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_8540717.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8540717.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8540717.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.89, per 1000 atoms: 0.56 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: 0.52 Conformation dependent library (CDL) restraints added in 193.0 milliseconds Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 0.94: 683 0.94 - 1.19: 987 1.19 - 1.44: 673 1.44 - 1.69: 784 1.69 - 1.94: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " ideal model delta sigma weight residual 1.326 1.116 0.210 1.10e-02 8.26e+03 3.65e+02 bond pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 1.450 1.657 -0.207 1.16e-02 7.43e+03 3.19e+02 bond pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta sigma weight residual 1.540 1.335 0.205 1.17e-02 7.31e+03 3.06e+02 bond pdb=" C GLU A 147 " pdb=" N LYS A 148 " ideal model delta sigma weight residual 1.332 1.113 0.219 1.26e-02 6.30e+03 3.01e+02 bond pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " ideal model delta sigma weight residual 1.354 1.164 0.190 1.10e-02 8.26e+03 3.00e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 2885 4.09 - 8.18: 1796 8.18 - 12.26: 829 12.26 - 16.35: 224 16.35 - 20.44: 43 Bond angle restraints: 5777 Sorted by residual: angle pdb=" N PRO A 54 " pdb=" CA PRO A 54 " pdb=" CB PRO A 54 " ideal model delta sigma weight residual 103.32 115.71 -12.39 8.40e-01 1.42e+00 2.18e+02 angle pdb=" CA VAL A 177 " pdb=" C VAL A 177 " pdb=" O VAL A 177 " ideal model delta sigma weight residual 121.17 106.15 15.02 1.06e+00 8.90e-01 2.01e+02 angle pdb=" O AGLN A 80 " pdb=" C AGLN A 80 " pdb=" N ASN A 81 " ideal model delta sigma weight residual 122.12 107.19 14.93 1.06e+00 8.90e-01 1.99e+02 angle pdb=" CA ASP A 55 " pdb=" C ASP A 55 " pdb=" O ASP A 55 " ideal model delta sigma weight residual 119.97 136.10 -16.13 1.15e+00 7.56e-01 1.97e+02 angle pdb=" CA LYS A 32 " pdb=" C LYS A 32 " pdb=" O LYS A 32 " ideal model delta sigma weight residual 120.54 134.83 -14.29 1.04e+00 9.25e-01 1.89e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 956 17.47 - 34.93: 96 34.93 - 52.40: 43 52.40 - 69.87: 14 69.87 - 87.33: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CD2ATYR A 67 " pdb=" CG ATYR A 67 " pdb=" CD1ATYR A 67 " pdb=" HD1ATYR A 67 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+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 -157.90 -22.10 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 89 0.183 - 0.366: 76 0.366 - 0.549: 44 0.549 - 0.731: 25 0.731 - 0.914: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB THR A 154 " pdb=" CA THR A 154 " pdb=" OG1 THR A 154 " pdb=" CG2 THR A 154 " both_signs ideal model delta sigma weight residual False 2.55 1.64 0.91 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -1.74 -0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -3.46 0.83 2.00e-01 2.50e+01 1.73e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.059 2.00e-02 2.50e+03 6.38e-02 1.22e+02 pdb=" CG BTYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.045 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.113 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.091 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.009 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.049 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.033 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.036 2.00e-02 2.50e+03 5.87e-02 1.03e+02 pdb=" CG PHE A 162 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.065 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.073 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.079 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.099 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.037 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 162 " 0.050 2.00e-02 2.50e+03 1.00e-01 1.00e+02 pdb=" C PHE A 162 " -0.173 2.00e-02 2.50e+03 pdb=" O PHE A 162 " 0.063 2.00e-02 2.50e+03 pdb=" N GLU A 163 " 0.060 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 641 2.26 - 2.84: 7707 2.84 - 3.43: 10608 3.43 - 4.01: 15403 4.01 - 4.60: 22229 Nonbonded