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_8736282.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8736282.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8736282.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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: 1.35, per 1000 atoms: 0.40 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: 0.40 Conformation dependent library (CDL) restraints added in 130.0 milliseconds Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.61 - 0.87: 288 0.87 - 1.13: 1291 1.13 - 1.39: 588 1.39 - 1.65: 919 1.65 - 1.91: 67 Bond restraints: 3153 Sorted by residual: bond pdb=" CA PRO A 73 " pdb=" C PRO A 73 " ideal model delta sigma weight residual 1.521 1.318 0.203 1.20e-02 6.94e+03 2.87e+02 bond pdb=" C LEU A 185 " pdb=" O LEU A 185 " ideal model delta sigma weight residual 1.236 1.013 0.223 1.32e-02 5.74e+03 2.85e+02 bond pdb=" CA ATYR A 67 " pdb=" C ATYR A 67 " ideal model delta sigma weight residual 1.522 1.322 0.200 1.19e-02 7.06e+03 2.83e+02 bond pdb=" C VAL A 51 " pdb=" O VAL A 51 " ideal model delta sigma weight residual 1.237 1.417 -0.180 1.08e-02 8.57e+03 2.77e+02 bond pdb=" CA ILE A 31 " pdb=" C ILE A 31 " ideal model delta sigma weight residual 1.523 1.333 0.190 1.14e-02 7.69e+03 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 3452 5.28 - 10.55: 1819 10.55 - 15.82: 448 15.82 - 21.09: 54 21.09 - 26.37: 4 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.35 108.99 14.36 9.50e-01 1.11e+00 2.28e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.57 135.23 -12.66 9.20e-01 1.18e+00 1.89e+02 angle pdb=" O GLY A 136 " pdb=" C GLY A 136 " pdb=" N GLY A 137 " ideal model delta sigma weight residual 122.42 105.72 16.70 1.31e+00 5.83e-01 1.62e+02 angle pdb=" OE1 GLN A 95 " pdb=" CD GLN A 95 " pdb=" NE2 GLN A 95 " ideal model delta sigma weight residual 122.60 109.95 12.65 1.00e+00 1.00e+00 1.60e+02 angle pdb=" O VAL A 35 " pdb=" C VAL A 35 " pdb=" N ALA A 36 " ideal model delta sigma weight residual 122.62 108.76 13.86 1.17e+00 7.31e-01 1.40e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.87: 958 17.87 - 35.74: 99 35.74 - 53.61: 38 53.61 - 71.48: 15 71.48 - 89.35: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 180.00 154.76 25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA VAL A 35 " pdb=" C VAL A 35 " pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta harmonic sigma weight residual -180.00 -156.61 -23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual -180.00 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.200: 92 0.200 - 0.397: 73 0.397 - 0.593: 41 0.593 - 0.789: 29 0.789 - 0.986: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PHE A 119 " pdb=" N PHE A 119 " pdb=" C PHE A 119 " pdb=" CB PHE A 119 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" CA VAL A 23 " pdb=" N VAL A 23 " pdb=" C VAL A 23 " pdb=" CB VAL A 23 " both_signs ideal model delta sigma weight residual False 2.44 3.36 -0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CA ALA A 183 " pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CB ALA A 183 " both_signs ideal model delta sigma weight residual False 2.48 3.39 -0.90 2.00e-01 2.50e+01 2.04e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.077 2.00e-02 2.50e+03 5.81e-02 1.01e+02 pdb=" CG ATYR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.101 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.008 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.085 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " -0.061 9.50e-02 1.11e+02 6.84e-02 9.63e+01 pdb=" NE ARG A 145 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " -0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " 0.077 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " -0.067 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " 0.099 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " 0.023 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.086 2.00e-02 2.50e+03 5.52e-02 9.13e+01 pdb=" CG PHE A 164 " 0.111 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.079 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.077 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.030 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.015 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1060 2.32 - 2.89: 8105 2.89 - 3.46: 10509 3.46 - 4.03: 15335 4.03 - 4.60: 21607 Nonbonded interactions: 56616 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.754 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.778 1.850 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.813 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.834 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.834 1.850 ... (remaining 56611 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_8736282_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= 0.2612 r_free= 0.1988 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.799588 | | target function (ml) not normalized (work): 233222.447168 | | target function (ml) not normalized (free): 11870.779398 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3018 0.2115 7.0143 4.9474| | 2: 3.57 - 2.84 1.00 2876 122 0.2418 0.1840 4.3513 4.3614| | 3: 2.84 - 2.48 1.00 2833 165 0.2372 0.1778 4.137 4.1642| | 4: 2.47 - 2.25 1.00 2825 136 0.2323 0.1464 3.8442 3.8312| | 5: 2.25 - 2.09 1.00 2756 127 0.2489 0.1678 3.8105 3.8507| | 6: 2.09 - 1.97 1.00 2846 113 0.2568 0.1744 3.4794 3.5643| | 7: 1.97 - 1.87 1.00 2787 165 0.2517 0.1824 3.1488 