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_6017437.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" 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_6017437.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6017437.pdb" } 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 3 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: 1.86, per 1000 atoms: 0.55 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: 0.56 Conformation dependent library (CDL) restraints added in 213.1 milliseconds Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.89: 392 0.89 - 1.16: 1231 1.16 - 1.43: 698 1.43 - 1.70: 807 1.70 - 1.97: 25 Bond restraints: 3153 Sorted by residual: bond pdb=" N MET A 17 " pdb=" CA MET A 17 " ideal model delta sigma weight residual 1.459 1.669 -0.210 1.19e-02 7.06e+03 3.11e+02 bond pdb=" CA ALA A 36 " pdb=" C ALA A 36 " ideal model delta sigma weight residual 1.525 1.309 0.216 1.28e-02 6.10e+03 2.85e+02 bond pdb=" C LYS A 122 " pdb=" N VAL A 123 " ideal model delta sigma weight residual 1.332 1.134 0.198 1.20e-02 6.94e+03 2.73e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.201 0.177 1.10e-02 8.26e+03 2.59e+02 bond pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 1.330 1.539 -0.209 1.30e-02 5.92e+03 2.58e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 2948 4.41 - 8.82: 1933 8.82 - 13.22: 713 13.22 - 17.63: 166 17.63 - 22.03: 17 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 181 " pdb=" C VAL A 181 " pdb=" N LYS A 182 " ideal model delta sigma weight residual 121.87 104.73 17.14 9.70e-01 1.06e+00 3.12e+02 angle pdb=" CA LEU A 58 " pdb=" C LEU A 58 " pdb=" O LEU A 58 " ideal model delta sigma weight residual 120.92 137.20 -16.28 1.12e+00 7.97e-01 2.11e+02 angle pdb=" O GLY A 120 " pdb=" C GLY A 120 " pdb=" N SER A 121 " ideal model delta sigma weight residual 122.77 110.06 12.71 9.40e-01 1.13e+00 1.83e+02 angle pdb=" N PRO A 43 " pdb=" CA PRO A 43 " pdb=" CB PRO A 43 " ideal model delta sigma weight residual 103.32 114.67 -11.35 8.40e-01 1.42e+00 1.83e+02 angle pdb=" O LYS A 130 " pdb=" C LYS A 130 " pdb=" N ASP A 131 " ideal model delta sigma weight residual 122.07 109.18 12.89 1.03e+00 9.43e-01 1.57e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.29: 943 17.29 - 34.58: 118 34.58 - 51.86: 32 51.86 - 69.15: 16 69.15 - 86.43: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 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 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 102 0.195 - 0.390: 66 0.390 - 0.585: 44 0.585 - 0.779: 22 0.779 - 0.974: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.74 0.97 2.00e-01 2.50e+01 2.37e+01 chirality pdb=" CA BGLU A 94 " pdb=" N BGLU A 94 " pdb=" C BGLU A 94 " pdb=" CB BGLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 3.42 -0.91 2.00e-01 2.50e+01 2.05e+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 -1.74 -0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.076 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG PHE A 119 " -0.087 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.107 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.072 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.022 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.049 2.00e-02 2.50e+03 5.91e-02 1.05e+02 pdb=" CG PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.138 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.035 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.089 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.014 2.00e-02 2.50e+03 6.46e-02 9.40e+01 pdb=" CG HIS A 115 " 0.072 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.094 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.115 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.065 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 900 2.30 - 2.88: 8022 2.88 - 3.45: 10553 3.45 - 4.03: 15292 4.03 - 4.60: 21823 Nonbonded interactions: 56590 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.726 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.817 1.850 x-y,-y,-z-4/3 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.832 1.850 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.839 1.850 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.850 1.850 ... (remaining 56585 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_6017437_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= 0.2605 r_free= 0.1931 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.785659 | | target function (ml) not normalized (work): 232062.075368 | | target function (ml) not normalized (free): 11820.510947 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3041 0.2080 7.005 4.9586| | 2: 3.57 - 2.84 1.00 2876 122 0.2434 0.1802 4.3557 4.3551| | 3: 2.84 - 2.48 1.00 2833 165 0.2386 0.1603 4.1408 4.1475| | 4: 2.47 - 2.25 1.00 2825 136 0.2324 0.1501 3.8411 3.8338| | 5: 2.25 - 2.09 1.00 2756 127 0.2453 0.1565 3.806 3.8356| | 6: 2.09 - 1.97 1.00 2846 113 0.2574 0.1807 3.4626 3.5551| | 7: 1.97 - 1.87 1.00 2787 165 0.2541 0.1856 3.1208 3.1782| | 8: 1.87 - 1.79 1.00 2789 144 0.2453 0.1745 3.0487 3.1004| | 9: 1.79 - 1.72 1.00 2745 138 0.2468 0.1878 2.9015 2.9352| | 10: 1.72 - 1.66 1.00 2789 158 0.2379 0.1954 2.7833 2.8796| | 11: 1.66 - 1.61 1.00 2740 147 0.2464 0.1935 2.7407 2.8169| | 12: 1.61 - 1.56 1.00 2787 146 0.2538 0.1933 2.6342 2.676| | 13: 1.56 - 1.52 1.00 2745 130 0.2563 0.1781 2.5858 2.5926| | 14: 1.52 - 1.48 1.00 2803 134 0.2556 0.1726 2.502 2.5018| | 15: 1.48 - 1.45 1.00 2738 128 0.2578 0.2187 2.4183 2.5555| | 16: 1.45 - 1.42 1.00 2756 161 0.2585 0.2236 2.3706 2.455| | 17: 1.42 - 1.39 1.00 2785 139 0.2658 0.2062 2.325 2.3612| | 18: 1.39 - 1.36 1.00 2741 179 0.2632 0.2171 2.2557 2.3173| | 19: 1.36 - 1.34 1.00 2807 134 0.2644 0.2311 2.2548 2.2717| | 20: 1.34 - 1.32 1.00 2696 147 0.2611 0.2274 2.18 2.2556| | 21: 1.32 - 1.30 1.00 2785 112 0.2686 0.2050 2.178 2.1406| | 22: 1.29 - 1.27 1.00 2704 152 0.2723 0.2576 2.1214 2.1849| | 23: 1.27 - 1.26 1.00 2802 156 0.2778 0.2400 2.1115 2.1539| | 24: 1.26 - 1.24 1.00 2744 132 0.2738 0.2677 2.0666 2.1933| | 25: 1.24 - 1.22 1.00 2734 148 0.2816 0.2682 2.038 2.0651| | 26: 1.22 - 1.21 1.00 2727 135 0.2843 0.2325 1.9962 2.0704| | 27: 1.21 - 1.19 1.00 2814 148 0.3009 0.2834 2.0091 2.0418| | 28: 1.19 - 1.18 1.00 2671 147 0.2964 0.2733 1.9716 2.0262| | 29: 1.18 - 1.16 1.00 2800 134 0.2942 0.2770 1.9569 2.0367| | 30: 1.16 - 1.15 1.00 2740 148 0.3064 0.2500 1.9321 1.9044| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.05 0.76 0.23 1525.77| | 2: 3.57 - 2.84 2876 122 0.80 26.44 1.27 0.23 1525.77| | 3: 2.84 - 2.48 2833 165 0.73 32.39 1.24 0.24 1264.11| | 4: 2.47 - 2.25 2825 136 0.81 25.74 1.25 0.25 585.06| | 5: 2.25 - 2.09 2756 127 0.77 29.57 1.28 0.25 585.06| | 6: 2.09 - 1.97 2846 113 0.83 22.94 1.30 0.25 318.32| | 7: 1.97 - 1.87 2787 165 0.90 16.48 1.29 0.26 90.82| | 8: 1.87 - 1.79 2789 144 0.86 20.98 1.25 0.26 90.82| | 9: 1.79 - 1.72 2745 138 0.88 18.84 1.24 0.25 55.33| | 10: 1.72 - 1.66 2789 158 0.86 20.30 1.22 0.25 48.22| | 11: 1.66 - 1.61 2740 147 0.85 21.45 1.23 0.25 46.56| | 12: 1.61 - 1.56 2787 146 0.88 18.73 1.24 0.25 29.75| | 13: 1.56 - 1.52 2745 130 0.86 20.64 1.24 0.25 29.75| | 14: 1.52 - 1.48 2803 134 0.86 20.93 1.23 0.25 26.46| | 15: 1.48 - 1.45 2738 128 0.87 19.96 1.23 0.25 20.43| | 16: 1.45 - 1.42 2756 161 0.86 21.54 1.23 0.25 20.43| | 17: 1.42 - 1.39 2785 139 0.87 20.72 1.23 0.25 17.49| | 18: 1.39 - 1.36 2741 179 0.87 20.92 1.23 0.25 15.78| | 19: 1.36 - 1.34 2807 134 0.85 22.12 1.21 0.25 15.78| | 20: 1.34 - 1.32 2696 147 0.87 20.91 1.20 0.25 13.19| | 21: 1.32 - 1.30 2785 112 0.86 21.92 1.19 0.24 13.01| | 22: 1.29 - 1.27 2704 152 0.85 22.55 1.22 0.24 12.72| | 23: 1.27 - 1.26 2802 156 0.85 22.48 1.21 0.24 11.29| | 24: 1.26 - 1.24 2744 132 0.85 23.00 1.20 0.24 11.29| | 25: 1.24 - 1.22 2734 148 0.84 23.51 1.20 0.24 10.66| | 26: 1.22 - 1.21 2727 135 0.84 23.95 1.21 0.23 9.96| | 27: 1.21 - 1.19 2814 148 0.83 24.90 1.21 0.23 9.96| | 28: 1.19 - 1.18 2671 147 0.83 24.78 1.18 0.23 9.01| | 29: 1.18 - 1.16 2800 134 0.83 24.81 1.16 0.23 8.66| | 30: 1.16 - 1.15 2740 148 0.82 26.36 1.15 0.23 8.66| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.66 max = 1525.77 mean = 220.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.93 mean = 22.63| |phase err.(test): min = 0.00 max = 89.85 mean = 22.49| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.273 1557 Z= 5.355 Angle : 5.322 17.136 2118 Z= 3.696 Chirality : 0.367 0.974 243 Planarity : 0.032 0.088 284 Dihedral : 13.812 86.433 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 4.35 % Favored : 95.03 % Cbeta Deviations : 32.97 % 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: -2.79 (0.45), residues: 224 helix: -2.86 (0.34), residues: 106 sheet: -2.09 (0.75), residues: 28 loop : -0.04 (0.57), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.083 0.017 ARG A 48 TYR 0.064 0.030 TYR A 141 PHE 0.103 0.044 PHE A 119 HIS 0.073 0.031 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= 0.2605 r_free= 0.1931 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.785659 | | target function (ml) not normalized (work): 232062.075368 | | target function (ml) not normalized (free): 11820.510947 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2564 0.2606 0.1931 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2564 0.2606 0.1931 n_refl.: 87602 remove outliers: r(all,work,free)=0.1975 0.1980 0.1931 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.1999 0.2004 0.1945 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1639 0.1632 0.1765 n_refl.: 87594 remove outliers: r(all,work,free)=0.1638 0.1632 0.1765 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 0.3794 386.428 360.028 0.669 1.003 0.407 11.894-9.307 99.02 97 4 0.1810 613.822 597.327 0.921 1.004 0.390 9.237-7.194 100.00 213 7 0.2154 502.031 490.818 0.955 1.004 0.360 7.162-5.571 100.00 427 22 0.2209 376.746 364.935 0.927 1.004 0.330 5.546-4.326 100.00 867 58 0.1296 517.179 510.956 0.959 1.004 0.230 4.315-3.360 100.00 1859 96 0.1160 491.841 487.941 1.006 1.004 0.199 3.356-2.611 100.00 3867 181 0.1456 323.114 319.407 0.996 1.003 0.043 2.608-2.026 99.99 8198 413 0.1352 214.195 211.981 1.005 1.001 0.000 2.025-1.573 100.00 17313 902 0.1620 104.602 104.014 1.015 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2046 46.385 45.121 1.003 0.996 0.000 1.221-1.150 99.97 13689 708 0.2566 29.226 26.987 0.978 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0455 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1632 r_free=0.1765 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1642 r_free=0.1781 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.078488 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2024.532548 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 0.1753 0.1867 0.0114 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1591 0.1730 0.0139 0.001 0.4 4.8 0.0 0.0 0 0.250 0.1458 0.1631 0.0174 0.002 0.4 4.2 0.0 0.0 0 0.500 0.1384 0.1577 0.0194 