1457 0.0201 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1228 0.1435 0.0207 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1221 0.1436 0.0216 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1212 0.1428 0.0216 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1206 0.1424 0.0218 0.004 0.7 3.8 0.5 0.0 0 6.000 0.1203 0.1423 0.0219 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1199 0.1426 0.0227 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1194 0.1423 0.0229 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1192 0.1430 0.0238 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1191 0.1432 0.0241 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1188 0.1430 0.0241 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1184 0.1427 0.0242 0.008 1.0 5.4 0.5 0.6 0 13.968 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1423 0.0219 0.005 0.8 4.5 0.5 0.0 0 7.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 14.23 2.19 3.773 21.794 1496.666 0.016 12.03 14.23 2.19 3.773 21.794 44.900 0.016 12.03 14.23 2.19 3.773 21.794 187.083 0.016 12.26 14.69 2.43 3.621 21.802 748.333 0.016 12.23 15.09 2.85 3.478 22.225 1496.666 0.015 12.01 14.87 2.86 3.436 22.107 2245.000 0.015 11.93 14.90 2.98 3.505 21.954 2993.333 0.014 11.82 14.77 2.95 3.480 22.015 3741.666 0.014 11.82 14.81 2.99 3.492 22.043 4489.999 0.014 11.85 14.88 3.03 3.514 22.169 5238.332 0.014 11.82 15.02 3.19 3.550 22.281 5986.665 0.014 11.81 15.03 3.21 3.576 22.301 6734.999 0.014 11.80 15.04 3.24 3.585 22.231 7483.332 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: 187.083 Accepted refinement result: 12.03 14.23 2.19 3.773 21.794 187.083 0.016 Individual atomic B min max mean iso aniso Overall: 9.12 115.00 22.22 3.31 195 1749 Protein: 9.12 115.00 17.02 3.31 0 1519 Water: 11.49 76.68 41.17 N/A 195 222 Other: 19.74 26.63 22.09 N/A 0 8 Chain A: 9.12 115.00 19.40 N/A 0 1749 Chain S: 14.66 60.00 47.55 N/A 195 0 Histogram: Values Number of atoms 9.12 - 19.70 1261 19.70 - 30.29 238 30.29 - 40.88 166 40.88 - 51.47 131 51.47 - 62.06 125 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1423 r_work=0.1203 r_free=0.1423 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1423 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 = 0.1202 r_free = 0.1421 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1202 r_free= 0.1421 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015394 | | target function (ls_wunit_k1) not normalized (work): 1282.250642 | | target function (ls_wunit_k1) not normalized (free): 103.361691 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1202 0.1421 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1603 0.1603 0.1638 n_refl.: 87593 remove outliers: r(all,work,free)=0.1603 0.1603 0.1638 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1605 0.1604 0.1640 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1200 0.1416 n_refl.: 87593 remove outliers: r(all,work,free)=0.1209 0.1199 0.1416 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 0.3375 303.487 274.294 0.601 1.003 0.350 11.894-9.307 99.02 97 4 0.1680 482.958 473.227 0.919 1.003 0.330 9.237-7.194 100.00 213 7 0.1778 395.000 394.918 0.987 1.003 0.264 7.162-5.571 100.00 427 22 0.1601 296.426 291.799 0.936 1.003 0.250 5.546-4.326 100.00 867 58 0.0903 406.919 403.457 0.960 