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_3941866.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_3941866.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3941866.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 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: 1.53, per 1000 atoms: 0.45 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: 0.29 Conformation dependent library (CDL) restraints added in 107.2 milliseconds Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 577 0.92 - 1.18: 1076 1.18 - 1.43: 652 1.43 - 1.68: 822 1.68 - 1.94: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.462 1.282 0.180 9.50e-03 1.11e+04 3.59e+02 bond pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.336 1.561 -0.225 1.25e-02 6.40e+03 3.25e+02 bond pdb=" CA ILE A 91 " pdb=" CB ILE A 91 " ideal model delta sigma weight residual 1.538 1.353 0.185 1.06e-02 8.90e+03 3.05e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.496 -0.175 1.00e-02 1.00e+04 3.05e+02 bond pdb=" C THR A 110 " pdb=" N ALA A 111 " ideal model delta sigma weight residual 1.335 1.560 -0.225 1.31e-02 5.83e+03 2.94e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 3369 5.06 - 10.13: 1881 10.13 - 15.19: 452 15.19 - 20.26: 64 20.26 - 25.32: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " ideal model delta sigma weight residual 123.46 109.43 14.03 9.90e-01 1.02e+00 2.01e+02 angle pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" O ALA A 56 " ideal model delta sigma weight residual 121.10 136.58 -15.48 1.10e+00 8.26e-01 1.98e+02 angle pdb=" O GLU A 84 " pdb=" C GLU A 84 " pdb=" N SER A 85 " ideal model delta sigma weight residual 122.34 137.76 -15.42 1.25e+00 6.40e-01 1.52e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.82 108.08 12.74 1.05e+00 9.07e-01 1.47e+02 angle pdb=" O BASN A 76 " pdb=" C BASN A 76 " pdb=" N LEU A 77 " ideal model delta sigma weight residual 122.07 134.36 -12.29 1.03e+00 9.43e-01 1.42e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 15.87: 910 15.87 - 31.71: 134 31.71 - 47.55: 42 47.55 - 63.39: 22 63.39 - 79.23: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.254: 108 0.254 - 0.503: 80 0.503 - 0.753: 42 0.753 - 1.002: 10 1.002 - 1.251: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -3.88 1.25 2.00e-01 2.50e+01 3.91e+01 chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.62 -1.18 2.00e-01 2.50e+01 3.49e+01 chirality pdb=" CA MET A 133 " pdb=" N MET A 133 " pdb=" C MET A 133 " pdb=" CB MET A 133 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.71e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.039 2.00e-02 2.50e+03 5.81e-02 1.01e+02 pdb=" CG ATYR A 67 " 0.127 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.009 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.043 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.008 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.020 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.066 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.089 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.069 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.058 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.068 2.00e-02 2.50e+03 5.36e-02 8.62e+01 pdb=" CG BTYR A 67 " 0.042 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.052 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.041 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.115 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.036 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.029 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.013 2.00e-02 2.50e+03 5.28e-02 8.37e+01 pdb=" CG TYR A 139 " -0.097 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.086 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.058 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.053 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 598 2.24 - 2.83: 7500 2.83 - 3.42: 10849 3.42 - 4.01: 15322 4.01 - 4.60: 22313 Nonbonded interactions: 56582 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.652 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.749 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.794 1.850 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.811 1.850 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.827 2.100 ... (remaining 56577 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_3941866_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1917 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793292 | | target function (ml) not normalized (work): 232697.977799 | | target function (ml) not normalized (free): 11828.129705 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3038 0.2035 7.0981 4.9489| | 2: 3.57 - 2.84 1.00 2876 122 0.2441 0.1763 4.3462 4.3358| | 3: 2.84 - 2.48 1.00 2833 165 0.2346 0.1570 4.1277 4.1494| | 4: 2.47 - 2.25 1.00 2825 136 0.2328 0.1466 3.8346 3.8379| | 5: 2.25 - 2.09 1.00 2756 127 0.2468 0.1676 3.7946 3.8071| | 6: 2.09 - 1.97 1.00 2846 113 0.2524 0.1655 3.4694 3.5037| | 7: 1.97 - 1.87 1.00 2787 165 0.2547 0.1737 3.1237 3.1525| | 8: 1.87 - 1.79 1.00 2789 144 0.2447 0.1895 3.0447 3.1421| | 9: 1.79 - 1.72 1.00 2745 138 0.2370 0.1826 2.891 2.9635| | 10: 1.72 - 1.66 1.00 2789 158 0.2483 0.1985 2.8018 2.8714| | 11: 1.66 - 1.61 1.00 2740 147 0.2509 0.1879 2.7508 2.7933| | 12: 1.61 - 1.56 1.00 2787 146 0.2512 0.2166 2.6225 2.7649| | 13: 1.56 - 1.52 1.00 2745 130 