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1354 0.1559 0.0205 0.002 0.5 4.2 0.0 0.0 0 1.000 0.1349 0.1554 0.0205 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1295 0.1510 0.0215 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1270 0.1494 0.0224 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1254 0.1481 0.0227 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1247 0.1477 0.0230 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1245 0.1479 0.0234 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1239 0.1474 0.0235 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1233 0.1466 0.0234 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1233 0.1477 0.0244 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1231 0.1469 0.0238 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1229 0.1470 0.0241 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1226 0.1473 0.0246 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1227 0.1481 0.0254 0.007 0.9 3.5 0.5 0.0 0 13.039 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1233 0.1466 0.0234 0.005 0.8 3.8 0.5 0.0 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.33 14.66 2.34 3.013 19.057 2024.533 0.018 12.33 14.66 2.33 2.998 19.057 60.736 0.018 12.39 14.65 2.26 2.668 19.057 253.067 0.018 12.75 15.38 2.63 2.800 19.277 1012.266 0.017 12.67 15.63 2.96 3.184 19.543 2024.533 0.016 12.48 15.51 3.03 3.378 19.681 3036.799 0.016 12.40 15.47 3.08 3.382 19.656 4049.065 0.015 12.34 15.49 3.15 3.343 19.625 5061.331 0.015 12.27 15.41 3.14 3.295 19.586 6073.598 0.015 12.28 15.47 3.19 3.356 19.613 7085.864 0.015 12.21 15.41 3.19 3.313 19.577 8098.130 0.015 12.23 15.53 3.29 3.557 19.702 9110.396 0.015 12.21 15.49 3.28 3.359 19.580 10122.663 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: 253.067 Accepted refinement result: 12.39 14.65 2.26 2.668 19.057 253.067 0.018 Individual atomic B min max mean iso aniso Overall: 9.04 119.44 20.08 3.31 0 1785 Protein: 9.04 114.99 16.99 3.32 0 1519 Water: 11.45 119.44 38.22 N/A 0 258 Other: 19.70 26.61 22.06 N/A 0 8 Chain A: 9.04 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.04 - 20.08 1272 20.08 - 31.12 227 31.12 - 42.16 125 42.16 - 53.20 94 53.20 - 64.24 42 64.24 - 75.28 11 75.28 - 86.32 7 86.32 - 97.36 4 97.36 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1465 r_work=0.1241 r_free=0.1468 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1241 r_free = 0.1468 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1234 r_free = 0.1460 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 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= 0.1234 r_free= 0.1460 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017049 | | target function (ls_wunit_k1) not normalized (work): 1420.171511 | | target function (ls_wunit_k1) not normalized (free): 109.003714 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1245 0.1234 0.1460 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1676 0.1678 0.1682 n_refl.: 87593 remove outliers: r(all,work,free)=0.1676 0.1678 0.1682 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1682 0.1684 0.1686 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1231 0.1450 n_refl.: 87593 remove outliers: r(all,work,free)=0.1241 0.1231 0.1450 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 0.3567 303.807 281.298 0.665 1.002 0.389 11.894-9.307 99.02 97 4 0.1628 482.583 470.826 0.926 1.003 0.382 9.237-7.194 100.00 213 7 0.1917 394.693 388.534 0.962 1.003 0.324 7.162-5.571 100.00 427 22 0.1842 296.195 290.274 0.937 1.003 0.263 5.546-4.326 100.00 867 58 0.1011 406.603 403.719 0.962 1.003 0.204 4.315-3.360 100.00 1859 96 0.0878 386.682 385.524 1.009 1.002 0.180 3.356-2.611 100.00 3867 181 0.1179 254.030 252.897 1.009 1.002 0.090 2.608-2.026 99.99 8198 413 0.1022 168.399 167.684 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1115 82.237 82.431 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1453 36.467 35.970 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2251 22.977 21.462 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0518 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1450 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** Total number of N/Q/H flips: 1 r_work=0.1232 r_free=0.1450 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1450 | n_water=258 | time (s): 1.890 (total time: 1.890) Filter (dist) r_work=0.1243 r_free=0.1447 | n_water=248 | time (s): 21.450 (total time: 23.340) Filter (q & B) r_work=0.1245 r_free=0.1447 | n_water=245 | time (s): 2.670 (total time: 26.010) Compute maps r_work=0.1245 r_free=0.1447 | n_water=245 | time (s): 1.330 (total time: 27.340) Filter (map) r_work=0.1262 r_free=0.1450 | n_water=223 | time (s): 2.670 (total time: 30.010) Find peaks r_work=0.1262 r_free=0.1450 | n_water=223 | time (s): 0.650 (total time: 30.660) Add new water r_work=0.1416 r_free=0.1622 | n_water=437 | time (s): 3.490 (total time: 34.150) Refine new water occ: r_work=0.1322 r_free=0.1482 adp: r_work=0.1233 r_free=0.1427 occ: r_work=0.1245 r_free=0.1410 adp: r_work=0.1209 r_free=0.1396 occ: r_work=0.1212 r_free=0.1385 adp: r_work=0.1201 r_free=0.1384 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1384 r_work=0.1201 r_free=0.1384 | n_water=437 | time (s): 52.620 (total time: 86.770) Filter (q & B) r_work=0.1206 r_free=0.1389 | n_water=423 | time (s): 2.470 (total time: 89.240) Filter (dist only) r_work=0.1206 r_free=0.1388 | n_water=422 | time (s): 35.360 (total time: 124.