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_1541177.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_1541177.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1541177.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: 1.52, 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: 0.57 Conformation dependent library (CDL) restraints added in 107.9 milliseconds Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.92: 575 0.92 - 1.17: 1067 1.17 - 1.42: 625 1.42 - 1.66: 843 1.66 - 1.91: 43 Bond restraints: 3153 Sorted by residual: bond pdb=" N BGLN A 80 " pdb=" CA BGLN A 80 " ideal model delta sigma weight residual 1.459 1.694 -0.235 1.19e-02 7.06e+03 3.88e+02 bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.692 -0.233 1.19e-02 7.06e+03 3.82e+02 bond pdb=" CA ALA A 61 " pdb=" C ALA A 61 " ideal model delta sigma weight residual 1.523 1.284 0.239 1.35e-02 5.49e+03 3.13e+02 bond pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " ideal model delta sigma weight residual 1.326 1.518 -0.192 1.10e-02 8.26e+03 3.03e+02 bond pdb=" C ALA A 36 " pdb=" O ALA A 36 " ideal model delta sigma weight residual 1.236 1.436 -0.200 1.22e-02 6.72e+03 2.70e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 3146 4.72 - 9.44: 1861 9.44 - 14.16: 655 14.16 - 18.88: 105 18.88 - 23.60: 10 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 140.59 -19.36 8.10e-01 1.52e+00 5.71e+02 angle pdb=" O ILE A 152 " pdb=" C ILE A 152 " pdb=" N ALEU A 153 " ideal model delta sigma weight residual 123.10 142.90 -19.80 1.17e+00 7.31e-01 2.86e+02 angle pdb=" O ILE A 91 " pdb=" C ILE A 91 " pdb=" N LEU A 92 " ideal model delta sigma weight residual 121.83 138.06 -16.23 1.03e+00 9.43e-01 2.48e+02 angle pdb=" C ACYS A 53 " pdb=" N PRO A 54 " pdb=" CA PRO A 54 " ideal model delta sigma weight residual 120.03 104.54 15.49 9.90e-01 1.02e+00 2.45e+02 angle pdb=" CA BLEU A 153 " pdb=" C BLEU A 153 " pdb=" O BLEU A 153 " ideal model delta sigma weight residual 120.30 105.59 14.71 1.07e+00 8.73e-01 1.89e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 930 16.51 - 33.01: 116 33.01 - 49.52: 49 49.52 - 66.03: 12 66.03 - 82.53: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 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 180.00 160.19 19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.019 - 0.214: 92 0.214 - 0.410: 75 0.410 - 0.605: 43 0.605 - 0.800: 23 0.800 - 0.996: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG BLEU A 153 " pdb=" CB BLEU A 153 " pdb=" CD1BLEU A 153 " pdb=" CD2BLEU A 153 " both_signs ideal model delta sigma weight residual False -2.59 -3.59 1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.64 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CA ALA A 79 " pdb=" N ALA A 79 " pdb=" C ALA A 79 " pdb=" CB ALA A 79 " both_signs ideal model delta sigma weight residual False 2.48 1.56 0.93 2.00e-01 2.50e+01 2.14e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.029 2.00e-02 2.50e+03 7.00e-02 1.47e+02 pdb=" CG PHE A 164 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.121 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.085 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.058 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.121 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.123 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.025 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.025 2.00e-02 2.50e+03 5.95e-02 1.06e+02 pdb=" CG TYR A 139 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.078 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.118 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.078 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.026 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.107 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.059 2.00e-02 2.50e+03 5.87e-02 1.03e+02 pdb=" CG BTYR A 67 " 0.093 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.002 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.096 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.060 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.018 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.003 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.096 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.027 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.24: 583 2.24 - 2.83: 7551 2.83 - 3.42: 10765 3.42 - 4.01: 15326 4.01 - 4.60: 22349 Nonbonded interactions: 56574 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.655 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.770 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.797 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.847 2.100 nonbonded pdb=" HB2BGLN A 80 " pdb="HE21BGLN A 80 " model vdw 1.849 2.270 ... (remaining 56569 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_1541177_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= 0.2613 r_free= 0.1952 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794678 | | target function (ml) not normalized (work): 232813.404500 | | target function (ml) not normalized (free): 11845.770782 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3046 0.2073 7.0243 4.9328| | 2: 3.57 - 2.84 1.00 2876 122 0.2440 0.1792 4.3565 4.359| | 3: 2.84 - 2.48 1.00 2833 165 0.2370 0.1753 4.1311 4.178| | 4: 2.47 - 2.25 1.00 2825 136 0.2320 0.1465 3.8329 3.8388| | 5: 2.25 - 2.09 1.00 2756 127 0.2450 0.1645 3.7967 3.8413| | 6: 2.09 - 1.97 1.00 2846 113 0.2568 0.1718 3.477 3.5504| | 7: 1.97 - 1.87 1.00 2787 165 