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_3495505.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3495505.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3495505.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" 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 2 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: 1.69, per 1000 atoms: 0.50 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: 0.61 Conformation dependent library (CDL) restraints added in 216.7 milliseconds Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.93: 636 0.93 - 1.19: 1040 1.19 - 1.45: 691 1.45 - 1.71: 768 1.71 - 1.97: 18 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.461 1.271 0.191 9.20e-03 1.18e+04 4.29e+02 bond pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 1.330 1.574 -0.244 1.26e-02 6.30e+03 3.74e+02 bond pdb=" N BGLU A 64 " pdb=" CA BGLU A 64 " ideal model delta sigma weight residual 1.456 1.686 -0.230 1.22e-02 6.72e+03 3.55e+02 bond pdb=" C ILE A 117 " pdb=" O ILE A 117 " ideal model delta sigma weight residual 1.238 1.455 -0.217 1.17e-02 7.31e+03 3.46e+02 bond pdb=" C BGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 1.335 1.556 -0.221 1.26e-02 6.30e+03 3.08e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.07: 3311 5.07 - 10.15: 1882 10.15 - 15.22: 508 15.22 - 20.29: 73 20.29 - 25.36: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.27 141.39 -19.12 1.23e+00 6.61e-01 2.42e+02 angle pdb=" N ILE A 91 " pdb=" CA ILE A 91 " pdb=" C ILE A 91 " ideal model delta sigma weight residual 110.62 125.23 -14.61 1.02e+00 9.61e-01 2.05e+02 angle pdb=" N PRO A 43 " pdb=" CA PRO A 43 " pdb=" CB PRO A 43 " ideal model delta sigma weight residual 103.25 115.48 -12.23 8.80e-01 1.29e+00 1.93e+02 angle pdb=" C ILE A 21 " pdb=" N PRO A 22 " pdb=" CA PRO A 22 " ideal model delta sigma weight residual 119.19 104.58 14.61 1.06e+00 8.90e-01 1.90e+02 angle pdb=" O GLN A 95 " pdb=" C GLN A 95 " pdb=" N BGLU A 96 " ideal model delta sigma weight residual 122.27 105.71 16.56 1.23e+00 6.61e-01 1.81e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 944 17.07 - 34.14: 112 34.14 - 51.21: 37 51.21 - 68.28: 16 68.28 - 85.35: 2 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 180.00 151.19 28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -156.69 -23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LEU A 172 " pdb=" C LEU A 172 " pdb=" N ASN A 173 " pdb=" CA ASN A 173 " ideal model delta harmonic sigma weight residual 180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.247: 116 0.247 - 0.494: 69 0.494 - 0.741: 43 0.741 - 0.988: 12 0.988 - 1.236: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 69 " pdb=" N VAL A 69 " pdb=" C VAL A 69 " pdb=" CB VAL A 69 " both_signs ideal model delta sigma weight residual False 2.44 3.68 -1.24 2.00e-01 2.50e+01 3.82e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.43 -1.16 2.00e-01 2.50e+01 3.36e+01 chirality pdb=" CA BGLU A 94 " pdb=" N BGLU A 94 " pdb=" C BGLU A 94 " pdb=" CB BGLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 3.54 -1.03 2.00e-01 2.50e+01 2.64e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.032 2.00e-02 2.50e+03 6.55e-02 1.29e+02 pdb=" CG TYR A 141 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.125 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.096 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.062 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.060 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 172 " -0.051 2.00e-02 2.50e+03 9.56e-02 9.14e+01 pdb=" C LEU A 172 " 0.165 2.00e-02 2.50e+03 pdb=" O LEU A 172 " -0.062 2.00e-02 2.50e+03 pdb=" N ASN A 173 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.067 2.00e-02 2.50e+03 5.22e-02 8.16e+01 pdb=" CG BTYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.076 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.040 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.050 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.002 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.079 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.077 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.042 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 1268 2.35 - 2.91: 8252 2.91 - 3.47: 10473 3.47 - 4.04: 15152 4.04 - 4.60: 21487 Nonbonded interactions: 56632 Sorted by model distance: nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.785 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.791 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.808 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.835 2.270 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.836 1.850 ... (remaining 56627 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_3495505_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= 0.2607 r_free= 0.1954 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794696 | | target function (ml) not normalized (work): 232814.910905 | | target function (ml) not normalized (free): 11852.326817 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3020 0.2200 6.9991 4.9684| | 2: 3.57 - 2.84 1.00 2876 122 0.2429 0.1766 4.3572 4.3533| | 3: 2.84 - 2.48 1.00 2833 165 0.2346 0.1643 4.1372 4.1688| | 4: 2.47 - 2.25 1.00 2825 136 0.2309 0.1444 3.8415 3.853| | 5: 2.25 - 2.09 1.00 2756 127 0.2486 0.1590 3.8093 3.8327| | 6: 2.09 - 1.97 1.00 2846 113 0.2550 0.1685 3.4774 3.5372| | 7: 1.97 - 1.87 1.00 2787 165 0.2589 0.1825 3.1464 3.2101| | 8: 1.87 - 1.79 1.00 2789 144 0.2502 0.1752 3.0746 3.0975| | 