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_8666014.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8666014.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8666014.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.30, per 1000 atoms: 0.38 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: 0.47 Conformation dependent library (CDL) restraints added in 195.6 milliseconds Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.90: 430 0.90 - 1.16: 1197 1.16 - 1.43: 670 1.43 - 1.69: 835 1.69 - 1.96: 21 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.244 1.430 -0.186 1.00e-02 1.00e+04 3.46e+02 bond pdb=" C LEU A 77 " pdb=" N GLY A 78 " ideal model delta sigma weight residual 1.334 1.544 -0.211 1.14e-02 7.69e+03 3.42e+02 bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.447 1.251 0.196 1.08e-02 8.57e+03 3.29e+02 bond pdb=" C ASP A 60 " pdb=" O ASP A 60 " ideal model delta sigma weight residual 1.236 1.451 -0.215 1.19e-02 7.06e+03 3.26e+02 bond pdb=" CD ARG A 145 " pdb=" NE ARG A 145 " ideal model delta sigma weight residual 1.458 1.209 0.249 1.40e-02 5.10e+03 3.15e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 2961 4.39 - 8.79: 1912 8.79 - 13.18: 728 13.18 - 17.57: 152 17.57 - 21.97: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 119.71 106.85 12.86 8.10e-01 1.52e+00 2.52e+02 angle pdb=" CA GLY A 137 " pdb=" C GLY A 137 " pdb=" O GLY A 137 " ideal model delta sigma weight residual 119.82 103.97 15.85 1.14e+00 7.69e-01 1.93e+02 angle pdb=" C LEU A 82 " pdb=" N SER A 83 " pdb=" CA SER A 83 " ideal model delta sigma weight residual 120.28 139.74 -19.46 1.44e+00 4.82e-01 1.83e+02 angle pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 108.40 95.27 13.13 1.00e+00 1.00e+00 1.72e+02 angle pdb=" ND1 HIS A 126 " pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " ideal model delta sigma weight residual 106.10 118.65 -12.55 1.00e+00 1.00e+00 1.57e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 925 16.76 - 33.53: 131 33.53 - 50.29: 34 50.29 - 67.05: 16 67.05 - 83.81: 5 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.240: 108 0.240 - 0.472: 75 0.472 - 0.705: 36 0.705 - 0.937: 19 0.937 - 1.170: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -1.42 -1.17 2.00e-01 2.50e+01 3.42e+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 -1.52 -1.07 2.00e-01 2.50e+01 2.88e+01 chirality pdb=" CA BGLU A 90 " pdb=" N BGLU A 90 " pdb=" C BGLU A 90 " pdb=" CB BGLU A 90 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.072 2.00e-02 2.50e+03 6.70e-02 1.35e+02 pdb=" CG TYR A 141 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.110 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.107 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.097 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.034 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.011 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.028 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.107 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.058 2.00e-02 2.50e+03 6.22e-02 1.16e+02 pdb=" CG BTYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.128 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.050 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.093 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.053 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.074 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.046 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.061 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.041 2.00e-02 2.50e+03 5.42e-02 8.82e+01 pdb=" CG TYR A 139 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.085 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.079 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.087 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.029 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.078 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.052 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1084 2.32 - 2.89: 8132 2.89 - 3.46: 10475 3.46 - 4.03: 15267 4.03 - 4.60: 21704 Nonbonded interactions: 56662 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.755 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.775 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.779 1.850 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.814 1.850 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.827 1.850 ... (remaining 56657 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_8666014_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= 0.2600 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787673 | | target function (ml) not normalized (work): 232229.914467 | | target function (ml) not normalized (free): 11810.873337 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3033 0.2194 7.022 4.9608| | 2: 3.57 - 2.84 1.00 2876 122 0.2424 0.1722 4.3528 4.3443| | 3: 2.84 - 2.48 1.00 2833 165 0.2330 0.1749 4.1334 4.1891| | 4: 2.47 - 2.25 1.00 2825 136 0.2353 0.1480 3.8344 3.8183| | 5: 2.25 - 2.09 1.00 2756 127 0.2458 0.1638 3.8059 3.8341| | 6: 2.09 - 1.97 1.00 2846 113 0.2536 0.1533 3.4748 3.4992| | 7: 1.97 - 1.87 1.00 2787 165 0.2511 0.1818 3.1343 3.2157| | 8: 1.87 - 1.79 1.00 2789 144 0.2453 0.1832 3.0569 3.1052| | 9: 1.79 - 1.72 1.00 2745 138 0.2412 0.1901 2.9022 2.9428| | 10: 1.72 - 1.66 1.00 2789 158 0.2393 0.1968 2.7987 2.8944| | 11: 1.66 - 1.61 1.00 2740 147 0.2496 0.2176 2.7534 2.8529| | 12: 1.61 - 1.56 1.00 2787 146 0.2509 0.1886 2.632 2.6199| | 13: 