0.2571 0.1967 2.5787 2.6387| | 14: 1.52 - 1.48 1.00 2803 134 0.2613 0.2028 2.5046 2.5727| | 15: 1.48 - 1.45 1.00 2738 128 0.2581 0.1963 2.4173 2.4259| | 16: 1.45 - 1.42 1.00 2756 161 0.2639 0.2085 2.3864 2.4205| | 17: 1.42 - 1.39 1.00 2785 139 0.2730 0.1929 2.3479 2.3398| | 18: 1.39 - 1.36 1.00 2741 179 0.2631 0.2255 2.2684 2.356| | 19: 1.36 - 1.34 1.00 2807 134 0.2678 0.2165 2.2603 2.2528| | 20: 1.34 - 1.32 1.00 2696 147 0.2684 0.2107 2.2114 2.2214| | 21: 1.32 - 1.30 1.00 2785 112 0.2672 0.2407 2.1621 2.2528| | 22: 1.29 - 1.27 1.00 2704 152 0.2748 0.2619 2.1384 2.1923| | 23: 1.27 - 1.26 1.00 2802 156 0.2782 0.2461 2.1232 2.1693| | 24: 1.26 - 1.24 1.00 2744 132 0.2792 0.2446 2.0933 2.0962| | 25: 1.24 - 1.22 1.00 2734 148 0.2864 0.2688 2.0445 2.1231| | 26: 1.22 - 1.21 1.00 2727 135 0.2911 0.2378 2.0143 2.0817| | 27: 1.21 - 1.19 1.00 2814 148 0.2962 0.2582 1.9938 2.0336| | 28: 1.19 - 1.18 1.00 2671 147 0.2997 0.2787 1.9894 1.9955| | 29: 1.18 - 1.16 1.00 2800 134 0.2987 0.2708 1.9724 2.0458| | 30: 1.16 - 1.15 1.00 2740 148 0.3053 0.2721 1.9298 1.9566| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.76 0.76 0.23 1479.57| | 2: 3.57 - 2.84 2876 122 0.80 25.98 1.27 0.23 1479.57| | 3: 2.84 - 2.48 2833 165 0.74 31.88 1.24 0.24 1225.64| | 4: 2.47 - 2.25 2825 136 0.81 25.35 1.25 0.25 566.65| | 5: 2.25 - 2.09 2756 127 0.77 29.17 1.28 0.25 566.65| | 6: 2.09 - 1.97 2846 113 0.84 22.39 1.29 0.25 308.32| | 7: 1.97 - 1.87 2787 165 0.90 16.37 1.29 0.26 88.01| | 8: 1.87 - 1.79 2789 144 0.86 20.61 1.25 0.26 88.01| | 9: 1.79 - 1.72 2745 138 0.88 18.56 1.23 0.25 55.15| | 10: 1.72 - 1.66 2789 158 0.86 20.51 1.23 0.25 48.57| | 11: 1.66 - 1.61 2740 147 0.85 21.52 1.24 0.25 46.95| | 12: 1.61 - 1.56 2787 146 0.88 18.78 1.24 0.25 30.48| | 13: 1.56 - 1.52 2745 130 0.86 20.68 1.24 0.25 30.48| | 14: 1.52 - 1.48 2803 134 0.86 21.22 1.24 0.25 27.09| | 15: 1.48 - 1.45 2738 128 0.87 20.29 1.24 0.25 20.88| | 16: 1.45 - 1.42 2756 161 0.86 21.54 1.23 0.25 20.88| | 17: 1.42 - 1.39 2785 139 0.86 21.05 1.24 0.25 17.61| | 18: 1.39 - 1.36 2741 179 0.86 21.30 1.22 0.25 15.71| | 19: 1.36 - 1.34 2807 134 0.86 21.89 1.22 0.25 15.71| | 20: 1.34 - 1.32 2696 147 0.87 20.78 1.21 0.25 13.03| | 21: 1.32 - 1.30 2785 112 0.86 21.74 1.20 0.25 12.84| | 22: 1.29 - 1.27 2704 152 0.85 22.52 1.21 0.25 12.56| | 23: 1.27 - 1.26 2802 156 0.86 22.05 1.20 0.24 11.16| | 24: 1.26 - 1.24 2744 132 0.85 22.38 1.20 0.24 11.16| | 25: 1.24 - 1.22 2734 148 0.84 23.88 1.20 0.24 10.67| | 26: 1.22 - 1.21 2727 135 0.84 23.92 1.21 0.24 10.13| | 27: 1.21 - 1.19 2814 148 0.83 24.94 1.21 0.24 10.13| | 28: 1.19 - 1.18 2671 147 0.83 25.36 1.19 0.23 9.59| | 29: 1.18 - 1.16 2800 134 0.82 25.62 1.16 0.23 9.38| | 30: 1.16 - 1.15 2740 148 0.80 27.42 1.16 0.23 9.38| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 9.38 max = 1479.57 mean = 214.27| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.62| |phase err.(test): min = 0.00 max = 89.97 mean = 22.49| |-----------------------------------------------------------------------------| ----------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 : 0.079 0.225 1557 Z= 5.386 Angle : 5.321 17.827 2118 Z= 3.702 Chirality : 0.409 1.251 243 Planarity : 0.032 0.116 284 Dihedral : 13.882 79.230 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 1.08 % Allowed : 5.41 % Favored : 93.51 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % 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: -2.87 (0.49), residues: 224 helix: -3.19 (0.32), residues: 103 sheet: -1.11 (0.77), residues: 38 loop : -0.05 (0.68), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.092 0.028 ARG A 5 TYR 0.072 0.032 TYR A 141 PHE 0.058 0.025 PHE A 164 HIS 0.050 0.017 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= 0.2608 r_free= 0.1917 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793292 | | target function (ml) not normalized (work): 232697.977799 | | target function (ml) not normalized (free): 11828.129705 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2608 0.1917 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2608 0.1917 n_refl.: 87602 remove outliers: r(all,work,free)=0.1978 0.1983 0.1917 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.2000 0.2005 0.1930 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1647 0.1641 0.1755 n_refl.: 87594 remove outliers: r(all,work,free)=0.1646 0.1640 0.1755 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.87 87 5 0.3809 382.009 359.448 0.682 1.002 0.413 11.894-9.307 99.02 97 4 0.1829 613.617 596.249 0.933 1.003 0.400 9.237-7.194 100.00 213 7 0.2135 501.863 489.693 0.965 1.003 0.345 7.162-5.571 100.00 427 22 0.2222 376.620 364.312 0.931 1.003 0.303 5.546-4.326 100.00 867 58 0.1293 517.006 510.837 0.969 1.003 0.233 4.315-3.360 100.00 1859 96 0.1129 491.677 487.512 1.007 1.003 0.158 3.356-2.611 100.00 3867 181 0.1448 323.006 319.646 0.996 1.002 0.057 2.608-2.026 99.99 8198 413 0.1363 214.124 212.034 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1643 104.567 103.837 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2074 46.369 45.064 1.003 0.996 0.000 1.221-1.150 99.97 13689 708 0.2587 29.216 26.953 0.980 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0414 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1640 r_free=0.1755 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1640 r_free=0.1755 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.889362 