3.2053| | 8: 1.87 - 1.79 1.00 2789 144 0.2514 0.1916 3.0909 3.1685| | 9: 1.79 - 1.72 1.00 2745 138 0.2470 0.1926 2.9163 2.9206| | 10: 1.72 - 1.66 1.00 2789 158 0.2388 0.2160 2.8368 2.9399| | 11: 1.66 - 1.61 1.00 2740 147 0.2531 0.1836 2.7522 2.7698| | 12: 1.61 - 1.56 1.00 2787 146 0.2574 0.2073 2.6593 2.7021| | 13: 1.56 - 1.52 1.00 2745 130 0.2568 0.1999 2.5905 2.6694| | 14: 1.52 - 1.48 1.00 2803 134 0.2552 0.1980 2.5124 2.5743| | 15: 1.48 - 1.45 1.00 2738 128 0.2577 0.1961 2.4258 2.4594| | 16: 1.45 - 1.42 1.00 2756 161 0.2668 0.2219 2.4077 2.4884| | 17: 1.42 - 1.39 1.00 2785 139 0.2707 0.2257 2.3424 2.3854| | 18: 1.39 - 1.36 1.00 2741 179 0.2702 0.2069 2.2704 2.2648| | 19: 1.36 - 1.34 1.00 2807 134 0.2727 0.2415 2.2598 2.3313| | 20: 1.34 - 1.32 1.00 2696 147 0.2688 0.2467 2.2038 2.2454| | 21: 1.32 - 1.30 1.00 2785 112 0.2698 0.2329 2.1657 2.1808| | 22: 1.29 - 1.27 1.00 2704 152 0.2712 0.2569 2.1278 2.1948| | 23: 1.27 - 1.26 1.00 2802 156 0.2853 0.2526 2.1172 2.1711| | 24: 1.26 - 1.24 1.00 2744 132 0.2789 0.2370 2.0779 2.0959| | 25: 1.24 - 1.22 1.00 2734 148 0.2887 0.2565 2.0526 2.0817| | 26: 1.22 - 1.21 1.00 2727 135 0.2845 0.2534 2.0077 2.1243| | 27: 1.21 - 1.19 1.00 2814 148 0.2947 0.2558 2.0064 2.0303| | 28: 1.19 - 1.18 1.00 2671 147 0.3042 0.2829 2.0015 1.9986| | 29: 1.18 - 1.16 1.00 2800 134 0.3023 0.2805 1.9842 2.0476| | 30: 1.16 - 1.15 1.00 2740 148 0.3063 0.2976 1.9392 1.992| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.04 0.76 0.23 1516.93| | 2: 3.57 - 2.84 2876 122 0.80 26.27 1.27 0.23 1516.93| | 3: 2.84 - 2.48 2833 165 0.73 32.42 1.25 0.24 1258.58| | 4: 2.47 - 2.25 2825 136 0.81 25.84 1.25 0.25 588.12| | 5: 2.25 - 2.09 2756 127 0.77 29.66 1.28 0.25 588.12| | 6: 2.09 - 1.97 2846 113 0.83 23.22 1.30 0.25 323.40| | 7: 1.97 - 1.87 2787 165 0.90 17.08 1.28 0.26 97.63| | 8: 1.87 - 1.79 2789 144 0.85 21.79 1.25 0.26 97.63| | 9: 1.79 - 1.72 2745 138 0.87 19.40 1.24 0.26 59.61| | 10: 1.72 - 1.66 2789 158 0.86 20.93 1.21 0.25 52.00| | 11: 1.66 - 1.61 2740 147 0.84 22.44 1.25 0.25 50.15| | 12: 1.61 - 1.56 2787 146 0.88 19.03 1.24 0.25 31.41| | 13: 1.56 - 1.52 2745 130 0.86 21.06 1.24 0.25 31.41| | 14: 1.52 - 1.48 2803 134 0.86 21.37 1.23 0.25 27.93| | 15: 1.48 - 1.45 2738 128 0.87 20.35 1.24 0.25 21.55| | 16: 1.45 - 1.42 2756 161 0.85 22.05 1.23 0.25 21.55| | 17: 1.42 - 1.39 2785 139 0.86 21.25 1.24 0.25 18.14| | 18: 1.39 - 1.36 2741 179 0.86 21.39 1.24 0.25 16.16| | 19: 1.36 - 1.34 2807 134 0.85 22.43 1.22 0.25 16.16| | 20: 1.34 - 1.32 2696 147 0.86 21.32 1.21 0.24 13.45| | 21: 1.32 - 1.30 2785 112 0.85 22.36 1.20 0.24 13.26| | 22: 1.29 - 1.27 2704 152 0.85 22.77 1.21 0.24 12.94| | 23: 1.27 - 1.26 2802 156 0.85 22.63 1.22 0.24 11.32| | 24: 1.26 - 1.24 2744 132 0.85 23.06 1.20 0.24 11.32| | 25: 1.24 - 1.22 2734 148 0.84 23.95 1.21 0.24 10.80| | 26: 1.22 - 1.21 2727 135 0.84 24.31 1.20 0.23 10.21| | 27: 1.21 - 1.19 2814 148 0.83 24.96 1.20 0.23 10.21| | 28: 1.19 - 1.18 2671 147 0.82 25.63 1.18 0.23 9.57| | 29: 1.18 - 1.16 2800 134 0.82 26.05 1.16 0.23 9.32| | 30: 1.16 - 1.15 2740 148 0.80 27.48 1.15 0.23 9.32| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.32 max = 1516.93 mean = 221.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.95 mean = 23.05| |phase err.(test): min = 0.00 max = 88.86 mean = 23.05| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.238 1557 Z= 5.499 Angle : 5.270 16.705 2118 Z= 3.642 Chirality : 0.390 0.986 243 Planarity : 0.033 0.085 284 Dihedral : 13.762 89.347 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 35.68 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.46), residues: 224 helix: -3.33 (0.31), residues: 103 sheet: -0.11 (0.89), residues: 28 loop : -0.66 (0.57), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.077 0.023 ARG A 145 TYR 0.087 0.040 TYR A 141 PHE 0.109 0.040 PHE A 164 HIS 0.107 0.036 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2612 r_free= 0.1988 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.799588 | | target function (ml) not normalized (work): 233222.447168 | | target function (ml) not normalized (free): 11870.779398 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2572 0.2613 0.1989 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2572 0.2613 0.1989 n_refl.: 87602 remove outliers: r(all,work,free)=0.1988 0.1991 0.1989 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2011 0.2015 0.2002 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1654 0.1646 0.1811 n_refl.: 87594 remove outliers: r(all,work,free)=0.1653 0.1645 0.1811 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 0.3884 386.541 355.242 0.670 1.002 0.403 11.894-9.307 99.02 97 4 0.1803 614.002 594.547 0.928 1.003 0.390 9.237-7.194 100.00 213 7 0.2131 502.178 492.214 0.957 1.004 0.354 7.162-5.571 100.00 427 22 0.2194 376.856 363.821 0.927 1.004 0.283 5.546-4.326 100.00 867 58 0.1285 517.331 511.869 0.964 1.004 0.249 4.315-3.360 100.00 1859 96 0.1155 491.985 488.056 1.004 1.003 0.189 3.356-2.611 100.00 3867 181 0.1427 323.209 319.857 0.995 1.003 0.099 2.608-2.026 99.99 8198 413 0.1355 214.258 211.986 1.007 1.002 0.000 2.025-1.573 100.00 17313 902 0.1675 104.632 103.834 1.012 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2071 46.398 45.119 1.004 0.997 0.000 1.221-1.150 99.97 13689 708 0.2621 29.234 26.954 0.975 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0442 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1645 r_free=0.1811 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** A 80 GLN B