interactions: 56588 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.671 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.797 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.799 1.850 nonbonded pdb="HH22 ARG A 5 " pdb=" O AGLU A 64 " model vdw 1.844 1.850 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.851 1.850 ... (remaining 56583 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_8540717_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= 0.2599 r_free= 0.1899 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787754 | | target function (ml) not normalized (work): 232236.593515 | | target function (ml) not normalized (free): 11767.052801 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3026 0.1987 7.1067 4.9352| | 2: 3.57 - 2.84 1.00 2876 122 0.2417 0.1770 4.3398 4.3347| | 3: 2.84 - 2.48 1.00 2833 165 0.2357 0.1640 4.1226 4.1399| | 4: 2.47 - 2.25 1.00 2825 136 0.2328 0.1420 3.8267 3.8163| | 5: 2.25 - 2.09 1.00 2756 127 0.2467 0.1539 3.7874 3.7969| | 6: 2.09 - 1.97 1.00 2846 113 0.2528 0.1696 3.4712 3.4813| | 7: 1.97 - 1.87 1.00 2787 165 0.2553 0.1905 3.1279 3.2287| | 8: 1.87 - 1.79 1.00 2789 144 0.2454 0.1796 3.0401 3.115| | 9: 1.79 - 1.72 1.00 2745 138 0.2410 0.1656 2.8956 2.836| | 10: 1.72 - 1.66 1.00 2789 158 0.2422 0.2027 2.7827 2.8897| | 11: 1.66 - 1.61 1.00 2740 147 0.2453 0.1731 2.7282 2.7494| | 12: 1.61 - 1.56 1.00 2787 146 0.2538 0.1966 2.6204 2.6268| | 13: 1.56 - 1.52 1.00 2745 130 0.2513 0.2068 2.5494 2.6321| | 14: 1.52 - 1.48 1.00 2803 134 0.2515 0.1836 2.4688 2.4938| | 15: 1.48 - 1.45 1.00 2738 128 0.2558 0.2125 2.4081 2.4917| | 16: 1.45 - 1.42 1.00 2756 161 0.2581 0.1976 2.3764 2.3762| | 17: 1.42 - 1.39 1.00 2785 139 0.2645 0.2233 2.3281 2.3993| | 18: 1.39 - 1.36 1.00 2741 179 0.2644 0.2007 2.2585 2.2839| | 19: 1.36 - 1.34 1.00 2807 134 0.2671 0.2173 2.2467 2.2603| | 20: 1.34 - 1.32 1.00 2696 147 0.2770 0.2270 2.2425 2.1939| | 21: 1.32 - 1.30 1.00 2785 112 0.2744 0.2308 2.1637 2.2233| | 22: 1.29 - 1.27 1.00 2704 152 0.2795 0.2476 2.1495 2.1837| | 23: 1.27 - 1.26 1.00 2802 156 0.2827 0.2441 2.1114 2.1888| | 24: 1.26 - 1.24 1.00 2744 132 0.2816 0.2622 2.0743 2.2204| | 25: 1.24 - 1.22 1.00 2734 148 0.2809 0.2627 2.0449 2.1201| | 26: 1.22 - 1.21 1.00 2727 135 0.2872 0.2325 2.0208 2.0562| | 27: 1.21 - 1.19 1.00 2814 148 0.2951 0.2545 2.0045 1.9886| | 28: 1.19 - 1.18 1.00 2671 147 0.2969 0.2632 1.9832 1.9584| | 29: 1.18 - 1.16 1.00 2800 134 0.2967 0.2645 1.9622 2.0003| | 30: 1.16 - 1.15 1.00 2740 148 0.3081 0.3186 1.9328 2.0075| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.64 0.76 0.23 1452.24| | 2: 3.57 - 2.84 2876 122 0.81 25.86 1.27 0.23 1452.24| | 3: 2.84 - 2.48 2833 165 0.74 31.60 1.24 0.24 1203.74| | 4: 2.47 - 2.25 2825 136 0.82 25.11 1.26 0.25 558.84| | 5: 2.25 - 2.09 2756 127 0.78 28.88 1.29 0.25 558.84| | 6: 2.09 - 1.97 2846 113 0.84 22.34 1.29 0.25 304.55| | 7: 1.97 - 1.87 2787 165 0.90 16.32 1.28 0.26 87.67| | 8: 1.87 - 1.79 2789 144 0.86 20.62 1.25 0.26 87.67| | 9: 1.79 - 1.72 2745 138 0.89 17.74 1.23 0.25 51.78| | 10: 1.72 - 1.66 2789 158 0.87 19.37 1.22 0.25 44.59| | 11: 1.66 - 1.61 2740 147 0.86 20.52 1.24 0.25 43.07| | 12: 1.61 - 1.56 2787 146 0.89 17.75 1.23 0.25 27.72| | 13: 1.56 - 1.52 2745 130 0.87 19.95 1.23 0.25 27.72| | 14: 1.52 - 1.48 2803 134 0.87 20.11 1.23 0.25 24.81| | 15: 1.48 - 1.45 2738 128 0.88 19.50 1.23 0.25 19.47| | 16: 1.45 - 1.42 2756 161 0.87 20.66 1.22 0.25 19.47| | 17: 1.42 - 1.39 2785 139 0.87 20.24 1.22 0.25 16.78| | 18: 1.39 - 1.36 2741 179 0.87 20.77 1.22 0.25 15.22| | 19: 1.36 - 1.34 2807 134 0.86 21.51 1.21 0.25 15.22| | 20: 1.34 - 1.32 2696 147 0.87 20.61 1.21 0.25 12.69| | 21: 1.32 - 1.30 2785 112 0.86 21.46 1.21 0.25 12.52| | 22: 1.29 - 1.27 2704 152 0.85 22.34 1.21 0.25 12.30| | 23: 1.27 - 1.26 2802 156 0.85 22.46 1.22 0.24 11.23| | 24: 1.26 - 1.24 2744 132 0.85 23.03 1.21 0.24 11.23| | 25: 1.24 - 1.22 2734 148 0.84 23.60 1.20 0.24 10.65| | 26: 1.22 - 1.21 2727 135 0.84 24.03 1.20 0.23 10.02| | 27: 1.21 - 1.19 2814 148 0.83 24.84 1.20 0.23 10.02| | 28: 1.19 - 1.18 2671 147 0.83 25.29 1.18 0.23 9.21| | 29: 1.18 - 1.16 2800 134 0.82 25.62 1.15 0.22 8.90| | 30: 1.16 - 1.15 2740 148 0.81 27.27 1.15 0.22 8.90| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 8.90 max = 1452.24 mean = 210.