1.003 0.200 4.315-3.360 100.00 1859 96 0.0804 386.983 386.060 1.004 1.002 0.190 3.356-2.611 100.00 3867 181 0.1109 254.228 253.143 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1014 168.530 168.003 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1114 82.301 82.492 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1453 36.496 36.025 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2259 22.995 21.506 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0157 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1416 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1416 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1416 | n_water=417 | time (s): 1.500 (total time: 1.500) Filter (dist) r_work=0.1201 r_free=0.1418 | n_water=412 | time (s): 38.970 (total time: 40.470) Filter (q & B) r_work=0.1201 r_free=0.1418 | n_water=412 | time (s): 1.170 (total time: 41.640) Compute maps r_work=0.1201 r_free=0.1418 | n_water=412 | time (s): 1.350 (total time: 42.990) Filter (map) r_work=0.1238 r_free=0.1401 | n_water=285 | time (s): 3.230 (total time: 46.220) Find peaks r_work=0.1238 r_free=0.1401 | n_water=285 | time (s): 0.570 (total time: 46.790) Add new water r_work=0.1359 r_free=0.1516 | n_water=469 | time (s): 2.350 (total time: 49.140) Refine new water occ: r_work=0.1266 r_free=0.1435 adp: r_work=0.1268 r_free=0.1437 occ: r_work=0.1244 r_free=0.1409 adp: r_work=0.1243 r_free=0.1412 occ: r_work=0.1226 r_free=0.1389 adp: r_work=0.1220 r_free=0.1389 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1389 r_work=0.1220 r_free=0.1389 | n_water=469 | time (s): 203.850 (total time: 252.990) Filter (q & B) r_work=0.1225 r_free=0.1391 | n_water=439 | time (s): 3.170 (total time: 256.160) Filter (dist only) r_work=0.1226 r_free=0.1389 | n_water=438 | time (s): 38.130 (total time: 294.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.712816 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.381067 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 0.1239 0.1356 0.0117 0.002 0.6 4.8 0.5 0.0 0 0.086 0.1198 0.1329 0.0130 0.003 0.7 3.8 0.5 0.0 0 0.257 0.1183 0.1317 0.0135 0.004 0.8 3.2 0.5 0.0 0 0.514 0.1174 0.1316 0.0142 0.005 0.9 3.2 0.5 0.0 0 0.771 0.1169 0.1318 0.0149 0.006 1.0 3.2 0.5 0.0 0 1.028 0.1166 0.1319 0.0153 0.006 1.0 3.8 0.5 0.0 0 1.285 0.1164 0.1313 0.0149 0.007 1.1 3.5 0.5 0.0 0 1.542 0.1163 0.1317 0.0155 0.008 1.1 3.8 0.5 0.0 0 1.798 0.1172 0.1314 0.0143 0.005 0.9 3.5 0.5 0.0 0 0.856 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1164 0.1313 0.0149 0.007 1.1 3.5 0.5 0.0 0 1.542 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 13.13 1.49 3.776 21.272 41.381 3.620 11.64 13.13 1.49 3.776 21.272 1.241 3.620 11.64 13.13 1.49 3.776 21.272 5.173 3.620 11.68 13.20 1.52 3.706 21.265 20.691 3.615 11.75 13.33 1.58 3.717 21.233 41.381 3.618 11.67 13.30 1.63 3.742 21.221 62.072 3.612 11.62 13.30 1.67 3.754 21.212 82.762 3.608 11.57 13.26 1.69 3.768 21.210 103.453 3.604 11.55 13.25 1.70 3.777 21.204 124.143 3.602 11.52 13.23 1.71 3.786 21.201 144.834 3.600 11.51 13.23 1.72 3.797 21.191 165.524 3.599 11.51 13.24 1.73 3.810 21.181 186.215 3.599 11.50 13.24 1.74 3.817 21.183 206.905 3.599 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.241 Accepted refinement result: 11.64 13.13 1.49 3.776 21.272 1.241 3.620 Individual