1.56 - 1.52 1.00 2745 130 0.2519 0.1693 2.5404 2.5569| | 14: 1.52 - 1.48 1.00 2803 134 0.2545 0.2057 2.5087 2.5808| | 15: 1.48 - 1.45 1.00 2738 128 0.2621 0.2156 2.4134 2.496| | 16: 1.45 - 1.42 1.00 2756 161 0.2675 0.2207 2.3848 2.417| | 17: 1.42 - 1.39 1.00 2785 139 0.2708 0.2246 2.3463 2.4075| | 18: 1.39 - 1.36 1.00 2741 179 0.2659 0.2297 2.2584 2.3119| | 19: 1.36 - 1.34 1.00 2807 134 0.2673 0.2536 2.2421 2.3562| | 20: 1.34 - 1.32 1.00 2696 147 0.2736 0.2266 2.2097 2.2585| | 21: 1.32 - 1.30 1.00 2785 112 0.2699 0.2031 2.1689 2.14| | 22: 1.29 - 1.27 1.00 2704 152 0.2748 0.2379 2.1478 2.144| | 23: 1.27 - 1.26 1.00 2802 156 0.2729 0.2486 2.0896 2.1688| | 24: 1.26 - 1.24 1.00 2744 132 0.2753 0.2522 2.0655 2.1617| | 25: 1.24 - 1.22 1.00 2734 148 0.2887 0.2324 2.0507 2.0403| | 26: 1.22 - 1.21 1.00 2727 135 0.2828 0.2328 1.9959 2.1194| | 27: 1.21 - 1.19 1.00 2814 148 0.2944 0.2583 1.9999 1.9651| | 28: 1.19 - 1.18 1.00 2671 147 0.2979 0.2778 1.9778 1.9888| | 29: 1.18 - 1.16 1.00 2800 134 0.2962 0.2772 1.9592 2.011| | 30: 1.16 - 1.15 1.00 2740 148 0.3040 0.2696 1.9153 1.9167| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 19.04 0.76 0.23 1508.78| | 2: 3.57 - 2.84 2876 122 0.80 26.29 1.27 0.23 1508.78| | 3: 2.84 - 2.48 2833 165 0.74 32.28 1.24 0.24 1250.38| | 4: 2.47 - 2.25 2825 136 0.81 25.90 1.26 0.25 579.78| | 5: 2.25 - 2.09 2756 127 0.77 29.43 1.28 0.25 579.78| | 6: 2.09 - 1.97 2846 113 0.83 22.60 1.29 0.25 315.73| | 7: 1.97 - 1.87 2787 165 0.90 16.35 1.28 0.26 90.53| | 8: 1.87 - 1.79 2789 144 0.86 21.05 1.25 0.26 90.53| | 9: 1.79 - 1.72 2745 138 0.88 18.46 1.23 0.25 55.06| | 10: 1.72 - 1.66 2789 158 0.86 20.27 1.22 0.25 47.96| | 11: 1.66 - 1.61 2740 147 0.86 21.27 1.24 0.25 46.34| | 12: 1.61 - 1.56 2787 146 0.89 18.43 1.23 0.25 29.90| | 13: 1.56 - 1.52 2745 130 0.86 20.61 1.24 0.25 29.90| | 14: 1.52 - 1.48 2803 134 0.86 20.81 1.23 0.25 26.95| | 15: 1.48 - 1.45 2738 128 0.86 20.70 1.24 0.25 21.55| | 16: 1.45 - 1.42 2756 161 0.85 22.16 1.25 0.25 21.55| | 17: 1.42 - 1.39 2785 139 0.86 21.21 1.24 0.25 18.27| | 18: 1.39 - 1.36 2741 179 0.86 21.69 1.23 0.25 16.37| | 19: 1.36 - 1.34 2807 134 0.85 22.65 1.22 0.25 16.37| | 20: 1.34 - 1.32 2696 147 0.86 21.27 1.21 0.24 13.38| | 21: 1.32 - 1.30 2785 112 0.86 22.13 1.20 0.24 13.17| | 22: 1.29 - 1.27 2704 152 0.85 22.71 1.20 0.24 12.82| | 23: 1.27 - 1.26 2802 156 0.86 22.21 1.21 0.24 11.04| | 24: 1.26 - 1.24 2744 132 0.85 22.92 1.20 0.24 11.04| | 25: 1.24 - 1.22 2734 148 0.84 23.69 1.21 0.24 10.40| | 26: 1.22 - 1.21 2727 135 0.84 23.86 1.19 0.23 9.69| | 27: 1.21 - 1.19 2814 148 0.84 24.35 1.20 0.23 9.69| | 28: 1.19 - 1.18 2671 147 0.83 24.99 1.18 0.23 8.97| | 29: 1.18 - 1.16 2800 134 0.83 24.76 1.16 0.23 8.69| | 30: 1.16 - 1.15 2740 148 0.81 26.63 1.16 0.23 8.69| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.69 max = 1508.78 mean = 218.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.96 mean = 22.69| |phase err.(test): min = 0.00 max = 89.19 mean = 22.55| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.249 1557 Z= 5.435 Angle : 5.396 19.459 2118 Z= 3.758 Chirality : 0.408 1.170 243 Planarity : 0.030 0.091 284 Dihedral : 13.832 83.813 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 32.43 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.45), residues: 224 helix: -3.25 (0.33), residues: 105 sheet: -0.98 (0.72), residues: 38 loop : -0.95 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.081 0.023 ARG A 98 TYR 0.085 0.037 TYR A 139 PHE 0.090 0.027 PHE A 164 HIS 0.047 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= 0.2600 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787673 | | target function (ml) not normalized (work): 232229.914467 | | target function (ml) not normalized (free): 11810.873337 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2559 0.2600 0.1963 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2559 0.2600 0.1963 n_refl.: 87602 remove outliers: r(all,work,free)=0.1972 0.1975 0.1963 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.1996 0.1999 0.1976 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1635 0.1628 0.1779 n_refl.: 87594 remove outliers: r(all,work,free)=0.1635 0.1627 0.1779 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 0.3852 386.280 356.231 0.660 1.002 0.401 11.894-9.307 99.02 97 4 0.1832 613.587 595.457 0.925 1.003 0.380 9.237-7.194 100.00 213 7 0.2207 501.839 491.027 0.961 1.004 0.344 7.162-5.571 100.00 427 22 0.2123 376.602 366.532 0.931 1.004 0.330 5.546-4.326 100.00 867 58 0.1296 516.982 512.007 0.965 1.003 0.230 4.315-3.360 100.00 1859 96 0.1128 491.653 488.217 1.006 1.003 0.199 3.356-2.611 100.00 3867 181 0.1443 322.991 319.632 0.996 1.002 0.048 2.608-2.026 99.99 8198 413 0.1337 214.113 212.197 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1642 104.562 103.886 1.010 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2047 46.367 45.078 1.006 0.996 0.000 1.221-1.150 99.97 13689 708 0.2568 29.214 26.945 0.976 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0438 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1627 r_free=0.1779 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1635 r_free=0.1785 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.101326 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2026.140199 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 0.1742 0.1861 0.0119 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1588 0.1734 0.0146 0.001 0.4 4.8 0.0 0.0 0 0.250 0.1469 0.1643 0.0175 0.002 0.4 4.2 0.0 0.0 