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 22.27| |phase err.(test): min = 0.00 max = 89.48 mean = 22.10| |-----------------------------------------------------------------------------| ----------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 0.227 1557 Z= 5.298 Angle : 5.387 17.599 2118 Z= 3.799 Chirality : 0.356 0.914 243 Planarity : 0.031 0.138 284 Dihedral : 14.041 87.333 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.41 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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: -3.30 (0.45), residues: 224 helix: -3.52 (0.31), residues: 103 sheet: -1.85 (0.65), residues: 40 loop : 0.05 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.020 ARG A 98 TYR 0.102 0.033 TYR A 139 PHE 0.077 0.036 PHE A 164 HIS 0.037 0.016 HIS A 138 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= 0.2599 r_free= 0.1899 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787754 | | target function (ml) not normalized (work): 232236.593515 | | target function (ml) not normalized (free): 11767.052801 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2557 0.2600 0.1899 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2557 0.2600 0.1899 n_refl.: 87602 remove outliers: r(all,work,free)=0.1967 0.1973 0.1899 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.1993 0.2000 0.1915 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1633 0.1628 0.1719 n_refl.: 87594 remove outliers: r(all,work,free)=0.1632 0.1627 0.1719 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 98.94 88 5 0.3806 386.321 361.406 0.677 1.004 0.414 11.894-9.307 98.04 96 4 0.1696 616.143 591.270 0.929 1.004 0.400 9.237-7.194 100.00 213 7 0.2108 501.892 492.926 0.953 1.004 0.339 7.162-5.571 100.00 427 22 0.2198 376.642 364.909 0.933 1.004 0.278 5.546-4.326 100.00 867 58 0.1271 517.037 511.590 0.962 1.004 0.239 4.315-3.360 100.00 1859 96 0.1139 491.706 487.869 1.002 1.003 0.179 3.356-2.611 100.00 3867 181 0.1407 323.025 320.097 0.996 1.003 0.099 2.608-2.026 99.99 8198 413 0.1355 214.136 212.167 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1640 104.573 103.919 1.012 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2054 46.372 45.026 1.003 0.996 0.000 1.221-1.150 99.97 13689 708 0.2599 29.218 26.967 0.974 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0498 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1627 r_free=0.1719 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=0.1627 r_free=0.1719 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.150229 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2031.353142 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 0.1206 0.1448 0.0242 0.007 0.9 3.2 0.5 0.0 0 13.075 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 14.48 2.42 3.013 19.076 2031.353 0.017 12.06 14.48 2.42 3.013 19.076 60.941 0.017 12.13 14.46 2.33 2.686 19.074 253.919 0.017 12.57 15.29 2.72 2.923 19.356 1015.677 0.016 12.36 15.34 2.99 3.200 19.555 2031.353 0.015 12.29 15.41 3.13 3.371 19.668 3047.030 0.015 12.16 15.33 3.17 3.384 19.664 4062.706 0.015 12.06 15.24 3.18 3.221 19.553 5078.383 0.015 12.02 15.22 3.20 3.252 19.566 6094.059 0.015 11.95 15.17 3.21 3.166 19.501 7109.736 0.014 11.95 15.22 3.27 3.264 19.550 8125.413 0.014 12.11 15.53 3.42 3.597 19.722 9141.089 0.014 12.04 15.42 3.38 3.598 19.714 10156.766 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: 253.919 Accepted refinement result: 12.13 14.46 2.33 2.686 19.074 253.919 0.017 Individual atomic B min max mean iso aniso Overall: 9.10 119.47 20.10 3.35 0 1785 Protein: 9.10 115.19 17.01 3.35 0 1519 Water: 11.49 119.47 38.24 N/A 0 258 Other: 19.70 26.62 22.06 N/A 0 8 Chain A: 9.10 119.47 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.10 - 20.13 1272 20.13 - 31.17 228 31.17 - 42.21 125 42.21 - 53.24 94 53.24 - 64.28 41 64.28 - 75.32 11 75.32 - 86.36 7 86.36 - 97.39 4 97.39 - 108.43 1 108.43 - 119.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1213 r_free=0.1446 r_work=0.1215 r_free=0.1450 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1215 r_free = 0.1450 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 = 0.1207 r_free = 0.1444 target_work(ls_wunit_k1) = 0.016 | | 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.