9: 1.79 - 1.72 1.00 2745 138 0.2387 0.1926 2.9097 2.9668| | 10: 1.72 - 1.66 1.00 2789 158 0.2415 0.1763 2.8208 2.857| | 11: 1.66 - 1.61 1.00 2740 147 0.2506 0.1869 2.7681 2.7695| | 12: 1.61 - 1.56 1.00 2787 146 0.2495 0.2161 2.614 2.706| | 13: 1.56 - 1.52 1.00 2745 130 0.2574 0.2017 2.5759 2.6583| | 14: 1.52 - 1.48 1.00 2803 134 0.2626 0.1987 2.5215 2.5117| | 15: 1.48 - 1.45 1.00 2738 128 0.2589 0.1963 2.4385 2.4334| | 16: 1.45 - 1.42 1.00 2756 161 0.2661 0.2118 2.3771 2.3786| | 17: 1.42 - 1.39 1.00 2785 139 0.2680 0.2065 2.3329 2.3852| | 18: 1.39 - 1.36 1.00 2741 179 0.2668 0.2401 2.2775 2.4032| | 19: 1.36 - 1.34 1.00 2807 134 0.2639 0.2372 2.2462 2.3548| | 20: 1.34 - 1.32 1.00 2696 147 0.2686 0.1990 2.1814 2.1427| | 21: 1.32 - 1.30 1.00 2785 112 0.2707 0.2247 2.1722 2.212| | 22: 1.29 - 1.27 1.00 2704 152 0.2801 0.2421 2.1492 2.2188| | 23: 1.27 - 1.26 1.00 2802 156 0.2777 0.2548 2.1012 2.19| | 24: 1.26 - 1.24 1.00 2744 132 0.2775 0.2291 2.0752 2.1007| | 25: 1.24 - 1.22 1.00 2734 148 0.2879 0.2618 2.0563 2.0802| | 26: 1.22 - 1.21 1.00 2727 135 0.2843 0.2553 2.0159 2.1759| | 27: 1.21 - 1.19 1.00 2814 148 0.3002 0.2588 2.0246 1.9784| | 28: 1.19 - 1.18 1.00 2671 147 0.3025 0.2904 1.9951 2.0199| | 29: 1.18 - 1.16 1.00 2800 134 0.3003 0.2732 1.9683 2.0713| | 30: 1.16 - 1.15 1.00 2740 148 0.3014 0.3055 1.9236 1.9798| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.11 0.76 0.23 1534.22| | 2: 3.57 - 2.84 2876 122 0.80 26.46 1.27 0.23 1534.22| | 3: 2.84 - 2.48 2833 165 0.73 32.45 1.24 0.24 1271.60| | 4: 2.47 - 2.25 2825 136 0.81 25.88 1.26 0.25 590.07| | 5: 2.25 - 2.09 2756 127 0.77 29.83 1.28 0.25 590.07| | 6: 2.09 - 1.97 2846 113 0.83 23.02 1.29 0.25 321.81| | 7: 1.97 - 1.87 2787 165 0.90 16.90 1.29 0.26 93.02| | 8: 1.87 - 1.79 2789 144 0.85 21.45 1.25 0.26 93.02| | 9: 1.79 - 1.72 2745 138 0.88 18.53 1.22 0.25 56.16| | 10: 1.72 - 1.66 2789 158 0.87 20.25 1.22 0.25 48.78| | 11: 1.66 - 1.61 2740 147 0.86 21.35 1.23 0.25 47.09| | 12: 1.61 - 1.56 2787 146 0.88 18.49 1.23 0.25 29.97| | 13: 1.56 - 1.52 2745 130 0.86 20.67 1.25 0.25 29.97| | 14: 1.52 - 1.48 2803 134 0.86 21.00 1.25 0.25 26.67| | 15: 1.48 - 1.45 2738 128 0.87 20.01 1.22 0.25 20.63| | 16: 1.45 - 1.42 2756 161 0.86 21.65 1.24 0.25 20.63| | 17: 1.42 - 1.39 2785 139 0.87 20.77 1.23 0.25 17.56| | 18: 1.39 - 1.36 2741 179 0.86 21.36 1.23 0.25 15.78| | 19: 1.36 - 1.34 2807 134 0.86 21.99 1.22 0.25 15.78| | 20: 1.34 - 1.32 2696 147 0.87 20.95 1.21 0.25 13.05| | 21: 1.32 - 1.30 2785 112 0.86 21.63 1.20 0.25 12.86| | 22: 1.29 - 1.27 2704 152 0.85 22.52 1.21 0.24 12.60| | 23: 1.27 - 1.26 2802 156 0.85 22.43 1.22 0.24 11.28| | 24: 1.26 - 1.24 2744 132 0.85 22.91 1.20 0.24 11.28| | 25: 1.24 - 1.22 2734 148 0.84 24.24 1.21 0.24 10.88| | 26: 1.22 - 1.21 2727 135 0.83 24.55 1.21 0.23 10.45| | 27: 1.21 - 1.19 2814 148 0.82 25.50 1.20 0.23 10.45| | 28: 1.19 - 1.18 2671 147 0.81 26.68 1.18 0.23 10.07| | 29: 1.18 - 1.16 2800 134 0.81 27.26 1.18 0.22 9.93| | 30: 1.16 - 1.15 2740 148 0.79 28.67 1.16 0.22 9.93| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.93 max = 1534.22 mean = 222.09| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 22.95| |phase err.(test): min = 0.00 max = 89.87 mean = 22.92| |-----------------------------------------------------------------------------| ----------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 0.278 1557 Z= 5.407 Angle : 5.466 19.351 2118 Z= 3.832 Chirality : 0.408 1.236 243 Planarity : 0.032 0.129 284 Dihedral : 13.528 85.348 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 33.51 % 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: -2.76 (0.48), residues: 224 helix: -2.98 (0.36), residues: 109 sheet: -0.21 (0.80), residues: 28 loop : -0.43 (0.61), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.077 0.022 ARG A 156 TYR 0.131 0.041 TYR A 141 PHE 0.124 0.029 PHE A 119 HIS 0.086 0.034 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= 0.2607 r_free= 0.1954 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794696 | | target function (ml) not normalized (work): 232814.910905 | | target function (ml) not normalized (free): 11852.326817 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2608 0.1954 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2608 0.1954 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1984 0.1954 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.2001 0.2006 0.1964 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1645 0.1639 0.1770 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1639 0.1770 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 0.3833 386.386 354.302 0.669 1.003 0.397 11.894-9.307 99.02 97 4 0.1798 613.756 594.557 0.928 1.004 0.380 9.237-7.194 100.00 213 7 0.2135 501.977 490.021 0.956 1.004 0.362 7.162-5.571 100.00 427 22 0.2213 376.706 364.462 0.930 1.004 0.295 5.546-4.326 100.00 867 58 0.1275 517.124 512.006 0.968 1.004 0.250 4.315-3.360 100.00 1859 96 0.1146 491.788 488.188 1.005 1.003 0.179 3.356-2.611 100.00 3867 181 0.1424 323.080 319.749 0.998 1.003 0.057 2.608-2.026 99.99 8198 413 0.1338 214.172 212.067 1.009 1.001 0.000 2.025-1.573 100.00 17313 902 0.1671 104.591 103.821 1.010 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2073 46.380 45.049 1.005 0.995 0.000 1.221-1.150 99.97 13689 708 0.2590 29.222 26.993 0.979 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0408 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1639 r_free=0.1770 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1640 r_free=0.1772 