A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1650 r_free=0.1814 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.459676 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2004.256912 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 0.1770 0.1883 0.0113 0.002 0.4 4.5 0.0 0.0 0 0.125 0.1577 0.1717 0.0140 0.001 0.5 3.5 0.0 0.0 0 0.250 0.1451 0.1618 0.0167 0.002 0.5 3.2 0.0 0.0 0 0.500 0.1386 0.1578 0.0192 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1362 0.1561 0.0199 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1349 0.1549 0.0200 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1288 0.1501 0.0213 0.002 0.6 2.6 0.5 0.0 0 2.000 0.1275 0.1500 0.0225 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1257 0.1487 0.0230 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1250 0.1481 0.0231 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1246 0.1477 0.0231 0.004 0.8 3.2 0.5 0.0 0 6.000 0.1243 0.1474 0.0231 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1239 0.1472 0.0232 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1238 0.1473 0.0235 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1235 0.1469 0.0234 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1232 0.1472 0.0240 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1230 0.1472 0.0242 0.007 0.9 3.8 0.5 0.6 0 12.000 0.1229 0.1477 0.0248 0.008 1.0 3.5 0.5 0.6 0 13.230 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1235 0.1469 0.0234 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 12.35 14.69 2.34 3.013 19.051 2004.257 0.018 12.35 14.68 2.33 2.989 19.051 60.128 0.018 12.41 14.66 2.25 2.657 19.051 250.532 0.018 12.72 15.32 2.59 2.738 19.216 1002.128 0.017 12.51 15.38 2.86 3.120 19.500 2004.257 0.016 12.48 15.45 2.97 3.345 19.643 3006.385 0.016 12.38 15.41 3.04 3.398 19.658 4008.514 0.015 12.33 15.42 3.08 3.354 19.623 5010.642 0.015 12.27 15.38 3.11 3.324 19.602 6012.771 0.015 12.27 15.44 3.18 3.471 19.686 7014.899 0.015 12.23 15.41 3.19 3.322 19.593 8017.028 0.015 12.24 15.49 3.25 3.466 19.660 9019.156 0.015 12.24 15.51 3.27 3.629 19.738 10021.285 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 250.532 Accepted refinement result: 12.41 14.66 2.25 2.657 19.051 250.532 0.018 Individual atomic B min max mean iso aniso Overall: 9.06 119.43 20.08 3.29 0 1785 Protein: 9.06 114.87 16.99 3.29 0 1519 Water: 11.44 119.43 38.22 N/A 0 258 Other: 19.74 26.60 22.07 N/A 0 8 Chain A: 9.06 119.43 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1272 20.10 - 31.14 227 31.14 - 42.17 125 42.17 - 53.21 94 53.21 - 64.25 42 64.25 - 75.28 11 75.28 - 86.32 7 86.32 - 97.36 4 97.36 - 108.39 1 108.39 - 119.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1241 r_free=0.1466 r_work=0.1243 r_free=0.1469 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1243 r_free = 0.1469 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1235 r_free = 0.1460 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= 0.1235 r_free= 0.1460 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016993 | | target function (ls_wunit_k1) not normalized (work): 1415.476236 | | target function (ls_wunit_k1) not normalized (free): 109.511799 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1246 0.1235 0.1460 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1676 0.1677 0.1700 n_refl.: 87593 remove outliers: r(all,work,free)=0.1676 0.1677 0.1700 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1683 0.1684 0.1704 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1244 0.1234 0.1453 n_refl.: 87593 remove outliers: r(all,work,free)=0.1244 0.1233 0.1453 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 0.3510 301.472 282.208 0.645 1.002 0.372 11.894-9.307 99.02 97 4 0.1685 482.941 470.530 0.921 1.003 0.367 9.237-7.194 100.00 213 7 0.1919 394.987 389.012 0.963 1.003 0.340 7.162-5.571 100.00 427 22 0.1834 296.416 290.477 0.935 1.003 0.259 5.546-4.326 100.00 867 58 0.0997 406.905 403.895 0.963 1.003 0.204 4.315-3.360 100.00 1859 96 0.0874 386.970 385.859 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1179 254.219 253.062 1.009 1.002 0.057 2.608-2.026 99.99 8198 413 0.1030 168.524 167.799 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1121 82.298 82.466 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1457 36.494 35.994 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 22.994 21.478 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0531 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1453 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 B A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1231 r_free=0.1450 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1450 | n_water=258 | time (s): 1.520 (total time: 1.520) Filter (dist) r_work=0.1239 r_free=0.1446 | n_water=252 | time (s): 22.150 (total time: 23.670) Filter (q & B) r_work=0.1241 r_free=0.1446 | n_water=249 | time (s): 2.990 (total time: 26.660) Compute maps r_work=0.1241 r_free=0.1446 | n_water=249 | time (s): 1.200 (total time: 27.860) Filter (map) r_work=0.1254 r_free=0.1447 | n_water=228 | time (s): 2.850 (total time: 30.710) Find peaks r_work=0.1254 r_free=0.1447 | n_water=228 | time (s): 0.540 (total time: 31.250) Add new water r_work=0.1399 r_free=0.1617 | n_water=440 | time (s): 3.240 (total time: 34.490) Refine new water occ: r_work=0.1306 r_free=0.1471 adp: r_work=0.1225 r_free=0.1423 occ: r_work=0.1237 r_free=0.1414 adp: r_work=0.1204 r_free=0.1401 occ: r_work=0.1208 r_free=0.1390 adp: r_work=0.1196 r_free=0.1387 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1387 r_work=0.1196 r_free=0.1387 | n_water=440 | time (s): 57.880 (total time: 92.370) Filter (q & B) r_work=0.1199 r_free=0.1386 | n_water=427 | time (s): 2.630 (total time: 95.000) Filter (dist only) r_work=0.1199 r_free=0.1386 | n_water=426 | time (s): 35.000 (total time: 130.