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1207 r_free= 0.1444 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.016228 | | target function (ls_wunit_k1) not normalized (work): 1351.740578 | | target function (ls_wunit_k1) not normalized (free): 108.136683 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1207 0.1444 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1661 0.1663 0.1669 n_refl.: 87592 remove outliers: r(all,work,free)=0.1661 0.1663 0.1669 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1666 0.1668 0.1673 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1205 0.1435 n_refl.: 87592 remove outliers: r(all,work,free)=0.1215 0.1204 0.1435 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3549 300.977 281.683 0.646 1.003 0.380 11.894-9.307 98.04 96 4 0.1551 484.104 472.504 0.932 1.003 0.380 9.237-7.194 100.00 213 7 0.1888 394.338 389.442 0.963 1.003 0.326 7.162-5.571 100.00 427 22 0.1822 295.928 290.396 0.936 1.003 0.265 5.546-4.326 100.00 867 58 0.1001 406.237 403.021 0.964 1.003 0.204 4.315-3.360 100.00 1859 96 0.0862 386.334 385.160 1.007 1.002 0.180 3.356-2.611 100.00 3867 181 0.1142 253.801 252.676 1.010 1.002 0.053 2.608-2.026 99.99 8198 413 0.0991 168.247 167.582 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1082 82.163 82.370 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1433 36.434 35.949 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2249 22.956 21.440 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0428 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1204 r_free=0.1435 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=0.1206 r_free=0.1436 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1206 r_free=0.1436 | n_water=258 | time (s): 1.880 (total time: 1.880) Filter (dist) r_work=0.1213 r_free=0.1435 | n_water=252 | time (s): 23.610 (total time: 25.490) Filter (q & B) r_work=0.1216 r_free=0.1434 | n_water=249 | time (s): 3.230 (total time: 28.720) Compute maps r_work=0.1216 r_free=0.1434 | n_water=249 | time (s): 1.170 (total time: 29.890) Filter (map) r_work=0.1226 r_free=0.1437 | n_water=237 | time (s): 3.250 (total time: 33.140) Find peaks r_work=0.1226 r_free=0.1437 | n_water=237 | time (s): 0.520 (total time: 33.660) Add new water r_work=0.1366 r_free=0.1602 | n_water=441 | time (s): 2.400 (total time: 36.060) Refine new water occ: r_work=0.1277 r_free=0.1477 adp: r_work=0.1198 r_free=0.1423 occ: r_work=0.1210 r_free=0.1404 adp: r_work=0.1179 r_free=0.1394 occ: r_work=0.1183 r_free=0.1383 adp: r_work=0.1172 r_free=0.1382 ADP+occupancy (water only), MIN, final r_work=0.1172 r_free=0.1382 r_work=0.1172 r_free=0.1382 | n_water=441 | time (s): 57.050 (total time: 93.110) Filter (q & B) r_work=0.1176 r_free=0.1383 | n_water=425 | time (s): 3.100 (total time: 96.210) Filter (dist only) r_work=0.1177 r_free=0.1382 | n_water=424 | time (s): 36.440 (total time: 132.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.510449 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1451.352347 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1644 0.1769 0.0125 0.001 0.4 6.7 0.0 0.0 0 0.125 0.1541 0.1678 0.0137 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1404 0.1562 0.0158 0.001 0.4 4.8 0.0 0.0 0 0.500 0.1324 0.1498 0.0174 0.001 0.5 4.8 0.0 0.0 0 0.750 0.1298 0.1478 0.0180 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1314 0.1495 0.0181 0.002 0.5 4.2 0.0 0.0 0 1.000 0.1245 0.1447 0.0202 0.002 0.5 3.8 0.5 0.0 0 2.000 0.1219 0.1430 0.0212 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1208 0.1424 0.0217 0.003 0.6 4.8 0.5 0.0 0 4.000 0.1197 0.1417 0.0220 0.004 0.7 5.1 0.5 0.0 0 5.000 0.1191 0.1410 0.0219 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1186 0.1410 0.0225 0.005 0.8 5.1 0.5 0.0 0 7.000 0.1183 0.1406 0.0222 0.005 0.8 5.1 0.5 0.0 0 8.000 0.1182 0.1407 0.0225 0.006 0.8 5.8 0.5 0.0 0 9.000 0.1178 0.1404 0.0226 0.006 0.8 5.8 0.5 0.0 0 10.000 0.1175 0.1404 0.0229 0.007 0.9 6.1 0.5 0.0 0 11.000 0.1175 0.1404 0.0228 0.007 0.9 5.4 