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.004545 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2005.166880 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 0.1703 0.1826 0.0123 0.002 0.4 4.5 0.0 0.0 0 0.125 0.1603 0.1743 0.0139 0.002 0.4 4.8 0.0 0.0 0 0.250 0.1478 0.1650 0.0172 0.002 0.4 4.2 0.0 0.0 0 0.500 0.1418 0.1614 0.0196 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1370 0.1572 0.0202 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1371 0.1577 0.0206 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1299 0.1516 0.0217 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1271 0.1499 0.0228 0.003 0.6 3.8 0.5 0.0 0 3.000 0.1255 0.1487 0.0232 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1248 0.1484 0.0236 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1244 0.1482 0.0238 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1238 0.1474 0.0236 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1234 0.1473 0.0239 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1233 0.1472 0.0239 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1230 0.1472 0.0242 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1227 0.1471 0.0245 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1228 0.1474 0.0246 0.007 0.9 4.2 0.5 0.6 0 12.000 0.1223 0.1473 0.0250 0.007 1.0 4.5 0.5 0.6 0 13.002 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1227 0.1471 0.0245 0.007 0.9 3.8 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.71 2.45 3.013 19.036 2005.167 0.017 12.27 14.71 2.45 3.013 19.036 60.155 0.017 12.33 14.67 2.34 2.667 19.035 250.646 0.017 12.68 15.32 2.64 2.744 19.199 1002.583 0.016 12.54 15.48 2.94 3.270 19.569 2005.167 0.016 12.42 15.45 3.03 3.273 19.579 3007.750 0.015 12.29 15.37 3.08 3.311 19.594 4010.334 0.015 12.29 15.44 3.15 3.356 19.604 5012.917 0.015 12.26 15.48 3.21 3.441 19.646 6015.501 0.015 12.23 15.50 3.27 3.290 19.558 7018.084 0.015 12.15 15.37 3.22 3.382 19.604 8020.668 0.015 12.17 15.48 3.31 3.408 19.605 9023.251 0.015 12.13 15.44 3.31 3.449 19.614 10025.834 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: 250.646 Accepted refinement result: 12.33 14.67 2.34 2.667 19.035 250.646 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.43 20.06 3.31 0 1785 Protein: 9.06 114.97 16.97 3.31 0 1519 Water: 11.45 119.43 38.20 N/A 0 258 Other: 19.70 26.58 22.03 N/A 0 8 Chain A: 9.06 119.43 20.06 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1272 20.10 - 31.13 227 31.13 - 42.17 125 42.17 - 53.21 94 53.21 - 64.24 42 64.24 - 75.28 11 75.28 - 86.32 7 86.32 - 97.35 4 97.35 - 108.39 1 108.39 - 119.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1467 r_work=0.1235 r_free=0.1471 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1471 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1468 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1230 r_free= 0.1468 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016903 | | target function (ls_wunit_k1) not normalized (work): 1407.961473 | | target function (ls_wunit_k1) not normalized (free): 111.705968 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1241 0.1230 0.1468 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1670 0.1671 0.1697 n_refl.: 87593 remove outliers: r(all,work,free)=0.1670 0.1671 0.1697 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1678 0.1678 0.1702 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1458 n_refl.: 87593 remove outliers: r(all,work,free)=0.1238 0.1227 0.1458 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 0.3487 303.977 280.424 0.634 1.003 0.370 11.894-9.307 99.02 97 4 0.1688 483.737 471.134 0.919 1.003 0.365 9.237-7.194 100.00 213 7 0.1898 395.638 389.852 0.963 1.003 0.345 7.162-5.571 100.00 427 22 0.1835 296.904 290.966 0.936 1.003 0.269 5.546-4.326 100.00 867 58 0.1005 407.576 404.571 0.962 1.003 0.204 4.315-3.360 100.00 1859 96 0.0872 387.608 386.525 1.008 1.003 0.170 3.356-2.611 100.00 3867 181 0.1171 254.638 253.513 1.010 1.002 0.053 2.608-2.026 99.99 8198 413 0.1022 168.802 168.130 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1111 82.434 82.621 1.025 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1450 36.555 36.065 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 23.032 21.513 0.979 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0629 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1458 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 A Total number of N/Q/H flips: 2 r_work=0.1228 r_free=0.1459 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1228 r_free=0.1459 | n_water=258 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1239 r_free=0.1457 | n_water=250 | time (s): 21.720 (total time: 24.020) Filter (q & B) r_work=0.1241 r_free=0.1457 | n_water=247 | time (s): 2.500 (total time: 26.520) Compute maps r_work=0.1241 r_free=0.1457 | n_water=247 | time (s): 1.320 (total time: 27.840) Filter (map) r_work=0.1255 r_free=0.1460 | n_water=227 | time (s): 3.070 (total time: 30.910) Find peaks r_work=0.1255 r_free=0.1460 | n_water=227 | time (s): 0.590 (total time: 31.500) Add new water r_work=0.1395 r_free=0.1623 | n_water=433 | time (s): 2.380 (total time: 33.880) Refine new water occ: r_work=0.1305 r_free=0.1497 adp: r_work=0.1225 r_free=0.1444 occ: r_work=0.1236 r_free=0.1430 adp: r_work=0.1205 r_free=0.1417 occ: r_work=0.1208 r_free=0.1407 adp: r_work=0.1198 r_free=0.1407 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1407 r_work=0.1198 r_free=0.1407 | n_water=433 | time (s): 59.770 (total time: 93.650) Filter (q & B) r_work=0.1201 r_free=0.1411 | n_water=418 | time (s): 3.520 (total time: 97.170) Filter (dist only) r_work=0.1202 r_free=0.1409 | n_water=417 | time (s): 34.800 (total time: 131.