0.2519 0.1836 3.1351 3.1888| | 8: 1.87 - 1.79 1.00 2789 144 0.2546 0.1847 3.0693 3.1302| | 9: 1.79 - 1.72 1.00 2745 138 0.2480 0.1890 2.9161 2.9704| | 10: 1.72 - 1.66 1.00 2789 158 0.2421 0.1823 2.8039 2.8368| | 11: 1.66 - 1.61 1.00 2740 147 0.2511 0.1926 2.7407 2.7808| | 12: 1.61 - 1.56 1.00 2787 146 0.2550 0.2176 2.6535 2.7062| | 13: 1.56 - 1.52 1.00 2745 130 0.2608 0.1882 2.5889 2.5928| | 14: 1.52 - 1.48 1.00 2803 134 0.2583 0.1922 2.5187 2.6005| | 15: 1.48 - 1.45 1.00 2738 128 0.2587 0.2102 2.4264 2.4872| | 16: 1.45 - 1.42 1.00 2756 161 0.2658 0.2287 2.3885 2.4613| | 17: 1.42 - 1.39 1.00 2785 139 0.2605 0.2213 2.3348 2.4106| | 18: 1.39 - 1.36 1.00 2741 179 0.2657 0.2230 2.2773 2.3371| | 19: 1.36 - 1.34 1.00 2807 134 0.2687 0.2343 2.2736 2.2996| | 20: 1.34 - 1.32 1.00 2696 147 0.2676 0.2340 2.2023 2.2717| | 21: 1.32 - 1.30 1.00 2785 112 0.2679 0.2124 2.1651 2.1135| | 22: 1.29 - 1.27 1.00 2704 152 0.2758 0.2539 2.1458 2.1742| | 23: 1.27 - 1.26 1.00 2802 156 0.2751 0.2341 2.1094 2.1595| | 24: 1.26 - 1.24 1.00 2744 132 0.2782 0.2573 2.0813 2.1922| | 25: 1.24 - 1.22 1.00 2734 148 0.2822 0.2522 2.0546 2.08| | 26: 1.22 - 1.21 1.00 2727 135 0.2804 0.2279 2.0088 2.0693| | 27: 1.21 - 1.19 1.00 2814 148 0.2997 0.2647 2.0063 2.0429| | 28: 1.19 - 1.18 1.00 2671 147 0.2960 0.2579 1.9936 1.9598| | 29: 1.18 - 1.16 1.00 2800 134 0.2894 0.2741 1.9452 2.0575| | 30: 1.16 - 1.15 1.00 2740 148 0.3044 0.2783 1.9291 1.9499| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.96 0.76 0.23 1493.56| | 2: 3.57 - 2.84 2876 122 0.80 26.28 1.27 0.23 1493.56| | 3: 2.84 - 2.48 2833 165 0.74 32.28 1.24 0.23 1237.96| | 4: 2.47 - 2.25 2825 136 0.81 25.61 1.26 0.25 574.64| | 5: 2.25 - 2.09 2756 127 0.77 29.44 1.28 0.25 574.64| | 6: 2.09 - 1.97 2846 113 0.83 22.87 1.29 0.25 313.43| | 7: 1.97 - 1.87 2787 165 0.90 16.43 1.28 0.25 90.65| | 8: 1.87 - 1.79 2789 144 0.86 21.19 1.26 0.25 90.65| | 9: 1.79 - 1.72 2745 138 0.88 18.52 1.24 0.25 55.02| | 10: 1.72 - 1.66 2789 158 0.87 20.19 1.23 0.25 47.88| | 11: 1.66 - 1.61 2740 147 0.86 21.42 1.25 0.25 46.29| | 12: 1.61 - 1.56 2787 146 0.88 18.79 1.23 0.25 30.14| | 13: 1.56 - 1.52 2745 130 0.86 20.89 1.24 0.25 30.14| | 14: 1.52 - 1.48 2803 134 0.86 21.19 1.23 0.25 27.14| | 15: 1.48 - 1.45 2738 128 0.86 20.68 1.23 0.25 21.63| | 16: 1.45 - 1.42 2756 161 0.85 22.33 1.23 0.25 21.63| | 17: 1.42 - 1.39 2785 139 0.86 21.10 1.22 0.25 18.37| | 18: 1.39 - 1.36 2741 179 0.86 21.89 1.22 0.25 16.48| | 19: 1.36 - 1.34 2807 134 0.85 22.47 1.21 0.25 16.48| | 20: 1.34 - 1.32 2696 147 0.86 21.50 1.21 0.24 13.59| | 21: 1.32 - 1.30 2785 112 0.85 22.46 1.20 0.24 13.39| | 22: 1.29 - 1.27 2704 152 0.85 22.93 1.21 0.24 13.05| | 23: 1.27 - 1.26 2802 156 0.86 22.06 1.21 0.24 11.31| | 24: 1.26 - 1.24 2744 132 0.85 23.22 1.20 0.24 11.31| | 25: 1.24 - 1.22 2734 148 0.84 23.85 1.20 0.24 10.70| | 26: 1.22 - 1.21 2727 135 0.84 23.88 1.19 0.23 10.02| | 27: 1.21 - 1.19 2814 148 0.83 25.09 1.20 0.23 10.02| | 28: 1.19 - 1.18 2671 147 0.83 24.94 1.17 0.23 9.23| | 29: 1.18 - 1.16 2800 134 0.83 25.08 1.16 0.23 8.93| | 30: 1.16 - 1.15 2740 148 0.81 26.89 1.15 0.23 8.93| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 8.93 max = 1493.56 mean = 216.63| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 22.82| |phase err.(test): min = 0.00 max = 89.83 mean = 22.74| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.239 1557 Z= 5.520 Angle : 5.413 19.796 2118 Z= 3.892 Chirality : 0.397 0.996 243 Planarity : 0.032 0.090 284 Dihedral : 14.027 82.534 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 2.48 % Allowed : 1.24 % Favored : 96.27 % Cbeta Deviations : 34.59 % 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: -2.69 (0.51), residues: 224 helix: -3.09 (0.37), residues: 108 sheet: -0.73 (0.78), residues: 38 loop : 0.17 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.089 0.020 ARG A 98 TYR 0.087 0.038 TYR A 139 PHE 0.138 0.046 PHE A 164 HIS 0.088 0.044 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= 0.2613 r_free= 0.1952 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794678 | | target function (ml) not normalized (work): 232813.404500 | | target function (ml) not normalized (free): 11845.770782 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2572 0.2614 0.1952 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2572 0.2614 0.1952 n_refl.: 87602 remove outliers: r(all,work,free)=0.1988 0.1992 0.1952 n_refl.: 87594 overall B=0.23 to atoms: r(all,work,free)=0.2016 0.2021 0.1969 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1651 0.1645 0.1778 n_refl.: 87594 remove outliers: r(all,work,free)=0.1650 0.1644 0.1778 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 0.3801 382.013 356.138 0.722 0.911 0.401 11.894-9.307 99.02 97 4 0.1884 613.622 592.086 1.016 0.911 0.380 9.237-7.194 100.00 213 7 0.2154 501.868 492.028 1.055 0.911 0.344 7.162-5.571 100.00 427 22 0.2229 376.624 364.999 1.022 0.912 0.282 5.546-4.326 100.00 867 58 0.1299 517.011 511.609 1.060 0.913 0.221 4.315-3.360 100.00 1859 96 0.1147 491.681 488.133 1.099 0.914 0.203 3.356-2.611 100.00 3867 181 0.1467 323.009 319.144 1.088 0.916 0.029 2.608-2.026 99.99 8198 413 0.1337 214.126 211.946 1.095 0.920 0.000 2.025-1.573 100.00 17313 902 0.1661 104.568 103.787 1.093 0.926 0.000 1.573-1.221 100.00 36679 1900 0.2071 46.370 45.012 1.067 0.936 0.000 1.221-1.150 99.97 13689 708 0.2578 29.216 26.965 1.027 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0531 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1644 r_free=0.1778 