atomic B min max mean iso aniso Overall: 9.13 115.01 21.26 3.31 219 1746 Protein: 9.13 115.01 17.03 3.31 0 1519 Water: 11.50 76.69 35.90 N/A 219 219 Other: 19.75 26.64 22.10 N/A 0 8 Chain A: 9.13 115.01 19.35 N/A 0 1746 Chain S: 14.67 60.01 36.46 N/A 219 0 Histogram: Values Number of atoms 9.13 - 19.71 1264 19.71 - 30.30 285 30.30 - 40.89 208 40.89 - 51.48 129 51.48 - 62.07 56 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1164 r_free=0.1313 r_work=0.1164 r_free=0.1313 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1164 r_free = 0.1313 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1155 r_free = 0.1305 target_work(ml) = 3.613 | | occupancies: max = 1.00 min = 0.19 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= 0.1155 r_free= 0.1305 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.613479 | | target function (ml) not normalized (work): 300984.729086 | | target function (ml) not normalized (free): 15832.311236 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1155 0.1305 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1495 0.1494 0.1530 n_refl.: 87591 remove outliers: r(all,work,free)=0.1495 0.1494 0.1530 n_refl.: 87591 overall B=-0.00 to atoms: r(all,work,free)=0.1494 0.1493 0.1530 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1149 0.1301 n_refl.: 87591 remove outliers: r(all,work,free)=0.1153 0.1145 0.1301 n_refl.: 87581 ======================== 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 0.3693 291.139 272.729 0.515 1.001 0.330 11.894-9.307 98.04 96 4 0.2201 483.083 467.027 0.876 1.002 0.330 9.237-7.194 98.18 209 7 0.2273 388.022 385.846 0.952 1.002 0.202 7.162-5.571 100.00 427 22 0.2163 296.426 285.211 0.920 1.003 0.173 5.546-4.326 100.00 867 58 0.1102 406.919 402.189 0.963 1.003 0.162 4.315-3.360 100.00 1859 96 0.0939 386.983 384.644 1.004 1.002 0.150 3.356-2.611 100.00 3867 181 0.1138 254.228 252.161 1.008 1.002 0.100 2.608-2.026 99.99 8198 413 0.0942 168.530 167.771 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0896 82.301 82.579 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1261 36.496 36.076 1.029 0.996 0.000 1.221-1.150 99.97 13689 708 0.2168 22.995 21.529 0.991 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0111 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1301 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=0.1145 r_free=0.1301 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1145 r_free=0.1301 | n_water=438 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1145 r_free=0.1301 | n_water=436 | time (s): 44.150 (total time: 46.540) Filter (q & B) r_work=0.1146 r_free=0.1302 | n_water=435 | time (s): 3.710 (total time: 50.250) Compute maps r_work=0.1146 r_free=0.1302 | n_water=435 | time (s): 1.670 (total time: 51.920) Filter (map) r_work=0.1171 r_free=0.1293 | n_water=324 | time (s): 3.640 (total time: 55.560) Find peaks r_work=0.1171 r_free=0.1293 | n_water=324 | time (s): 0.680 (total time: 56.240) Add new water r_work=0.1246 r_free=0.1360 | n_water=492 | time (s): 3.620 (total time: 59.860) Refine new water occ: r_work=0.1168 r_free=0.1314 adp: r_work=0.1169 r_free=0.1315 occ: r_work=0.1153 r_free=0.1303 adp: r_work=0.1152 r_free=0.1302 occ: r_work=0.1141 r_free=0.1298 adp: r_work=0.1137 r_free=0.1294 ADP+occupancy (water only), MIN, final r_work=0.1137 r_free=0.1294 r_work=0.1137 r_free=0.1294 | n_water=492 | time (s): 190.830 (total time: 250.690) Filter (q & B) r_work=0.1144 r_free=0.1300 | n_water=454 | time (s): 3.920 (total time: 254.610) Filter (dist only) r_work=0.1144 r_free=0.1299 | n_water=453 | time (s): 45.670 (total time: 300.