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2021.335354 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 0.1772 0.1888 0.0116 0.001 0.4 5.4 0.0 0.0 0 0.125 0.1608 0.1753 0.0145 0.001 0.4 5.4 0.0 0.0 0 0.250 0.1444 0.1622 0.0179 0.001 0.5 4.5 0.0 0.0 0 0.500 0.1386 0.1587 0.0200 0.002 0.5 4.2 0.0 0.0 0 0.750 0.1355 0.1561 0.0206 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1348 0.1554 0.0205 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1299 0.1521 0.0223 0.002 0.6 4.2 0.5 0.0 0 2.000 0.1267 0.1498 0.0230 0.003 0.6 3.8 0.5 0.0 0 3.000 0.1257 0.1493 0.0236 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1245 0.1483 0.0238 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1237 0.1475 0.0237 0.004 0.8 4.2 0.5 0.0 0 6.000 0.1235 0.1473 0.0238 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1231 0.1468 0.0236 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1227 0.1466 0.0239 0.006 0.9 4.5 0.5 0.0 0 9.000 0.1227 0.1468 0.0242 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1224 0.1470 0.0245 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1220 0.1473 0.0253 0.007 1.0 3.8 0.5 0.6 0 12.945 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1227 0.1466 0.0239 0.006 0.9 4.5 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.66 2.39 3.013 19.038 2021.335 0.017 12.27 14.66 2.39 3.007 19.038 60.640 0.017 12.34 14.63 2.29 2.669 19.037 252.667 0.017 12.69 15.29 2.60 2.747 19.196 1010.668 0.016 12.52 15.41 2.89 3.144 19.490 2021.335 0.016 12.43 15.47 3.04 3.378 19.640 3032.003 0.015 12.44 15.58 3.14 3.533 19.705 4042.671 0.015 12.26 15.36 3.10 3.299 19.570 5053.338 0.015 12.21 15.33 3.11 3.296 19.557 6064.006 0.015 12.20 15.37 3.17 3.369 19.586 7074.674 0.015 12.20 15.42 3.22 3.415 19.591 8085.341 0.015 12.15 15.34 3.19 3.356 19.563 9096.009 0.015 12.19 15.47 3.28 3.479 19.621 10106.677 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 252.667 Accepted refinement result: 12.34 14.63 2.29 2.669 19.037 252.667 0.017 Individual atomic B min max mean iso aniso Overall: 9.04 119.43 20.06 3.31 0 1785 Protein: 9.04 114.98 16.97 3.32 0 1519 Water: 11.45 119.43 38.20 N/A 0 258 Other: 19.69 26.59 22.04 N/A 0 8 Chain A: 9.04 119.43 20.06 N/A 0 1785 Histogram: Values Number of atoms 9.04 - 20.08 1272 20.08 - 31.12 227 31.12 - 42.16 125 42.16 - 53.20 94 53.20 - 64.23 42 64.23 - 75.27 11 75.27 - 86.31 7 86.31 - 97.35 4 97.35 - 108.39 1 108.39 - 119.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1463 r_work=0.1236 r_free=0.1467 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1467 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1461 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1229 r_free= 0.1461 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016790 | | target function (ls_wunit_k1) not normalized (work): 1398.553190 | | target function (ls_wunit_k1) not normalized (free): 110.197642 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1240 0.1229 0.1461 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1669 0.1670 0.1681 n_refl.: 87592 remove outliers: r(all,work,free)=0.1669 0.1670 0.1681 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1676 0.1678 0.1686 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1227 0.1453 n_refl.: 87592 remove outliers: r(all,work,free)=0.1238 0.1227 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 0.3457 301.487 282.012 0.666 1.002 0.395 11.894-9.307 99.02 97 4 0.1624 484.274 471.518 0.929 1.003 0.385 9.237-7.194 100.00 213 7 0.1874 396.077 390.391 0.968 1.003 0.348 7.162-5.571 100.00 427 22 0.1809 297.234 291.809 0.937 1.003 0.265 5.546-4.326 100.00 867 58 0.1010 408.028 404.987 0.965 1.003 0.199 4.315-3.360 100.00 1859 96 0.0878 388.038 386.854 1.008 1.002 0.170 3.356-2.611 100.00 3867 181 0.1175 254.921 253.787 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1022 168.989 168.297 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1110 82.525 82.713 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1449 36.595 36.100 1.017 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 23.058 21.536 0.979 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0606 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1453 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1228 r_free=0.1455 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1228 r_free=0.1455 | n_water=258 | time (s): 2.040 (total time: 2.040) Filter (dist) r_work=0.1235 r_free=0.1455 | n_water=252 | time (s): 20.960 (total time: 23.000) Filter (q & B) r_work=0.1238 r_free=0.1455 | n_water=249 | time (s): 2.680 (total time: 25.680) Compute maps r_work=0.1238 r_free=0.1455 | n_water=249 | time (s): 1.320 (total time: 27.000) Filter (map) r_work=0.1258 r_free=0.1467 | n_water=223 | time (s): 2.720 (total time: 29.720) Find peaks r_work=0.1258 r_free=0.1467 | n_water=223 | time (s): 0.630 (total time: 30.350) Add new water r_work=0.1406 r_free=0.1642 | n_water=428 | time (s): 2.290 (total time: 32.640) Refine new water occ: r_work=0.1305 r_free=0.1503 adp: r_work=0.1228 r_free=0.1447 occ: r_work=0.1239 r_free=0.1437 adp: r_work=0.1208 r_free=0.1423 occ: r_work=0.1209 r_free=0.1407 adp: r_work=0.1200 r_free=0.1408 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1408 r_work=0.1200 r_free=0.1408 | n_water=428 | time (s): 47.840 (total time: 80.480) Filter (q & B) r_work=0.1204 r_free=0.1413 | n_water=414 | time (s): 3.090 (total time: 83.570) Filter (dist only) r_work=0.1204 r_free=0.1412 | n_water=413 | time (s): 36.060 (total time: 119.