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=0.1649 r_free=0.1782 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.264472 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1970.540816 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 0.1689 0.1802 0.0113 0.002 0.4 4.5 0.0 0.0 0 0.125 0.1592 0.1724 0.0132 0.002 0.4 4.5 0.0 0.0 0 0.250 0.1450 0.1611 0.0162 0.001 0.5 3.8 0.0 0.0 0 0.500 0.1398 0.1577 0.0179 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1365 0.1560 0.0195 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1369 0.1565 0.0197 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1293 0.1502 0.0209 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1267 0.1487 0.0220 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1257 0.1482 0.0224 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1246 0.1472 0.0226 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1242 0.1471 0.0229 0.004 0.8 3.2 0.5 0.0 0 6.000 0.1238 0.1472 0.0234 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1233 0.1463 0.0230 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1231 0.1471 0.0240 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1227 0.1463 0.0236 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1226 0.1468 0.0242 0.007 0.9 3.2 0.5 0.0 0 11.000 0.1225 0.1467 0.0242 0.007 0.9 3.5 0.5 0.6 0 12.000 0.1224 0.1472 0.0248 0.007 1.0 3.5 0.5 0.6 0 13.132 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1227 0.1463 0.0236 0.006 0.9 3.5 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.63 2.36 3.013 19.090 1970.541 0.017 12.27 14.62 2.35 2.989 19.090 59.116 0.017 12.34 14.60 2.26 2.668 19.088 246.318 0.017 12.71 15.28 2.57 2.843 19.324 985.270 0.016 12.54 15.43 2.89 3.177 19.557 1970.541 0.016 12.37 15.29 2.92 3.084 19.523 2955.811 0.015 12.36 15.39 3.03 3.370 19.680 3941.082 0.015 12.29 15.38 3.09 3.357 19.655 4926.352 0.015 12.21 15.31 3.10 3.390 19.671 5911.622 0.015 12.21 15.39 3.18 3.469 19.713 6896.893 0.015 12.20 15.40 3.20 3.397 19.665 7882.163 0.015 12.20 15.46 3.26 3.603 19.766 8867.434 0.015 12.15 15.37 3.22 3.507 19.694 9852.704 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: 246.318 Accepted refinement result: 12.34 14.60 2.26 2.668 19.088 246.318 0.017 Individual atomic B min max mean iso aniso Overall: 9.09 119.47 20.11 3.31 0 1785 Protein: 9.09 115.03 17.02 3.32 0 1519 Water: 11.48 119.47 38.26 N/A 0 258 Other: 19.73 26.62 22.08 N/A 0 8 Chain A: 9.09 119.47 20.11 N/A 0 1785 Histogram: Values Number of atoms 9.09 - 20.13 1272 20.13 - 31.17 227 31.17 - 42.21 125 42.21 - 53.24 94 53.24 - 64.28 42 64.28 - 75.32 11 75.32 - 86.36 7 86.36 - 97.40 4 97.40 - 108.43 1 108.43 - 119.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1460 r_work=0.1235 r_free=0.1462 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1462 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 = 0.1228 r_free = 0.1454 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 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= 0.1228 r_free= 0.1454 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.016778 | | target function (ls_wunit_k1) not normalized (work): 1397.540970 | | target function (ls_wunit_k1) not normalized (free): 108.744195 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1239 0.1228 0.1454 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1677 0.1678 0.1689 n_refl.: 87592 remove outliers: r(all,work,free)=0.1677 0.1678 0.1689 n_refl.: 87592 overall B=0.02 to atoms: r(all,work,free)=0.1681 0.1683 0.1692 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1226 0.1449 n_refl.: 87592 remove outliers: r(all,work,free)=0.1237 0.1226 0.1449 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 0.3555 300.011 276.040 0.654 1.003 0.390 11.894-9.307 99.02 97 4 0.1637 481.904 469.107 0.921 1.003 0.365 9.237-7.194 100.00 213 7 0.1882 394.138 388.059 0.965 1.003 0.350 7.162-5.571 100.00 427 22 0.1844 295.779 289.803 0.937 1.003 0.254 5.546-4.326 100.00 867 58 0.0995 406.031 403.189 0.965 1.003 0.209 4.315-3.360 100.00 1859 96 0.0872 386.139 385.045 1.008 1.003 0.190 3.356-2.611 100.00 3867 181 0.1175 253.673 252.514 1.009 1.002 0.090 2.608-2.026 99.99 8198 413 0.1021 168.162 167.429 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1111 82.122 82.308 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1448 36.416 35.920 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2251 22.945 21.433 0.984 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0363 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1449 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=0.1226 r_free=0.1449 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1449 | n_water=258 | time (s): 1.920 (total time: 1.920) Filter (dist) r_work=0.1236 r_free=0.1449 | n_water=251 | time (s): 21.550 (total time: 23.470) Filter (q & B) r_work=0.1239 r_free=0.1449 | n_water=248 | time (s): 2.320 (total time: 25.790) Compute maps r_work=0.1239 r_free=0.1449 | n_water=248 | time (s): 1.150 (total time: 26.940) Filter (map) r_work=0.1257 r_free=0.1451 | n_water=224 | time (s): 2.450 (total time: 29.390) Find peaks r_work=0.1257 r_free=0.1451 | n_water=224 | time (s): 0.500 (total time: 29.890) Add new water r_work=0.1410 r_free=0.1625 | n_water=438 | time (s): 2.760 (total time: 32.650) Refine new water occ: r_work=0.1313 r_free=0.1481 adp: r_work=0.1230 r_free=0.1427 occ: r_work=0.1242 r_free=0.1417 adp: r_work=0.1208 r_free=0.1402 occ: r_work=0.1210 r_free=0.1394 adp: r_work=0.1201 r_free=0.1391 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1391 r_work=0.1201 r_free=0.1391 | n_water=438 | time (s): 57.320 (total time: 89.970) Filter (q & B) r_work=0.1204 r_free=0.1393 | n_water=425 | time (s): 2.790 (total time: 92.760) Filter (dist only) r_work=0.1204 r_free=0.1392 | n_water=424 | time (s): 34.960 (total time: 127.