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.778552 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.374642 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 0.1206 0.1339 0.0133 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1170 0.1314 0.0144 0.003 0.8 3.2 0.5 0.0 0 0.267 0.1156 0.1306 0.0150 0.005 0.9 3.5 0.5 0.0 0 0.534 0.1149 0.1304 0.0154 0.006 1.0 3.5 0.5 0.0 0 0.800 0.1145 0.1302 0.0156 0.007 1.0 3.2 0.5 0.0 0 1.067 0.1143 0.1300 0.0157 0.007 1.1 3.5 0.5 0.0 0 1.334 0.1140 0.1301 0.0161 0.008 1.1 3.5 0.5 0.0 0 1.601 0.1139 0.1300 0.0161 0.009 1.1 3.5 0.5 0.0 0 1.867 0.1147 0.1301 0.0154 0.006 1.0 3.2 0.5 0.0 0 0.889 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1143 0.1300 0.0157 0.007 1.1 3.5 0.5 0.0 0 1.334 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.43 13.00 1.57 3.777 21.242 43.375 3.609 11.43 13.00 1.57 3.777 21.242 1.301 3.609 11.43 13.00 1.57 3.777 21.242 5.422 3.609 11.46 13.05 1.59 3.714 21.235 21.687 3.603 11.53 13.19 1.66 3.731 21.199 43.375 3.606 11.45 13.16 1.71 3.755 21.188 65.062 3.600 11.42 13.15 1.73 3.766 21.182 86.749 3.596 11.38 13.11 1.74 3.779 21.184 108.437 3.594 11.36 13.11 1.75 3.791 21.171 130.124 3.592 11.34 13.11 1.77 3.802 21.173 151.811 3.591 11.33 13.12 1.78 3.813 21.165 173.499 3.590 11.32 13.10 1.78 3.823 21.160 195.186 3.588 11.33 13.12 1.79 3.833 21.156 216.873 3.588 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.301 Accepted refinement result: 11.43 13.00 1.57 3.777 21.242 1.301 3.609 Individual atomic B min max mean iso aniso Overall: 9.12 115.01 21.20 3.31 236 1744 Protein: 9.12 115.01 17.03 3.31 0 1519 Water: 11.50 76.69 35.20 N/A 236 217 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.12 115.01 19.33 N/A 0 1744 Chain S: 14.66 60.01 35.08 N/A 236 0 Histogram: Values Number of atoms 9.12 - 19.71 1263 19.71 - 30.30 303 30.30 - 40.89 215 40.89 - 51.48 127 51.48 - 62.06 49 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=0.1143 r_free=0.1300 r_work=0.1143 r_free=0.1300 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1300 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1301 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1140 r_free= 0.1301 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.606813 | | target function (ml) not normalized (work): 300393.390376 | | target function (ml) not normalized (free): 15821.579931 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1147 0.1140 0.1301 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1472 0.1471 0.1527 n_refl.: 87581 remove outliers: r(all,work,free)=0.1472 0.1471 0.1527 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1471 0.1470 0.1526 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1146 0.1138 0.1299 n_refl.: 87581 remove outliers: r(all,work,free)=0.1144 0.1136 0.1299 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 88.54 80 5 0.3889 286.396 258.302 0.440 0.999 0.287 11.894-9.307 96.08 94 4 0.2429 476.321 463.446 0.863 1.001 0.270 9.237-7.194 97.73 208 7 0.2330 