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.230815 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1487.817293 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 0.1617 0.1739 0.0122 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1521 0.1656 0.0135 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1403 0.1561 0.0159 0.001 0.4 6.1 0.0 0.0 0 0.500 0.1348 0.1521 0.0173 0.002 0.5 5.1 0.0 0.0 0 0.750 0.1315 0.1495 0.0180 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1325 0.1506 0.0181 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1263 0.1454 0.0191 0.002 0.5 4.8 0.5 0.0 0 2.000 0.1234 0.1444 0.0210 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1220 0.1438 0.0218 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1213 0.1437 0.0224 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1206 0.1430 0.0224 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1204 0.1430 0.0226 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1200 0.1428 0.0228 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1197 0.1429 0.0231 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1194 0.1428 0.0233 0.006 0.9 5.1 0.5 0.0 0 10.000 0.1193 0.1429 0.0236 0.007 0.9 5.4 0.5 0.0 0 11.000 0.1192 0.1432 0.0240 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1190 0.1430 0.0240 0.008 0.9 5.4 0.5 0.6 0 13.000 0.1185 0.1424 0.0239 0.008 0.9 6.4 0.5 0.6 0 14.115 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1185 0.1424 0.0239 0.008 0.9 6.4 0.5 0.6 0 14.115 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.85 14.24 2.39 3.772 21.714 1487.817 0.016 11.85 14.24 2.39 3.772 21.714 44.635 0.016 11.85 14.24 2.39 3.772 21.714 185.977 0.016 11.99 14.60 2.62 3.638 21.714 743.909 0.015 11.99 14.86 2.87 3.540 21.790 1487.817 0.015 11.88 14.89 3.01 3.459 21.933 2231.726 0.014 11.81 14.93 3.12 3.512 21.867 2975.635 0.014 11.72 14.84 3.12 3.534 21.848 3719.543 0.014 11.73 14.93 3.20 3.521 22.086 4463.452 0.014 11.70 14.97 3.27 3.520 21.991 5207.361 0.014 11.65 14.88 3.22 3.542 22.052 5951.269 0.014 11.63 14.90 3.27 3.563 22.084 6695.178 0.014 11.62 14.92 3.30 3.565 22.012 7439.086 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 185.977 Accepted refinement result: 11.85 14.24 2.39 3.772 21.714 185.977 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.01 22.09 3.31 190 1754 Protein: 9.10 115.01 17.01 3.31 0 1519 Water: 11.49 76.68 40.58 N/A 190 227 Other: 19.74 26.62 22.07 N/A 0 8 Chain A: 9.10 115.01 19.46 N/A 0 1754 Chain S: 13.42 60.00 46.36 N/A 190 0 Histogram: Values Number of atoms 9.10 - 19.69 1261 19.69 - 30.28 245 30.28 - 40.87 166 40.87 - 51.46 131 51.46 - 62.05 118 62.05 - 72.64 12 72.64 - 83.23 5 83.23 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1185 r_free=0.1424 r_work=0.1185 r_free=0.1424 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1185 r_free = 0.1424 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1182 r_free = 0.1417 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1182 r_free= 0.1417 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014727 | | target function (ls_wunit_k1) not normalized (work): 1226.725019 | | target function (ls_wunit_k1) not normalized (free): 104.528165 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1182 0.1417 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1531 0.1528 0.1618 n_refl.: 87591 remove outliers: r(all,work,free)=0.1531 0.1528 0.1618 n_refl.: 87591 overall B=0.02 to atoms: r(all,work,free)=0.1533 0.1530 0.1620 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1178 0.1412 n_refl.: 87591 remove outliers: r(all,work,free)=0.1189 0.1178 0.1412 n_refl.: 87590 ======================== 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 93.75 85 5 0.3434 300.514 284.251 0.599 1.003 0.350 11.894-9.307 99.02 97 4 0.1660 483.737 476.338 0.916 1.003 0.342 9.237-7.194 100.00 213 7 0.1719 395.638 395.082 0.984 1.003 0.280 7.162-5.571 100.00 427 22 0.1553 296.904 292.662 0.936 1.003 0.220 5.546-4.326 100.00 867 58 0.0873 407.576 404.336 0.960 1.003 0.195 4.315-3.360 100.00 1859 96 0.0767 387.608 386.751 1.006 1.002 0.190 3.356-2.611 100.00 3867 181 0.1074 254.638 253.645 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1005 168.802 168.264 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1094 82.434 82.640 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.555 36.086 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 23.032 21.541 0.986 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0232 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1178 r_free=0.1412 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1178 r_free=0.1412 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1412 | n_water=417 | time (s): 2.210 (total time: 2.210) Filter (dist) r_work=0.1178 r_free=0.1410 | n_water=413 | time (s): 35.320 (total time: 37.530) Filter (q & B) r_work=0.1178 r_free=0.1410 | n_water=413 | time (s): 0.820 (total time: 38.350) Compute maps r_work=0.1178 r_free=0.1410 | n_water=413 | time (s): 1.270 (total time: 39.620) Filter (map) r_work=0.1213 r_free=0.1411 | n_water=289 | time (s): 3.350 (total time: 42.970) Find peaks r_work=0.1213 r_free=0.1411 | n_water=289 | time (s): 0.570 (total time: 43.540) Add new water r_work=0.1324 r_free=0.1519 | n_water=473 | time (s): 2.620 (total time: 46.160) Refine new water occ: r_work=0.1238 r_free=0.1427 adp: r_work=0.1240 r_free=0.1429 occ: r_work=0.1216 r_free=0.1403 adp: r_work=0.1216 r_free=0.1404 occ: r_work=0.1199 r_free=0.1387 adp: r_work=0.1195 r_free=0.1386 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1386 r_work=0.1195 r_free=0.1386 | n_water=473 | time (s): 170.630 (total time: 216.790) Filter (q & B) r_work=0.1199 r_free=0.1388 | n_water=442 | time (s): 2.980 (total time: 219.770) Filter (dist only) r_work=0.1199 r_free=0.1387 | n_water=441 | time (s): 38.160 (total time: 257.