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.516327 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1496.684855 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1695 0.1797 0.0102 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1556 0.1671 0.0115 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1415 0.1553 0.0138 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1340 0.1493 0.0153 0.002 0.5 5.4 0.0 0.0 0 0.750 0.1320 0.1482 0.0162 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1298 0.1461 0.0163 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1246 0.1434 0.0188 0.002 0.6 4.8 0.5 0.0 0 2.000 0.1227 0.1431 0.0204 0.003 0.6 5.1 0.5 0.0 0 3.000 0.1207 0.1417 0.0210 0.004 0.7 4.8 0.5 0.0 0 4.000 0.1207 0.1417 0.0211 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1205 0.1421 0.0216 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1199 0.1423 0.0224 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1193 0.1417 0.0224 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1191 0.1419 0.0228 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1191 0.1423 0.0232 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1189 0.1423 0.0234 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1189 0.1421 0.0233 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1186 0.1422 0.0235 0.008 0.9 4.2 0.5 0.0 0 13.758 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1417 0.0210 0.004 0.7 4.8 0.5 0.0 0 4.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 14.17 2.10 3.775 21.873 1496.685 0.016 12.07 14.17 2.10 3.775 21.873 44.901 0.016 12.07 14.17 2.10 3.775 21.873 187.086 0.016 12.27 14.62 2.35 3.624 21.879 748.342 0.015 12.19 14.90 2.71 3.484 22.004 1496.685 0.015 12.11 14.99 2.88 3.478 22.049 2245.027 0.014 12.00 14.95 2.95 3.481 22.050 2993.370 0.014 11.89 14.81 2.92 3.473 22.074 3741.712 0.014 11.86 14.76 2.90 3.474 22.186 4490.055 0.014 11.83 14.74 2.91 3.496 22.144 5238.397 0.014 11.80 14.74 2.94 3.502 22.142 5986.739 0.014 11.80 14.79 2.98 3.522 22.190 6735.082 0.014 11.80 14.84 3.05 3.535 22.198 7483.424 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.901 Accepted refinement result: 12.07 14.17 2.10 3.775 21.873 44.901 0.016 Individual atomic B min max mean iso aniso Overall: 9.08 115.03 22.36 3.31 199 1750 Protein: 9.08 115.03 17.03 3.32 0 1519 Water: 11.48 76.69 41.56 N/A 199 223 Other: 19.73 26.65 22.09 N/A 0 8 Chain A: 9.08 115.03 19.40 N/A 0 1750 Chain S: 16.02 60.00 48.34 N/A 199 0 Histogram: Values Number of atoms 9.08 - 19.67 1257 19.67 - 30.27 241 30.27 - 40.86 165 40.86 - 51.46 131 51.46 - 62.05 132 62.05 - 72.65 12 72.65 - 83.24 5 83.24 - 93.84 4 93.84 - 104.43 0 104.43 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1207 r_free=0.1417 r_work=0.1207 r_free=0.1417 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1417 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1418 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 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= 0.1207 r_free= 0.1418 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015414 | | target function (ls_wunit_k1) not normalized (work): 1283.916267 | | target function (ls_wunit_k1) not normalized (free): 97.861211 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1207 0.1418 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1604 0.1601 0.1693 n_refl.: 87593 remove outliers: r(all,work,free)=0.1604 0.1601 0.1693 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1606 0.1603 0.1695 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1206 0.1414 n_refl.: 87593 remove outliers: r(all,work,free)=0.1215 0.1205 0.1414 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 0.3333 299.797 276.549 0.603 1.002 0.350 11.894-9.307 99.02 97 4 0.1647 482.583 478.865 0.921 1.003 0.333 9.237-7.194 100.00 213 7 0.1732 394.693 393.724 0.981 1.003 0.280 7.162-5.571 100.00 427 22 0.1675 296.195 291.486 0.938 1.003 0.240 5.546-4.326 100.00 867 58 0.0907 406.603 403.790 0.958 1.003 0.195 4.315-3.360 100.00 1859 96 0.0811 386.682 385.652 1.005 1.002 0.190 3.356-2.611 100.00 3867 181 0.1099 254.030 252.825 1.011 1.002 0.090 2.608-2.026 99.99 8198 413 0.1013 168.399 167.827 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1123 82.237 82.433 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1473 36.467 35.997 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2269 22.977 21.491 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=0.0172 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1205 r_free=0.1414 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1205 r_free=0.1414 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1205 r_free=0.1414 | n_water=422 | time (s): 1.950 (total time: 1.950) Filter (dist) r_work=0.1204 r_free=0.1416 | n_water=420 | time (s): 35.530 (total time: 37.480) Filter (q & B) r_work=0.1204 r_free=0.1416 | n_water=420 | time (s): 1.170 (total time: 38.650) Compute maps r_work=0.1204 r_free=0.1416 | n_water=420 | time (s): 1.670 (total time: 40.320) Filter (map) r_work=0.1259 r_free=0.1415 | n_water=287 | time (s): 3.360 (total time: 43.680) Find peaks r_work=0.1259 r_free=0.1415 | n_water=287 | time (s): 0.680 (total time: 44.360) Add new water r_work=0.1376 r_free=0.1523 | n_water=465 | time (s): 2.910 (total time: 47.270) Refine new water occ: r_work=0.1273 r_free=0.1433 adp: r_work=0.1274 r_free=0.1434 occ: r_work=0.1250 r_free=0.1406 adp: r_work=0.1249 r_free=0.1408 occ: r_work=0.1233 r_free=0.1385 adp: r_work=0.1227 r_free=0.1386 ADP+occupancy (water only), MIN, final r_work=0.1227 r_free=0.1386 r_work=0.1227 r_free=0.1386 | n_water=465 | time (s): 201.500 (total time: 248.770) Filter (q & B) r_work=0.1231 r_free=0.1389 | n_water=443 | time (s): 3.530 (total time: 252.300) Filter (dist only) r_work=0.1231 r_free=0.1390 | n_water=441 | time (s): 38.180 (total time: 290.