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.503851 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1497.633282 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 0.1710 0.1817 0.0107 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1463 0.1598 0.0135 0.001 0.4 5.4 0.0 0.0 0 0.250 0.1408 0.1559 0.0150 0.001 0.4 5.1 0.0 0.0 0 0.500 0.1361 0.1522 0.0161 0.001 0.4 4.5 0.0 0.0 0 0.750 0.1339 0.1509 0.0170 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1341 0.1513 0.0172 0.002 0.5 4.2 0.0 0.0 0 1.000 0.1262 0.1463 0.0200 0.002 0.5 3.8 0.5 0.0 0 2.000 0.1231 0.1437 0.0206 0.003 0.6 3.8 0.5 0.0 0 3.000 0.1221 0.1432 0.0211 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1211 0.1425 0.0214 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1209 0.1421 0.0211 0.005 0.7 4.2 0.5 0.0 0 6.000 0.1203 0.1416 0.0213 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1201 0.1419 0.0218 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1198 0.1420 0.0223 0.006 0.8 4.5 0.5 0.0 0 9.000 0.1196 0.1426 0.0230 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1195 0.1427 0.0232 0.007 0.9 5.1 0.5 0.6 0 11.000 0.1194 0.1423 0.0229 0.007 0.9 4.5 0.5 0.6 0 12.000 0.1194 0.1428 0.0235 0.008 0.9 5.1 0.5 0.6 0 13.000 0.1192 0.1427 0.0236 0.008 1.0 4.8 0.5 0.6 0 14.252 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1416 0.0213 0.005 0.8 3.5 0.5 0.0 0 7.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 14.16 2.13 3.778 21.814 1497.633 0.016 12.03 14.16 2.13 3.778 21.814 44.929 0.016 12.03 14.16 2.13 3.778 21.814 187.204 0.016 12.23 14.57 2.35 3.619 21.820 748.817 0.016 12.20 14.87 2.66 3.508 21.927 1497.633 0.015 12.04 14.74 2.70 3.471 22.181 2246.450 0.015 11.99 14.77 2.78 3.511 22.192 2995.267 0.015 11.95 14.78 2.83 3.535 22.227 3744.083 0.015 11.90 14.78 2.88 3.535 22.190 4492.900 0.014 11.84 14.76 2.92 3.532 22.147 5241.716 0.014 11.80 14.74 2.93 3.545 22.142 5990.533 0.014 11.79 14.79 2.99 3.557 22.099 6739.350 0.014 11.77 14.77 3.00 3.571 22.113 7488.166 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 187.204 Accepted refinement result: 12.03 14.16 2.13 3.778 21.814 187.204 0.016 Individual atomic B min max mean iso aniso Overall: 9.12 115.05 22.23 3.31 200 1751 Protein: 9.12 115.05 17.05 3.32 0 1519 Water: 11.51 76.71 40.80 N/A 200 224 Other: 19.76 26.64 22.10 N/A 0 8 Chain A: 9.12 115.05 19.45 N/A 0 1751 Chain S: 13.43 60.00 46.59 N/A 200 0 Histogram: Values Number of atoms 9.12 - 19.71 1260 19.71 - 30.30 249 30.30 - 40.90 166 40.90 - 51.49 125 51.49 - 62.08 128 62.08 - 72.68 12 72.68 - 83.27 5 83.27 - 93.86 4 93.86 - 104.46 0 104.46 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1416 r_work=0.1203 r_free=0.1416 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1416 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 = 0.1204 r_free = 0.1411 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1204 r_free= 0.1411 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015624 | | target function (ls_wunit_k1) not normalized (work): 1301.452192 | | target function (ls_wunit_k1) not normalized (free): 101.508195 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1204 0.1411 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1603 0.1602 0.1652 n_refl.: 87592 remove outliers: r(all,work,free)=0.1603 0.1602 0.1652 n_refl.: 87592 overall B=0.00 to atoms: r(all,work,free)=0.1603 0.1602 0.1653 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1202 0.1407 n_refl.: 87592 remove outliers: r(all,work,free)=0.1210 0.1200 0.1407 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 0.3420 299.376 273.576 0.586 1.003 0.350 11.894-9.307 99.02 97 4 0.1689 481.904 474.685 0.912 1.003 0.333 9.237-7.194 100.00 213 7 0.1785 394.138 392.974 0.982 1.003 0.290 7.162-5.571 100.00 427 22 0.1616 295.779 291.173 0.937 1.003 0.240 5.546-4.326 100.00 867 58 0.0913 406.031 402.979 0.959 1.003 0.205 4.315-3.360 100.00 1859 96 0.0820 386.139 384.721 1.006 1.003 0.200 3.356-2.611 100.00 3867 181 0.1109 253.673 252.609 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1014 168.162 167.595 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1110 82.122 82.339 1.031 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1452 36.416 35.950 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2259 22.945 21.465 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0036 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1407 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1407 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1407 | n_water=424 | time (s): 2.000 (total time: 2.000) Filter (dist) r_work=0.1200 r_free=0.1408 | n_water=422 | time (s): 36.030 (total time: 38.030) Filter (q & B) r_work=0.1200 r_free=0.1408 | n_water=422 | time (s): 1.650 (total time: 39.680) Compute maps r_work=0.1200 r_free=0.1408 | n_water=422 | time (s): 1.360 (total time: 41.040) Filter (map) r_work=0.1242 r_free=0.1394 | n_water=284 | time (s): 2.680 (total time: 43.720) Find peaks r_work=0.1242 r_free=0.1394 | n_water=284 | time (s): 0.640 (total time: 44.360) Add new water r_work=0.1357 r_free=0.1527 | n_water=463 | time (s): 2.610 (total time: 46.970) Refine new water occ: r_work=0.1264 r_free=0.1444 adp: r_work=0.1265 r_free=0.1445 occ: r_work=0.1241 r_free=0.1418 adp: r_work=0.1240 r_free=0.1419 occ: r_work=0.1223 r_free=0.1397 adp: r_work=0.1218 r_free=0.1395 ADP+occupancy (water only), MIN, final r_work=0.1218 r_free=0.1395 r_work=0.1218 r_free=0.1395 | n_water=463 | time (s): 186.160 (total time: 233.130) Filter (q & B) r_work=0.1224 r_free=0.1396 | n_water=437 | time (s): 3.290 (total time: 236.420) Filter (dist only) r_work=0.1224 r_free=0.1394 | n_water=436 | time (s): 38.730 (total time: 275.