0 0.500 0.1388 0.1590 0.0202 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1351 0.1557 0.0206 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1357 0.1566 0.0209 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1297 0.1520 0.0223 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1269 0.1500 0.0232 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1257 0.1488 0.0231 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1249 0.1484 0.0235 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1241 0.1474 0.0233 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1236 0.1474 0.0237 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1232 0.1466 0.0235 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1231 0.1472 0.0241 0.006 0.8 3.5 0.5 0.0 0 9.000 0.1230 0.1472 0.0242 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1229 0.1473 0.0245 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1227 0.1472 0.0244 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1228 0.1481 0.0253 0.008 0.9 4.2 0.5 0.6 0 13.051 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1232 0.1466 0.0235 0.005 0.8 3.5 0.5 0.0 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.66 2.35 3.013 19.050 2026.140 0.018 12.32 14.66 2.34 2.986 19.050 60.784 0.018 12.39 14.64 2.25 2.653 19.049 253.268 0.017 12.75 15.32 2.57 2.762 19.217 1013.070 0.017 12.57 15.46 2.89 3.130 19.496 2026.140 0.016 12.41 15.39 2.98 3.270 19.603 3039.210 0.016 12.42 15.48 3.06 3.398 19.651 4052.280 0.015 12.33 15.42 3.09 3.334 19.611 5065.350 0.015 12.31 15.44 3.13 3.436 19.658 6078.421 0.015 12.19 15.36 3.17 3.380 19.627 7091.491 0.015 12.24 15.44 3.21 3.531 19.690 8104.561 0.015 12.24 15.47 3.23 3.429 19.626 9117.631 0.015 12.21 15.47 3.26 3.547 19.688 10130.701 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: 253.268 Accepted refinement result: 12.39 14.64 2.25 2.653 19.049 253.268 0.017 Individual atomic B min max mean iso aniso Overall: 9.05 119.43 20.08 3.28 0 1785 Protein: 9.05 114.82 16.98 3.28 0 1519 Water: 11.45 119.43 38.21 N/A 0 258 Other: 19.72 26.59 22.06 N/A 0 8 Chain A: 9.05 119.43 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.05 - 20.09 1270 20.09 - 31.13 229 31.13 - 42.17 125 42.17 - 53.20 94 53.20 - 64.24 42 64.24 - 75.28 11 75.28 - 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=0.1239 r_free=0.1464 r_work=0.1240 r_free=0.1467 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1240 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 = 0.1235 r_free = 0.1463 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1235 r_free= 0.1463 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017051 | | target function (ls_wunit_k1) not normalized (work): 1420.269914 | | target function (ls_wunit_k1) not normalized (free): 109.590317 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1246 0.1235 0.1463 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1677 0.1679 0.1692 n_refl.: 87593 remove outliers: r(all,work,free)=0.1677 0.1679 0.1692 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1684 0.1685 0.1696 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1243 0.1233 0.1455 n_refl.: 87593 remove outliers: r(all,work,free)=0.1243 0.1233 0.1455 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3512 304.211 283.126 0.660 1.002 0.387 11.894-9.307 99.02 97 4 0.1643 483.224 470.950 0.924 1.002 0.370 9.237-7.194 100.00 213 7 0.1896 395.218 389.750 0.968 1.003 0.321 7.162-5.571 100.00 427 22 0.1856 296.589 290.515 0.933 1.003 0.269 5.546-4.326 100.00 867 58 0.1018 407.144 403.855 0.964 1.002 0.214 4.315-3.360 100.00 1859 96 0.0880 387.196 386.021 1.009 1.002 0.190 3.356-2.611 100.00 3867 181 0.1180 254.368 253.222 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1023 168.623 167.899 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1118 82.347 82.543 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1454 36.516 36.019 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2256 23.008 21.489 0.980 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0553 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1455 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 180 GLN Total number of N/Q/H flips: 2 r_work=0.1232 r_free=0.1454 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1454 | n_water=258 | time (s): 2.210 (total time: 2.210) Filter (dist) r_work=0.1239 r_free=0.1453 | n_water=251 | time (s): 20.610 (total time: 22.820) Filter (q & B) r_work=0.1241 r_free=0.1452 | n_water=248 | time (s): 3.060 (total time: 25.880) Compute maps r_work=0.1241 r_free=0.1452 | n_water=248 | time (s): 1.500 (total time: 27.380) Filter (map) r_work=0.1261 r_free=0.1459 | n_water=223 | time (s): 3.020 (total time: 30.400) Find peaks r_work=0.1261 r_free=0.1459 | n_water=223 | time (s): 0.620 (total time: 31.020) Add new water r_work=0.1412 r_free=0.1637 | n_water=426 | time (s): 2.440 (total time: 33.460) Refine new water occ: r_work=0.1314 r_free=0.1483 adp: r_work=0.1234 r_free=0.1433 occ: r_work=0.1245 r_free=0.1419 adp: r_work=0.1212 r_free=0.1406 occ: r_work=0.1213 r_free=0.1394 adp: r_work=0.1205 r_free=0.1390 ADP+occupancy (water only), MIN, final r_work=0.1205 r_free=0.1390 r_work=0.1205 r_free=0.1390 | n_water=426 | time (s): 51.010 (total time: 84.470) Filter (q & B) r_work=0.1209 r_free=0.1393 | n_water=412 | time (s): 2.440 (total time: 86.910) Filter (dist only) r_work=0.1209 r_free=0.1393 | n_water=411 | time (s): 34.430 (total time: 121.