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.513892 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1508.725953 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 0.1816 0.0122 0.001 0.4 8.6 0.0 0.0 0 0.125 0.1539 0.1681 0.0142 0.001 0.4 8.0 0.0 0.0 0 0.250 0.1402 0.1568 0.0166 0.001 0.4 7.4 0.0 0.0 0 0.500 0.1334 0.1517 0.0184 0.001 0.5 6.4 0.0 0.0 0 0.750 0.1328 0.1515 0.0187 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1324 0.1513 0.0188 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1255 0.1468 0.0213 0.002 0.6 5.4 0.5 0.0 0 2.000 0.1235 0.1453 0.0218 0.003 0.6 5.1 0.5 0.0 0 3.000 0.1218 0.1440 0.0223 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1212 0.1435 0.0223 0.004 0.7 5.4 0.5 0.0 0 5.000 0.1205 0.1434 0.0229 0.004 0.7 5.1 0.5 0.0 0 6.000 0.1203 0.1430 0.0227 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1202 0.1428 0.0226 0.005 0.8 5.4 0.5 0.0 0 8.000 0.1197 0.1423 0.0227 0.006 0.8 5.4 0.5 0.0 0 9.000 0.1195 0.1420 0.0225 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1194 0.1418 0.0223 0.007 0.9 5.8 0.5 0.0 0 11.000 0.1192 0.1414 0.0222 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1190 0.1417 0.0227 0.008 1.0 5.1 0.5 0.0 0 13.757 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1414 0.0222 0.007 0.9 5.1 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 14.14 2.22 3.774 21.743 1508.726 0.016 11.92 14.14 2.22 3.774 21.743 45.262 0.016 11.92 14.14 2.22 3.774 21.743 188.591 0.016 12.12 14.63 2.51 3.621 21.750 754.363 0.015 12.04 14.83 2.78 3.505 21.857 1508.726 0.015 11.90 14.80 2.89 3.446 22.062 2263.089 0.014 11.81 14.78 2.96 3.495 21.906 3017.452 0.014 11.81 14.88 3.07 3.488 21.985 3771.815 0.014 11.72 14.77 3.05 3.502 21.943 4526.178 0.014 11.75 14.79 3.05 3.507 22.110 5280.541 0.014 11.72 14.81 3.09 3.519 22.104 6034.904 0.014 11.73 14.90 3.17 3.559 22.181 6789.267 0.014 11.67 14.80 3.12 3.545 22.142 7543.630 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: 188.591 Accepted refinement result: 11.92 14.14 2.22 3.774 21.743 188.591 0.016 Individual atomic B min max mean iso aniso Overall: 9.08 115.02 22.14 3.31 190 1750 Protein: 9.08 115.02 17.01 3.32 0 1519 Water: 11.49 76.67 41.01 N/A 190 223 Other: 19.73 26.63 22.08 N/A 0 8 Chain A: 9.08 115.02 19.39 N/A 0 1750 Chain S: 14.47 60.00 47.47 N/A 190 0 Histogram: Values Number of atoms 9.08 - 19.67 1258 19.67 - 30.27 241 30.27 - 40.86 163 40.86 - 51.46 134 51.46 - 62.05 121 62.05 - 72.64 12 72.64 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1414 r_work=0.1192 r_free=0.1414 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1414 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 = 0.1191 r_free = 0.1408 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.16 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= 0.1191 r_free= 0.1408 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015028 | | target function (ls_wunit_k1) not normalized (work): 1251.774467 | | target function (ls_wunit_k1) not normalized (free): 102.710612 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1191 0.1408 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1586 0.1584 0.1647 n_refl.: 87592 remove outliers: r(all,work,free)=0.1586 0.1584 0.1647 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1588 0.1587 0.1648 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1187 0.1401 n_refl.: 87592 remove outliers: r(all,work,free)=0.1197 0.1186 0.1401 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 0.3371 300.848 274.105 0.609 1.002 0.360 11.894-9.307 99.02 97 4 0.1622 484.274 476.341 0.924 1.003 0.353 9.237-7.194 100.00 213 7 0.1668 396.077 395.403 0.990 1.003 0.290 7.162-5.571 100.00 427 22 0.1544 297.234 292.102 0.937 1.003 0.224 5.546-4.326 100.00 867 58 0.0877 408.028 405.387 0.962 1.003 0.200 4.315-3.360 100.00 1859 96 0.0796 388.038 387.060 1.004 1.003 0.190 3.356-2.611 100.00 3867 181 0.1094 254.921 253.818 1.008 1.002 0.130 2.608-2.026 99.99 8198 413 0.1019 168.989 168.377 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1097 82.525 82.744 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.595 36.129 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2248 23.058 21.563 0.986 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0206 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1401 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=0.1186 r_free=0.1401 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1401 | n_water=413 | time (s): 1.470 (total time: 1.470) Filter (dist) r_work=0.1186 r_free=0.1397 | n_water=409 | time (s): 33.270 (total time: 34.740) Filter (q & B) r_work=0.1186 r_free=0.1397 | n_water=409 | time (s): 1.080 (total time: 35.820) Compute maps r_work=0.1186 r_free=0.1397 | n_water=409 | time (s): 1.710 (total time: 37.530) Filter (map) r_work=0.1217 r_free=0.1403 | n_water=283 | time (s): 3.100 (total time: 40.630) Find peaks r_work=0.1217 r_free=0.1403 | n_water=283 | time (s): 0.630 (total time: 41.260) Add new water r_work=0.1343 r_free=0.1529 | n_water=482 | time (s): 2.490 (total time: 43.750) Refine new water occ: r_work=0.1247 r_free=0.1433 adp: r_work=0.1248 r_free=0.1437 occ: r_work=0.1222 r_free=0.1405 adp: r_work=0.1221 r_free=0.1410 occ: r_work=0.1203 r_free=0.1383 adp: r_work=0.1198 r_free=0.1388 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1388 r_work=0.1198 r_free=0.1388 | n_water=482 | time (s): 191.920 (total time: 235.670) Filter (q & B) r_work=0.1203 r_free=0.1394 | n_water=450 | time (s): 2.530 (total time: 238.200) Filter (dist only) r_work=0.1203 r_free=0.1393 | n_water=449 | time (s): 36.550 (total time: 274.