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.695638 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 53.014532 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 0.1238 0.1347 0.0109 0.002 0.6 4.5 0.5 0.0 0 0.085 0.1191 0.1314 0.0122 0.003 0.7 3.8 0.5 0.0 0 0.254 0.1174 0.1306 0.0132 0.004 0.8 3.2 0.5 0.0 0 0.509 0.1167 0.1304 0.0137 0.005 0.9 3.5 0.5 0.0 0 0.763 0.1162 0.1306 0.0144 0.006 0.9 3.5 0.5 0.0 0 1.017 0.1159 0.1307 0.0148 0.006 1.0 3.2 0.5 0.0 0 1.272 0.1157 0.1309 0.0152 0.007 1.0 3.2 0.5 0.0 0 1.526 0.1156 0.1310 0.0154 0.008 1.1 3.5 0.5 0.0 0 1.780 0.1166 0.1306 0.0140 0.005 0.9 3.5 0.5 0.0 0 0.848 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1167 0.1304 0.0137 0.005 0.9 3.5 0.5 0.0 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.67 13.04 1.37 3.779 21.301 53.015 3.625 11.67 13.04 1.37 3.779 21.301 1.590 3.625 11.69 13.04 1.35 3.747 21.301 6.627 3.625 11.72 13.14 1.42 3.715 21.284 26.507 3.619 11.70 13.24 1.54 3.738 21.256 53.015 3.618 11.64 13.22 1.58 3.757 21.248 79.522 3.612 11.60 13.20 1.60 3.773 21.240 106.029 3.608 11.56 13.19 1.62 3.788 21.235 132.536 3.605 11.55 13.20 1.65 3.806 21.225 159.044 3.604 11.53 13.15 1.62 3.814 21.220 185.551 3.601 11.51 13.12 1.61 3.822 21.220 212.058 3.599 11.52 13.14 1.63 3.831 21.219 238.565 3.600 11.51 13.13 1.63 3.839 21.219 265.073 3.599 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.590 Accepted refinement result: 11.67 13.04 1.37 3.779 21.301 1.590 3.625 Individual atomic B min max mean iso aniso Overall: 9.09 115.04 21.30 3.31 222 1746 Protein: 9.09 115.04 17.04 3.32 0 1519 Water: 11.49 76.70 35.99 N/A 222 219 Other: 19.74 26.66 22.10 N/A 0 8 Chain A: 9.09 115.04 19.37 N/A 0 1746 Chain S: 16.03 60.01 36.50 N/A 222 0 Histogram: Values Number of atoms 9.09 - 19.68 1260 19.68 - 30.28 288 30.28 - 40.87 209 40.87 - 51.47 130 51.47 - 62.06 58 62.06 - 72.66 12 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1167 r_free=0.1304 r_work=0.1167 r_free=0.1304 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1167 r_free = 0.1304 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1159 r_free = 0.1309 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1159 r_free= 0.1309 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.619332 | | target function (ml) not normalized (work): 301468.674928 | | target function (ml) not normalized (free): 15854.730860 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1167 0.1159 0.1309 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1509 0.1508 0.1545 n_refl.: 87590 remove outliers: r(all,work,free)=0.1509 0.1508 0.1545 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1508 0.1507 0.1544 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1163 0.1156 0.1307 n_refl.: 87590 remove outliers: r(all,work,free)=0.1161 0.1153 0.1307 n_refl.: 87584 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3792 291.707 270.198 0.515 1.001 0.330 11.894-9.307 99.02 97 4 0.2261 482.583 472.370 0.889 1.002 0.330 9.237-7.194 98.18 209 7 0.2212 386.172 387.221 0.957 1.003 0.240 7.162-5.571 100.00 427 22 0.2121 296.195 285.034 0.918 1.003 0.207 5.546-4.326 100.00 867 58 0.1107 406.603 401.317 0.965 1.003 0.166 4.315-3.360 100.00 1859 96 0.0927 386.682 384.044 1.005 1.002 0.147 3.356-2.611 100.00 3867 181 0.1149 254.030 251.801 1.008 1.002 0.053 2.608-2.026 99.99 8198 413 0.0947 168.399 167.552 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0915 82.237 82.505 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1275 36.467 36.039 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2172 22.977 21.509 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0158 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1153 r_free=0.1307 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=0.1153 r_free=0.1307 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1153 r_free=0.1307 | n_water=441 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1155 r_free=0.1305 | n_water=439 | time (s): 48.550 (total time: 50.970) Filter (q & B) r_work=0.1156 r_free=0.1306 | n_water=438 | time (s): 3.800 (total time: 54.770) Compute maps r_work=0.1156 r_free=0.1306 | n_water=438 | time (s): 1.830 (total time: 56.600) Filter (map) r_work=0.1174 r_free=0.1306 | n_water=328 | time (s): 3.880 (total time: 60.480) Find peaks r_work=0.1174 r_free=0.1306 | n_water=328 | time (s): 0.670 (total time: 61.150) Add new water r_work=0.1252 r_free=0.1402 | n_water=485 | time (s): 3.560 (total time: 64.710) Refine new water occ: r_work=0.1182 r_free=0.1341 adp: r_work=0.1183 r_free=0.1344 occ: r_work=0.1166 r_free=0.1323 adp: r_work=0.1166 r_free=0.1325 occ: r_work=0.1153 r_free=0.1307 adp: r_work=0.1150 r_free=0.1307 ADP+occupancy (water only), MIN, final r_work=0.1150 r_free=0.1307 r_work=0.1150 r_free=0.1307 | n_water=485 | time (s): 223.730 (total time: 288.440) Filter (q & B) r_work=0.1157 r_free=0.1310 | n_water=448 | time (s): 3.920 (total time: 292.360) Filter (dist only) r_work=0.1164 r_free=0.1306 | n_water=446 | time (s): 45.720 (total time: 338.