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.008448 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1483.116354 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 0.1695 0.1809 0.0114 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1503 0.1636 0.0133 0.001 0.4 6.1 0.0 0.0 0 0.250 0.1396 0.1548 0.0152 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1321 0.1485 0.0164 0.002 0.5 5.8 0.0 0.0 0 0.750 0.1319 0.1488 0.0169 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1311 0.1477 0.0167 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1251 0.1439 0.0188 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1222 0.1419 0.0197 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1210 0.1411 0.0202 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1202 0.1412 0.0210 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1197 0.1411 0.0214 0.004 0.7 5.4 0.5 0.0 0 6.000 0.1194 0.1409 0.0215 0.005 0.8 5.4 0.5 0.0 0 7.000 0.1191 0.1410 0.0218 0.005 0.8 5.8 0.5 0.0 0 8.000 0.1188 0.1406 0.0218 0.006 0.8 5.4 0.5 0.0 0 9.000 0.1185 0.1403 0.0219 0.006 0.9 5.4 0.5 0.0 0 10.000 0.1183 0.1405 0.0222 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1181 0.1402 0.0221 0.007 0.9 5.8 0.5 0.0 0 12.000 0.1181 0.1412 0.0232 0.008 0.9 5.4 0.5 0.6 0 13.504 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1181 0.1402 0.0221 0.007 0.9 5.8 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.81 14.02 2.21 3.764 21.835 1483.116 0.016 11.81 14.02 2.21 3.764 21.835 44.493 0.016 11.81 14.02 2.21 3.764 21.835 185.390 0.016 12.05 14.49 2.43 3.588 21.861 741.558 0.015 11.99 14.73 2.74 3.453 22.052 1483.116 0.015 11.89 14.77 2.87 3.490 21.988 2224.675 0.014 11.75 14.64 2.89 3.468 22.143 2966.233 0.014 11.73 14.71 2.99 3.481 22.160 3707.791 0.014 11.61 14.62 3.01 3.509 22.019 4449.349 0.014 11.66 14.73 3.07 3.517 22.117 5190.907 0.014 11.60 14.67 3.08 3.529 22.151 5932.465 0.014 11.64 14.86 3.22 3.584 22.239 6674.024 0.014 11.60 14.80 3.20 3.606 22.294 7415.582 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.493 Accepted refinement result: 11.81 14.02 2.21 3.764 21.835 44.493 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 114.90 22.30 3.29 198 1755 Protein: 9.10 114.90 17.02 3.29 0 1519 Water: 11.48 76.68 41.11 N/A 198 228 Other: 19.77 26.63 22.10 N/A 0 8 Chain A: 9.10 114.90 19.49 N/A 0 1755 Chain S: 17.42 60.00 47.14 N/A 198 0 Histogram: Values Number of atoms 9.10 - 19.68 1259 19.68 - 30.26 243 30.26 - 40.84 168 40.84 - 51.42 134 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=0.1181 r_free=0.1402 r_work=0.1181 r_free=0.1402 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1181 r_free = 0.1402 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1180 r_free = 0.1407 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= 0.1180 r_free= 0.1407 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014919 | | target function (ls_wunit_k1) not normalized (work): 1242.706973 | | target function (ls_wunit_k1) not normalized (free): 99.813307 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1180 0.1407 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1574 0.1573 0.1638 n_refl.: 87592 remove outliers: r(all,work,free)=0.1574 0.1573 0.1638 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1576 0.1574 0.1639 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1188 0.1177 0.1405 n_refl.: 87592 remove outliers: r(all,work,free)=0.1187 0.1176 0.1405 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3353 297.375 274.847 0.584 1.002 0.340 11.894-9.307 99.02 97 4 0.1676 482.941 476.403 0.920 1.003 0.333 9.237-7.194 100.00 213 7 0.1696 394.987 394.190 0.982 1.003 0.290 7.162-5.571 100.00 427 22 0.1588 296.416 292.293 0.937 1.003 0.224 5.546-4.326 100.00 867 58 0.0862 406.905 403.660 0.961 1.003 0.210 4.315-3.360 100.00 1859 96 0.0768 386.970 385.916 1.005 1.002 0.190 3.356-2.611 100.00 3867 181 0.1067 254.219 253.413 1.009 1.002 0.130 2.608-2.026 99.99 8198 413 0.1004 168.524 167.975 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1091 82.298 82.517 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.494 36.035 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 22.994 21.507 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0136 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1176 r_free=0.1405 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1176 r_free=0.1405 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1176 r_free=0.1405 | n_water=426 | time (s): 2.040 (total time: 2.040) Filter (dist) r_work=0.1176 r_free=0.1402 | n_water=421 | time (s): 38.260 (total time: 40.300) Filter (q & B) r_work=0.1176 r_free=0.1402 | n_water=421 | time (s): 1.030 (total time: 41.330) Compute maps r_work=0.1176 r_free=0.1402 | n_water=421 | time (s): 1.400 (total time: 42.730) Filter (map) r_work=0.1213 r_free=0.1395 | n_water=290 | time (s): 2.310 (total time: 45.040) Find peaks r_work=0.1213 r_free=0.1395 | n_water=290 | time (s): 0.590 (total time: 45.630) Add new water r_work=0.1329 r_free=0.1531 | n_water=484 | time (s): 3.110 (total time: 48.740) Refine new water occ: r_work=0.1238 r_free=0.1437 adp: r_work=0.1240 r_free=0.1440 occ: r_work=0.1216 r_free=0.1413 adp: r_work=0.1216 r_free=0.1416 occ: r_work=0.1199 r_free=0.1391 adp: r_work=0.1195 r_free=0.1390 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1390 r_work=0.1195 r_free=0.1390 | n_water=484 | time (s): 176.830 (total time: 225.570) Filter (q & B) r_work=0.1201 r_free=0.1396 | n_water=443 | time (s): 2.860 (total time: 228.430) Filter (dist only) r_work=0.1201 r_free=0.1395 | n_water=442 | time (s): 38.740 (total time: 267.