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.824283 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.198807 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 0.1234 0.1363 0.0129 0.002 0.6 4.5 0.5 0.0 0 0.091 0.1188 0.1324 0.0137 0.003 0.7 3.2 0.5 0.0 0 0.274 0.1171 0.1311 0.0140 0.004 0.8 3.2 0.5 0.0 0 0.547 0.1163 0.1302 0.0140 0.005 0.9 3.2 0.5 0.0 0 0.821 0.1159 0.1301 0.0142 0.006 1.0 3.5 0.5 0.0 0 1.095 0.1157 0.1302 0.0145 0.007 1.0 3.5 0.5 0.0 0 1.368 0.1154 0.1300 0.0146 0.007 1.1 3.8 0.5 0.0 0 1.642 0.1153 0.1299 0.0146 0.008 1.1 3.8 0.5 0.0 0 1.915 0.1162 0.1303 0.0140 0.006 0.9 2.9 0.5 0.0 0 0.912 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1153 0.1299 0.0146 0.008 1.1 3.8 0.5 0.0 0 1.915 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.53 12.99 1.46 3.777 21.318 49.199 3.619 11.53 12.99 1.46 3.777 21.318 1.476 3.619 11.54 13.00 1.46 3.766 21.318 6.150 3.619 11.60 13.11 1.50 3.712 21.301 24.599 3.614 11.57 13.16 1.59 3.740 21.275 49.199 3.612 11.53 13.16 1.63 3.756 21.260 73.798 3.607 11.47 13.11 1.64 3.769 21.260 98.398 3.602 11.44 13.09 1.66 3.782 21.255 122.997 3.600 11.44 13.14 1.70 3.803 21.239 147.596 3.600 11.42 13.12 1.70 3.816 21.229 172.196 3.598 11.42 13.12 1.70 3.825 21.228 196.795 3.597 11.41 13.12 1.71 3.835 21.222 221.395 3.596 11.39 13.09 1.70 3.839 21.224 245.994 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: 1.476 Accepted refinement result: 11.53 12.99 1.46 3.777 21.318 1.476 3.619 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.35 3.31 227 1749 Protein: 9.09 115.03 17.02 3.32 0 1519 Water: 11.50 76.68 35.96 N/A 227 222 Other: 19.75 26.64 22.09 N/A 0 8 Chain A: 9.09 115.03 19.38 N/A 0 1749 Chain S: 14.48 60.01 36.49 N/A 227 0 Histogram: Values Number of atoms 9.09 - 19.69 1262 19.69 - 30.28 290 30.28 - 40.87 206 40.87 - 51.47 139 51.47 - 62.06 56 62.06 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1153 r_free=0.1299 r_work=0.1153 r_free=0.1299 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1299 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1144 r_free = 0.1305 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1144 r_free= 0.1305 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.613941 | | target function (ml) not normalized (work): 301019.600796 | | target function (ml) not normalized (free): 15848.273869 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1152 0.1144 0.1305 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1482 0.1480 0.1548 n_refl.: 87590 remove outliers: r(all,work,free)=0.1482 0.1480 0.1548 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1481 0.1479 0.1547 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1146 0.1138 0.1302 n_refl.: 87590 remove outliers: r(all,work,free)=0.1144 0.1135 0.1302 n_refl.: 87584 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3826 294.910 265.930 0.485 0.999 0.307 11.894-9.307 98.04 96 4 0.2372 484.400 464.605 0.879 1.001 0.290 9.237-7.194 99.09 211 7 0.2231 390.557 390.562 0.962 1.002 0.180 7.162-5.571 100.00 427 22 0.1977 297.234 287.810 0.927 1.002 0.168 5.546-4.326 100.00 867 58 0.1101 408.028 403.791 0.964 1.002 0.141 4.315-3.360 100.00 1859 96 0.0932 388.038 385.535 1.004 1.002 0.127 3.356-2.611 100.00 3867 181 0.1133 254.921 252.775 1.007 1.001 0.090 2.608-2.026 99.99 8198 413 0.0925 168.989 168.268 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0892 82.525 82.828 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.595 36.188 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2162 23.058 21.600 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0108 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1135 r_free=0.1302 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1135 r_free=0.1302 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1135 r_free=0.1302 | n_water=449 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1135 r_free=0.1301 | n_water=447 | time (s): 45.250 (total time: 47.690) Filter (q & B) r_work=0.1136 r_free=0.1301 | n_water=446 | time (s): 4.290 (total time: 51.980) Compute maps r_work=0.1136 r_free=0.1301 | n_water=446 | time (s): 1.840 (total time: 53.820) Filter (map) r_work=0.1167 r_free=0.1296 | n_water=336 | time (s): 3.820 (total time: 57.640) Find peaks r_work=0.1167 r_free=0.1296 | n_water=336 | time (s): 0.690 (total time: 58.330) Add new water r_work=0.1232 r_free=0.1359 | n_water=508 | time (s): 3.520 (total time: 61.850) Refine new water occ: r_work=0.1158 r_free=0.1311 adp: r_work=0.1158 r_free=0.1314 occ: r_work=0.1141 r_free=0.1297 adp: r_work=0.1140 r_free=0.1298 occ: r_work=0.1129 r_free=0.1290 adp: r_work=0.1125 r_free=0.1289 ADP+occupancy (water only), MIN, final r_work=0.1125 r_free=0.1289 r_work=0.1125 r_free=0.1289 | n_water=508 | time (s): 221.010 (total time: 282.860) Filter (q & B) r_work=0.1133 r_free=0.1298 | n_water=469 | time (s): 3.900 (total time: 286.760) Filter (dist only) r_work=0.1133 r_free=0.1298 | n_water=468 | time (s): 47.730 (total time: 334.