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.757683 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.631816 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1240 0.1360 0.0121 0.002 0.6 4.8 0.5 0.0 0 0.088 0.1188 0.1325 0.0137 0.003 0.7 3.8 0.5 0.0 0 0.264 0.1173 0.1310 0.0137 0.004 0.8 3.8 0.5 0.0 0 0.527 0.1165 0.1304 0.0139 0.005 0.9 3.5 0.5 0.0 0 0.791 0.1161 0.1302 0.0142 0.006 1.0 3.5 0.5 0.0 0 1.055 0.1157 0.1300 0.0143 0.007 1.0 4.2 0.5 0.6 0 1.318 0.1155 0.1302 0.0147 0.007 1.1 4.2 0.5 0.6 0 1.582 0.1153 0.1301 0.0148 0.008 1.1 4.2 0.5 0.6 0 1.846 0.1163 0.1303 0.0140 0.005 0.9 3.5 0.5 0.0 0 0.879 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1157 0.1300 0.0143 0.007 1.0 4.2 0.5 0.6 0 1.318 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 13.00 1.43 3.776 21.292 45.632 3.621 11.57 13.00 1.43 3.776 21.292 1.369 3.621 11.58 13.00 1.42 3.764 21.292 5.704 3.621 11.62 13.08 1.46 3.709 21.281 22.816 3.614 11.63 13.18 1.55 3.728 21.249 45.632 3.614 11.53 13.12 1.59 3.757 21.242 68.448 3.608 11.51 13.11 1.59 3.769 21.234 91.264 3.604 11.46 13.06 1.60 3.779 21.234 114.080 3.600 11.47 13.12 1.65 3.800 21.213 136.895 3.600 11.46 13.11 1.65 3.813 21.209 159.711 3.599 11.43 13.09 1.66 3.822 21.207 182.527 3.597 11.41 13.07 1.66 3.826 21.208 205.343 3.596 11.40 13.06 1.66 3.833 21.207 228.159 3.595 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.369 Accepted refinement result: 11.57 13.00 1.43 3.776 21.292 1.369 3.621 Individual atomic B min max mean iso aniso Overall: 9.12 115.02 21.30 3.31 216 1752 Protein: 9.12 115.02 17.03 3.31 0 1519 Water: 11.50 76.69 36.00 N/A 216 225 Other: 19.75 26.63 22.09 N/A 0 8 Chain A: 9.12 115.02 19.43 N/A 0 1752 Chain S: 13.43 60.02 36.43 N/A 216 0 Histogram: Values Number of atoms 9.12 - 19.71 1264 19.71 - 30.30 286 30.30 - 40.89 206 40.89 - 51.48 134 51.48 - 62.07 55 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1157 r_free=0.1300 r_work=0.1158 r_free=0.1300 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1158 r_free = 0.1300 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1149 r_free = 0.1298 target_work(ml) = 3.613 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1149 r_free= 0.1298 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.612953 | | target function (ml) not normalized (work): 300937.285082 | | target function (ml) not normalized (free): 15825.081230 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1156 0.1149 0.1298 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1495 0.1495 0.1527 n_refl.: 87590 remove outliers: r(all,work,free)=0.1495 0.1495 0.1527 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1494 0.1494 0.1527 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1152 0.1145 0.1290 n_refl.: 87590 remove outliers: r(all,work,free)=0.1148 0.1141 0.1290 n_refl.: 87580 ======================== 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 0.3603 299.463 267.452 0.505 1.000 0.330 11.894-9.307 97.06 95 4 0.2154 485.066 466.310 0.889 1.002 0.330 9.237-7.194 98.18 209 7 0.2170 387.096 389.514 0.971 1.002 0.200 7.162-5.571 100.00 427 22 0.2008 296.904 287.348 0.921 1.002 0.190 5.546-4.326 100.00 867 58 0.1122 407.576 403.175 0.964 1.002 0.170 4.315-3.360 100.00 1859 96 0.0919 387.608 385.214 1.004 1.002 0.160 3.356-2.611 100.00 3867 181 0.1142 254.638 252.578 1.007 1.002 0.090 2.608-2.026 99.99 8198 413 0.0937 168.802 168.119 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0906 82.434 82.738 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1261 36.555 36.150 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 23.032 21.581 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=-0.0093 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1141 r_free=0.1290 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=0.1141 r_free=0.1290 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1141 r_free=0.1290 | n_water=441 | time (s): 2.520 (total time: 2.520) Filter (dist) r_work=0.1141 r_free=0.1289 | n_water=439 | time (s): 47.850 (total time: 50.370) Filter (q & B) r_work=0.1142 r_free=0.1289 | n_water=438 | time (s): 3.870 (total time: 54.240) Compute maps r_work=0.1142 r_free=0.1289 | n_water=438 | time (s): 1.850 (total time: 56.090) Filter (map) r_work=0.1158 r_free=0.1288 | n_water=334 | time (s): 3.890 (total time: 59.980) Find peaks r_work=0.1158 r_free=0.1288 | n_water=334 | time (s): 0.730 (total time: 60.710) Add new water r_work=0.1234 r_free=0.1364 | n_water=500 | time (s): 3.720 (total time: 64.430) Refine new water occ: r_work=0.1161 r_free=0.1294 adp: r_work=0.1162 r_free=0.1296 occ: r_work=0.1146 r_free=0.1280 adp: r_work=0.1144 r_free=0.1279 occ: r_work=0.1133 r_free=0.1271 adp: r_work=0.1130 r_free=0.1267 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1267 r_work=0.1130 r_free=0.1267 | n_water=500 | time (s): 216.930 (total time: 281.360) Filter (q & B) r_work=0.1135 r_free=0.1271 | n_water=459 | time (s): 4.030 (total time: 285.390) Filter (dist only) r_work=0.1135 r_free=0.1270 | n_water=458 | time (s): 48.110 (total time: 333.