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.773263 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.032034 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 0.1237 0.1377 0.0139 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1193 0.1341 0.0148 0.003 0.7 3.5 0.5 0.0 0 0.266 0.1177 0.1327 0.0150 0.004 0.8 3.2 0.5 0.0 0 0.532 0.1167 0.1322 0.0155 0.005 0.9 3.8 0.5 0.0 0 0.798 0.1164 0.1323 0.0159 0.006 1.0 3.8 0.5 0.0 0 1.064 0.1161 0.1323 0.0161 0.007 1.0 3.8 0.5 0.0 0 1.330 0.1160 0.1324 0.0164 0.007 1.1 3.5 0.5 0.0 0 1.596 0.1156 0.1322 0.0166 0.008 1.1 3.8 0.5 0.0 0 1.862 0.1166 0.1323 0.0157 0.005 0.9 3.5 0.5 0.0 0 0.887 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1156 0.1322 0.0166 0.008 1.1 3.8 0.5 0.0 0 1.862 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.56 13.22 1.66 3.768 21.281 44.032 3.623 11.56 13.22 1.66 3.768 21.281 1.321 3.623 11.57 13.22 1.65 3.756 21.281 5.504 3.623 11.60 13.27 1.67 3.703 21.270 22.016 3.616 11.65 13.37 1.72 3.729 21.236 44.032 3.617 11.57 13.35 1.78 3.751 21.225 66.048 3.611 11.51 13.32 1.81 3.766 21.221 88.064 3.606 11.50 13.35 1.84 3.780 21.205 110.080 3.604 11.49 13.36 1.87 3.796 21.198 132.096 3.603 11.46 13.35 1.88 3.808 21.193 154.112 3.601 11.45 13.33 1.88 3.818 21.189 176.128 3.600 11.43 13.32 1.89 3.823 21.189 198.144 3.599 11.43 13.32 1.88 3.835 21.181 220.160 3.598 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.321 Accepted refinement result: 11.56 13.22 1.66 3.768 21.281 1.321 3.623 Individual atomic B min max mean iso aniso Overall: 9.11 114.91 21.28 3.29 216 1753 Protein: 9.11 114.91 17.03 3.29 0 1519 Water: 11.48 76.69 35.85 N/A 216 226 Other: 19.78 26.64 22.11 N/A 0 8 Chain A: 9.11 114.91 19.46 N/A 0 1753 Chain S: 16.41 60.01 35.98 N/A 216 0 Histogram: Values Number of atoms 9.11 - 19.69 1263 19.69 - 30.27 287 30.27 - 40.85 212 40.85 - 51.43 128 51.43 - 62.01 56 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1156 r_free=0.1322 r_work=0.1156 r_free=0.1322 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1322 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1148 r_free = 0.1314 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1148 r_free= 0.1314 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.614600 | | target function (ml) not normalized (work): 301070.909850 | | target function (ml) not normalized (free): 15856.258989 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1156 0.1148 0.1314 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1487 0.1486 0.1540 n_refl.: 87589 remove outliers: r(all,work,free)=0.1487 0.1486 0.1540 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1487 0.1485 0.1539 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1141 0.1306 n_refl.: 87589 remove outliers: r(all,work,free)=0.1148 0.1140 0.1306 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 0.4028 297.375 268.296 0.486 1.001 0.320 11.894-9.307 97.06 95 4 0.2289 485.039 460.511 0.874 1.002 0.320 9.237-7.194 99.09 211 7 0.2242 389.482 388.949 0.958 1.003 0.190 7.162-5.571 100.00 427 22 0.2075 296.416 286.420 0.926 1.003 0.170 5.546-4.326 100.00 867 58 0.1133 406.905 402.002 0.964 1.003 0.160 4.315-3.360 100.00 1859 96 0.0931 386.970 384.544 1.003 1.002 0.150 3.356-2.611 100.00 3867 181 0.1127 254.219 252.246 1.008 1.002 0.100 2.608-2.026 99.99 8198 413 0.0924 168.524 167.781 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0894 82.298 82.587 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.494 36.088 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2164 22.994 21.538 0.991 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0135 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1140 r_free=0.1306 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 B Total number of N/Q/H flips: 1 r_work=0.1140 r_free=0.1306 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1140 r_free=0.1306 | n_water=442 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1140 r_free=0.1308 | n_water=439 | time (s): 45.050 (total time: 47.510) Filter (q & B) r_work=0.1140 r_free=0.1308 | n_water=437 | time (s): 3.860 (total time: 51.370) Compute maps r_work=0.1140 r_free=0.1308 | n_water=437 | time (s): 1.870 (total time: 53.240) Filter (map) r_work=0.1159 r_free=0.1313 | n_water=337 | time (s): 3.970 (total time: 57.210) Find peaks r_work=0.1159 r_free=0.1313 | n_water=337 | time (s): 0.700 (total time: 57.910) Add new water r_work=0.1224 r_free=0.1387 | n_water=487 | time (s): 3.800 (total time: 61.710) Refine new water occ: r_work=0.1164 r_free=0.1326 adp: r_work=0.1164 r_free=0.1328 occ: r_work=0.1149 r_free=0.1307 adp: r_work=0.1148 r_free=0.1310 occ: r_work=0.1138 r_free=0.1295 adp: r_work=0.1134 r_free=0.1295 ADP+occupancy (water only), MIN, final r_work=0.1134 r_free=0.1295 r_work=0.1134 r_free=0.1295 | n_water=487 | time (s): 150.820 (total time: 212.530) Filter (q & B) r_work=0.1139 r_free=0.1301 | n_water=451 | time (s): 3.980 (total time: 216.510) Filter (dist only) r_work=0.1146 r_free=0.1298 | n_water=449 | time (s): 46.060 (total time: 262.