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 29.129742 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1501.063067 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1644 0.1752 0.0108 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1575 0.1693 0.0119 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1433 0.1578 0.0146 0.001 0.4 5.1 0.0 0.0 0 0.500 0.1375 0.1539 0.0164 0.002 0.4 4.5 0.0 0.0 0 0.750 0.1327 0.1505 0.0178 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1331 0.1507 0.0176 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1255 0.1455 0.0200 0.002 0.6 4.5 0.5 0.0 0 2.000 0.1234 0.1452 0.0219 0.003 0.6 3.8 0.5 0.0 0 3.000 0.1218 0.1437 0.0219 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1213 0.1434 0.0221 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1207 0.1431 0.0225 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1203 0.1429 0.0226 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1200 0.1426 0.0226 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1196 0.1426 0.0230 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1192 0.1426 0.0233 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1190 0.1422 0.0232 0.007 0.9 5.8 0.5 0.0 0 11.000 0.1190 0.1428 0.0238 0.007 0.9 5.8 0.5 0.0 0 12.000 0.1190 0.1429 0.0239 0.007 0.9 5.8 0.5 0.0 0 13.000 0.1188 0.1430 0.0242 0.008 1.0 5.4 0.5 0.0 0 14.565 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1422 0.0232 0.007 0.9 5.8 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 14.22 2.32 3.760 21.691 1501.063 0.016 11.90 14.22 2.32 3.760 21.691 45.032 0.016 11.90 14.22 2.32 3.760 21.691 187.633 0.016 12.12 14.65 2.53 3.624 21.691 750.532 0.015 12.07 14.95 2.88 3.440 21.969 1501.063 0.015 11.89 14.81 2.92 3.449 22.071 2251.595 0.014 11.81 14.75 2.94 3.450 22.051 3002.126 0.014 11.77 14.77 3.00 3.473 22.044 3752.658 0.014 11.79 14.88 3.08 3.504 22.093 4503.189 0.014 11.78 14.94 3.17 3.543 22.154 5253.721 0.014 11.78 14.98 3.20 3.566 22.157 6004.252 0.014 11.67 14.85 3.18 3.538 22.030 6754.784 0.014 11.61 14.77 3.17 3.544 22.056 7505.315 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: 45.032 Accepted refinement result: 11.90 14.22 2.32 3.760 21.691 45.032 0.016 Individual atomic B min max mean iso aniso Overall: 9.09 114.86 22.04 3.28 188 1750 Protein: 9.09 114.86 17.02 3.28 0 1519 Water: 11.49 76.66 40.57 N/A 188 223 Other: 19.75 26.63 22.10 N/A 0 8 Chain A: 9.09 114.86 19.40 N/A 0 1750 Chain S: 16.66 60.00 46.55 N/A 188 0 Histogram: Values Number of atoms 9.09 - 19.67 1256 19.67 - 30.24 245 30.24 - 40.82 168 40.82 - 51.40 129 51.40 - 61.97 117 61.97 - 72.55 11 72.55 - 83.13 6 83.13 - 93.70 4 93.70 - 104.28 0 104.28 - 114.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1422 r_work=0.1190 r_free=0.1422 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1422 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1413 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1190 r_free= 0.1413 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015079 | | target function (ls_wunit_k1) not normalized (work): 1256.048886 | | target function (ls_wunit_k1) not normalized (free): 100.608008 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1190 0.1413 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1587 0.1587 0.1636 n_refl.: 87593 remove outliers: r(all,work,free)=0.1587 0.1587 0.1636 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1589 0.1588 0.1637 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1187 0.1409 n_refl.: 87593 remove outliers: r(all,work,free)=0.1196 0.1186 0.1409 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 0.3410 300.196 277.641 0.600 1.003 0.360 11.894-9.307 99.02 97 4 0.1658 483.224 474.997 0.918 1.003 0.350 9.237-7.194 100.00 213 7 0.1707 395.218 394.427 0.984 1.003 0.280 7.162-5.571 100.00 427 22 0.1585 296.589 292.197 0.933 1.003 0.240 5.546-4.326 100.00 867 58 0.0894 407.144 404.075 0.960 1.003 0.209 4.315-3.360 100.00 1859 96 0.0777 387.196 386.273 1.007 1.003 0.200 3.356-2.611 100.00 3867 181 0.1081 254.368 253.517 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1015 168.623 168.088 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1102 82.347 82.566 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1443 36.516 36.050 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2249 23.008 21.524 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0152 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1409 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1186 r_free=0.1409 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1409 | n_water=411 | time (s): 1.770 (total time: 1.770) Filter (dist) r_work=0.1187 r_free=0.1412 | n_water=408 | time (s): 33.830 (total time: 35.600) Filter (q & B) r_work=0.1187 r_free=0.1412 | n_water=408 | time (s): 1.000 (total time: 36.600) Compute maps r_work=0.1187 r_free=0.1412 | n_water=408 | time (s): 1.390 (total time: 37.990) Filter (map) r_work=0.1223 r_free=0.1415 | n_water=285 | time (s): 2.540 (total time: 40.530) Find peaks r_work=0.1223 r_free=0.1415 | n_water=285 | time (s): 0.610 (total time: 41.140) Add new water r_work=0.1340 r_free=0.1540 | n_water=464 | time (s): 3.210 (total time: 44.350) Refine new water occ: r_work=0.1249 r_free=0.1450 adp: r_work=0.1250 r_free=0.1452 occ: r_work=0.1228 r_free=0.1427 adp: r_work=0.1226 r_free=0.1427 occ: r_work=0.1211 r_free=0.1408 adp: r_work=0.1205 r_free=0.1407 ADP+occupancy (water only), MIN, final r_work=0.1205 r_free=0.1407 r_work=0.1205 r_free=0.1407 | n_water=464 | time (s): 167.020 (total time: 211.370) Filter (q & B) r_work=0.1209 r_free=0.1412 | n_water=435 | time (s): 2.690 (total time: 214.060) Filter (dist only) r_work=0.1209 r_free=0.1411 | n_water=434 | time (s): 35.770 (total time: 249.