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.780159 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.025129 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 0.1220 0.1346 0.0125 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1181 0.1316 0.0135 0.003 0.7 3.2 0.5 0.0 0 0.267 0.1167 0.1309 0.0142 0.004 0.9 3.5 0.5 0.0 0 0.534 0.1161 0.1311 0.0150 0.006 0.9 3.8 0.5 0.0 0 0.801 0.1157 0.1302 0.0145 0.007 1.0 4.2 0.5 0.0 0 1.068 0.1154 0.1307 0.0152 0.007 1.0 3.5 0.5 0.0 0 1.335 0.1152 0.1308 0.0156 0.008 1.1 3.8 0.5 0.0 0 1.602 0.1151 0.1308 0.0157 0.008 1.1 3.8 0.5 0.0 0 1.869 0.1159 0.1307 0.0148 0.006 1.0 3.8 0.5 0.0 0 0.890 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1157 0.1302 0.0145 0.007 1.0 4.2 0.5 0.0 0 1.068 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 13.02 1.45 3.780 21.244 36.025 3.617 11.57 13.02 1.45 3.780 21.244 1.081 3.617 11.57 13.02 1.45 3.780 21.244 4.503 3.617 11.61 13.08 1.46 3.708 21.237 18.013 3.612 11.64 13.19 1.55 3.729 21.219 36.025 3.613 11.58 13.16 1.59 3.745 21.210 54.038 3.608 11.57 13.21 1.64 3.760 21.196 72.050 3.607 11.54 13.20 1.66 3.771 21.193 90.063 3.604 11.52 13.19 1.67 3.780 21.191 108.075 3.602 11.54 13.25 1.71 3.793 21.180 126.088 3.602 11.51 13.22 1.71 3.803 21.178 144.101 3.600 11.49 13.21 1.72 3.811 21.179 162.113 3.599 11.48 13.20 1.72 3.819 21.177 180.126 3.599 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.081 Accepted refinement result: 11.57 13.02 1.45 3.780 21.244 1.081 3.617 Individual atomic B min max mean iso aniso Overall: 9.08 115.03 21.20 3.31 230 1743 Protein: 9.08 115.03 17.03 3.32 0 1519 Water: 11.49 76.70 35.40 N/A 230 216 Other: 19.74 26.65 22.10 N/A 0 8 Chain A: 9.08 115.03 19.36 N/A 0 1743 Chain S: 16.03 60.01 35.21 N/A 230 0 Histogram: Values Number of atoms 9.08 - 19.68 1261 19.68 - 30.27 289 30.27 - 40.87 219 40.87 - 51.46 131 51.46 - 62.06 50 62.06 - 72.65 12 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1157 r_free=0.1302 r_work=0.1157 r_free=0.1302 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1157 r_free = 0.1302 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1152 r_free = 0.1300 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1152 r_free= 0.1300 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.614544 | | target function (ml) not normalized (work): 301048.171690 | | target function (ml) not normalized (free): 15844.527280 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1160 0.1152 0.1300 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1502 0.1502 0.1521 n_refl.: 87584 remove outliers: r(all,work,free)=0.1502 0.1502 0.1521 n_refl.: 87584 overall B=-0.00 to atoms: r(all,work,free)=0.1501 0.1502 0.1521 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1150 0.1295 n_refl.: 87584 remove outliers: r(all,work,free)=0.1155 0.1148 0.1295 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3822 296.516 255.325 0.466 1.000 0.314 11.894-9.307 95.10 93 4 0.2362 469.730 458.790 0.864 1.001 0.244 9.237-7.194 98.18 209 7 0.2452 386.172 378.584 0.924 1.001 0.180 7.162-5.571 100.00 427 22 0.2145 296.195 285.338 0.914 1.001 0.180 5.546-4.326 100.00 867 58 0.1152 406.603 400.975 0.962 1.002 0.130 4.315-3.360 100.00 1859 96 0.0932 386.682 384.599 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1126 254.030 252.219 1.010 1.002 0.040 2.608-2.026 99.99 8198 413 0.0931 168.399 167.807 1.023 1.002 0.000 2.025-1.573 100.00 17313 902 0.0903 82.237 82.608 1.033 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1262 36.467 36.069 1.023 1.001 0.000 1.221-1.150 99.97 13689 708 0.2170 22.977 21.440 0.979 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0032 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1148 r_free=0.1295 After: r_work=0.1149 r_free=0.1295 ================================== NQH flips ================================== r_work=0.1149 r_free=0.1295 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=0.1149 r_free=0.1295 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1149 r_free=0.1295 | n_water=446 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1149 r_free=0.1296 | n_water=445 | time (s): 49.230 (total time: 51.570) Filter (q & B) r_work=0.1149 r_free=0.1297 | n_water=444 | time (s): 3.800 (total time: 55.370) Compute maps r_work=0.1149 r_free=0.1297 | n_water=444 | time (s): 1.670 (total time: 57.040) Filter (map) r_work=0.1172 r_free=0.1308 | n_water=350 | time (s): 3.560 (total time: 60.600) Find peaks r_work=0.1172 r_free=0.1308 | n_water=350 | time (s): 0.680 (total time: 61.280) Add new water r_work=0.1222 r_free=0.1360 | n_water=483 | time (s): 3.780 (total time: 65.060) Refine new water occ: r_work=0.1171 r_free=0.1301 adp: r_work=0.1171 r_free=0.1302 occ: r_work=0.1159 r_free=0.1289 adp: r_work=0.1158 r_free=0.1289 occ: r_work=0.1150 r_free=0.1281 adp: r_work=0.1146 r_free=0.1279 ADP+occupancy (water only), MIN, final r_work=0.1146 r_free=0.1279 r_work=0.1146 r_free=0.1279 | n_water=483 | time (s): 232.400 (total time: 297.460) Filter (q & B) r_work=0.1151 r_free=0.1291 | n_water=459 | time (s): 3.770 (total time: 301.230) Filter (dist only) r_work=0.1151 r_free=0.1291 | n_water=458 | time (s): 47.530 (total time: 348.