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.712470 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.891425 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 0.1208 0.1338 0.0130 0.002 0.6 4.2 0.5 0.0 0 0.086 0.1175 0.1316 0.0141 0.003 0.7 3.5 0.5 0.0 0 0.257 0.1160 0.1306 0.0146 0.004 0.9 3.5 0.5 0.0 0 0.514 0.1153 0.1304 0.0150 0.005 0.9 3.5 0.5 0.0 0 0.771 0.1149 0.1300 0.0151 0.006 1.0 3.5 0.5 0.0 0 1.027 0.1146 0.1300 0.0154 0.007 1.0 3.5 0.5 0.0 0 1.284 0.1144 0.1301 0.0157 0.008 1.1 3.5 0.5 0.0 0 1.541 0.1143 0.1297 0.0155 0.008 1.1 3.5 0.5 0.0 0 1.798 0.1152 0.1304 0.0153 0.006 1.0 3.5 0.5 0.0 0 0.856 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1143 0.1297 0.0155 0.008 1.1 3.5 0.5 0.0 0 1.798 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.43 12.97 1.55 3.768 21.270 43.891 3.611 11.43 12.97 1.55 3.768 21.270 1.317 3.611 11.43 12.97 1.54 3.766 21.270 5.486 3.611 11.46 13.03 1.57 3.704 21.262 21.946 3.605 11.54 13.18 1.65 3.723 21.230 43.891 3.608 11.45 13.14 1.69 3.749 21.220 65.837 3.602 11.39 13.09 1.71 3.763 21.217 87.783 3.597 11.37 13.10 1.73 3.774 21.213 109.729 3.596 11.34 13.09 1.74 3.784 21.210 131.674 3.594 11.33 13.09 1.76 3.799 21.203 153.620 3.593 11.34 13.11 1.77 3.815 21.191 175.566 3.593 11.32 13.08 1.76 3.822 21.191 197.511 3.591 11.30 13.06 1.76 3.824 21.193 219.457 3.590 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.486 Accepted refinement result: 11.43 12.97 1.54 3.766 21.270 5.486 3.611 Individual atomic B min max mean iso aniso Overall: 9.10 114.88 21.26 3.28 225 1751 Protein: 9.10 114.88 17.03 3.29 0 1519 Water: 11.48 76.69 35.56 N/A 225 224 Other: 19.77 26.62 22.10 N/A 0 8 Chain A: 9.10 114.88 19.43 N/A 0 1751 Chain S: 16.41 60.00 35.52 N/A 225 0 Histogram: Values Number of atoms 9.10 - 19.68 1263 19.68 - 30.26 284 30.26 - 40.84 226 40.84 - 51.41 133 51.41 - 61.99 48 61.99 - 72.57 11 72.57 - 83.15 5 83.15 - 93.72 4 93.72 - 104.30 0 104.30 - 114.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1143 r_free=0.1297 r_work=0.1143 r_free=0.1297 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1297 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1138 r_free = 0.1291 target_work(ml) = 3.608 | | 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= 0.1138 r_free= 0.1291 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.608352 | | target function (ml) not normalized (work): 300536.035795 | | target function (ml) not normalized (free): 15827.060409 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1145 0.1138 0.1291 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1479 0.1478 0.1516 n_refl.: 87585 remove outliers: r(all,work,free)=0.1479 0.1478 0.1516 n_refl.: 87585 overall B=-0.00 to atoms: r(all,work,free)=0.1478 0.1477 0.1515 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1145 0.1138 0.1291 n_refl.: 87585 remove outliers: r(all,work,free)=0.1141 0.1133 0.1291 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 0.3838 285.969 258.284 0.458 0.999 0.294 11.894-9.307 93.14 91 4 0.2320 475.648 461.426 0.874 1.001 0.276 9.237-7.194 97.73 208 7 0.2315 387.543 382.797 0.934 1.002 0.162 7.162-5.571 100.00 427 22 0.2175 296.416 285.792 0.918 1.002 0.149 5.546-4.326 100.00 867 58 0.1115 406.905 401.502 0.964 1.002 0.130 4.315-3.360 100.00 1859 96 0.0927 386.970 384.510 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1107 254.219 252.340 1.010 1.002 0.014 2.608-2.026 99.99 8198 413 0.0913 168.524 167.841 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.298 82.605 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.494 36.089 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 22.994 21.531 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0081 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1133 r_free=0.1291 After: r_work=0.1134 r_free=0.1291 ================================== NQH flips ================================== r_work=0.1134 r_free=0.1291 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=0.1291 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1134 r_free=0.1291 | n_water=449 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1135 r_free=0.1290 | n_water=448 | time (s): 49.700 (total time: 52.160) Filter (q & B) r_work=0.1135 r_free=0.1289 | n_water=447 | time (s): 3.830 (total time: 55.990) Compute maps r_work=0.1135 r_free=0.1289 | n_water=447 | time (s): 1.820 (total time: 57.810) Filter (map) r_work=0.1162 r_free=0.1301 | n_water=355 | time (s): 3.920 (total time: 61.730) Find peaks r_work=0.1162 r_free=0.1301 | n_water=355 | time (s): 0.710 (total time: 62.440) Add new water r_work=0.1207 r_free=0.1349 | n_water=493 | time (s): 3.400 (total time: 65.840) Refine new water occ: r_work=0.1153 r_free=0.1300 adp: r_work=0.1153 r_free=0.1302 occ: r_work=0.1142 r_free=0.1286 adp: r_work=0.1141 r_free=0.1288 occ: r_work=0.1134 r_free=0.1276 adp: r_work=0.1132 r_free=0.1276 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1276 r_work=0.1132 r_free=0.1276 | n_water=493 | time (s): 235.370 (total time: 301.210) Filter (q & B) r_work=0.1137 r_free=0.1285 | n_water=458 | time (s): 3.740 (total time: 304.950) Filter (dist only) r_work=0.1137 r_free=0.1284 | n_water=457 | time (s): 48.040 (total time: 352.