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.795400 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.216194 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 0.1242 0.1366 0.0124 0.002 0.6 4.8 0.5 0.0 0 0.090 0.1195 0.1333 0.0138 0.003 0.7 4.2 0.5 0.0 0 0.269 0.1179 0.1326 0.0146 0.004 0.8 3.2 0.5 0.0 0 0.539 0.1172 0.1321 0.0149 0.005 0.9 3.5 0.5 0.0 0 0.808 0.1168 0.1319 0.0151 0.006 1.0 3.5 0.5 0.0 0 1.077 0.1166 0.1319 0.0154 0.007 1.0 3.5 0.5 0.0 0 1.347 0.1163 0.1318 0.0155 0.007 1.0 3.8 0.5 0.0 0 1.616 0.1161 0.1316 0.0155 0.008 1.1 3.8 0.5 0.0 0 1.885 0.1171 0.1320 0.0150 0.005 0.9 3.5 0.5 0.0 0 0.898 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1161 0.1316 0.0155 0.008 1.1 3.8 0.5 0.0 0 1.885 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.61 13.16 1.55 3.781 21.252 50.216 3.618 11.61 13.16 1.55 3.781 21.252 1.506 3.618 11.62 13.16 1.54 3.771 21.252 6.277 3.618 11.66 13.27 1.61 3.718 21.233 25.108 3.612 11.62 13.32 1.70 3.750 21.209 50.216 3.609 11.59 13.36 1.77 3.766 21.194 75.324 3.605 11.55 13.34 1.79 3.782 21.185 100.432 3.601 11.51 13.31 1.80 3.797 21.180 125.540 3.598 11.51 13.33 1.82 3.815 21.164 150.649 3.597 11.48 13.29 1.81 3.826 21.161 175.757 3.594 11.46 13.29 1.82 3.833 21.165 200.865 3.594 11.44 13.26 1.82 3.838 21.164 225.973 3.592 11.44 13.28 1.84 3.850 21.159 251.081 3.592 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 6.277 Accepted refinement result: 11.62 13.16 1.54 3.771 21.252 6.277 3.618 Individual atomic B min max mean iso aniso Overall: 9.13 114.93 21.20 3.28 214 1749 Protein: 9.13 114.93 17.05 3.28 0 1519 Water: 11.51 76.71 35.66 N/A 214 222 Other: 19.69 26.59 22.09 N/A 0 8 Chain A: 9.13 114.93 19.42 N/A 0 1749 Chain S: 13.44 60.00 35.76 N/A 214 0 Histogram: Values Number of atoms 9.13 - 19.71 1264 19.71 - 30.29 293 30.29 - 40.87 200 40.87 - 51.45 123 51.45 - 62.03 60 62.03 - 72.61 11 72.61 - 83.19 6 83.19 - 93.77 4 93.77 - 104.35 0 104.35 - 114.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.1162 r_free=0.1316 r_work=0.1162 r_free=0.1316 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1162 r_free = 0.1316 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1154 r_free = 0.1309 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.13 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= 0.1154 r_free= 0.1309 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.610309 | | target function (ml) not normalized (work): 300717.087194 | | target function (ml) not normalized (free): 15820.910034 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1161 0.1154 0.1309 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1496 0.1496 0.1525 n_refl.: 87590 remove outliers: r(all,work,free)=0.1496 0.1496 0.1525 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1494 0.1494 0.1523 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1149 0.1300 n_refl.: 87590 remove outliers: r(all,work,free)=0.1153 0.1146 0.1300 n_refl.: 87581 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3794 287.936 268.276 0.490 1.000 0.308 11.894-9.307 97.06 95 4 0.2288 482.128 462.772 0.861 1.002 0.300 9.237-7.194 98.18 209 7 0.2327 385.629 384.057 0.944 1.002 0.219 7.162-5.571 100.00 427 22 0.2122 295.779 284.629 0.912 1.002 0.184 5.546-4.326 100.00 867 58 0.1099 406.031 401.396 0.954 1.002 0.170 4.315-3.360 100.00 1859 96 0.0957 386.139 383.355 0.997 1.002 0.170 3.356-2.611 100.00 3867 181 0.1148 253.673 251.577 0.997 1.002 0.043 2.608-2.026 99.99 8198 413 0.0938 168.162 167.361 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0895 82.122 82.422 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.416 36.008 1.019 0.998 0.000 1.221-1.150 99.97 13689 708 0.2162 22.945 21.500 0.982 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0303 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 r_free=0.1300 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=0.1300 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1300 | n_water=436 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1146 r_free=0.1300 | n_water=434 | time (s): 44.340 (total time: 46.790) Filter (q & B) r_work=0.1146 r_free=0.1301 | n_water=432 | time (s): 3.900 (total time: 50.690) Compute maps r_work=0.1146 r_free=0.1301 | n_water=432 | time (s): 1.810 (total time: 52.500) Filter (map) r_work=0.1171 r_free=0.1293 | n_water=316 | time (s): 3.890 (total time: 56.390) Find peaks r_work=0.1171 r_free=0.1293 | n_water=316 | time (s): 0.700 (total time: 57.090) Add new water r_work=0.1242 r_free=0.1362 | n_water=470 | time (s): 3.640 (total time: 60.730) Refine new water occ: r_work=0.1168 r_free=0.1292 adp: r_work=0.1168 r_free=0.1296 occ: r_work=0.1152 r_free=0.1280 adp: r_work=0.1151 r_free=0.1282 occ: r_work=0.1140 r_free=0.1271 adp: r_work=0.1136 r_free=0.1271 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1271 r_work=0.1136 r_free=0.1271 | n_water=470 | time (s): 257.120 (total time: 317.850) Filter (q & B) r_work=0.1140 r_free=0.1279 | n_water=445 | time (s): 3.820 (total time: 321.670) Filter (dist only) r_work=0.1147 r_free=0.1278 | n_water=443 | time (s): 45.700 (total time: 367.