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.674767 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.788716 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 0.1347 0.0105 0.003 0.7 6.7 0.0 0.0 0 0.084 0.1183 0.1308 0.0125 0.004 0.8 6.4 0.0 0.0 0 0.251 0.1160 0.1296 0.0136 0.005 0.9 7.0 0.5 0.0 0 0.502 0.1153 0.1292 0.0139 0.006 1.0 6.4 0.5 0.0 0 0.754 0.1151 0.1291 0.0140 0.006 1.0 6.4 0.5 0.0 0 1.005 0.1150 0.1291 0.0141 0.007 1.0 6.4 0.5 0.0 0 1.256 0.1149 0.1291 0.0142 0.007 1.0 6.4 0.5 0.0 0 1.507 0.1147 0.1291 0.0143 0.008 1.1 6.4 0.5 0.0 0 1.759 0.1152 0.1292 0.0140 0.006 1.0 6.4 0.5 0.0 0 0.837 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1147 0.1291 0.0143 0.008 1.1 6.4 0.5 0.0 0 1.759 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.47 12.91 1.43 3.779 21.270 48.789 3.609 11.47 12.91 1.43 3.779 21.270 1.464 3.609 11.48 12.90 1.42 3.763 21.270 6.099 3.609 11.53 12.96 1.43 3.712 21.257 24.394 3.605 11.49 13.00 1.51 3.738 21.243 48.789 3.602 11.46 13.04 1.58 3.761 21.227 73.183 3.599 11.41 13.02 1.60 3.774 21.225 97.577 3.595 11.41 13.05 1.64 3.785 21.220 121.972 3.593 11.41 13.07 1.66 3.803 21.211 146.366 3.593 11.38 13.04 1.66 3.815 21.210 170.761 3.591 11.36 13.01 1.65 3.821 21.210 195.155 3.589 11.34 13.00 1.66 3.827 21.211 219.549 3.587 11.34 13.00 1.66 3.832 21.212 243.944 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: 6.099 Accepted refinement result: 11.48 12.90 1.42 3.763 21.270 6.099 3.609 Individual atomic B min max mean iso aniso Overall: 9.10 114.84 21.25 3.26 244 1741 Protein: 9.10 114.84 17.03 3.26 0 1519 Water: 11.50 76.69 35.25 N/A 244 214 Other: 19.70 26.59 22.09 N/A 0 8 Chain A: 9.10 114.84 19.31 N/A 0 1741 Chain S: 16.00 60.00 35.15 N/A 244 0 Histogram: Values Number of atoms 9.10 - 19.67 1260 19.67 - 30.25 301 30.25 - 40.82 218 40.82 - 51.40 130 51.40 - 61.97 54 61.97 - 72.54 11 72.54 - 83.12 5 83.12 - 93.69 4 93.69 - 104.27 0 104.27 - 114.84 2 =========================== Idealize ADP of riding H ========================== r_work=0.1148 r_free=0.1290 r_work=0.1148 r_free=0.1290 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1148 r_free = 0.1290 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1144 r_free = 0.1289 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1144 r_free= 0.1289 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607091 | | target function (ml) not normalized (work): 300405.792761 | | target function (ml) not normalized (free): 15806.887080 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1354 0.1316 5.6703 5.5804| | 2: 3.57 - 2.84 1.00 2888 124 0.1067 0.1425 5.1571 5.2294| | 3: 2.83 - 2.48 1.00 2820 163 0.1116 0.1196 4.9433 4.9587| | 4: 2.47 - 2.25 1.00 2825 136 0.0921 0.0992 4.631 4.6505| | 5: 2.25 - 2.09 1.00 2756 127 0.0888 0.0961 4.5758 4.6293| | 6: 2.09 - 1.97 1.00 2846 113 0.0874 0.1027 4.2712 4.3694| | 7: 1.97 - 1.87 1.00 2787 165 0.0898 0.1132 3.9905 4.1072| | 8: 1.87 - 1.79 1.00 2789 144 0.0927 0.1118 3.9008 4.0068| | 9: 1.79 - 1.72 1.00 2745 138 0.0881 0.1216 3.6551 3.8255| | 10: 1.72 - 1.66 1.00 2831 160 0.0930 0.1187 3.5736 3.7208| | 11: 1.66 - 1.61 1.00 2712 147 0.0881 0.1049 3.5035 3.5774| | 12: 1.61 - 1.56 1.00 2773 144 0.0916 0.1137 3.3382 3.4587| | 13: 1.56 - 1.52 1.00 2745 130 0.0959 0.1046 3.3154 3.4005| | 14: 1.52 - 1.48 1.00 2803 134 0.0990 0.1052 3.2441 3.3254| | 15: 1.48 - 1.45 1.00 2738 128 0.1007 0.1230 3.1555 3.2576| | 16: 1.45 - 1.42 1.00 2756 161 0.1058 0.1261 3.1351 3.2373| | 17: 1.42 - 1.39 1.00 2785 139 0.1149 0.1288 3.1214 3.2235| | 18: 1.39 - 1.36 1.00 2741 179 0.1199 0.1316 3.1037 3.2357| | 19: 1.36 - 1.34 1.00 2807 134 0.1265 0.1557 3.1136 3.2657| | 20: 1.34 - 1.32 1.00 2696 147 0.1364 0.1477 3.1124 3.1592| | 21: 1.32 - 1.30 1.00 2785 112 0.1467 0.1523 3.1132 3.1149| | 22: 1.29 - 1.27 1.00 2704 152 0.1564 0.1973 3.124 3.2947| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1781 3.134 3.1965| | 24: 1.26 - 1.24 1.00 2744 132 0.1702 0.1829 3.1261 3.2284| | 25: 1.24 - 1.22 1.00 2733 148 0.1873 0.2159 3.1413 3.2698| | 26: 1.22 - 1.21 1.00 2727 135 0.1914 0.1778 3.1492 3.2044| | 27: 1.21 - 1.19 1.00 2814 148 0.2079 0.2156 3.172 3.1577| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2289 3.1649 3.1694| | 29: 1.18 - 1.16 1.00 2800 134 0.2260 0.2362 3.1469 3.2241| | 30: 1.16 - 1.15 1.00 2739 148 0.2443 0.2436 3.1434 3.1663| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2920 171 0.95 8.39 1.00 0.97 5586.87| | 2: 3.57 - 2.84 2888 124 0.93 12.28 1.01 0.97 5586.87| | 3: 2.83 - 2.48 2820 163 0.90 16.24 0.99 0.97 4672.59| | 4: 2.47 - 2.25 2825 136 0.92 13.35 1.00 0.98 2314.95| | 5: 2.25 - 2.09 2756 127 0.91 15.40 1.01 0.98 2314.95| | 6: 2.09 - 1.97 2846 113 0.93 12.31 1.02 0.98 1346.25| | 7: 1.97 - 1.87 2787 165 0.95 9.40 1.02 0.98 520.08| | 8: 1.87 - 1.79 2789 144 0.93 12.72 1.00 0.98 520.08| | 9: 1.79 - 1.72 2745 138 0.94 10.16 0.98 0.97 293.29| | 10: 1.72 - 1.66 2831 160 0.94 11.19 0.98 0.97 247.87| | 11: 1.66 - 1.61 2712 147 0.93 11.86 0.98 0.97 237.41| | 12: 1.61 - 1.56 2773 144 0.95 8.97 0.99 0.97 138.74| | 13: 1.56 - 1.52 2745 130 0.95 10.50 1.03 0.97 138.74| | 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 9.91 1.02 0.99 97.88| | 16: 1.45 - 1.42 2756 161 0.94 11.12 1.02 0.99 97.88| | 17: 1.42 - 1.39 2785 139 0.95 10.91 1.01 0.99 89.05| | 18: 1.39 - 1.36 2741 179 0.94 11.54 1.01 0.99 83.94| | 19: 1.36 - 1.34 2807 134 0.94 11.89 1.00 0.99 83.94| | 20: 1.34 - 1.32 2696 147 0.94 12.12 0.99 0.97 80.05| | 21: 1.32 - 1.30 2785 112 0.94 13.10 0.98 0.97 79.78| | 22: 1.29 - 1.27 2704 152 0.93 13.66 0.98 0.96 80.18| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.97 0.95 82.19| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.95 82.19| | 25: 1.24 - 1.22 2733 148 0.91 16.31 0.96 0.94 84.07| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.03 0.94 86.15| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.03 0.94 86.15| | 28: 1.19 - 1.18 2671 147 0.88 20.31 1.01 0.93 89.44| | 29: 1.18 - 1.16 2800 134 0.88 20.40 0.99 0.93 90.68| | 30: 1.16 - 1.15 2739 148 0.86 21.90 0.98 0.93 90.68| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.78 max = 5586.87 mean = 868.75| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.85 mean = 13.42| |phase err.