0.5 0.6 0 12.000 0.1175 0.1408 0.0233 0.007 0.9 6.4 0.5 0.6 0 13.000 0.1173 0.1405 0.0231 0.008 0.9 5.4 0.5 0.6 0 14.255 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1178 0.1404 0.0226 0.006 0.8 5.8 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.78 14.04 2.26 3.793 21.859 1451.352 0.015 11.78 14.04 2.26 3.793 21.859 43.541 0.015 11.78 14.04 2.26 3.793 21.859 181.419 0.015 12.00 14.51 2.52 3.623 21.875 725.676 0.015 11.99 14.80 2.81 3.453 22.166 1451.352 0.014 11.84 14.72 2.87 3.477 22.262 2177.029 0.014 11.72 14.72 3.00 3.473 22.078 2902.705 0.014 11.63 14.70 3.07 3.509 22.041 3628.381 0.014 11.71 14.77 3.06 3.539 22.322 4354.057 0.013 11.68 14.78 3.10 3.547 22.286 5079.733 0.013 11.58 14.61 3.03 3.530 22.234 5805.409 0.013 11.50 14.64 3.14 3.540 22.173 6531.086 0.013 11.54 14.68 3.15 3.554 22.296 7256.762 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 181.419 Accepted refinement result: 11.78 14.04 2.26 3.793 21.859 181.419 0.015 Individual atomic B min max mean iso aniso Overall: 9.12 115.22 22.32 3.35 187 1764 Protein: 9.12 115.22 17.04 3.35 0 1519 Water: 11.52 79.17 41.26 N/A 187 237 Other: 19.73 26.65 22.09 N/A 0 8 Chain A: 9.12 115.22 19.67 N/A 0 1764 Chain S: 12.54 60.00 47.29 N/A 187 0 Histogram: Values Number of atoms 9.12 - 19.73 1261 19.73 - 30.34 239 30.34 - 40.95 168 40.95 - 51.56 138 51.56 - 62.17 120 62.17 - 72.78 13 72.78 - 83.39 6 83.39 - 94.00 4 94.00 - 104.61 0 104.61 - 115.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1178 r_free=0.1404 r_work=0.1178 r_free=0.1404 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1178 r_free = 0.1404 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1177 r_free = 0.1405 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1177 r_free= 0.1405 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014636 | | target function (ls_wunit_k1) not normalized (work): 1219.080980 | | target function (ls_wunit_k1) not normalized (free): 97.556148 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1188 0.1177 0.1405 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1576 0.1576 0.1613 n_refl.: 87591 remove outliers: r(all,work,free)=0.1576 0.1576 0.1613 n_refl.: 87591 overall B=0.00 to atoms: r(all,work,free)=0.1576 0.1577 0.1613 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1185 0.1174 0.1400 n_refl.: 87591 remove outliers: r(all,work,free)=0.1183 0.1172 0.1400 n_refl.: 87588 ======================== 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 92.71 84 5 0.3198 296.887 277.970 0.611 1.004 0.358 11.894-9.307 98.04 96 4 0.1446 484.104 477.873 0.932 1.004 0.350 9.237-7.194 100.00 213 7 0.1696 394.338 394.235 0.987 1.004 0.280 7.162-5.571 100.00 427 22 0.1576 295.928 292.089 0.934 1.004 0.220 5.546-4.326 100.00 867 58 0.0873 406.237 403.168 0.963 1.003 0.210 4.315-3.360 100.00 1859 96 0.0769 386.334 385.229 1.002 1.003 0.170 3.356-2.611 100.00 3867 181 0.1079 253.801 252.529 1.009 1.002 0.080 2.608-2.026 99.99 8198 413 0.1002 168.247 167.669 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1087 82.163 82.368 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1433 36.434 35.977 1.025 0.998 0.000 1.221-1.150 99.97 13689 708 0.2248 22.956 21.472 0.988 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0055 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1172 r_free=0.1400 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=0.1172 r_free=0.1400 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1172 r_free=0.1400 | n_water=424 | time (s): 2.140 (total time: 2.140) Filter (dist) r_work=0.1173 r_free=0.1400 | n_water=421 | time (s): 35.910 (total time: 38.050) Filter (q & B) r_work=0.1173 r_free=0.1400 | n_water=421 | time (s): 0.910 (total time: 38.960) Compute maps r_work=0.1173 r_free=0.1400 | n_water=421 | time (s): 1.570 (total time: 40.530) Filter (map) r_work=0.1213 r_free=0.1389 | n_water=298 | time (s): 2.630 (total time: 43.160) Find peaks r_work=0.1213 r_free=0.1389 | n_water=298 | time (s): 0.670 (total time: 43.830) Add new water r_work=0.1324 r_free=0.1504 | n_water=483 | time (s): 2.850 (total time: 46.680) Refine new water occ: r_work=0.1234 r_free=0.1424 adp: r_work=0.1235 r_free=0.1426 occ: r_work=0.1211 r_free=0.1402 adp: r_work=0.1209 r_free=0.1403 occ: r_work=0.1194 r_free=0.1386 adp: r_work=0.1188 r_free=0.1385 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1385 r_work=0.1188 r_free=0.1385 | n_water=483 | time (s): 194.540 (total time: 241.220) Filter (q & B) r_work=0.1193 r_free=0.1388 | n_water=451 | time (s): 2.670 (total time: 243.890) Filter (dist only) r_work=0.1193 r_free=0.1387 | n_water=450 | time (s): 36.880 (total time: 280.