389.123 379.063 0.926 1.001 0.160 7.162-5.571 100.00 427 22 0.2204 296.426 284.066 0.911 1.002 0.117 5.546-4.326 100.00 867 58 0.1137 406.919 402.335 0.964 1.002 0.101 4.315-3.360 100.00 1859 96 0.0920 386.983 385.115 1.004 1.001 0.097 3.356-2.611 100.00 3867 181 0.1115 254.228 252.357 1.011 1.001 0.060 2.608-2.026 99.99 8198 413 0.0920 168.530 167.852 1.026 1.000 0.000 2.025-1.573 100.00 17313 902 0.0883 82.301 82.625 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.496 36.091 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2172 22.995 21.527 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0143 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1136 r_free=0.1299 After: r_work=0.1137 r_free=0.1299 ================================== NQH flips ================================== r_work=0.1137 r_free=0.1299 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=0.1137 r_free=0.1299 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1299 | n_water=453 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1137 r_free=0.1301 | n_water=452 | time (s): 46.780 (total time: 49.140) Filter (q & B) r_work=0.1138 r_free=0.1300 | n_water=450 | time (s): 3.640 (total time: 52.780) Compute maps r_work=0.1138 r_free=0.1300 | n_water=450 | time (s): 1.770 (total time: 54.550) Filter (map) r_work=0.1169 r_free=0.1313 | n_water=344 | time (s): 3.790 (total time: 58.340) Find peaks r_work=0.1169 r_free=0.1313 | n_water=344 | time (s): 0.720 (total time: 59.060) Add new water r_work=0.1217 r_free=0.1364 | n_water=504 | time (s): 3.570 (total time: 62.630) Refine new water occ: r_work=0.1154 r_free=0.1293 adp: r_work=0.1154 r_free=0.1296 occ: r_work=0.1142 r_free=0.1280 adp: r_work=0.1141 r_free=0.1282 occ: r_work=0.1132 r_free=0.1270 adp: r_work=0.1129 r_free=0.1270 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1270 r_work=0.1129 r_free=0.1270 | n_water=504 | time (s): 178.210 (total time: 240.840) Filter (q & B) r_work=0.1137 r_free=0.1280 | n_water=463 | time (s): 3.930 (total time: 244.770) Filter (dist only) r_work=0.1138 r_free=0.1279 | n_water=462 | time (s): 47.960 (total time: 292.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.817140 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.112171 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 0.1214 0.1328 0.0113 0.004 0.7 5.8 0.0 0.0 0 0.091 0.1177 0.1303 0.0127 0.004 0.8 5.8 0.0 0.0 0 0.273 0.1155 0.1289 0.0134 0.005 0.9 5.1 0.5 0.0 0 0.545 0.1144 0.1282 0.0137 0.006 1.0 4.8 0.5 0.0 0 0.818 0.1139 0.1279 0.0141 0.007 1.1 4.5 0.5 0.0 0 1.090 0.1137 0.1279 0.0141 0.007 1.1 4.5 0.5 0.0 0 1.363 0.1137 0.1279 0.0142 0.008 1.1 4.8 0.5 0.0 0 1.635 0.1136 0.1279 0.0143 0.008 1.1 4.8 0.5 0.0 0 1.908 0.1142 0.1281 0.0138 0.006 1.0 4.5 0.5 0.0 0 0.909 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1137 0.1279 0.0142 0.008 1.1 4.8 0.5 0.0 0 1.635 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.37 12.79 1.42 3.777 21.275 37.112 3.603 11.37 12.79 1.42 3.777 21.275 1.113 3.603 11.37 12.79 1.42 3.776 21.275 4.639 3.603 11.40 12.85 1.44 3.706 21.270 18.556 3.599 11.42 12.93 1.51 3.725 21.255 37.112 3.599 11.38 12.93 1.54 3.747 21.233 55.668 3.596 11.35 12.92 1.57 3.759 21.226 74.224 3.593 11.32 12.90 1.57 3.769 21.223 92.780 3.590 11.29 12.87 1.59 3.777 21.224 111.337 3.587 11.28 