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.731647 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.455258 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 0.1192 0.1309 0.0117 0.002 0.6 4.5 0.5 0.0 0 0.087 0.1158 0.1288 0.0129 0.003 0.7 3.2 0.5 0.0 0 0.260 0.1143 0.1279 0.0136 0.005 0.9 4.5 0.5 0.0 0 0.519 0.1136 0.1279 0.0142 0.006 0.9 4.5 0.5 0.0 0 0.779 0.1134 0.1278 0.0145 0.006 1.0 4.5 0.5 0.0 0 1.039 0.1130 0.1276 0.0146 0.007 1.1 4.5 0.5 0.0 0 1.299 0.1130 0.1275 0.0145 0.008 1.1 4.5 0.5 0.0 0 1.558 0.1125 0.1273 0.0148 0.008 1.1 4.5 0.5 0.6 0 1.818 0.1136 0.1279 0.0143 0.006 1.0 4.2 0.5 0.0 0 0.866 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1125 0.1273 0.0148 0.008 1.1 4.5 0.5 0.6 0 1.818 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.25 12.73 1.48 3.778 21.294 44.455 3.603 11.25 12.73 1.48 3.778 21.294 1.334 3.603 11.25 12.73 1.48 3.778 21.294 5.557 3.603 11.29 12.78 1.49 3.711 21.286 22.228 3.598 11.36 12.95 1.59 3.731 21.257 44.455 3.602 11.27 12.91 1.64 3.755 21.249 66.683 3.595 11.23 12.89 1.66 3.767 21.246 88.911 3.591 11.20 12.89 1.68 3.780 21.241 111.138 3.589 11.17 12.87 1.70 3.789 21.239 133.366 3.586 11.16 12.89 1.73 3.803 21.233 155.593 3.586 11.16 12.91 1.75 3.817 21.227 177.821 3.586 11.14 12.87 1.73 3.821 21.225 200.049 3.584 11.13 12.87 1.74 3.828 21.225 222.276 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.557 Accepted refinement result: 11.25 12.73 1.48 3.778 21.294 5.557 3.603 Individual atomic B min max mean iso aniso Overall: 9.11 115.02 21.30 3.31 234 1751 Protein: 9.11 115.02 17.02 3.31 0 1519 Water: 11.50 76.69 35.49 N/A 234 224 Other: 19.75 26.63 22.08 N/A 0 8 Chain A: 9.11 115.02 19.43 N/A 0 1751 Chain S: 13.43 60.01 35.35 N/A 234 0 Histogram: Values Number of atoms 9.11 - 19.70 1266 19.70 - 30.29 298 30.29 - 40.89 210 40.89 - 51.48 140 51.48 - 62.07 48 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1125 r_free=0.1273 r_work=0.1125 r_free=0.1273 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1125 r_free = 0.1273 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1120 r_free = 0.1273 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1120 r_free= 0.1273 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601363 | | target function (ml) not normalized (work): 299935.928302 | | target function (ml) not normalized (free): 15808.944541 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1128 0.1120 0.1273 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1448 0.1446 0.1502 n_refl.: 87580 remove outliers: r(all,work,free)=0.1448 0.1446 0.1502 n_refl.: 87580 overall B=-0.00 to atoms: r(all,work,free)=0.1447 0.1446 0.1501 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1119 0.1276 n_refl.: 87580 remove outliers: r(all,work,free)=0.1126 0.1118 0.1276 n_refl.: 87578 ======================== 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 0.3762 293.829 265.979 0.478 1.001 0.306 11.894-9.307 96.08 94 4 0.2289 485.179 471.769 0.877 1.002 0.290 9.237-7.194 98.18 209 7 0.2288 387.096 384.140 0.942 1.002 0.190 7.162-5.571 100.00 427 22 0.2010 296.904 287.442 0.920 1.003 0.150 5.546-4.326 100.00 867 58 0.1083 407.576 403.422 0.964 1.003 0.130 4.315-3.360 100.00 1859 96 0.0881 387.608 385.731 1.002 1.002 0.130 3.356-2.611 100.00 3867 181 0.1103 254.638 252.688 1.009 1.002 0.034 2.608-2.026 99.99 8198 413 0.0908 168.802 168.198 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0880 82.434 82.784 1.034 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.555 36.164 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2164 23.032 21.586 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=-0.0102 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1118 r_free=0.1276 After: r_work=0.1119 r_free=0.1276 ================================== NQH flips ================================== r_work=0.1119 r_free=0.1276 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=0.1119 r_free=0.1276 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1119 r_free=0.1276 | n_water=458 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1120 r_free=0.1276 | n_water=456 | time (s): 49.520 (total time: 52.000) Filter (q & B) r_work=0.1121 r_free=0.1276 | n_water=454 | time (s): 3.970 (total time: 55.970) Compute maps r_work=0.1121 r_free=0.1276 | n_water=454 | time (s): 1.860 (total time: 57.830) Filter (map) r_work=0.1158 r_free=0.1300 | n_water=356 | time (s): 4.000 (total time: 61.830) Find peaks r_work=0.1158 r_free=0.1300 | n_water=356 | time (s): 0.700 (total time: 62.530) Add new water r_work=0.1211 r_free=0.1351 | n_water=504 | time (s): 3.760 (total time: 66.290) Refine new water occ: r_work=0.1140 r_free=0.1282 adp: r_work=0.1140 r_free=0.1282 occ: r_work=0.1128 r_free=0.1270 adp: r_work=0.1127 r_free=0.1270 occ: r_work=0.1119 r_free=0.1263 adp: r_work=0.1117 r_free=0.1261 ADP+occupancy (water only), MIN, final r_work=0.1117 r_free=0.1261 r_work=0.1117 r_free=0.1261 | n_water=504 | time (s): 282.490 (total time: 348.780) Filter (q & B) r_work=0.1124 r_free=0.1271 | n_water=467 | time (s): 3.960 (total time: 352.740) Filter (dist only) r_work=0.1124 r_free=0.1271 | n_water=466 | time (s): 49.540 (total time: 402.