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.813249 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.646454 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 0.1365 0.0145 0.002 0.6 4.2 0.5 0.0 0 0.091 0.1177 0.1331 0.0154 0.003 0.7 3.5 0.5 0.0 0 0.272 0.1162 0.1321 0.0159 0.004 0.8 3.5 0.5 0.0 0 0.544 0.1153 0.1317 0.0164 0.005 0.9 3.5 0.5 0.0 0 0.816 0.1151 0.1318 0.0168 0.006 1.0 3.5 0.5 0.0 0 1.088 0.1147 0.1317 0.0170 0.007 1.0 4.2 0.5 0.0 0 1.360 0.1146 0.1316 0.0170 0.007 1.1 4.5 0.5 0.0 0 1.632 0.1144 0.1317 0.0173 0.008 1.1 4.5 0.5 0.0 0 1.904 0.1153 0.1316 0.0163 0.006 0.9 3.5 0.5 0.0 0 0.907 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1153 0.1316 0.0163 0.006 0.9 3.5 0.5 0.0 0 0.907 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.53 13.16 1.63 3.796 21.439 47.646 3.619 11.53 13.16 1.63 3.796 21.439 1.429 3.619 11.54 13.16 1.62 3.780 21.439 5.956 3.619 11.61 13.25 1.64 3.720 21.425 23.823 3.615 11.54 13.23 1.69 3.742 21.416 47.646 3.611 11.55 13.29 1.74 3.756 21.388 71.470 3.609 11.49 13.26 1.77 3.772 21.384 95.293 3.605 11.47 13.28 1.80 3.781 21.374 119.116 3.603 11.45 13.28 1.83 3.797 21.365 142.939 3.601 11.41 13.24 1.83 3.804 21.371 166.763 3.599 11.41 13.24 1.83 3.817 21.357 190.586 3.598 11.40 13.25 1.85 3.826 21.355 214.409 3.597 11.38 13.22 1.84 3.830 21.355 238.232 3.596 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.429 Accepted refinement result: 11.53 13.16 1.63 3.796 21.439 1.429 3.619 Individual atomic B min max mean iso aniso Overall: 9.13 115.22 21.55 3.35 215 1762 Protein: 9.13 115.22 17.04 3.35 0 1519 Water: 11.52 79.17 36.76 N/A 215 235 Other: 19.73 26.65 22.09 N/A 0 8 Chain A: 9.13 115.22 19.65 N/A 0 1762 Chain S: 12.55 60.00 37.11 N/A 215 0 Histogram: Values Number of atoms 9.13 - 19.74 1264 19.74 - 30.35 278 30.35 - 40.96 207 40.96 - 51.56 144 51.56 - 62.17 59 62.17 - 72.78 13 72.78 - 83.39 6 83.39 - 94.00 4 94.00 - 104.61 0 104.61 - 115.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1153 r_free=0.1316 r_work=0.1153 r_free=0.1316 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1316 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1144 r_free = 0.1308 target_work(ml) = 3.613 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1144 r_free= 0.1308 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.612543 | | target function (ml) not normalized (work): 300895.935129 | | target function (ml) not normalized (free): 15836.250827 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1152 0.1144 0.1308 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1484 0.1484 0.1515 n_refl.: 87588 remove outliers: r(all,work,free)=0.1484 0.1484 0.1515 n_refl.: 87588 overall B=-0.00 to atoms: r(all,work,free)=0.1484 0.1483 0.1514 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1146 0.1139 0.1296 n_refl.: 87588 remove outliers: r(all,work,free)=0.1143 0.1135 0.1296 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3721 290.239 266.671 0.508 1.002 0.330 11.894-9.307 96.08 94 4 0.2241 484.370 463.025 0.880 1.002 0.283 9.237-7.194 98.64 210 7 0.2172 387.850 388.743 0.963 1.002 0.190 7.162-5.571 100.00 427 22 0.2087 295.928 285.078 0.916 1.003 0.165 5.546-4.326 100.00 867 58 0.1102 406.237 402.468 0.965 1.002 0.160 4.315-3.360 100.00 1859 96 0.0905 386.334 384.501 1.004 1.002 0.140 3.356-2.611 100.00 3867 181 0.1115 253.801 251.942 1.008 1.002 0.100 2.608-2.026 99.99 8198 413 0.0931 168.247 167.526 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0901 82.163 82.469 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1262 36.434 36.026 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.956 21.499 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0127 