12.89 1.61 3.786 21.214 129.893 3.586 11.26 12.87 1.61 3.793 21.215 148.449 3.584 11.24 12.84 1.60 3.796 21.217 167.005 3.583 11.28 12.92 1.64 3.820 21.199 185.561 3.585 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.113 Accepted refinement result: 11.37 12.79 1.42 3.777 21.275 1.113 3.603 Individual atomic B min max mean iso aniso Overall: 9.12 115.00 21.27 3.31 245 1744 Protein: 9.12 115.00 17.02 3.31 0 1519 Water: 11.49 76.68 35.22 N/A 245 217 Other: 19.74 26.63 22.09 N/A 0 8 Chain A: 9.12 115.00 19.32 N/A 0 1744 Chain S: 14.66 60.00 35.13 N/A 245 0 Histogram: Values Number of atoms 9.12 - 19.71 1264 19.71 - 30.29 303 30.29 - 40.88 222 40.88 - 51.47 128 51.47 - 62.06 49 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1137 r_free=0.1279 r_work=0.1137 r_free=0.1279 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1137 r_free = 0.1279 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1134 r_free = 0.1277 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.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1134 r_free= 0.1277 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601691 | | target function (ml) not normalized (work): 299952.417750 | | target function (ml) not normalized (free): 15784.518620 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1349 0.1327 5.6851 5.5833| | 2: 3.57 - 2.84 1.00 2888 124 0.1054 0.1379 5.1461 5.2026| | 3: 2.83 - 2.48 1.00 2820 163 0.1101 0.1192 4.9309 4.9518| | 4: 2.47 - 2.25 1.00 2825 136 0.0899 0.1005 4.6139 4.6528| | 5: 2.25 - 2.09 1.00 2756 127 0.0866 0.0935 4.5609 4.6029| | 6: 2.09 - 1.97 1.00 2846 113 0.0851 0.0970 4.2547 4.3469| | 7: 1.97 - 1.87 1.00 2787 165 0.0888 0.1107 3.9754 4.0906| | 8: 1.87 - 1.79 1.00 2789 144 0.0907 0.1090 3.8807 3.989| | 9: 1.79 - 1.72 1.00 2745 138 0.0872 0.1171 3.6393 3.8229| | 10: 1.72 - 1.66 1.00 2831 160 0.0913 0.1170 3.5583 3.6931| | 11: 1.66 - 1.61 1.00 2712 147 0.0861 0.1016 3.4883 3.5668| | 12: 1.61 - 1.56 1.00 2773 144 0.0905 0.1116 3.3273 3.4466| | 13: 1.56 - 1.52 1.00 2745 130 0.0947 0.1046 3.3041 3.3976| | 14: 1.52 - 1.48 1.00 2803 134 0.0986 0.1038 3.2354 3.3132| | 15: 1.48 - 1.45 1.00 2738 128 0.1004 0.1231 3.1514 3.2719| | 16: 1.45 - 1.42 1.00 2756 161 0.1056 0.1236 3.1341 3.2327| | 17: 1.42 - 1.39 1.00 2785 139 0.1138 0.1268 3.1174 3.2093| | 18: 1.39 - 1.36 1.00 2741 179 0.1202 0.1325 3.1058 3.2405| | 19: 1.36 - 1.34 1.00 2807 134 0.1263 0.1556 3.1119 3.2681| | 20: 1.34 - 1.32 1.00 2696 147 0.1371 0.1463 3.1137 3.1596| | 21: 1.32 - 1.30 1.00 2785 112 0.1475 0.1509 3.1153 3.1047| | 22: 1.29 - 1.27 1.00 2704 152 0.1568 0.1965 3.1254 3.2882| | 23: 1.27 - 1.26 1.00 2802 156 0.1651 0.1780 3.1344 3.2008| | 24: 1.26 - 1.24 1.00 2744 132 0.1710 0.1862 3.1276 3.2407| | 25: 1.24 - 1.22 1.00 2733 148 0.1885 0.2157 3.1438 3.2641| | 26: 1.22 - 1.21 1.00 2727 135 0.1911 0.1778 3.1498 3.2057| | 27: 1.21 - 1.19 1.00 2814 148 0.2078 0.2169 3.1735 3.1627| | 28: 1.19 - 1.18 1.00 2671 147 0.2204 0.2304 3.1676 3.1747| | 29: 1.18 - 1.16 1.00 2800 134 0.2269 0.2388 3.1492 3.2297| | 30: 1.16 - 1.15 1.00 2739 148 0.2453 0.2456 3.1447 3.1692| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2919 171 0.95 8.11 1.00 0.97 5459.95| | 2: 3.57 - 2.84 2888 124 0.93 12.13 1.01 0.97 5459.95| | 3: 2.83 - 2.48 2820 163 0.90 16.00 0.99 0.97 4565.32| | 4: 2.47 - 2.25 2825 