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.788437 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.599431 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1239 0.1378 0.0139 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1194 0.1348 0.0154 0.003 0.7 3.8 0.5 0.0 0 0.268 0.1178 0.1337 0.0159 0.004 0.8 3.2 0.5 0.0 0 0.537 0.1170 0.1332 0.0162 0.005 0.9 2.9 0.5 0.0 0 0.805 0.1165 0.1330 0.0165 0.006 1.0 2.9 0.5 0.0 0 1.073 0.1163 0.1331 0.0168 0.007 1.0 2.9 0.5 0.0 0 1.341 0.1160 0.1332 0.0171 0.007 1.1 3.2 0.5 0.0 0 1.610 0.1159 0.1330 0.0171 0.008 1.1 3.5 0.5 0.0 0 1.878 0.1169 0.1334 0.0165 0.005 0.9 2.9 0.5 0.0 0 0.894 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1165 0.1330 0.0165 0.006 1.0 2.9 0.5 0.0 0 1.073 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.65 13.30 1.65 3.764 21.233 47.599 3.628 11.65 13.30 1.65 3.764 21.233 1.428 3.628 11.65 13.30 1.65 3.747 21.233 5.950 3.628 11.72 13.38 1.66 3.701 21.216 23.800 3.623 11.70 13.45 1.76 3.729 21.187 47.599 3.621 11.61 13.42 1.81 3.749 21.180 71.399 3.614 11.61 13.46 1.85 3.758 21.166 95.199 3.612 11.56 13.42 1.86 3.774 21.160 118.999 3.608 11.55 13.44 1.89 3.792 21.150 142.798 3.607 11.53 13.41 1.89 3.802 21.140 166.598 3.605 11.51 13.42 1.90 3.814 21.140 190.398 3.605 11.50 13.40 1.90 3.820 21.139 214.197 3.603 11.49 13.40 1.91 3.826 21.139 237.997 3.603 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.428 Accepted refinement result: 11.65 13.30 1.65 3.764 21.233 1.428 3.628 Individual atomic B min max mean iso aniso Overall: 9.10 114.87 21.19 3.28 214 1747 Protein: 9.10 114.87 17.03 3.28 0 1519 Water: 11.50 76.67 35.72 N/A 214 220 Other: 19.76 26.64 22.11 N/A 0 8 Chain A: 9.10 114.87 19.35 N/A 0 1747 Chain S: 15.76 60.01 36.16 N/A 214 0 Histogram: Values Number of atoms 9.10 - 19.68 1259 19.68 - 30.25 289 30.25 - 40.83 213 40.83 - 51.41 121 51.41 - 61.98 56 61.98 - 72.56 11 72.56 - 83.14 6 83.14 - 93.71 4 93.71 - 104.29 0 104.29 - 114.87 2 =========================== Idealize ADP of riding H ========================== r_work=0.1165 r_free=0.1330 r_work=0.1165 r_free=0.1330 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1165 r_free = 0.1330 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1155 r_free = 0.1317 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.17 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= 0.1155 r_free= 0.1317 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.621389 | | target function (ml) not normalized (work): 301640.004478 | | target function (ml) not normalized (free): 15863.323646 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1163 0.1155 0.1317 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1495 0.1494 0.1534 n_refl.: 87590 remove outliers: r(all,work,free)=0.1495 0.1494 0.1534 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1494 0.1494 0.1533 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1158 0.1151 0.1306 n_refl.: 87590 remove outliers: r(all,work,free)=0.1154 0.1146 0.1306 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 0.3860 289.615 262.609 0.490 1.000 0.301 11.894-9.307 97.06 95 4 0.2345 476.553 463.796 0.878 1.001 0.287 9.237-7.194 98.18 209 7 0.2264 386.685 387.227 0.954 1.001 0.217 7.162-5.571 100.00 427 22 0.2092 296.589 286.763 0.917 1.002 0.187 5.546-4.326 100.00 867 58 0.1112 407.144 402.259 0.964 1.002 0.156 4.315-3.360 100.00 1859 96 0.0935 387.196 384.732 1.006 1.002 0.133 3.356-2.611 100.00 3867 181 0.1137 254.368 252.096 1.009 1.001 0.070 2.608-2.026 99.99 8198 413 0.0925 168.623 167.819 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0910 82.347 82.611 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1269 36.516 36.090 1.027 0.998 0.000 1.221-1.150 99.97 13689 708 0.2169 23.008 21.540 0.988 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0124 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 r_free=0.1306 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1146 r_free=0.1306 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1306 | n_water=434 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1147 r_free=0.1307 | n_water=432 | time (s): 46.340 (total time: 48.680) Filter (q & B) r_work=0.1147 r_free=0.1309 | n_water=429 | time (s): 3.860 (total time: 52.540) Compute maps r_work=0.1147 r_free=0.1309 | n_water=429 | time (s): 1.810 (total time: 54.350) Filter (map) r_work=0.1166 r_free=0.1299 | n_water=329 | time (s): 3.830 (total time: 58.180) Find peaks r_work=0.1166 r_free=0.1299 | n_water=329 | time (s): 0.700 (total time: 58.880) Add new water r_work=0.1238 r_free=0.1357 | n_water=504 | time (s): 3.740 (total time: 62.620) Refine new water occ: r_work=0.1168 r_free=0.1305 adp: r_work=0.1169 r_free=0.1306 occ: r_work=0.1153 r_free=0.1296 adp: r_work=0.1152 r_free=0.1296 occ: r_work=0.1142 r_free=0.1290 adp: r_work=0.1138 r_free=0.1289 ADP+occupancy (water only), MIN, final r_work=0.1138 r_free=0.1289 r_work=0.1138 r_free=0.1289 | n_water=504 | time (s): 265.080 (total time: 327.700) Filter (q & B) r_work=0.1144 r_free=0.1296 | n_water=468 | time (s): 3.850 (total time: 331.550) Filter (dist only) r_work=0.1145 r_free=0.1297 | n_water=466 | time (s): 48.420 (total time: 379.