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1135 r_free=0.1296 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1135 r_free=0.1296 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1135 r_free=0.1296 | n_water=450 | time (s): 2.320 (total time: 2.320) Filter (dist) r_work=0.1135 r_free=0.1294 | n_water=449 | time (s): 37.460 (total time: 39.780) Filter (q & B) r_work=0.1135 r_free=0.1295 | n_water=448 | time (s): 3.210 (total time: 42.990) Compute maps r_work=0.1135 r_free=0.1295 | n_water=448 | time (s): 1.640 (total time: 44.630) Filter (map) r_work=0.1160 r_free=0.1302 | n_water=342 | time (s): 3.440 (total time: 48.070) Find peaks r_work=0.1160 r_free=0.1302 | n_water=342 | time (s): 0.520 (total time: 48.590) Add new water r_work=0.1221 r_free=0.1362 | n_water=502 | time (s): 3.080 (total time: 51.670) Refine new water occ: r_work=0.1157 r_free=0.1316 adp: r_work=0.1157 r_free=0.1317 occ: r_work=0.1143 r_free=0.1305 adp: r_work=0.1142 r_free=0.1305 occ: r_work=0.1131 r_free=0.1294 adp: r_work=0.1128 r_free=0.1294 ADP+occupancy (water only), MIN, final r_work=0.1128 r_free=0.1294 r_work=0.1128 r_free=0.1294 | n_water=502 | time (s): 331.710 (total time: 383.380) Filter (q & B) r_work=0.1135 r_free=0.1292 | n_water=461 | time (s): 4.040 (total time: 387.420) Filter (dist only) r_work=0.1135 r_free=0.1290 | n_water=460 | time (s): 48.460 (total time: 435.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.777362 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.361075 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 0.1187 0.1329 0.0142 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1153 0.1305 0.0152 0.003 0.7 3.5 0.5 0.0 0 0.267 0.1137 0.1292 0.0156 0.005 0.9 4.2 0.5 0.0 0 0.533 0.1131 0.1292 0.0162 0.006 0.9 4.2 0.5 0.0 0 0.800 0.1127 0.1289 0.0161 0.006 1.0 4.5 0.5 0.0 0 1.066 0.1124 0.1291 0.0167 0.007 1.1 4.5 0.5 0.0 0 1.333 0.1122 0.1291 0.0169 0.008 1.1 4.5 0.5 0.0 0 1.600 0.1121 0.1288 0.0167 0.008 1.1 4.5 0.5 0.0 0 1.866 0.1129 0.1291 0.0162 0.006 1.0 4.2 0.5 0.0 0 0.889 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1121 0.1288 0.0167 0.008 1.1 4.5 0.5 0.0 0 1.866 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.21 12.88 1.67 3.796 21.381 43.361 3.599 11.21 12.88 1.67 3.796 21.381 1.301 3.599 11.21 12.88 1.67 3.788 21.381 5.420 3.599 11.28 12.95 1.67 3.721 21.369 21.681 3.596 11.26 12.99 1.72 3.743 21.356 43.361 3.595 11.24 13.02 1.78 3.763 21.337 65.042 3.591 11.21 13.01 1.79 3.774 21.329 86.722 3.588 11.17 12.98 1.81 3.787 21.328 108.403 3.585 11.16 12.99 1.83 3.794 21.324 130.083 3.584 11.12 12.95 1.83 3.800 21.325 151.764 3.581 11.14 13.02 1.88 3.820 21.306 173.444 3.583 11.12 13.00 1.88 3.826 21.304 195.125 3.581 11.12 13.01 1.89 3.834 21.301 216.805 3.580 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.301 Accepted refinement result: 11.21 12.88 1.67 3.796 21.381 1.301 3.599 Individual atomic B min max mean iso aniso Overall: 9.12 115.22 21.45 3.35 225 1762 Protein: 9.12 115.22 17.03 3.35 0 1519 Water: 11.52 79.17 36.01 N/A 225 235 Other: 19.73 26.65 22.08 N/A 0 8 Chain A: 9.12 115.22 19.65 N/A 0 1762 Chain S: 12.54 60.00 35.56 N/A 225 0 Histogram: Values Number of atoms 9.12 - 19.73 1266 19.73 - 30.34 290 30.34 - 40.95 217 40.95 - 51.56 134 51.56 - 62.17 55 62.17 - 72.78 13 72.78 - 83.39 6 83.39 - 94.00 4 94.00 - 104.61 0 104.61 - 115.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1121 r_free=0.1288 r_work=0.1121 r_free=0.1288 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1121 r_free = 0.1288 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1117 r_free = 0.1286 target_work(ml) = 3.597 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1117 r_free= 0.1286 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.597166 | | target function (ml) not normalized (work): 299586.350337 | | target function (ml) not normalized (free): 15798.463317 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1117 0.1286 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1440 0.1437 0.1525 n_refl.: 87580 remove outliers: r(all,work,free)=0.1440 0.1437 0.1525 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1439 0.1436 0.1524 