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.789896 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.480515 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 0.1224 0.1341 0.0117 0.004 0.7 6.1 0.0 0.0 0 0.089 0.1175 0.1307 0.0132 0.004 0.8 6.7 0.0 0.0 0 0.268 0.1156 0.1295 0.0139 0.005 0.9 6.4 0.5 0.0 0 0.537 0.1148 0.1289 0.0141 0.006 1.0 6.1 0.5 0.0 0 0.805 0.1143 0.1285 0.0142 0.006 1.1 6.1 0.5 0.0 0 1.074 0.1139 0.1283 0.0144 0.008 1.1 5.8 0.5 0.0 0 1.342 0.1137 0.1283 0.0146 0.008 1.1 5.8 0.5 0.0 0 1.611 0.1137 0.1283 0.0146 0.008 1.1 6.1 0.5 0.0 0 1.879 0.1146 0.1288 0.0141 0.006 1.0 6.1 0.5 0.0 0 0.895 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1137 0.1283 0.0146 0.008 1.1 5.8 0.5 0.0 0 1.611 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.37 12.83 1.46 3.764 21.251 46.481 3.608 11.37 12.83 1.46 3.764 21.251 1.394 3.608 11.37 12.83 1.46 3.764 21.251 5.810 3.608 11.39 12.89 1.50 3.704 21.241 23.240 3.601 11.47 13.07 1.60 3.726 21.207 46.481 3.604 11.39 13.04 1.65 3.748 21.198 69.721 3.598 11.32 12.97 1.65 3.766 21.199 92.961 3.593 11.30 12.95 1.65 3.775 21.196 116.201 3.591 11.29 12.97 1.68 3.791 21.189 139.442 3.590 11.29 13.00 1.70 3.809 21.177 162.682 3.590 11.28 12.98 1.70 3.818 21.177 185.922 3.589 11.26 12.95 1.70 3.821 21.178 209.162 3.587 11.25 12.95 1.70 3.828 21.177 232.403 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: 1.394 Accepted refinement result: 11.37 12.83 1.46 3.764 21.251 1.394 3.608 Individual atomic B min max mean iso aniso Overall: 9.10 114.88 21.23 3.28 235 1749 Protein: 9.10 114.88 17.02 3.29 0 1519 Water: 11.48 76.68 35.19 N/A 235 222 Other: 19.77 26.62 22.10 N/A 0 8 Chain A: 9.10 114.88 19.39 N/A 0 1749 Chain S: 15.91 60.00 34.92 N/A 235 0 Histogram: Values Number of atoms 9.10 - 19.68 1263 19.68 - 30.26 294 30.26 - 40.83 223 40.83 - 51.41 133 51.41 - 61.99 49 61.99 - 72.57 11 72.57 - 83.14 5 83.14 - 93.72 4 93.72 - 104.30 0 104.30 - 114.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1137 r_free=0.1283 r_work=0.1137 r_free=0.1283 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1137 r_free = 0.1283 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1133 r_free = 0.1278 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1133 r_free= 0.1278 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605387 | | target function (ml) not normalized (work): 300249.418391 | | target function (ml) not normalized (free): 15813.989774 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1327 0.1352 5.6351 5.6141| | 2: 3.57 - 2.84 1.00 2888 124 0.1068 0.1322 5.159 5.2041| | 3: 2.83 - 2.48 1.00 2820 163 0.1092 0.1168 4.9375 4.9617| | 4: 2.47 - 2.25 1.00 2825 136 0.0893 0.1004 4.6239 4.6749| | 5: 2.25 - 2.09 1.00 2756 127 0.0860 0.0925 4.5701 4.6112| | 6: 2.09 - 1.97 1.00 2846 113 0.0859 0.1012 4.2659 4.3732| | 7: 1.97 - 1.87 1.00 2787 165 0.0896 0.1087 3.9852 4.0867| | 8: 1.87 - 1.79 1.00 2789 144 0.0923 0.1132 3.8939 3.9997| | 9: 1.79 - 1.72 1.00 2745 138 0.0878 0.1161 3.6509 3.8213| | 10: 1.72 - 1.66 1.00 2831 160 0.0923 0.1201 3.569 3.7219| | 11: 1.66 - 1.61 1.00 2712 147 0.0874 0.1023 3.4998 3.5765| | 12: 1.61 - 1.56 1.00 2773 144 0.0906 0.1127 3.3337 3.454| | 13: 1.56 - 1.52 1.00 2745 130 0.0953 0.1045 3.3147 3.4076| | 14: 1.52 - 1.48 1.00 2803 134 0.0990 0.1030 3.2477 3.325| | 15: 1.48 - 1.45 1.00 2738 128 0.1011 0.1225 3.1584 3.2632| | 16: 1.45 - 1.42 1.00 2756 161 0.1060 0.1260 3.1396 3.2505| | 17: 1.42 - 1.39 1.00 2785 139 0.1147 0.1322 3.1246 3.2442| | 18: 1.39 - 1.36 1.00 2741 179 0.1205 0.1333 3.1096 3.2458| | 19: 1.36 - 1.34 1.00 2807 134 0.1263 0.1571 3.1154 3.2714| | 20: 1.34 - 1.32 1.00 2696 147 0.1370 0.1464 3.1138 3.1575| | 21: 1.32 - 1.30 1.00 2785 112 0.1476 0.1509 3.1157 3.1109| | 22: 1.29 - 1.27 1.00 2704 152 0.1568 0.1974 3.1262 3.2884| | 23: 1.27 - 1.26 1.00 2802 156 0.1654 0.1780 3.1353 3.197| | 24: 1.26 - 1.24 1.00 2744 132 0.1708 0.1838 3.1284 3.2296| | 25: 1.24 - 1.22 1.00 2733 148 0.1887 0.2156 3.1449 3.2592| | 26: 1.22 - 1.21 1.00 2727 135 0.1909 0.1769 3.1492 3.2024| | 27: 1.21 - 1.19 1.00 2814 148 0.2076 0.2174 3.1725 3.1647| | 28: 1.19 - 1.18 1.00 2671 147 0.2204 0.2298 3.1674 3.1721| | 29: 1.18 - 1.16 1.00 2800 134 0.2267 0.2381 3.149 3.2297| | 30: 1.16 - 1.15 1.00 2739 148 0.2448 0.2445 3.1442 3.1665| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2916 171 0.95 8.43 1.00 0.97 5654.18| | 2: 3.57 - 2.84 2888 124 0.93 12.47 1.01 0.97 5654.18| | 3: 2.83 - 2.48 2820 163 0.90 16.36 0.99 0.97 4725.38| | 4: 2.47 - 2.25 2825 136 0.92 13.40 1.00 0.98 2330.29| | 5: 2.25 - 2.09 2756 127 0.90 15.50 1.01 0.98 2330.29| | 6: 2.09 - 1.97 2846 113 0.93 12.26 1.02 0.98 1349.41| | 7: 1.97 - 1.87 2787 165 0.95 9.34 1.02 0.98 512.85| | 8: 1.87 - 1.79 2789 144 0.93 12.65 1.00 0.98 512.85| | 9: 1.79 - 1.72 2745 138 0.94 10.15 0.98 0.97 291.92| | 10: 1.72 - 1.66 2831 160 0.94 11.21 0.98 0.97 247.68| | 11: 1.66 - 1.61 2712 147 0.93 11.84 0.98 0.97 237.25| | 12: 1.61 - 1.56 2773 144 0.95 8.97 0.99 0.97 138.90| | 13: 1.56 - 1.52 2745 130 0.95 10.47 1.03 0.97 138.90| | 14: 1.52 - 1.48 2803 134 0.94 10.85 1.02 0.98 124.58| | 15: 1.48 - 1.45 2738 128 0.95 9.98 1.02 0.98 98.37| | 16: 1.45 - 1.42 2756 161 0.94 11.13 1.02 0.98 98.37| | 17: 1.42 - 1.39 2785 139 0.95 10.98 1.01 0.98 89.70| | 18: 1.39 - 1.36 2741 179 0.94 11.60 1.01 0.98 84.68| | 19: 1.36 - 1.34 2807 134 0.94 11.93 1.00 0.98 84.68| | 20: 1.34 - 1.32 2696 147 0.94 12.15 0.98 0.97 80.47| | 21: 1.32 - 1.30 2785 112 0.94 13.16 0.98 0.96 80.17| | 22: 1.29 - 1.27 2704 152 0.93 13.68 0.98 0.96 80.54| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.97 0.94 82.40| | 24: 1.26 - 1.24 2744 132 0.92 14.88 0.96 0.94 82.40| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.94 84.29| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.02 0.93 86.39| | 27: 1.21 - 1.19 2814 148 0.89 18.79 1.02 0.93 86.39| | 28: 1.19 - 1.18 2671 147 0.88 20.41 1.01 0.93 90.10| | 29: 1.18 - 1.16 2800 134 0.88 20.51 0.99 0.92 91.50| | 30: 1.16 - 1.15 2739 148 0.86 22.05 0.98 0.92 91.50| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 80.17 max = 5654.18 mean = 875.87| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.46| |phase err.