(test): min = 0.00 max = 89.41 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1151 0.1144 0.1289 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1473 0.1473 0.1511 n_refl.: 87578 remove outliers: r(all,work,free)=0.1473 0.1473 0.1511 n_refl.: 87578 overall B=-0.00 to atoms: r(all,work,free)=0.1473 0.1472 0.1510 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1151 0.1144 0.1288 n_refl.: 87578 remove outliers: r(all,work,free)=0.1148 0.1141 0.1288 n_refl.: 87571 ======================== 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 0.3842 288.358 259.022 0.455 0.998 0.297 11.894-9.307 93.14 91 4 0.2310 474.768 456.030 0.850 1.000 0.218 9.237-7.194 96.82 206 7 0.2333 387.884 377.519 0.918 1.001 0.160 7.162-5.571 100.00 427 22 0.2231 296.195 284.878 0.901 1.001 0.130 5.546-4.326 100.00 867 58 0.1116 406.603 401.150 0.964 1.001 0.130 4.315-3.360 100.00 1859 96 0.0934 386.682 384.622 1.004 1.002 0.130 3.356-2.611 100.00 3867 181 0.1114 254.030 252.354 1.010 1.002 0.050 2.608-2.026 99.99 8198 413 0.0931 168.399 167.819 1.025 1.002 0.000 2.025-1.573 100.00 17313 902 0.0899 82.237 82.618 1.034 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.467 36.077 1.024 1.001 0.000 1.221-1.150 99.97 13689 708 0.2167 22.977 21.453 0.981 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0119 ================= 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 : 0.2605 0.1931 0.081 5.322 8.8 119.3 19.9 258 0.000 1_bss: 0.1632 0.1765 0.081 5.322 9.0 119.5 20.1 258 0.000 1_settarget: 0.1632 0.1765 0.081 5.322 9.0 119.5 20.1 258 0.000 1_nqh: 0.1642 0.1781 0.081 5.322 9.0 119.5 20.1 258 0.007 1_weight: 0.1642 0.1781 0.081 5.322 9.0 119.5 20.1 258 0.007 1_xyzrec: 0.1233 0.1466 0.005 0.819 9.0 119.5 20.1 258 0.138 1_adp: 0.1239 0.1465 0.005 0.819 9.0 119.4 20.1 258 0.138 1_regHadp: 0.1241 0.1468 0.005 0.819 9.0 119.4 20.1 258 0.138 1_occ: 0.1234 0.1460 0.005 0.819 9.0 119.4 20.1 258 0.138 2_bss: 0.1231 0.1450 0.005 0.819 9.1 119.5 20.1 258 0.138 2_settarget: 0.1231 0.1450 0.005 0.819 9.1 119.5 20.1 258 0.138 2_updatecdl: 0.1231 0.1450 0.005 0.841 9.1 119.5 20.1 258 0.138 2_nqh: 0.1232 0.1450 0.005 0.841 9.1 119.5 20.1 258 0.134 2_sol: 0.1206 0.1388 0.005 0.841 9.1 115.0 22.4 422 n/a 2_weight: 0.1206 0.1388 0.005 0.841 9.1 115.0 22.4 422 n/a 2_xyzrec: 0.1207 0.1417 0.004 0.668 9.1 115.0 22.4 422 n/a 2_adp: 0.1207 0.1417 0.004 0.668 9.1 115.0 22.4 422 n/a 2_regHadp: 0.1207 0.1417 0.004 0.668 9.1 115.0 22.4 422 n/a 2_occ: 0.1207 0.1418 0.004 0.668 9.1 115.0 22.4 422 n/a 3_bss: 0.1205 0.1414 0.004 0.668 9.1 115.0 22.4 422 n/a 3_settarget: 0.1205 0.1414 0.004 0.668 9.1 115.0 22.4 422 n/a 3_updatecdl: 0.1205 0.1414 0.004 0.669 9.1 115.0 22.4 422 n/a 3_nqh: 0.1205 0.1414 0.004 0.669 9.1 115.0 22.4 422 n/a 3_sol: 0.1231 0.1390 0.004 0.669 9.1 115.0 21.3 441 n/a 3_weight: 0.1231 0.1390 0.004 0.669 9.1 115.0 21.3 441 n/a 3_xyzrec: 0.1167 0.1304 0.005 0.893 9.1 115.0 21.3 441 n/a 3_adp: 0.1167 0.1304 0.005 0.893 9.1 115.0 21.3 441 n/a 3_regHadp: 0.1167 0.1304 0.005 0.893 9.1 115.0 21.3 441 n/a 3_occ: 0.1159 0.1309 0.005 0.893 9.1 115.0 21.3 441 n/a 4_bss: 0.1153 0.1307 0.005 0.893 9.1 115.0 21.3 441 n/a 4_settarget: 0.1153 0.1307 0.005 0.893 9.1 115.0 21.3 441 n/a 4_updatecdl: 0.1153 0.1307 0.005 0.895 9.1 115.0 21.3 441 n/a 4_nqh: 0.1153 0.1307 0.005 0.895 9.1 115.0 21.3 441 n/a 4_sol: 0.1164 0.1306 0.005 0.895 9.1 115.0 21.2 446 n/a 4_weight: 0.1164 0.1306 0.005 0.895 9.1 115.0 21.2 446 n/a 4_xyzrec: 0.1157 0.1302 0.007 1.001 9.1 115.0 21.2 446 n/a 4_adp: 0.1157 0.1302 0.007 1.001 9.1 115.0 21.2 446 n/a 4_regHadp: 0.1157 0.1302 0.007 1.001 9.1 115.0 21.2 446 n/a 4_occ: 0.1152 0.1300 0.007 1.001 9.1 115.0 21.2 446 n/a 5_bss: 0.1148 0.1295 0.007 1.001 9.1 115.0 21.2 446 n/a 5_settarget: 0.1148 0.1295 0.007 1.001 9.1 115.0 21.2 446 n/a 5_updatecdl: 0.1148 0.1295 0.007 1.001 9.1 115.0 21.2 446 n/a 5_setrh: 0.1149 0.1295 0.007 1.001 9.1 115.0 21.2 446 n/a 5_nqh: 0.1149 0.1295 0.007 1.001 9.1 115.0 21.2 446 n/a 5_sol: 0.1151 0.1291 0.007 1.001 9.1 115.0 21.3 458 n/a 5_weight: 0.1151 0.1291 0.007 1.001 9.1 115.0 21.3 458 n/a 5_xyzrec: 0.1147 0.1291 0.008 1.066 9.1 115.0 21.3 458 n/a 5_adp: 0.1148 0.1290 0.008 1.066 9.1 114.8 21.3 458 n/a 5_regHadp: 0.1148 0.1290 0.008 1.066 9.1 114.8 21.3 458 n/a 5_occ: 0.1144 0.1289 0.008 1.066 9.1 114.8 21.3 458 n/a end: 0.1141 0.1288 0.008 1.066 9.1 114.8 21.2 458 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6017437_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6017437_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8100 Refinement macro-cycles (run) : 13431.9000 Write final files (write_after_run_outputs) : 94.4000 Total : 13530.1100 Total CPU time: 3.77 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:07:13 PST -0800 (1735366033.42 s) Start R-work = 0.1632, R-free = 0.1765 Final R-work = 0.1141, R-free = 0.1288 =============================================================================== Job complete usr+sys time: 13721.87 seconds wall clock time: 251 minutes 35.15 seconds (15095.15 seconds total)