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.776874 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.329476 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1208 0.1315 0.0107 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1171 0.1291 0.0120 0.003 0.8 3.2 0.5 0.0 0 0.267 0.1157 0.1283 0.0126 0.005 0.9 3.5 0.5 0.0 0 0.533 0.1151 0.1280 0.0129 0.006 1.0 3.5 0.5 0.0 0 0.800 0.1147 0.1279 0.0132 0.007 1.0 3.8 0.5 0.0 0 1.066 0.1144 0.1278 0.0133 0.007 1.1 3.8 0.5 0.0 0 1.333 0.1142 0.1278 0.0136 0.008 1.1 3.8 0.5 0.0 0 1.599 0.1140 0.1281 0.0140 0.009 1.1 3.5 0.5 0.0 0 1.866 0.1149 0.1282 0.0133 0.006 1.0 3.5 0.5 0.0 0 0.888 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1144 0.1278 0.0133 0.007 1.1 3.8 0.5 0.0 0 1.333 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.44 12.78 1.33 3.766 21.180 36.329 3.603 11.44 12.78 1.33 3.766 21.180 1.090 3.603 11.44 12.78 1.33 3.766 21.180 4.541 3.603 11.48 12.81 1.34 3.700 21.171 18.165 3.599 11.47 12.88 1.41 3.719 21.158 36.329 3.598 11.50 12.99 1.49 3.735 21.133 54.494 3.599 11.43 12.94 1.51 3.754 21.129 72.659 3.593 11.38 12.91 1.52 3.764 21.128 90.824 3.590 11.37 12.91 1.54 3.772 21.123 108.988 3.588 11.35 12.89 1.55 3.780 21.122 127.153 3.586 11.34 12.90 1.56 3.792 21.116 145.318 3.586 11.36 12.94 1.59 3.808 21.099 163.483 3.586 11.33 12.91 1.58 3.815 21.102 181.647 3.584 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.541 Accepted refinement result: 11.44 12.78 1.33 3.766 21.180 4.541 3.603 Individual atomic B min max mean iso aniso Overall: 9.12 114.92 21.08 3.28 224 1746 Protein: 9.12 114.92 17.04 3.28 0 1519 Water: 11.50 76.69 34.94 N/A 224 219 Other: 19.68 26.58 22.08 N/A 0 8 Chain A: 9.12 114.92 19.38 N/A 0 1746 Chain S: 13.43 59.99 34.32 N/A 224 0 Histogram: Values Number of atoms 9.12 - 19.70 1264 19.70 - 30.28 301 30.28 - 40.86 213 40.86 - 51.44 120 51.44 - 62.02 49 62.02 - 72.60 11 72.60 - 83.18 6 83.18 - 93.76 4 93.76 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1144 r_free=0.1278 r_work=0.1144 r_free=0.1278 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1144 r_free = 0.1278 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1139 r_free = 0.1278 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1139 r_free= 0.1278 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601301 | | target function (ml) not normalized (work): 299934.376005 | | target function (ml) not normalized (free): 15779.740996 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1146 0.1139 0.1278 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1481 0.1483 0.1479 n_refl.: 87581 remove outliers: r(all,work,free)=0.1481 0.1483 0.1479 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1480 0.1481 0.1478 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1145 0.1139 0.1278 n_refl.: 87581 remove outliers: r(all,work,free)=0.1143 0.1136 0.1278 n_refl.: 87575 ======================== 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 0.3824 285.354 252.836 0.442 1.000 0.285 11.894-9.307 93.14 91 4 0.2174 482.190 470.556 0.864 1.002 0.267 9.237-7.194 98.18 209 7 0.2387 385.629 380.452 0.923 1.002 0.170 7.162-5.571 100.00 427 22 0.2106 295.779 285.083 0.906 1.002 0.150 5.546-4.326 100.00 867 58 0.1127 406.031 401.525 0.955 1.002 0.150 4.315-3.360 100.00 1859 96 0.0929 386.139 383.858 0.995 1.002 0.130 3.356-2.611 100.00 3867 181 0.1124 253.673 251.866 1.001 1.002 0.024 2.608-2.026 99.99 8198 413 0.0921 168.162 167.536 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.122 82.465 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.416 36.022 1.018 0.998 0.000 1.221-1.150 99.97 13689 708 0.2168 22.945 21.498 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0209 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1136 r_free=0.1278 After: r_work=0.1137 r_free=0.1277 ================================== NQH flips ================================== r_work=0.1137 r_free=0.1277 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1137 r_free=0.1277 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1277 | n_water=443 | time (s): 2.160 (total time: 2.160) Filter (dist) r_work=0.1137 r_free=0.1279 | n_water=442 | time (s): 44.830 (total time: 46.990) Filter (q & B) r_work=0.1137 r_free=0.1279 | n_water=442 | time (s): 1.300 (total time: 48.290) Compute maps r_work=0.1137 r_free=0.1279 | n_water=442 | time (s): 1.800 (total time: 50.090) Filter (map) r_work=0.1164 r_free=0.1287 | n_water=357 | time (s): 3.670 (total time: 53.760) Find peaks r_work=0.1164 r_free=0.1287 | n_water=357 | time (s): 0.720 (total time: 54.480) Add new water r_work=0.1211 r_free=0.1320 | n_water=485 | time (s): 3.650 (total time: 58.130) Refine new water occ: r_work=0.1159 r_free=0.1272 adp: r_work=0.1160 r_free=0.1273 occ: r_work=0.1147 r_free=0.1263 adp: r_work=0.1146 r_free=0.1265 occ: r_work=0.1138 r_free=0.1259 adp: r_work=0.1135 r_free=0.1259 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1259 r_work=0.1135 r_free=0.1259 | n_water=485 | time (s): 223.670 (total time: 281.800) Filter (q & B) r_work=0.1138 r_free=0.1267 | n_water=459 | time (s): 3.690 (total time: 285.490) Filter (dist only) r_work=0.1139 r_free=0.1266 | n_water=458 | time (s): 47.440 (total time: 332.