136 0.92 13.15 1.00 0.98 2258.35| | 5: 2.25 - 2.09 2756 127 0.91 15.22 1.01 0.98 2258.35| | 6: 2.09 - 1.97 2846 113 0.93 12.11 1.02 0.98 1311.44| | 7: 1.97 - 1.87 2787 165 0.95 9.21 1.02 0.98 503.86| | 8: 1.87 - 1.79 2789 144 0.93 12.53 1.00 0.98 503.86| | 9: 1.79 - 1.72 2745 138 0.94 9.91 0.98 0.97 284.65| | 10: 1.72 - 1.66 2831 160 0.94 10.97 0.98 0.97 240.75| | 11: 1.66 - 1.61 2712 147 0.94 11.59 0.98 0.97 230.67| | 12: 1.61 - 1.56 2773 144 0.96 8.78 0.99 0.97 135.58| | 13: 1.56 - 1.52 2745 130 0.95 10.28 1.03 0.97 135.58| | 14: 1.52 - 1.48 2803 134 0.94 10.68 1.02 0.98 121.75| | 15: 1.48 - 1.45 2738 128 0.95 9.80 1.02 0.98 96.43| | 16: 1.45 - 1.42 2756 161 0.94 10.97 1.02 0.98 96.43| | 17: 1.42 - 1.39 2785 139 0.95 10.79 1.01 0.98 88.06| | 18: 1.39 - 1.36 2741 179 0.94 11.45 1.01 0.98 83.21| | 19: 1.36 - 1.34 2807 134 0.94 11.79 0.99 0.98 83.21| | 20: 1.34 - 1.32 2696 147 0.94 12.12 0.98 0.96 79.83| | 21: 1.32 - 1.30 2785 112 0.94 13.08 0.98 0.96 79.59| | 22: 1.29 - 1.27 2704 152 0.93 13.65 0.98 0.96 80.05| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.97 0.94 82.41| | 24: 1.26 - 1.24 2744 132 0.92 14.88 0.96 0.94 82.41| | 25: 1.24 - 1.22 2733 148 0.91 16.38 0.96 0.94 84.50| | 26: 1.22 - 1.21 2727 135 0.90 18.17 1.02 0.93 86.81| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.02 0.93 86.81| | 28: 1.19 - 1.18 2671 147 0.88 20.46 1.01 0.93 90.44| | 29: 1.18 - 1.16 2800 134 0.88 20.55 0.99 0.92 91.81| | 30: 1.16 - 1.15 2739 148 0.86 22.11 0.98 0.92 91.81| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.59 max = 5459.95 mean = 849.09| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.93 mean = 13.33| |phase err.(test): min = 0.00 max = 88.42 mean = 13.31| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1141 0.1134 0.1277 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1456 0.1456 0.1488 n_refl.: 87577 remove outliers: r(all,work,free)=0.1456 0.1456 0.1488 n_refl.: 87577 overall B=-0.00 to atoms: r(all,work,free)=0.1456 0.1455 0.1487 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1141 0.1134 0.1276 n_refl.: 87577 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 0.4124 286.396 249.554 0.436 0.999 0.307 11.894-9.307 94.12 92 4 0.2390 480.257 459.341 0.859 1.001 0.298 9.237-7.194 97.27 207 7 0.2311 388.114 381.662 0.928 1.002 0.150 7.162-5.571 100.00 427 22 0.2208 296.426 285.284 0.907 1.002 0.118 5.546-4.326 100.00 867 58 0.1145 406.919 401.985 0.961 1.002 0.087 4.315-3.360 100.00 1859 96 0.0915 386.983 385.083 1.004 1.002 0.080 3.356-2.611 100.00 3867 181 0.1102 254.228 252.469 1.011 1.001 0.030 2.608-2.026 99.99 8198 413 0.0909 168.530 167.923 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0885 82.301 82.642 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.496 36.101 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2172 22.995 21.537 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0121 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2609 0.1941 0.083 5.182 8.8 119.3 19.9 258 0.000 1_bss: 0.1642 0.1756 0.083 5.182 9.0 119.5 20.1 258 0.000 1_settarget: 0.1642 0.1756 0.083 5.182 9.0 119.5 20.1 258 0.000 1_nqh: 0.1643 0.1754 0.083 5.182 9.0 119.5 20.1 258 0.003 1_weight: 0.1643 0.1754 0.083 5.182 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1231 0.1469 0.006 0.856 9.0 119.5 20.1 