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.823009 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.919099 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 0.1332 0.0130 0.002 0.6 4.8 0.5 0.0 0 0.091 0.1165 0.1307 0.0142 0.003 0.7 3.5 0.5 0.0 0 0.273 0.1151 0.1299 0.0148 0.005 0.9 3.8 0.5 0.0 0 0.547 0.1145 0.1301 0.0156 0.006 0.9 3.5 0.5 0.0 0 0.820 0.1141 0.1300 0.0160 0.007 1.0 3.8 0.5 0.0 0 1.094 0.1138 0.1300 0.0162 0.007 1.1 3.8 0.5 0.0 0 1.367 0.1136 0.1299 0.0163 0.008 1.1 3.8 0.5 0.0 0 1.641 0.1135 0.1300 0.0166 0.009 1.1 3.8 0.5 0.0 0 1.914 0.1144 0.1302 0.0158 0.006 1.0 3.5 0.5 0.0 0 0.912 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1151 0.1299 0.0148 0.005 0.9 3.8 0.5 0.0 0 0.547 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.51 12.99 1.48 3.765 21.281 48.919 3.618 11.51 12.99 1.48 3.765 21.281 1.468 3.618 11.51 12.98 1.47 3.754 21.281 6.115 3.617 11.55 13.06 1.51 3.700 21.271 24.460 3.612 11.54 13.15 1.61 3.728 21.247 48.919 3.611 11.47 13.14 1.67 3.747 21.241 73.379 3.605 11.45 13.14 1.70 3.756 21.239 97.838 3.602 11.41 13.12 1.71 3.771 21.234 122.298 3.599 11.40 13.15 1.75 3.789 21.227 146.757 3.598 11.39 13.14 1.76 3.800 21.222 171.217 3.597 11.36 13.12 1.76 3.806 21.223 195.676 3.595 11.35 13.11 1.76 3.811 21.224 220.136 3.594 11.33 13.09 1.76 3.813 21.225 244.595 3.593 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 6.115 Accepted refinement result: 11.51 12.98 1.47 3.754 21.281 6.115 3.617 Individual atomic B min max mean iso aniso Overall: 9.11 114.73 21.28 3.25 246 1747 Protein: 9.11 114.73 17.03 3.25 0 1519 Water: 11.49 76.67 35.12 N/A 246 220 Other: 19.71 26.59 22.09 N/A 0 8 Chain A: 9.11 114.73 19.35 N/A 0 1747 Chain S: 16.14 60.00 34.96 N/A 246 0 Histogram: Values Number of atoms 9.11 - 19.67 1258 19.67 - 30.23 306 30.23 - 40.80 224 40.80 - 51.36 134 51.36 - 61.92 48 61.92 - 72.48 11 72.48 - 83.05 6 83.05 - 93.61 4 93.61 - 104.17 0 104.17 - 114.73 2 =========================== Idealize ADP of riding H ========================== r_work=0.1151 r_free=0.1298 r_work=0.1151 r_free=0.1298 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1151 r_free = 0.1298 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1146 r_free = 0.1294 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.20 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= 0.1146 r_free= 0.1294 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.615135 | | target function (ml) not normalized (work): 301082.884129 | | target function (ml) not normalized (free): 15828.677504 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1153 0.1146 0.1294 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1464 0.1463 0.1517 n_refl.: 87580 remove outliers: r(all,work,free)=0.1464 0.1463 0.1517 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1463 0.1462 0.1516 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1152 0.1145 0.1296 n_refl.: 87580 remove outliers: r(all,work,free)=0.1150 0.1142 0.1296 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 0.4060 288.741 250.853 0.441 0.999 0.298 11.894-9.307 93.14 91 4 0.2399 467.580 451.469 0.856 1.001 0.238 9.237-7.194 98.18 209 7 0.2317 386.685 381.899 0.931 1.002 0.190 7.162-5.571 100.00 427 22 0.2193 296.589 285.564 0.911 1.002 0.144 5.546-4.326 100.00 867 58 0.1120 407.144 402.564 0.964 1.002 0.120 4.315-3.360 100.00 1859 96 0.0927 387.196 385.192 1.006 1.002 0.102 3.356-2.611 100.00 3867 181 0.1099 254.368 252.439 1.011 1.001 0.040 2.608-2.026 99.99 8198 413 0.0918 168.623 168.001 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0908 82.347 82.693 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1273 36.516 36.121 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2176 23.008 21.552 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=-0.0162 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1142 r_free=0.1296 After: r_work=0.1143 r_free=0.1296 ================================== NQH flips ================================== r_work=0.1143 r_free=0.1296 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=0.1143 r_free=0.1296 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1296 | n_water=466 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1143 r_free=0.1296 | n_water=466 | time (s): 44.170 (total time: 46.510) Filter (q & B) r_work=0.1143 r_free=0.1296 | n_water=466 | time (s): 1.310 (total time: 47.820) Compute maps r_work=0.1143 r_free=0.1296 | n_water=466 | time (s): 1.760 (total time: 49.580) Filter (map) r_work=0.1167 r_free=0.1297 | n_water=356 | time (s): 3.790 (total time: 53.370) Find peaks r_work=0.1167 r_free=0.1297 | n_water=356 | time (s): 0.710 (total time: 54.080) Add new water r_work=0.1212 r_free=0.1340 | n_water=504 | time (s): 3.750 (total time: 57.830) Refine new water occ: r_work=0.1159 r_free=0.1299 adp: r_work=0.1160 r_free=0.1300 occ: r_work=0.1148 r_free=0.1292 adp: r_work=0.1147 r_free=0.1290 occ: r_work=0.1139 r_free=0.1286 adp: r_work=0.1136 r_free=0.1283 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1283 r_work=0.1136 r_free=0.1283 | n_water=504 | time (s): 320.620 (total time: 378.450) Filter (q & B) r_work=0.1144 r_free=0.1287 | n_water=465 | time (s): 3.660 (total time: 382.110) Filter (dist only) r_work=0.1144 r_free=0.1288 | n_water=463 | time (s): 48.420 (total time: 430.