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.755532 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.584839 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 0.1205 0.1326 0.0121 0.004 0.7 6.7 0.0 0.0 0 0.088 0.1162 0.1296 0.0133 0.004 0.8 6.4 0.0 0.0 0 0.263 0.1144 0.1284 0.0140 0.005 0.9 6.1 0.5 0.0 0 0.527 0.1136 0.1279 0.0142 0.006 1.0 6.1 0.5 0.6 0 0.790 0.1132 0.1275 0.0143 0.006 1.1 6.1 0.5 0.6 0 1.053 0.1128 0.1273 0.0145 0.007 1.1 6.1 0.5 0.6 0 1.317 0.1125 0.1272 0.0146 0.008 1.1 5.8 0.5 0.6 0 1.580 0.1124 0.1271 0.0147 0.009 1.2 5.8 0.5 0.6 0 1.843 0.1134 0.1277 0.0143 0.006 1.0 6.1 0.5 0.6 0 0.878 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1124 0.1271 0.0147 0.009 1.2 5.8 0.5 0.6 0 1.843 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.24 12.71 1.47 3.777 21.270 35.585 3.602 11.24 12.71 1.47 3.777 21.270 1.068 3.602 11.24 12.71 1.47 3.777 21.270 4.448 3.602 11.29 12.77 1.48 3.707 21.263 17.792 3.599 11.32 12.88 1.56 3.729 21.244 35.585 3.600 11.27 12.88 1.61 3.747 21.229 53.377 3.596 11.23 12.88 1.65 3.761 21.224 71.170 3.593 11.19 12.85 1.66 3.770 21.223 88.962 3.590 11.17 12.83 1.66 3.777 21.219 106.755 3.587 11.14 12.79 1.66 3.781 21.223 124.547 3.585 11.17 12.88 1.71 3.802 21.206 142.339 3.587 11.15 12.86 1.71 3.811 21.205 160.132 3.586 11.14 12.84 1.70 3.817 21.204 177.924 3.584 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.068 Accepted refinement result: 11.24 12.71 1.47 3.777 21.270 1.068 3.602 Individual atomic B min max mean iso aniso Overall: 9.11 115.01 21.26 3.31 243 1750 Protein: 9.11 115.01 17.02 3.31 0 1519 Water: 11.49 76.68 35.09 N/A 243 223 Other: 19.75 26.62 22.08 N/A 0 8 Chain A: 9.11 115.01 19.42 N/A 0 1750 Chain S: 13.43 60.01 34.51 N/A 243 0 Histogram: Values Number of atoms 9.11 - 19.70 1267 19.70 - 30.29 301 30.29 - 40.88 220 40.88 - 51.47 138 51.47 - 62.06 44 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=0.1124 r_free=0.1271 r_work=0.1124 r_free=0.1271 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1124 r_free = 0.1271 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1121 r_free = 0.1270 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1121 r_free= 0.1270 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600383 | | target function (ml) not normalized (work): 299847.088869 | | target function (ml) not normalized (free): 15792.122062 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1311 0.1270 5.6414 5.5498| | 2: 3.57 - 2.84 1.00 2888 124 0.1045 0.1366 5.1348 5.2292| | 3: 2.83 - 2.48 1.00 2820 163 0.1071 0.1199 4.9196 4.9645| | 4: 2.47 - 2.25 1.00 2825 136 0.0885 0.1011 4.6082 4.653| | 5: 2.25 - 2.09 1.00 2756 127 0.0857 0.0967 4.5534 4.6092| | 6: 2.09 - 1.97 1.00 2846 113 0.0847 0.0993 4.2516 4.3299| | 7: 1.97 - 1.87 1.00 2787 165 0.0882 0.1105 3.9745 4.0856| | 8: 1.87 - 1.79 1.00 2789 144 0.0921 0.1104 3.8881 3.9985| | 9: 1.79 - 1.72 1.00 2745 138 0.0870 0.1185 3.6451 3.8228| | 10: 1.72 - 1.66 1.00 2831 160 0.0920 0.1180 3.5635 3.7037| | 11: 1.66 - 1.61 1.00 2712 147 0.0873 0.1030 3.4954 3.5672| | 12: 1.61 - 1.56 1.00 2773 144 0.0900 0.1161 3.3277 3.4787| | 13: 1.56 - 1.52 1.00 2745 130 0.0951 0.1029 3.3115 3.396| | 14: 1.52 - 1.48 1.00 2803 134 0.0983 0.1038 3.2412 3.3211| | 15: 1.48 - 1.45 1.00 2738 128 0.1000 0.1196 3.1551 3.2607| | 16: 1.45 - 1.42 1.00 2756 161 0.1051 0.1212 3.1354 3.236| | 17: 1.42 - 1.39 1.00 2785 139 0.1135 0.1296 3.1193 3.235| | 18: 1.39 - 1.36 1.00 2741 179 0.1194 0.1328 3.105 3.2375| | 19: 1.36 - 1.34 1.00 2807 134 0.1261 0.1573 3.1133 3.2714| | 20: 1.34 - 1.32 1.00 2696 147 0.1364 0.1469 3.1127 3.1506| | 21: 1.32 - 1.30 1.00 2785 112 0.1468 0.1543 3.1149 3.1153| | 22: 1.29 - 1.27 1.00 2704 152 0.1555 0.1980 3.1229 3.2956| | 23: 1.27 - 1.26 1.00 2802 156 0.1644 0.1798 3.1333 3.202| | 24: 1.26 - 1.24 1.00 2744 132 0.1710 0.1848 3.1295 3.2305| | 25: 1.24 - 1.22 1.00 2733 148 0.1881 0.2132 3.145 3.2581| | 26: 1.22 - 1.21 1.00 2727 135 0.1908 0.1762 3.1508 3.2026| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2157 3.1736 3.1645| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2277 3.1682 3.1705| | 29: 1.18 - 1.16 1.00 2800 134 0.2266 0.2391 3.1501 3.2331| | 30: 1.16 - 1.15 1.00 2739 148 0.2441 0.2451 3.1443 3.1698| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2920 171 0.95 7.90 1.00 0.97 5368.64| | 2: 3.57 - 2.84 2888 124 0.93 11.99 1.01 0.97 5368.64| | 3: 2.83 - 2.48 2820 163 0.90 15.88 0.99 0.98 4491.57| | 4: 2.47 - 2.25 2825 136 0.92 12.95 1.00 0.98 2229.86| | 5: 2.25 - 2.09 2756 127 0.91 15.11 1.01 0.98 2229.86| | 6: 2.09 - 1.97 2846 113 0.93 12.06 1.02 0.98 1300.04| | 7: 1.97 - 1.87 2787 165 0.95 9.23 1.02 0.98 507.03| | 8: 1.87 - 1.79 2789 144 0.93 12.56 0.99 0.98 507.03| | 9: 1.79 - 1.72 2745 138 0.94 9.98 0.98 0.98 287.74| | 10: 1.72 - 1.66 2831 160 0.94 11.06 0.98 0.97 243.83| | 11: 1.66 - 1.61 2712 147 0.93 11.70 0.98 0.97 233.65| | 12: 1.61 - 1.56 2773 144 0.96 8.88 0.99 0.97 137.66| | 13: 1.56 - 1.52 2745 130 0.95 10.40 1.03 0.97 137.66| | 14: 1.52 - 1.48 2803 134 0.94 10.76 1.02 0.98 123.47| | 15: 1.48 - 1.45 2738 128 0.95 9.84 1.02 0.98 97.48| | 16: 1.45 - 1.42 2756 161 0.94 11.05 1.02 0.98 97.48| | 17: 1.42 - 1.39 2785 139 0.95 10.88 1.01 0.98 89.01| | 18: 1.39 - 1.36 2741 179 0.94 11.50 1.01 0.98 84.10| | 19: 1.36 - 1.34 2807 134 0.94 11.84 1.00 0.98 84.10| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.97 80.30| | 21: 1.32 - 1.30 2785 112 0.94 13.08 0.98 0.97 80.04| | 22: 1.29 - 1.27 2704 152 0.93 13.63 0.98 0.96 80.44| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.97 0.95 82.52| | 24: 1.26 - 1.24 2744 132 0.92 14.86 0.96 0.95 82.52| | 25: 1.24 - 1.22 2733 148 0.91 16.31 0.96 0.94 84.41| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.02 0.93 86.51| | 27: 1.21 - 1.19 2814 148 0.89 18.73 1.02 0.93 86.51| | 28: 1.19 - 1.18 2671 147 0.88 20.33 1.01 0.93 90.11| | 29: 1.18 - 1.16 2800 134 0.88 20.45 0.99 0.93 91.46| | 30: 1.16 - 1.15 2739 148 0.86 21.94 0.98 0.93 91.46| |alpha: min = 0.93 max = 0.98 mean = 0.97| |beta: min = 80.04 max = 5368.64 mean = 838.85| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.31| |phase err.