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.761342 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.193129 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 0.1218 0.1314 0.0096 0.004 0.7 6.1 0.0 0.0 0 0.088 0.1172 0.1286 0.0114 0.004 0.8 6.7 0.0 0.0 0 0.264 0.1155 0.1275 0.0120 0.005 0.9 6.1 0.5 0.0 0 0.528 0.1147 0.1270 0.0123 0.006 1.0 6.4 0.5 0.0 0 0.793 0.1140 0.1266 0.0126 0.007 1.1 6.1 0.5 0.0 0 1.057 0.1139 0.1266 0.0127 0.007 1.1 6.1 0.5 0.0 0 1.321 0.1138 0.1266 0.0128 0.008 1.1 5.8 0.5 0.0 0 1.585 0.1137 0.1265 0.0128 0.008 1.1 5.8 0.5 0.0 0 1.849 0.1144 0.1268 0.0124 0.006 1.0 6.4 0.5 0.0 0 0.881 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1137 0.1265 0.0128 0.008 1.1 5.8 0.5 0.0 0 1.849 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.37 12.65 1.28 3.765 21.218 38.193 3.599 11.37 12.65 1.28 3.765 21.218 1.146 3.599 11.37 12.65 1.28 3.765 21.218 4.774 3.599 11.41 12.69 1.28 3.699 21.209 19.097 3.596 11.43 12.80 1.38 3.722 21.186 38.193 3.596 11.40 12.82 1.42 3.738 21.172 57.290 3.594 11.33 12.76 1.44 3.756 21.170 76.386 3.588 11.30 12.76 1.46 3.766 21.168 95.483 3.585 11.28 12.76 1.47 3.774 21.166 114.579 3.583 11.27 12.77 1.50 3.787 21.160 133.676 3.582 11.27 12.79 1.51 3.801 21.150 152.773 3.582 11.24 12.76 1.52 3.808 21.151 171.869 3.581 11.24 12.75 1.51 3.813 21.148 190.966 3.579 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.146 Accepted refinement result: 11.37 12.65 1.28 3.765 21.218 1.146 3.599 Individual atomic B min max mean iso aniso Overall: 9.11 114.92 21.16 3.28 240 1745 Protein: 9.11 114.92 17.03 3.28 0 1519 Water: 11.49 76.69 34.84 N/A 240 218 Other: 19.67 26.57 22.07 N/A 0 8 Chain A: 9.11 114.92 19.36 N/A 0 1745 Chain S: 13.43 59.98 34.25 N/A 240 0 Histogram: Values Number of atoms 9.11 - 19.69 1265 19.69 - 30.27 308 30.27 - 40.85 216 40.85 - 51.43 124 51.43 - 62.01 49 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1137 r_free=0.1265 r_work=0.1137 r_free=0.1265 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1137 r_free = 0.1265 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1134 r_free = 0.1265 target_work(ml) = 3.598 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1134 r_free= 0.1265 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.598440 | | target function (ml) not normalized (work): 299674.474594 | | target function (ml) not normalized (free): 15774.892099 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1319 0.1266 5.6506 5.5645| | 2: 3.57 - 2.84 1.00 2888 124 0.1082 0.1335 5.1524 5.1919| | 3: 2.83 - 2.48 1.00 2820 163 0.1108 0.1206 4.9217 4.9526| | 4: 2.47 - 2.25 1.00 2825 136 0.0904 0.0983 4.6078 4.6345| | 5: 2.25 - 2.09 1.00 2756 127 0.0870 0.0959 4.5515 4.603| | 6: 2.09 - 1.97 1.00 2846 113 0.0866 0.0997 4.257 4.347| | 7: 1.97 - 1.87 1.00 2787 165 0.0881 0.1080 3.9726 4.0744| | 8: 1.87 - 1.79 1.00 2789 144 0.0923 0.1073 3.8836 3.9734| | 9: 1.79 - 1.72 1.00 2745 138 0.0875 0.1199 3.6411 3.8363| | 10: 1.72 - 1.66 1.00 2831 160 0.0918 0.1201 3.5615 3.7054| | 11: 1.66 - 1.61 1.00 2712 147 0.0869 0.1046 3.4927 3.568| | 12: 1.61 - 1.56 1.00 2773 144 0.0903 0.1170 3.329 3.4732| | 13: 1.56 - 1.52 1.00 2745 130 0.0945 0.1025 3.3078 3.3889| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1059 3.2405 3.3265| | 15: 1.48 - 1.45 1.00 2738 128 0.0998 0.1255 3.1515 3.2718| | 16: 1.45 - 1.42 1.00 2756 161 0.1050 0.1248 3.1311 3.2377| | 17: 1.42 - 1.39 1.00 2785 139 0.1139 0.1298 3.1162 3.2261| | 18: 1.39 - 1.36 1.00 2741 179 0.1193 0.1321 3.0998 3.236| | 19: 1.36 - 1.34 1.00 2807 134 0.1257 0.1546 3.1069 3.2525| | 20: 1.34 - 1.32 1.00 2696 147 0.1363 0.1447 3.1083 3.1453| | 21: 1.32 - 1.30 1.00 2785 112 0.1472 0.1513 3.1112 3.1044| | 22: 1.29 - 1.27 1.00 2704 152 0.1559 0.1981 3.1182 3.2968| | 23: 1.27 - 1.26 1.00 2802 156 0.1645 0.1778 3.1305 3.197| | 24: 1.26 - 1.24 1.00 2744 132 0.1707 0.1830 3.1244 3.2261| | 25: 1.24 - 1.22 1.00 2733 148 0.1877 0.2141 3.1397 3.261| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1773 3.1446 3.2001| | 27: 1.21 - 1.19 1.00 2814 148 0.2070 0.2165 3.1679 3.1591| | 28: 1.19 - 1.18 1.00 2671 147 0.2201 0.2280 3.1638 3.169| | 29: 1.18 - 1.16 1.00 2800 134 0.2266 0.2381 3.1464 3.2271| | 30: 1.16 - 1.15 1.00 2739 148 0.2442 0.2453 3.1407 3.1672| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2917 171 0.95 8.11 1.00 0.98 5310.98| | 2: 3.57 - 2.84 2888 124 0.93 11.99 1.01 0.98 5310.98| | 3: 2.83 - 2.48 2820 163 0.90 15.87 0.99 0.98 4442.02| | 4: 2.47 - 2.25 2825 136 0.92 12.94 1.00 0.99 2201.23| | 5: 2.25 - 2.09 2756 127 0.91 15.02 1.01 0.99 2201.23| | 6: 2.09 - 1.97 2846 113 0.93 12.05 1.02 0.98 1282.05| | 7: 1.97 - 1.87 2787 165 0.95 9.19 1.02 0.98 498.12| | 8: 1.87 - 1.79 2789 144 0.93 12.43 1.00 0.98 498.12| | 9: 1.79 - 1.72 2745 138 0.94 10.06 0.98 0.98 286.65| | 10: 1.72 - 1.66 2831 160 0.94 11.14 0.98 0.98 244.30| | 11: 1.66 - 1.61 2712 147 0.93 11.75 0.98 0.98 234.18| | 12: 1.61 - 1.56 2773 144 0.95 8.99 0.99 0.98 138.75| | 13: 1.56 - 1.52 2745 130 0.95 10.47 1.02 0.98 138.75| | 14: 1.52 - 1.48 2803 134 0.94 10.80 1.02 0.98 124.30| | 15: 1.48 - 1.45 2738 128 0.95 9.96 1.02 0.99 97.83| | 16: 1.45 - 1.42 2756 161 0.94 11.11 1.02 0.99 97.83| | 17: 1.42 - 1.39 2785 139 0.95 10.96 1.01 0.99 88.78| | 18: 1.39 - 1.36 2741 179 0.94 11.51 1.01 0.99 83.54| | 19: 1.36 - 1.34 2807 134 0.94 11.85 1.00 0.99 83.54| | 20: 1.34 - 1.32 2696 147 0.94 12.07 0.98 0.97 79.29| | 21: 1.32 - 1.30 2785 112 0.94 13.07 0.98 0.97 79.00| | 22: 1.29 - 1.27 2704 152 0.93 13.62 0.98 0.97 79.43| | 23: 1.27 - 1.26 2802 156 0.92 14.79 0.97 0.95 81.61| | 24: 1.26 - 1.24 2744 132 0.92 14.84 0.96 0.95 81.61| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.95 83.62| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.02 0.94 85.86| | 27: 1.21 - 1.19 2814 148 0.89 18.71 1.02 0.94 85.86| | 28: 1.19 - 1.18 2671 147 0.88 20.33 1.01 0.93 89.53| | 29: 1.18 - 1.16 2800 134 0.88 20.47 0.99 0.93 90.91| | 30: 1.16 - 1.15 2739 148 0.86 21.99 0.98 0.93 90.91| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.00 max = 5310.98 mean = 829.64| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.33| |phase err.