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.734844 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.935121 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 0.1195 0.1323 0.0127 0.004 0.7 5.4 0.0 0.0 0 0.087 0.1153 0.1293 0.0140 0.004 0.8 5.1 0.5 0.0 0 0.260 0.1144 0.1288 0.0144 0.005 0.9 4.8 0.5 0.0 0 0.520 0.1143 0.1287 0.0144 0.005 0.9 4.8 0.5 0.0 0 0.781 0.1139 0.1285 0.0145 0.006 1.0 4.8 0.5 0.0 0 1.041 0.1136 0.1283 0.0146 0.007 1.0 4.8 0.5 0.0 0 1.301 0.1135 0.1282 0.0147 0.008 1.1 4.8 0.5 0.0 0 1.561 0.1134 0.1281 0.0147 0.008 1.1 4.8 0.5 0.0 0 1.822 0.1141 0.1286 0.0145 0.005 0.9 4.8 0.5 0.0 0 0.867 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1134 0.1281 0.0147 0.008 1.1 4.8 0.5 0.0 0 1.822 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.34 12.81 1.47 3.749 21.240 36.935 3.607 11.34 12.81 1.47 3.749 21.240 1.108 3.607 11.34 12.81 1.47 3.749 21.240 4.617 3.607 11.37 12.85 1.48 3.685 21.235 18.468 3.602 11.38 12.95 1.56 3.708 21.219 36.935 3.602 11.40 13.03 1.63 3.726 21.198 55.403 3.602 11.31 12.97 1.66 3.745 21.195 73.870 3.595 11.32 13.00 1.69 3.750 21.192 92.338 3.594 11.27 12.97 1.70 3.764 21.191 110.805 3.591 11.24 12.95 1.71 3.774 21.188 129.273 3.589 11.24 12.97 1.73 3.789 21.180 147.740 3.588 11.23 12.97 1.73 3.798 21.177 166.208 3.587 11.23 12.95 1.73 3.805 21.177 184.676 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: 1.108 Accepted refinement result: 11.34 12.81 1.47 3.749 21.240 1.108 3.607 Individual atomic B min max mean iso aniso Overall: 9.10 114.73 21.21 3.25 243 1747 Protein: 9.10 114.73 17.02 3.25 0 1519 Water: 11.49 76.66 34.94 N/A 243 220 Other: 19.71 26.58 22.09 N/A 0 8 Chain A: 9.10 114.73 19.34 N/A 0 1747 Chain S: 16.06 60.00 34.62 N/A 243 0 Histogram: Values Number of atoms 9.10 - 19.66 1259 19.66 - 30.23 315 30.23 - 40.79 214 40.79 - 51.35 131 51.35 - 61.91 48 61.91 - 72.48 11 72.48 - 83.04 6 83.04 - 93.60 4 93.60 - 104.17 0 104.17 - 114.73 2 =========================== Idealize ADP of riding H ========================== r_work=0.1134 r_free=0.1281 r_work=0.1134 r_free=0.1281 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1134 r_free = 0.1281 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1131 r_free = 0.1280 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1131 r_free= 0.1280 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.606030 | | target function (ml) not normalized (work): 300302.929055 | | target function (ml) not normalized (free): 15816.221218 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1337 0.1363 5.6388 5.614| | 2: 3.57 - 2.84 1.00 2888 124 0.1050 0.1370 5.1553 5.2262| | 3: 2.83 - 2.48 1.00 2820 163 0.1094 0.1150 4.9483 4.9788| | 4: 2.47 - 2.25 1.00 2825 136 0.0889 0.0952 4.6311 4.6524| | 5: 2.25 - 2.09 1.00 2756 127 0.0866 0.0934 4.5803 4.6229| | 6: 2.09 - 1.97 1.00 2846 113 0.0851 0.1039 4.2648 4.3725| | 7: 1.97 - 1.87 1.00 2787 165 0.0893 0.1114 3.9815 4.1056| | 8: 1.87 - 1.79 1.00 2789 144 0.0919 0.1120 3.8933 4.0028| | 9: 1.79 - 1.72 1.00 2745 138 0.0883 0.1169 3.6525 3.8204| | 10: 1.72 - 1.66 1.00 2831 160 0.0924 0.1155 3.5722 3.6946| | 11: 1.66 - 1.61 1.00 2712 147 0.0873 0.1038 3.5007 3.5824| | 12: 1.61 - 1.56 1.00 2773 144 0.0912 0.1111 3.337 3.4464| | 13: 1.56 - 1.52 1.00 2745 130 0.0950 0.1034 3.3122 3.4013| | 14: 1.52 - 1.48 1.00 2803 134 0.0981 0.1050 3.2403 3.322| | 15: 1.48 - 1.45 1.00 2738 128 0.1009 0.1236 3.1583 3.2831| | 16: 1.45 - 1.42 1.00 2756 161 0.1057 0.1245 3.1379 3.2394| | 17: 1.42 - 1.39 1.00 2785 139 0.1151 0.1274 3.1254 3.2212| | 18: 1.39 - 1.36 1.00 2741 179 0.1201 0.1322 3.107 3.237| | 19: 1.36 - 1.34 1.00 2807 134 0.1264 0.1567 3.1164 3.2757| | 20: 1.34 - 1.32 1.00 2696 147 0.1368 0.1454 3.1133 3.1586| | 21: 1.32 - 1.30 1.00 2785 112 0.1474 0.1531 3.1161 3.1167| | 22: 1.29 - 1.27 1.00 2704 152 0.1562 0.1984 3.1253 3.2981| | 23: 1.27 - 1.26 1.00 2802 156 0.1651 0.1791 3.1361 3.1986| | 24: 1.26 - 1.24 1.00 2744 132 0.1711 0.1828 3.1295 3.2308| | 25: 1.24 - 1.22 1.00 2733 148 0.1886 0.2162 3.1458 3.2666| | 26: 1.22 - 1.21 1.00 2727 135 0.1909 0.1777 3.1492 3.2052| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2157 3.1717 3.1602| | 28: 1.19 - 1.18 1.00 2671 147 0.2199 0.2302 3.167 3.1753| | 29: 1.18 - 1.16 1.00 2800 134 0.2263 0.2373 3.1484 3.229| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2446 3.144 3.1686| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2916 171 0.95 8.61 1.00 0.97 5783.82| | 2: 3.57 - 2.84 2888 124 0.93 12.58 1.01 0.97 5783.82| | 3: 2.83 - 2.48 2820 163 0.89 16.52 0.99 0.98 4831.68| | 4: 2.47 - 2.25 2825 136 0.92 13.47 1.00 0.98 2376.39| | 5: 2.25 - 2.09 2756 127 0.90 15.65 1.01 0.98 2376.39| | 6: 2.09 - 1.97 2846 113 0.92 12.37 1.02 0.98 1371.91| | 7: 1.97 - 1.87 2787 165 0.95 9.30 1.02 0.98 515.23| | 8: 1.87 - 1.79 2789 144 0.93 12.65 1.00 0.98 515.23| | 9: 1.79 - 1.72 2745 138 0.94 10.12 0.98 0.98 291.35| | 10: 1.72 - 1.66 2831 160 0.94 11.09 0.98 0.98 246.51| | 11: 1.66 - 1.61 2712 147 0.93 11.76 0.98 0.98 236.15| | 12: 1.61 - 1.56 2773 144 0.96 8.86 0.99 0.97 138.43| | 13: 1.56 - 1.52 2745 130 0.95 10.48 1.03 0.97 138.43| | 14: 1.52 - 1.48 2803 134 0.94 10.79 1.02 0.98 124.30| | 15: 1.48 - 1.45 2738 128 0.95 9.94 1.02 0.98 98.42| | 16: 1.45 - 1.42 2756 161 0.94 11.13 1.02 0.98 98.42| | 17: 1.42 - 1.39 2785 139 0.95 10.94 1.01 0.98 89.59| | 18: 1.39 - 1.36 2741 179 0.94 11.57 1.01 0.98 84.48| | 19: 1.36 - 1.34 2807 134 0.94 11.89 1.00 0.98 84.48| | 20: 1.34 - 1.32 2696 147 0.94 12.14 0.98 0.97 80.55| | 21: 1.32 - 1.30 2785 112 0.94 13.13 0.98 0.96 80.27| | 22: 1.29 - 1.27 2704 152 0.93 13.69 0.98 0.96 80.65| | 23: 1.27 - 1.26 2802 156 0.92 14.86 0.97 0.94 82.59| | 24: 1.26 - 1.24 2744 132 0.92 14.87 0.96 0.94 82.59| | 25: 1.24 - 1.22 2733 148 0.91 16.38 0.96 0.94 84.57| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.03 0.93 86.76| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.02 0.93 86.76| | 28: 1.19 - 1.18 2671 147 0.88 20.42 1.01 0.93 90.44| | 29: 1.18 - 1.16 2800 134 0.88 20.50 0.99 0.93 91.82| | 30: 1.16 - 1.15 2739 148 0.86 22.06 0.98 0.93 91.82| |alpha: min = 0.93 max = 0.98 mean = 0.97| |beta: min = 80.27 max = 5783.82 mean = 892.47| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.47| |phase err.