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.685719 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.353066 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 0.1202 0.1348 0.0146 0.002 0.6 4.5 0.5 0.0 0 0.084 0.1162 0.1321 0.0159 0.003 0.7 3.5 0.5 0.0 0 0.253 0.1148 0.1308 0.0160 0.004 0.9 3.5 0.5 0.0 0 0.506 0.1141 0.1306 0.0164 0.005 0.9 3.2 0.5 0.0 0 0.759 0.1138 0.1306 0.0168 0.006 1.0 3.2 0.5 0.0 0 1.011 0.1135 0.1304 0.0170 0.007 1.0 3.5 0.5 0.0 0 1.264 0.1133 0.1298 0.0165 0.008 1.1 3.5 0.5 0.0 0 1.517 0.1131 0.1298 0.0167 0.008 1.1 3.8 0.5 0.0 0 1.770 0.1140 0.1306 0.0166 0.006 0.9 3.2 0.5 0.0 0 0.843 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1131 0.1298 0.0167 0.008 1.1 3.8 0.5 0.0 0 1.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 12.98 1.67 3.779 21.316 48.353 3.608 11.31 12.98 1.67 3.779 21.316 1.451 3.608 11.31 12.98 1.67 3.778 21.316 6.044 3.608 11.36 13.06 1.70 3.713 21.303 24.177 3.604 11.38 13.16 1.78 3.742 21.276 48.353 3.604 11.31 13.13 1.82 3.762 21.269 72.530 3.598 11.29 13.12 1.83 3.774 21.266 96.706 3.595 11.22 13.06 1.83 3.779 21.269 120.883 3.591 11.22 13.09 1.86 3.798 21.260 145.059 3.590 11.24 13.12 1.88 3.819 21.248 169.236 3.590 11.22 13.10 1.87 3.828 21.245 193.412 3.589 11.21 13.08 1.88 3.835 21.245 217.589 3.588 11.19 13.07 1.88 3.840 21.246 241.765 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.451 Accepted refinement result: 11.31 12.98 1.67 3.779 21.316 1.451 3.608 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.34 3.31 247 1748 Protein: 9.09 115.03 17.02 3.32 0 1519 Water: 11.49 76.68 35.37 N/A 247 221 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.09 115.03 19.38 N/A 0 1748 Chain S: 14.48 60.01 35.27 N/A 247 0 Histogram: Values Number of atoms 9.09 - 19.68 1263 19.68 - 30.28 301 30.28 - 40.87 223 40.87 - 51.46 136 51.46 - 62.06 49 62.06 - 72.65 12 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1298 r_work=0.1131 r_free=0.1298 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1298 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1125 r_free = 0.1296 target_work(ml) = 3.606 | | 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.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1125 r_free= 0.1296 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605630 | | target function (ml) not normalized (work): 300305.701241 | | target function (ml) not normalized (free): 15819.744339 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1133 0.1125 0.1296 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1443 0.1441 0.1513 n_refl.: 87584 remove outliers: r(all,work,free)=0.1443 0.1441 0.1513 n_refl.: 87584 overall B=0.00 to atoms: r(all,work,free)=0.1444 0.1442 0.1514 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1133 0.1125 0.1303 n_refl.: 87584 remove outliers: r(all,work,free)=0.1131 0.1123 0.1303 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3995 292.865 252.091 0.452 0.997 0.320 11.894-9.307 96.08 94 4 0.2268 477.619 464.144 0.867 1.000 0.233 9.237-7.194 98.64 210 7 0.2343 388.536 384.674 0.935 1.001 0.150 7.162-5.571 100.00 427 22 0.2057 297.234 288.418 0.920 1.001 0.133 5.546-4.326 100.00 867 58 0.1112 408.028 403.157 0.962 1.001 0.127 4.315-3.360 100.00 1859 96 0.0910 388.038 386.571 1.004 1.001 0.097 3.356-2.611 100.00 3867 181 0.1093 254.921 253.014 1.008 1.002 0.024 2.608-2.026 99.99 8198 413 0.0904 168.989 168.393 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0882 82.525 82.872 1.033 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.595 36.174 1.023 1.001 0.000 1.221-1.150 99.97 13689 708 0.2164 23.058 21.499 0.979 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0050 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1123 r_free=0.1303 After: r_work=0.1124 r_free=0.1303 ================================== NQH flips ================================== r_work=0.1124 r_free=0.1303 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=0.1124 r_free=0.1303 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1124 r_free=0.1303 | n_water=468 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1124 r_free=0.1303 | n_water=468 | time (s): 46.070 (total time: 48.610) Filter (q & B) r_work=0.1124 r_free=0.1302 | n_water=467 | time (s): 4.130 (total time: 52.740) Compute maps r_work=0.1124 r_free=0.1302 | n_water=467 | time (s): 1.910 (total time: 54.650) Filter (map) r_work=0.1153 r_free=0.1301 | n_water=368 | time (s): 4.020 (total time: 58.670) Find peaks r_work=0.1153 r_free=0.1301 | n_water=368 | time (s): 0.710 (total time: 59.380) Add new water r_work=0.1198 r_free=0.1346 | n_water=519 | time (s): 3.690 (total time: 63.070) Refine new water occ: r_work=0.1140 r_free=0.1302 adp: r_work=0.1140 r_free=0.1304 occ: r_work=0.1128 r_free=0.1293 adp: r_work=0.1127 r_free=0.1293 occ: r_work=0.1119 r_free=0.1283 adp: r_work=0.1116 r_free=0.1283 ADP+occupancy (water only), MIN, final r_work=0.1116 r_free=0.1283 r_work=0.1116 r_free=0.1283 | n_water=519 | time (s): 211.850 (total time: 274.920) Filter (q & B) r_work=0.1124 r_free=0.1286 | n_water=478 | time (s): 4.150 (total time: 279.070) Filter (dist only) r_work=0.1124 r_free=0.1286 | n_water=477 | time (s): 49.480 (total time: 328.