(test): min = 0.00 max = 89.31 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1140 0.1133 0.1278 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1458 0.1458 0.1481 n_refl.: 87574 remove outliers: r(all,work,free)=0.1458 0.1458 0.1481 n_refl.: 87574 overall B=-0.00 to atoms: r(all,work,free)=0.1457 0.1457 0.1480 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1139 0.1132 0.1277 n_refl.: 87574 remove outliers: r(all,work,free)=0.1139 0.1132 0.1277 n_refl.: 87572 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3975 283.398 253.163 0.445 1.002 0.308 11.894-9.307 93.14 91 4 0.2302 475.648 461.524 0.871 1.002 0.300 9.237-7.194 97.27 207 7 0.2269 387.065 382.333 0.926 1.003 0.181 7.162-5.571 100.00 427 22 0.2162 296.416 285.354 0.910 1.003 0.120 5.546-4.326 100.00 867 58 0.1129 406.905 401.361 0.961 1.003 0.120 4.315-3.360 100.00 1859 96 0.0916 386.970 384.469 1.004 1.003 0.120 3.356-2.611 100.00 3867 181 0.1111 254.219 252.325 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0906 168.524 167.861 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.298 82.626 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.494 36.093 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.994 21.536 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=-0.0087 ================= 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 : 0.2612 0.1988 0.082 5.270 8.8 119.3 19.9 258 0.000 1_bss: 0.1645 0.1811 0.082 5.270 9.0 119.5 20.1 258 0.000 1_settarget: 0.1645 0.1811 0.082 5.270 9.0 119.5 20.1 258 0.000 1_nqh: 0.1650 0.1814 0.082 5.270 9.0 119.5 20.1 258 0.009 1_weight: 0.1650 0.1814 0.082 5.270 9.0 119.5 20.1 258 0.009 1_xyzrec: 0.1235 0.1469 0.006 0.897 9.0 119.5 20.1 258 0.146 1_adp: 0.1241 0.1466 0.006 0.897 9.1 119.4 20.1 258 0.146 1_regHadp: 0.1243 0.1469 0.006 0.897 9.1 119.4 20.1 258 0.146 1_occ: 0.1235 0.1460 0.006 0.897 9.1 119.4 20.1 258 0.146 2_bss: 0.1233 0.1453 0.006 0.897 9.1 119.5 20.1 258 0.146 2_settarget: 0.1233 0.1453 0.006 0.897 9.1 119.5 20.1 258 0.146 2_updatecdl: 0.1233 0.1453 0.006 0.895 9.1 119.5 20.1 258 0.146 2_nqh: 0.1231 0.1450 0.006 0.895 9.1 119.5 20.1 258 0.140 2_sol: 0.1199 0.1386 0.006 0.895 9.1 114.9 22.3 426 n/a 2_weight: 0.1199 0.1386 0.006 0.895 9.1 114.9 22.3 426 n/a 2_xyzrec: 0.1181 0.1402 0.007 0.897 9.1 114.9 22.3 426 n/a 2_adp: 0.1181 0.1402 0.007 0.897 9.1 114.9 22.3 426 n/a 2_regHadp: 0.1181 0.1402 0.007 0.897 9.1 114.9 22.3 426 n/a 2_occ: 0.1180 0.1407 0.007 0.897 9.1 114.9 22.3 426 n/a 3_bss: 0.1176 0.1405 0.007 0.897 9.1 114.9 22.3 426 n/a 3_settarget: 0.1176 0.1405 0.007 0.897 9.1 114.9 22.3 426 n/a 3_updatecdl: 0.1176 0.1405 0.007 0.899 9.1 114.9 22.3 426 n/a 3_nqh: 0.1176 0.1405 0.007 0.899 9.1 114.9 22.3 426 n/a 3_sol: 0.1201 0.1395 0.007 0.899 9.1 114.9 21.3 442 n/a 3_weight: 0.1201 0.1395 0.007 0.899 9.1 114.9 21.3 442 n/a 3_xyzrec: 0.1156 0.1322 0.008 1.082 9.1 114.9 21.3 442 n/a 3_adp: 0.1156 0.1322 0.008 1.082 9.1 114.9 21.3 442 n/a 3_regHadp: 0.1156 0.1322 0.008 1.082 9.1 114.9 21.3 442 n/a 3_occ: 0.1148 0.1314 0.008 1.082 9.1 114.9 21.3 442 n/a 4_bss: 0.1140 0.1306 0.008 1.082 9.1 114.9 21.3 442 n/a 4_settarget: 0.1140 0.1306 0.008 1.082 9.1 114.9 21.3 442 n/a 4_updatecdl: 0.1140 0.1306 0.008 1.086 9.1 114.9 21.3 442 n/a 4_nqh: 0.1140 0.1306 0.008 1.086 9.1 114.9 21.3 442 n/a 4_sol: 0.1146 0.1298 0.008 1.086 9.1 114.9 21.3 449 n/a 4_weight: 0.1146 0.1298 0.008 1.086 9.1 114.9 21.3 449 n/a 4_xyzrec: 0.1143 0.1297 0.008 1.119 9.1 114.9 21.3 449 n/a 4_adp: 0.1143 0.1297 0.008 1.119 9.1 114.9 21.3 449 n/a 4_regHadp: 0.1143 0.1297 0.008 1.119 9.1 114.9 21.3 449 n/a 4_occ: 0.1138 0.1291 0.008 1.119 9.1 114.9 21.3 449 n/a 5_bss: 0.1133 0.1291 0.008 1.119 9.1 114.9 21.3 449 n/a 5_settarget: 0.1133 0.1291 0.008 1.119 9.1 114.9 21.3 449 n/a 5_updatecdl: 0.1133 0.1291 0.008 1.117 9.1 114.9 21.3 449 n/a 5_setrh: 0.1134 0.1291 0.008 1.117 9.1 114.9 21.3 449 n/a 5_nqh: 0.1134 0.1291 0.008 1.117 9.1 114.9 21.3 449 n/a 5_sol: 0.1137 0.1284 0.008 1.117 9.1 114.9 21.2 457 n/a 5_weight: 0.1137 0.1284 0.008 1.117 9.1 114.9 21.2 457 n/a 5_xyzrec: 0.1137 0.1283 0.008 1.120 9.1 114.9 21.2 457 n/a 5_adp: 0.1137 0.1283 0.008 1.120 9.1 114.9 21.2 457 n/a 5_regHadp: 0.1137 0.1283 0.008 1.120 9.1 114.9 21.2 457 n/a 5_occ: 0.1133 0.1278 0.008 1.120 9.1 114.9 21.2 457 n/a end: 0.1132 0.1277 0.008 1.120 9.1 114.9 21.2 457 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8736282_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8736282_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9800 Refinement macro-cycles (run) : 13619.2900 Write final files (write_after_run_outputs) : 99.2100 Total : 13722.4800 Total CPU time: 3.82 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:08:00 PST -0800 (1735366080.70 s) Start R-work = 0.1645, R-free = 0.1811 Final R-work = 0.1132, R-free = 0.1277 =============================================================================== Job complete usr+sys time: 13914.44 seconds wall clock time: 252 minutes 22.82 seconds (15142.82 seconds total)