(test): min = 0.00 max = 87.83 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1131 0.1280 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1446 0.1444 0.1501 n_refl.: 87574 remove outliers: r(all,work,free)=0.1446 0.1444 0.1501 n_refl.: 87574 overall B=-0.00 to atoms: r(all,work,free)=0.1445 0.1443 0.1500 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1131 0.1282 n_refl.: 87574 remove outliers: r(all,work,free)=0.1138 0.1131 0.1282 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 0.4281 288.741 247.685 0.434 1.000 0.304 11.894-9.307 93.14 91 4 0.2496 467.580 452.560 0.858 1.002 0.233 9.237-7.194 98.18 209 7 0.2378 386.685 380.153 0.922 1.002 0.170 7.162-5.571 100.00 427 22 0.2165 296.589 285.942 0.909 1.003 0.130 5.546-4.326 100.00 867 58 0.1105 407.144 402.473 0.962 1.003 0.110 4.315-3.360 100.00 1859 96 0.0920 387.196 384.955 1.003 1.002 0.073 3.356-2.611 100.00 3867 181 0.1089 254.368 252.472 1.010 1.002 0.020 2.608-2.026 99.99 8198 413 0.0908 168.623 167.993 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.347 82.703 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.516 36.120 1.029 0.996 0.000 1.221-1.150 99.97 13689 708 0.2167 23.008 21.555 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0142 ================= 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 : 0.2600 0.1963 0.081 5.396 8.8 119.3 19.9 258 0.000 1_bss: 0.1627 0.1779 0.081 5.396 9.0 119.5 20.1 258 0.000 1_settarget: 0.1627 0.1779 0.081 5.396 9.0 119.5 20.1 258 0.000 1_nqh: 0.1635 0.1785 0.081 5.396 9.0 119.5 20.1 258 0.006 1_weight: 0.1635 0.1785 0.081 5.396 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1232 0.1466 0.005 0.820 9.0 119.5 20.1 258 0.137 1_adp: 0.1239 0.1464 0.005 0.820 9.1 119.4 20.1 258 0.137 1_regHadp: 0.1240 0.1467 0.005 0.820 9.1 119.4 20.1 258 0.137 1_occ: 0.1235 0.1463 0.005 0.820 9.1 119.4 20.1 258 0.137 2_bss: 0.1233 0.1455 0.005 0.820 9.1 119.5 20.1 258 0.137 2_settarget: 0.1233 0.1455 0.005 0.820 9.1 119.5 20.1 258 0.137 2_updatecdl: 0.1233 0.1455 0.005 0.837 9.1 119.5 20.1 258 0.137 2_nqh: 0.1232 0.1454 0.005 0.837 9.1 119.5 20.1 258 0.137 2_sol: 0.1209 0.1393 0.005 0.837 9.1 114.9 22.0 411 n/a 2_weight: 0.1209 0.1393 0.005 0.837 9.1 114.9 22.0 411 n/a 2_xyzrec: 0.1190 0.1422 0.007 0.877 9.1 114.9 22.0 411 n/a 2_adp: 0.1190 0.1422 0.007 0.877 9.1 114.9 22.0 411 n/a 2_regHadp: 0.1190 0.1422 0.007 0.877 9.1 114.9 22.0 411 n/a 2_occ: 0.1190 0.1413 0.007 0.877 9.1 114.9 22.0 411 n/a 3_bss: 0.1186 0.1409 0.007 0.877 9.1 114.9 22.0 411 n/a 3_settarget: 0.1186 0.1409 0.007 0.877 9.1 114.9 22.0 411 n/a 3_updatecdl: 0.1186 0.1409 0.007 0.876 9.1 114.9 22.0 411 n/a 3_nqh: 0.1186 0.1409 0.007 0.876 9.1 114.9 22.0 411 n/a 3_sol: 0.1209 0.1411 0.007 0.876 9.1 114.9 21.2 434 n/a 3_weight: 0.1209 0.1411 0.007 0.876 9.1 114.9 21.2 434 n/a 3_xyzrec: 0.1165 0.1330 0.006 0.967 9.1 114.9 21.2 434 n/a 3_adp: 0.1165 0.1330 0.006 0.967 9.1 114.9 21.2 434 n/a 3_regHadp: 0.1165 0.1330 0.006 0.967 9.1 114.9 21.2 434 n/a 3_occ: 0.1155 0.1317 0.006 0.967 9.1 114.9 21.2 434 n/a 4_bss: 0.1146 0.1306 0.006 0.967 9.1 114.9 21.2 434 n/a 4_settarget: 0.1146 0.1306 0.006 0.967 9.1 114.9 21.2 434 n/a 4_updatecdl: 0.1146 0.1306 0.006 0.970 9.1 114.9 21.2 434 n/a 4_nqh: 0.1146 0.1306 0.006 0.970 9.1 114.9 21.2 434 n/a 4_sol: 0.1145 0.1297 0.006 0.970 9.1 114.9 21.3 466 n/a 4_weight: 0.1145 0.1297 0.006 0.970 9.1 114.9 21.3 466 n/a 4_xyzrec: 0.1151 0.1299 0.005 0.891 9.1 114.9 21.3 466 n/a 4_adp: 0.1151 0.1298 0.005 0.891 9.1 114.7 21.3 466 n/a 4_regHadp: 0.1151 0.1298 0.005 0.891 9.1 114.7 21.3 466 n/a 4_occ: 0.1146 0.1294 0.005 0.891 9.1 114.7 21.3 466 n/a 5_bss: 0.1142 0.1296 0.005 0.891 9.1 114.7 21.3 466 n/a 5_settarget: 0.1142 0.1296 0.005 0.891 9.1 114.7 21.3 466 n/a 5_updatecdl: 0.1142 0.1296 0.005 0.891 9.1 114.7 21.3 466 n/a 5_setrh: 0.1143 0.1296 0.005 0.891 9.1 114.7 21.3 466 n/a 5_nqh: 0.1143 0.1296 0.005 0.891 9.1 114.7 21.3 466 n/a 5_sol: 0.1144 0.1288 0.005 0.891 9.1 114.7 21.2 463 n/a 5_weight: 0.1144 0.1288 0.005 0.891 9.1 114.7 21.2 463 n/a 5_xyzrec: 0.1134 0.1281 0.008 1.097 9.1 114.7 21.2 463 n/a 5_adp: 0.1134 0.1281 0.008 1.097 9.1 114.7 21.2 463 n/a 5_regHadp: 0.1134 0.1281 0.008 1.097 9.1 114.7 21.2 463 n/a 5_occ: 0.1131 0.1280 0.008 1.097 9.1 114.7 21.2 463 n/a end: 0.1131 0.1282 0.008 1.097 9.1 114.7 21.2 463 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8666014_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8666014_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3700 Refinement macro-cycles (run) : 13349.3300 Write final files (write_after_run_outputs) : 94.7900 Total : 13447.4900 Total CPU time: 3.74 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:02:33 PST -0800 (1735365753.35 s) Start R-work = 0.1627, R-free = 0.1779 Final R-work = 0.1131, R-free = 0.1282 =============================================================================== Job complete usr+sys time: 13626.48 seconds wall clock time: 246 minutes 55.15 seconds (14815.15 seconds total)