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.799600 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.569974 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1214 0.1349 0.0135 0.004 0.7 8.3 0.5 0.0 0 0.090 0.1159 0.1308 0.0148 0.004 0.8 7.0 0.0 0.0 0 0.270 0.1144 0.1297 0.0153 0.005 0.9 6.7 0.5 0.0 0 0.540 0.1132 0.1290 0.0157 0.006 1.0 6.4 0.5 0.0 0 0.810 0.1130 0.1288 0.0158 0.007 1.1 6.4 0.5 0.0 0 1.080 0.1127 0.1286 0.0160 0.008 1.1 6.4 0.5 0.0 0 1.350 0.1125 0.1286 0.0161 0.008 1.1 6.4 0.5 0.0 0 1.620 0.1124 0.1286 0.0161 0.008 1.1 6.4 0.5 0.0 0 1.890 0.1132 0.1289 0.0158 0.006 1.0 6.4 0.5 0.0 0 0.900 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1125 0.1286 0.0161 0.008 1.1 6.4 0.5 0.0 0 1.620 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.25 12.86 1.61 3.778 21.333 37.570 3.605 11.25 12.86 1.61 3.778 21.333 1.127 3.605 11.25 12.86 1.61 3.778 21.333 4.696 3.605 11.28 12.90 1.62 3.709 21.327 18.785 3.600 11.40 13.08 1.69 3.718 21.302 37.570 3.607 11.31 13.05 1.74 3.744 21.291 56.355 3.600 11.22 12.98 1.76 3.763 21.288 75.140 3.594 11.19 12.96 1.77 3.773 21.286 93.925 3.591 11.17 12.95 1.78 3.778 21.286 112.710 3.589 11.15 12.95 1.79 3.786 21.285 131.495 3.587 11.16 12.99 1.83 3.805 21.273 150.280 3.588 11.14 12.98 1.84 3.811 21.272 169.065 3.586 11.14 12.99 1.84 3.821 21.269 187.850 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: 4.696 Accepted refinement result: 11.25 12.86 1.61 3.778 21.333 4.696 3.605 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.37 3.31 257 1747 Protein: 9.09 115.03 17.02 3.32 0 1519 Water: 11.50 76.68 35.22 N/A 257 220 Other: 19.75 26.64 22.09 N/A 0 8 Chain A: 9.09 115.03 19.35 N/A 0 1747 Chain S: 14.48 60.01 35.15 N/A 257 0 Histogram: Values Number of atoms 9.09 - 19.69 1265 19.69 - 30.28 308 30.28 - 40.87 220 40.87 - 51.47 136 51.47 - 62.06 53 62.06 - 72.65 12 72.65 - 83.25 4 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1125 r_free=0.1286 r_work=0.1125 r_free=0.1286 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1125 r_free = 0.1286 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1121 r_free = 0.1285 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1121 r_free= 0.1285 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603358 | | target function (ml) not normalized (work): 300098.484516 | | target function (ml) not normalized (free): 15809.386476 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1308 0.1387 5.636 5.6107| | 2: 3.57 - 2.84 1.00 2888 124 0.1050 0.1366 5.1556 5.2289| | 3: 2.83 - 2.48 1.00 2820 163 0.1079 0.1147 4.9407 4.9547| | 4: 2.47 - 2.25 1.00 2825 136 0.0887 0.0963 4.6287 4.6571| | 5: 2.25 - 2.09 1.00 2756 127 0.0852 0.0969 4.5755 4.6315| | 6: 2.09 - 1.97 1.00 2846 113 0.0843 0.0992 4.2631 4.356| | 7: 1.97 - 1.87 1.00 2787 165 0.0878 0.1111 3.9741 4.0898| | 8: 1.87 - 1.79 1.00 2789 144 0.0913 0.1079 3.8867 3.9829| | 9: 1.79 - 1.72 1.00 2745 138 0.0867 0.1173 3.6418 3.8262| | 10: 1.72 - 1.66 1.00 2831 160 0.0915 0.1215 3.5648 3.7188| | 11: 1.66 - 1.61 1.00 2712 147 0.0864 0.1032 3.4924 3.571| | 12: 1.61 - 1.56 1.00 2773 144 0.0903 0.1141 3.3317 3.461| | 13: 1.56 - 1.52 1.00 2745 130 0.0944 0.1020 3.3075 3.3922| | 14: 1.52 - 1.48 1.00 2803 134 0.0981 0.1047 3.2383 3.3175| | 15: 1.48 - 1.45 1.00 2738 128 0.0997 0.1216 3.1506 3.2639| | 16: 1.45 - 1.42 1.00 2756 161 0.1050 0.1238 3.1342 3.2352| | 17: 1.42 - 1.39 1.00 2785 139 0.1133 0.1312 3.1181 3.2394| | 18: 1.39 - 1.36 1.00 2741 179 0.1194 0.1319 3.104 3.2304| | 19: 1.36 - 1.34 1.00 2807 134 0.1259 0.1568 3.1128 3.2746| | 20: 1.34 - 1.32 1.00 2696 147 0.1362 0.1455 3.1124 3.1563| | 21: 1.32 - 1.30 1.00 2785 112 0.1469 0.1510 3.1152 3.1085| | 22: 1.29 - 1.27 1.00 2704 152 0.1563 0.1976 3.1256 3.2962| | 23: 1.27 - 1.26 1.00 2802 156 0.1646 0.1795 3.1356 3.1998| | 24: 1.26 - 1.24 1.00 2744 132 0.1710 0.1843 3.1311 3.2394| | 25: 1.24 - 1.22 1.00 2733 148 0.1884 0.2148 3.1455 3.2663| | 26: 1.22 - 1.21 1.00 2727 135 0.1914 0.1762 3.1538 3.2041| | 27: 1.21 - 1.19 1.00 2814 148 0.2076 0.2172 3.1752 3.1666| | 28: 1.19 - 1.18 1.00 2671 147 0.2201 0.2303 3.1689 3.18| | 29: 1.18 - 1.16 1.00 2800 134 0.2259 0.2374 3.15 3.2333| | 30: 1.16 - 1.15 1.00 2739 148 0.2441 0.2436 3.1459 3.1669| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2921 171 0.95 8.39 1.00 0.97 5755.44| | 2: 3.57 - 2.84 2888 124 0.93 12.43 1.01 0.97 5755.44| | 3: 2.83 - 2.48 2820 163 0.90 16.44 0.99 0.98 4806.86| | 4: 2.47 - 2.25 2825 136 0.92 13.35 1.00 0.98 2360.77| | 5: 2.25 - 2.09 2756 127 0.90 15.57 1.01 0.98 2360.77| | 6: 2.09 - 1.97 2846 113 0.92 12.32 1.02 0.98 1361.58| | 7: 1.97 - 1.87 2787 165 0.95 9.27 1.02 0.98 509.39| | 8: 1.87 - 1.79 2789 144 0.93 12.59 0.99 0.98 509.39| | 9: 1.79 - 1.72 2745 138 0.94 9.98 0.98 0.98 288.57| | 10: 1.72 - 1.66 2831 160 0.94 11.06 0.98 0.98 244.34| | 11: 1.66 - 1.61 2712 147 0.93 11.70 0.98 0.98 234.15| | 12: 1.61 - 1.56 2773 144 0.96 8.83 0.99 0.98 137.97| | 13: 1.56 - 1.52 2745 130 0.95 10.38 1.03 0.98 137.97| | 14: 1.52 - 1.48 2803 134 0.94 10.73 1.02 0.98 123.62| | 15: 1.48 - 1.45 2738 128 0.95 9.85 1.02 0.99 97.33| | 16: 1.45 - 1.42 2756 161 0.94 11.00 1.02 0.99 97.33| | 17: 1.42 - 1.39 2785 139 0.95 10.84 1.01 0.99 88.81| | 18: 1.39 - 1.36 2741 179 0.94 11.47 1.01 0.99 83.88| | 19: 1.36 - 1.34 2807 134 0.94 11.82 0.99 0.99 83.88| | 20: 1.34 - 1.32 2696 147 0.94 12.09 0.98 0.97 80.17| | 21: 1.32 - 1.30 2785 112 0.94 13.09 0.98 0.97 79.91| | 22: 1.29 - 1.27 2704 152 0.93 13.64 0.98 0.96 80.36| | 23: 1.27 - 1.26 2802 156 0.92 14.81 0.97 0.95 82.66| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.95 82.66| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.94 84.69| | 26: 1.22 - 1.21 2727 135 0.90 18.14 1.03 0.94 86.93| | 27: 1.21 - 1.19 2814 148 0.89 18.79 1.03 0.94 86.93| | 28: 1.19 - 1.18 2671 147 0.88 20.42 1.01 0.93 90.59| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.99 0.93 91.97| | 30: 1.16 - 1.15 2739 148 0.86 22.03 0.98 0.93 91.97| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.91 max = 5755.44 mean = 887.73| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.40| |phase err.