(test): min = 0.00 max = 88.88 mean = 13.29| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1128 0.1121 0.1270 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1441 0.1439 0.1493 n_refl.: 87578 remove outliers: r(all,work,free)=0.1441 0.1439 0.1493 n_refl.: 87578 overall B=-0.00 to atoms: r(all,work,free)=0.1440 0.1439 0.1493 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1121 0.1273 n_refl.: 87578 remove outliers: r(all,work,free)=0.1127 0.1120 0.1273 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 87.50 79 5 0.3885 289.048 254.563 0.456 1.000 0.307 11.894-9.307 93.14 91 4 0.2276 475.904 470.075 0.885 1.002 0.237 9.237-7.194 98.18 209 7 0.2320 387.096 383.236 0.934 1.002 0.180 7.162-5.571 100.00 427 22 0.2047 296.904 287.242 0.915 1.003 0.136 5.546-4.326 100.00 867 58 0.1125 407.576 403.284 0.963 1.003 0.126 4.315-3.360 100.00 1859 96 0.0897 387.608 385.327 1.002 1.002 0.120 3.356-2.611 100.00 3867 181 0.1089 254.638 252.598 1.009 1.002 0.024 2.608-2.026 99.99 8198 413 0.0896 168.802 168.156 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0886 82.434 82.758 1.034 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.555 36.151 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 23.032 21.572 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=-0.0060 ================= 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 : 0.2607 0.1954 0.083 5.466 8.8 119.3 19.9 258 0.000 1_bss: 0.1639 0.1770 0.083 5.466 9.0 119.5 20.1 258 0.000 1_settarget: 0.1639 0.1770 0.083 5.466 9.0 119.5 20.1 258 0.000 1_nqh: 0.1640 0.1772 0.083 5.466 9.0 119.5 20.1 258 0.003 1_weight: 0.1640 0.1772 0.083 5.466 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1227 0.1471 0.007 0.903 9.0 119.5 20.1 258 0.139 1_adp: 0.1233 0.1467 0.007 0.903 9.1 119.4 20.1 258 0.139 1_regHadp: 0.1235 0.1471 0.007 0.903 9.1 119.4 20.1 258 0.139 1_occ: 0.1230 0.1468 0.007 0.903 9.1 119.4 20.1 258 0.139 2_bss: 0.1227 0.1458 0.007 0.903 9.1 119.5 20.1 258 0.139 2_settarget: 0.1227 0.1458 0.007 0.903 9.1 119.5 20.1 258 0.139 2_updatecdl: 0.1227 0.1458 0.007 0.911 9.1 119.5 20.1 258 0.139 2_nqh: 0.1228 0.1459 0.007 0.911 9.1 119.5 20.1 258 0.139 2_sol: 0.1202 0.1409 0.007 0.911 9.1 115.0 22.1 417 n/a 2_weight: 0.1202 0.1409 0.007 0.911 9.1 115.0 22.1 417 n/a 2_xyzrec: 0.1185 0.1424 0.008 0.947 9.1 115.0 22.1 417 n/a 2_adp: 0.1185 0.1424 0.008 0.947 9.1 115.0 22.1 417 n/a 2_regHadp: 0.1185 0.1424 0.008 0.947 9.1 115.0 22.1 417 n/a 2_occ: 0.1182 0.1417 0.008 0.947 9.1 115.0 22.1 417 n/a 3_bss: 0.1178 0.1412 0.008 0.947 9.1 115.0 22.1 417 n/a 3_settarget: 0.1178 0.1412 0.008 0.947 9.1 115.0 22.1 417 n/a 3_updatecdl: 0.1178 0.1412 0.008 0.947 9.1 115.0 22.1 417 n/a 3_nqh: 0.1178 0.1412 0.008 0.947 9.1 115.0 22.1 417 n/a 3_sol: 0.1199 0.1387 0.008 0.947 9.1 115.0 21.3 441 n/a 3_weight: 0.1199 0.1387 0.008 0.947 9.1 115.0 21.3 441 n/a 3_xyzrec: 0.1157 0.1300 0.007 1.021 9.1 115.0 21.3 441 n/a 3_adp: 0.1157 0.1300 0.007 1.021 9.1 115.0 21.3 441 n/a 3_regHadp: 0.1158 0.1300 0.007 1.021 9.1 115.0 21.3 441 n/a 3_occ: 0.1149 0.1298 0.007 1.021 9.1 115.0 21.3 441 n/a 4_bss: 0.1141 0.1290 0.007 1.021 9.1 115.0 21.3 441 n/a 4_settarget: 0.1141 0.1290 0.007 1.021 9.1 115.0 21.3 441 n/a 4_updatecdl: 0.1141 0.1290 0.007 1.023 9.1 115.0 21.3 441 n/a 4_nqh: 0.1141 0.1290 0.007 1.023 9.1 115.0 21.3 441 n/a 4_sol: 0.1135 0.1270 0.007 1.023 9.1 115.0 21.3 458 n/a 4_weight: 0.1135 0.1270 0.007 1.023 9.1 115.0 21.3 458 n/a 4_xyzrec: 0.1125 0.1273 0.008 1.134 9.1 115.0 21.3 458 n/a 4_adp: 0.1125 0.1273 0.008 1.134 9.1 115.0 21.3 458 n/a 4_regHadp: 0.1125 0.1273 0.008 1.134 9.1 115.0 21.3 458 n/a 4_occ: 0.1120 0.1273 0.008 1.134 9.1 115.0 21.3 458 n/a 5_bss: 0.1118 0.1276 0.008 1.134 9.1 115.0 21.3 458 n/a 5_settarget: 0.1118 0.1276 0.008 1.134 9.1 115.0 21.3 458 n/a 5_updatecdl: 0.1118 0.1276 0.008 1.135 9.1 115.0 21.3 458 n/a 5_setrh: 0.1119 0.1276 0.008 1.135 9.1 115.0 21.3 458 n/a 5_nqh: 0.1119 0.1276 0.008 1.135 9.1 115.0 21.3 458 n/a 5_sol: 0.1124 0.1271 0.008 1.135 9.1 115.0 21.3 466 n/a 5_weight: 0.1124 0.1271 0.008 1.135 9.1 115.0 21.3 466 n/a 5_xyzrec: 0.1124 0.1271 0.009 1.156 9.1 115.0 21.3 466 n/a 5_adp: 0.1124 0.1271 0.009 1.156 9.1 115.0 21.3 466 n/a 5_regHadp: 0.1124 0.1271 0.009 1.156 9.1 115.0 21.3 466 n/a 5_occ: 0.1121 0.1270 0.009 1.156 9.1 115.0 21.3 466 n/a end: 0.1120 0.1273 0.009 1.156 9.1 115.0 21.3 466 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3495505_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3495505_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9500 Refinement macro-cycles (run) : 14067.7000 Write final files (write_after_run_outputs) : 86.4800 Total : 14158.1300 Total CPU time: 3.94 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:17:05 PST -0800 (1735366625.29 s) Start R-work = 0.1639, R-free = 0.1770 Final R-work = 0.1120, R-free = 0.1273 =============================================================================== Job complete usr+sys time: 14317.25 seconds wall clock time: 260 minutes 53.77 seconds (15653.77 seconds total)