(test): min = 0.00 max = 89.85 mean = 13.33| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1140 0.1134 0.1265 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1457 0.1458 0.1462 n_refl.: 87575 remove outliers: r(all,work,free)=0.1457 0.1458 0.1462 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1456 0.1457 0.1461 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1140 0.1133 0.1266 n_refl.: 87575 remove outliers: r(all,work,free)=0.1139 0.1132 0.1266 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 88.54 80 5 0.4013 285.354 249.516 0.442 1.000 0.304 11.894-9.307 91.18 89 4 0.2090 484.930 473.269 0.858 1.002 0.300 9.237-7.194 98.18 209 7 0.2403 385.629 377.963 0.915 1.002 0.177 7.162-5.571 100.00 427 22 0.2096 295.779 286.385 0.905 1.003 0.150 5.546-4.326 100.00 867 58 0.1115 406.031 401.546 0.953 1.003 0.130 4.315-3.360 100.00 1859 96 0.0923 386.139 383.932 0.995 1.002 0.120 3.356-2.611 100.00 3867 181 0.1124 253.673 251.881 1.000 1.002 0.014 2.608-2.026 99.99 8198 413 0.0915 168.162 167.552 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0890 82.122 82.461 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.416 36.027 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2164 22.945 21.506 0.981 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0205 ================= 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 : 0.2613 0.1952 0.082 5.413 8.8 119.3 19.9 258 0.000 1_bss: 0.1644 0.1778 0.082 5.413 9.1 119.5 20.1 258 0.000 1_settarget: 0.1644 0.1778 0.082 5.413 9.1 119.5 20.1 258 0.000 1_nqh: 0.1649 0.1782 0.082 5.413 9.1 119.5 20.1 258 0.003 1_weight: 0.1649 0.1782 0.082 5.413 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1227 0.1463 0.006 0.883 9.1 119.5 20.1 258 0.134 1_adp: 0.1234 0.1460 0.006 0.883 9.1 119.5 20.1 258 0.134 1_regHadp: 0.1235 0.1462 0.006 0.883 9.1 119.5 20.1 258 0.134 1_occ: 0.1228 0.1454 0.006 0.883 9.1 119.5 20.1 258 0.134 2_bss: 0.1226 0.1449 0.006 0.883 9.1 119.5 20.1 258 0.134 2_settarget: 0.1226 0.1449 0.006 0.883 9.1 119.5 20.1 258 0.134 2_updatecdl: 0.1226 0.1449 0.006 0.891 9.1 119.5 20.1 258 0.134 2_nqh: 0.1226 0.1449 0.006 0.891 9.1 119.5 20.1 258 0.134 2_sol: 0.1204 0.1392 0.006 0.891 9.1 115.1 22.2 424 n/a 2_weight: 0.1204 0.1392 0.006 0.891 9.1 115.1 22.2 424 n/a 2_xyzrec: 0.1203 0.1416 0.005 0.776 9.1 115.1 22.2 424 n/a 2_adp: 0.1203 0.1416 0.005 0.776 9.1 115.1 22.2 424 n/a 2_regHadp: 0.1203 0.1416 0.005 0.776 9.1 115.1 22.2 424 n/a 2_occ: 0.1204 0.1411 0.005 0.776 9.1 115.1 22.2 424 n/a 3_bss: 0.1200 0.1407 0.005 0.776 9.1 115.1 22.2 424 n/a 3_settarget: 0.1200 0.1407 0.005 0.776 9.1 115.1 22.2 424 n/a 3_updatecdl: 0.1200 0.1407 0.005 0.776 9.1 115.1 22.2 424 n/a 3_nqh: 0.1200 0.1407 0.005 0.776 9.1 115.1 22.2 424 n/a 3_sol: 0.1224 0.1394 0.005 0.776 9.1 115.1 21.2 436 n/a 3_weight: 0.1224 0.1394 0.005 0.776 9.1 115.1 21.2 436 n/a 3_xyzrec: 0.1161 0.1316 0.008 1.080 9.1 115.1 21.2 436 n/a 3_adp: 0.1162 0.1316 0.008 1.080 9.1 114.9 21.2 436 n/a 3_regHadp: 0.1162 0.1316 0.008 1.080 9.1 114.9 21.2 436 n/a 3_occ: 0.1154 0.1309 0.008 1.080 9.1 114.9 21.2 436 n/a 4_bss: 0.1146 0.1300 0.008 1.080 9.1 114.9 21.2 436 n/a 4_settarget: 0.1146 0.1300 0.008 1.080 9.1 114.9 21.2 436 n/a 4_updatecdl: 0.1146 0.1300 0.008 1.083 9.1 114.9 21.2 436 n/a 4_nqh: 0.1146 0.1300 0.008 1.083 9.1 114.9 21.2 436 n/a 4_sol: 0.1147 0.1278 0.008 1.083 9.1 114.9 21.1 443 n/a 4_weight: 0.1147 0.1278 0.008 1.083 9.1 114.9 21.1 443 n/a 4_xyzrec: 0.1144 0.1278 0.007 1.060 9.1 114.9 21.1 443 n/a 4_adp: 0.1144 0.1278 0.007 1.060 9.1 114.9 21.1 443 n/a 4_regHadp: 0.1144 0.1278 0.007 1.060 9.1 114.9 21.1 443 n/a 4_occ: 0.1139 0.1278 0.007 1.060 9.1 114.9 21.1 443 n/a 5_bss: 0.1136 0.1278 0.007 1.060 9.1 114.9 21.1 443 n/a 5_settarget: 0.1136 0.1278 0.007 1.060 9.1 114.9 21.1 443 n/a 5_updatecdl: 0.1136 0.1278 0.007 1.059 9.1 114.9 21.1 443 n/a 5_setrh: 0.1137 0.1277 0.007 1.059 9.1 114.9 21.1 443 n/a 5_nqh: 0.1137 0.1277 0.007 1.059 9.1 114.9 21.1 443 n/a 5_sol: 0.1139 0.1266 0.007 1.059 9.1 114.9 21.2 458 n/a 5_weight: 0.1139 0.1266 0.007 1.059 9.1 114.9 21.2 458 n/a 5_xyzrec: 0.1137 0.1265 0.008 1.113 9.1 114.9 21.2 458 n/a 5_adp: 0.1137 0.1265 0.008 1.113 9.1 114.9 21.2 458 n/a 5_regHadp: 0.1137 0.1265 0.008 1.113 9.1 114.9 21.2 458 n/a 5_occ: 0.1134 0.1265 0.008 1.113 9.1 114.9 21.2 458 n/a end: 0.1132 0.1266 0.008 1.113 9.1 114.9 21.2 458 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1541177_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1541177_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2700 Refinement macro-cycles (run) : 13155.1900 Write final files (write_after_run_outputs) : 89.2700 Total : 13247.7300 Total CPU time: 3.69 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 21:58:27 PST -0800 (1735365507.29 s) Start R-work = 0.1644, R-free = 0.1778 Final R-work = 0.1132, R-free = 0.1266 =============================================================================== Job complete usr+sys time: 13425.24 seconds wall clock time: 242 minutes 48.97 seconds (14568.97 seconds total)