(test): min = 0.00 max = 89.56 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1121 0.1285 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1438 0.1437 0.1497 n_refl.: 87579 remove outliers: r(all,work,free)=0.1438 0.1437 0.1497 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1438 0.1436 0.1497 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1128 0.1120 0.1284 n_refl.: 87579 remove outliers: r(all,work,free)=0.1126 0.1118 0.1284 n_refl.: 87573 ======================== 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 0.4110 289.369 252.623 0.444 0.998 0.302 11.894-9.307 92.16 90 4 0.2296 472.546 457.230 0.865 1.001 0.222 9.237-7.194 98.18 209 7 0.2327 387.525 382.679 0.927 1.002 0.160 7.162-5.571 100.00 427 22 0.2071 297.234 287.323 0.916 1.002 0.130 5.546-4.326 100.00 867 58 0.1089 408.028 403.663 0.964 1.002 0.120 4.315-3.360 100.00 1859 96 0.0899 388.038 386.187 1.005 1.002 0.110 3.356-2.611 100.00 3867 181 0.1090 254.921 253.020 1.009 1.002 0.024 2.608-2.026 99.99 8198 413 0.0895 168.989 168.373 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0882 82.525 82.839 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.595 36.198 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 23.058 21.602 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0098 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2608 0.1917 0.079 5.321 8.8 119.3 19.9 258 0.000 1_bss: 0.1640 0.1755 0.079 5.321 9.0 119.5 20.1 258 0.000 1_settarget: 0.1640 0.1755 0.079 5.321 9.0 119.5 20.1 258 0.000 1_nqh: 0.1640 0.1755 0.079 5.321 9.0 119.5 20.1 258 0.000 1_weight: 0.1640 0.1755 0.079 5.321 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1227 0.1466 0.006 0.853 9.0 119.5 20.1 258 0.135 1_adp: 0.1234 0.1463 0.006 0.853 9.0 119.4 20.1 258 0.135 1_regHadp: 0.1236 0.1467 0.006 0.853 9.0 119.4 20.1 258 0.135 1_occ: 0.1229 0.1461 0.006 0.853 9.0 119.4 20.1 258 0.135 2_bss: 0.1227 0.1453 0.006 0.853 9.1 119.5 20.1 258 0.135 2_settarget: 0.1227 0.1453 0.006 0.853 9.1 119.5 20.1 258 0.135 2_updatecdl: 0.1227 0.1453 0.006 0.871 9.1 119.5 20.1 258 0.135 2_nqh: 0.1228 0.1455 0.006 0.871 9.1 119.5 20.1 258 0.138 2_sol: 0.1204 0.1412 0.006 0.871 9.1 115.0 22.1 413 n/a 2_weight: 0.1204 0.1412 0.006 0.871 9.1 115.0 22.1 413 n/a 2_xyzrec: 0.1192 0.1414 0.007 0.916 9.1 115.0 22.1 413 n/a 2_adp: 0.1192 0.1414 0.007 0.916 9.1 115.0 22.1 413 n/a 2_regHadp: 0.1192 0.1414 0.007 0.916 9.1 115.0 22.1 413 n/a 2_occ: 0.1191 0.1408 0.007 0.916 9.1 115.0 22.1 413 n/a 3_bss: 0.1186 0.1401 0.007 0.916 9.1 115.0 22.2 413 n/a 3_settarget: 0.1186 0.1401 0.007 0.916 9.1 115.0 22.2 413 n/a 3_updatecdl: 0.1186 0.1401 0.007 0.920 9.1 115.0 22.2 413 n/a 3_nqh: 0.1186 0.1401 0.007 0.920 9.1 115.0 22.2 413 n/a 3_sol: 0.1203 0.1393 0.007 0.920 9.1 115.0 21.3 449 n/a 3_weight: 0.1203 0.1393 0.007 0.920 9.1 115.0 21.3 449 n/a 3_xyzrec: 0.1153 0.1299 0.008 1.098 9.1 115.0 21.3 449 n/a 3_adp: 0.1153 0.1299 0.008 1.098 9.1 115.0 21.3 449 n/a 3_regHadp: 0.1153 0.1299 0.008 1.098 9.1 115.0 21.3 449 n/a 3_occ: 0.1144 0.1305 0.008 1.098 9.1 115.0 21.3 449 n/a 4_bss: 0.1135 0.1302 0.008 1.098 9.1 115.0 21.3 449 n/a 4_settarget: 0.1135 0.1302 0.008 1.098 9.1 115.0 21.3 449 n/a 4_updatecdl: 0.1135 0.1302 0.008 1.098 9.1 115.0 21.3 449 n/a 4_nqh: 0.1135 0.1302 0.008 1.098 9.1 115.0 21.3 449 n/a 4_sol: 0.1133 0.1298 0.008 1.098 9.1 115.0 21.3 468 n/a 4_weight: 0.1133 0.1298 0.008 1.098 9.1 115.0 21.3 468 n/a 4_xyzrec: 0.1131 0.1298 0.008 1.114 9.1 115.0 21.3 468 n/a 4_adp: 0.1131 0.1298 0.008 1.114 9.1 115.0 21.3 468 n/a 4_regHadp: 0.1131 0.1298 0.008 1.114 9.1 115.0 21.3 468 n/a 4_occ: 0.1125 0.1296 0.008 1.114 9.1 115.0 21.3 468 n/a 5_bss: 0.1123 0.1303 0.008 1.114 9.1 115.0 21.3 468 n/a 5_settarget: 0.1123 0.1303 0.008 1.114 9.1 115.0 21.3 468 n/a 5_updatecdl: 0.1123 0.1303 0.008 1.116 9.1 115.0 21.3 468 n/a 5_setrh: 0.1124 0.1303 0.008 1.116 9.1 115.0 21.3 468 n/a 5_nqh: 0.1124 0.1303 0.008 1.116 9.1 115.0 21.3 468 n/a 5_sol: 0.1124 0.1286 0.008 1.116 9.1 115.0 21.4 477 n/a 5_weight: 0.1124 0.1286 0.008 1.116 9.1 115.0 21.4 477 n/a 5_xyzrec: 0.1125 0.1286 0.008 1.119 9.1 115.0 21.4 477 n/a 5_adp: 0.1125 0.1286 0.008 1.119 9.1 115.0 21.4 477 n/a 5_regHadp: 0.1125 0.1286 0.008 1.119 9.1 115.0 21.4 477 n/a 5_occ: 0.1121 0.1285 0.008 1.119 9.1 115.0 21.4 477 n/a end: 0.1118 0.1284 0.008 1.119 9.1 115.0 21.4 477 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3941866_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3941866_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.0700 Refinement macro-cycles (run) : 13282.0200 Write final files (write_after_run_outputs) : 97.9800 Total : 13384.0700 Total CPU time: 3.73 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:03:58 PST -0800 (1735365838.57 s) Start R-work = 0.1640, R-free = 0.1755 Final R-work = 0.1118, R-free = 0.1284 =============================================================================== Job complete usr+sys time: 13575.04 seconds wall clock time: 248 minutes 28.98 seconds (14908.98 seconds total)