258 0.134 1_adp: 0.1238 0.1466 0.006 0.856 9.1 119.4 20.1 258 0.134 1_regHadp: 0.1239 0.1469 0.006 0.856 9.1 119.4 20.1 258 0.134 1_occ: 0.1231 0.1462 0.006 0.856 9.1 119.4 20.1 258 0.134 2_bss: 0.1230 0.1455 0.006 0.856 9.1 119.5 20.1 258 0.134 2_settarget: 0.1230 0.1455 0.006 0.856 9.1 119.5 20.1 258 0.134 2_updatecdl: 0.1230 0.1455 0.006 0.870 9.1 119.5 20.1 258 0.134 2_nqh: 0.1230 0.1455 0.006 0.870 9.1 119.5 20.1 258 0.134 2_sol: 0.1207 0.1404 0.006 0.870 9.1 115.0 22.2 417 n/a 2_weight: 0.1207 0.1404 0.006 0.870 9.1 115.0 22.2 417 n/a 2_xyzrec: 0.1203 0.1423 0.005 0.768 9.1 115.0 22.2 417 n/a 2_adp: 0.1203 0.1423 0.005 0.768 9.1 115.0 22.2 417 n/a 2_regHadp: 0.1203 0.1423 0.005 0.768 9.1 115.0 22.2 417 n/a 2_occ: 0.1202 0.1421 0.005 0.768 9.1 115.0 22.2 417 n/a 3_bss: 0.1199 0.1416 0.005 0.768 9.1 115.0 22.2 417 n/a 3_settarget: 0.1199 0.1416 0.005 0.768 9.1 115.0 22.2 417 n/a 3_updatecdl: 0.1199 0.1416 0.005 0.770 9.1 115.0 22.2 417 n/a 3_nqh: 0.1199 0.1416 0.005 0.770 9.1 115.0 22.2 417 n/a 3_sol: 0.1226 0.1389 0.005 0.770 9.1 115.0 21.3 438 n/a 3_weight: 0.1226 0.1389 0.005 0.770 9.1 115.0 21.3 438 n/a 3_xyzrec: 0.1164 0.1313 0.007 1.053 9.1 115.0 21.3 438 n/a 3_adp: 0.1164 0.1313 0.007 1.053 9.1 115.0 21.3 438 n/a 3_regHadp: 0.1164 0.1313 0.007 1.053 9.1 115.0 21.3 438 n/a 3_occ: 0.1155 0.1305 0.007 1.053 9.1 115.0 21.3 438 n/a 4_bss: 0.1145 0.1301 0.007 1.053 9.1 115.0 21.3 438 n/a 4_settarget: 0.1145 0.1301 0.007 1.053 9.1 115.0 21.3 438 n/a 4_updatecdl: 0.1145 0.1301 0.007 1.053 9.1 115.0 21.3 438 n/a 4_nqh: 0.1145 0.1301 0.007 1.053 9.1 115.0 21.3 438 n/a 4_sol: 0.1144 0.1299 0.007 1.053 9.1 115.0 21.2 453 n/a 4_weight: 0.1144 0.1299 0.007 1.053 9.1 115.0 21.2 453 n/a 4_xyzrec: 0.1143 0.1300 0.007 1.062 9.1 115.0 21.2 453 n/a 4_adp: 0.1143 0.1300 0.007 1.062 9.1 115.0 21.2 453 n/a 4_regHadp: 0.1143 0.1300 0.007 1.062 9.1 115.0 21.2 453 n/a 4_occ: 0.1140 0.1301 0.007 1.062 9.1 115.0 21.2 453 n/a 5_bss: 0.1136 0.1299 0.007 1.062 9.1 115.0 21.2 453 n/a 5_settarget: 0.1136 0.1299 0.007 1.062 9.1 115.0 21.2 453 n/a 5_updatecdl: 0.1136 0.1299 0.007 1.061 9.1 115.0 21.2 453 n/a 5_setrh: 0.1137 0.1299 0.007 1.061 9.1 115.0 21.2 453 n/a 5_nqh: 0.1137 0.1299 0.007 1.061 9.1 115.0 21.2 453 n/a 5_sol: 0.1138 0.1279 0.007 1.061 9.1 115.0 21.3 462 n/a 5_weight: 0.1138 0.1279 0.007 1.061 9.1 115.0 21.3 462 n/a 5_xyzrec: 0.1137 0.1279 0.008 1.080 9.1 115.0 21.3 462 n/a 5_adp: 0.1137 0.1279 0.008 1.080 9.1 115.0 21.3 462 n/a 5_regHadp: 0.1137 0.1279 0.008 1.080 9.1 115.0 21.3 462 n/a 5_occ: 0.1134 0.1277 0.008 1.080 9.1 115.0 21.3 462 n/a end: 0.1132 0.1276 0.008 1.080 9.1 115.0 21.3 462 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8569971_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8569971_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.5000 Refinement macro-cycles (run) : 12974.2400 Write final files (write_after_run_outputs) : 97.0800 Total : 13074.8200 Total CPU time: 3.64 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 21:55:43 PST -0800 (1735365343.25 s) Start R-work = 0.1642, R-free = 0.1756 Final R-work = 0.1132, R-free = 0.1276 =============================================================================== Job complete usr+sys time: 13267.25 seconds wall clock time: 240 minutes 32.11 seconds (14432.11 seconds total)