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1124 0.1116 0.1290 n_refl.: 87580 remove outliers: r(all,work,free)=0.1123 0.1114 0.1290 n_refl.: 87576 ======================== 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 0.3797 288.098 257.401 0.454 1.000 0.290 11.894-9.307 95.10 93 4 0.2426 485.617 465.389 0.880 1.002 0.269 9.237-7.194 98.18 209 7 0.2214 385.824 383.997 0.938 1.002 0.151 7.162-5.571 100.00 427 22 0.2091 295.928 285.978 0.918 1.002 0.143 5.546-4.326 100.00 867 58 0.1075 406.237 402.237 0.967 1.002 0.130 4.315-3.360 100.00 1859 96 0.0874 386.334 384.478 1.002 1.002 0.120 3.356-2.611 100.00 3867 181 0.1098 253.801 251.959 1.010 1.002 0.050 2.608-2.026 99.99 8198 413 0.0907 168.247 167.645 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0873 82.163 82.498 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1241 36.434 36.041 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2163 22.956 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=-0.0166 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1114 r_free=0.1290 After: r_work=0.1116 r_free=0.1289 ================================== NQH flips ================================== r_work=0.1116 r_free=0.1289 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=0.1116 r_free=0.1289 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1116 r_free=0.1289 | n_water=460 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1116 r_free=0.1290 | n_water=459 | time (s): 50.180 (total time: 52.720) Filter (q & B) r_work=0.1116 r_free=0.1290 | n_water=458 | time (s): 4.210 (total time: 56.930) Compute maps r_work=0.1116 r_free=0.1290 | n_water=458 | time (s): 1.920 (total time: 58.850) Filter (map) r_work=0.1138 r_free=0.1299 | n_water=373 | time (s): 4.070 (total time: 62.920) Find peaks r_work=0.1138 r_free=0.1299 | n_water=373 | time (s): 0.760 (total time: 63.680) Add new water r_work=0.1183 r_free=0.1348 | n_water=515 | time (s): 3.980 (total time: 67.660) Refine new water occ: r_work=0.1130 r_free=0.1297 adp: r_work=0.1130 r_free=0.1298 occ: r_work=0.1119 r_free=0.1290 adp: r_work=0.1118 r_free=0.1290 occ: r_work=0.1111 r_free=0.1286 adp: r_work=0.1108 r_free=0.1284 ADP+occupancy (water only), MIN, final r_work=0.1108 r_free=0.1284 r_work=0.1108 r_free=0.1284 | n_water=515 | time (s): 133.710 (total time: 201.370) Filter (q & B) r_work=0.1117 r_free=0.1290 | n_water=474 | time (s): 3.960 (total time: 205.330) Filter (dist only) r_work=0.1117 r_free=0.1288 | n_water=473 | time (s): 49.170 (total time: 254.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.725752 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.452062 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 0.1209 0.1348 0.0139 0.004 0.7 7.4 0.5 0.0 0 0.086 0.1155 0.1310 0.0155 0.004 0.8 6.1 0.0 0.0 0 0.259 0.1138 0.1301 0.0162 0.005 0.9 5.4 0.5 0.0 0 0.518 0.1130 0.1295 0.0165 0.006 1.0 5.1 0.5 0.0 0 0.777 0.1124 0.1291 0.0167 0.006 1.1 5.1 0.5 0.0 0 1.035 0.1121 0.1289 0.0168 0.007 1.1 4.8 0.5 0.0 0 1.294 0.1118 0.1288 0.0171 0.008 1.1 4.8 0.5 0.0 0 1.553 0.1117 0.1288 0.0171 0.008 1.1 4.8 0.5 0.0 0 1.812 0.1128 0.1293 0.0166 0.006 1.0 5.1 0.5 0.0 0 0.863 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1118 0.1288 0.0171 0.008 1.1 4.8 0.5 0.0 0 1.553 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.18 12.88 1.71 3.796 21.431 41.452 3.597 11.18 12.88 1.71 3.796 21.431 1.244 3.597 11.18 12.88 1.71 3.793 21.431 5.182 3.597 11.23 12.94 1.71 3.721 21.422 20.726 3.594 11.24 13.01 1.77 3.742 21.405 41.452 3.595 11.24 13.06 1.82 3.748 21.384 62.178 3.592 11.16 13.00 1.83 3.775 21.382 82.904 3.587 11.13 12.97 1.84 3.785 21.380 103.630 3.584 11.12 12.98 1.87 3.793 21.374 124.356 3.583 11.09 12.96 1.87 3.801 21.374 145.082 3.581 11.08 12.96 1.88 3.811 21.370 165.808 3.580 11.08 12.98 1.90 3.826 21.361 186.534 3.580 11.06 12.96 1.90 3.832 21.360 207.260 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: 1.244 Accepted refinement result: 11.18 12.88 1.71 3.796 21.431 1.244 3.597 Individual atomic B min max mean iso aniso Overall: 9.12 115.21 21.54 3.35 238 1762 Protein: 9.12 115.21 17.03 3.35 0 1519 Water: 11.51 79.16 36.03 N/A 238 235 Other: 19.72 26.64 22.08 N/A 0 8 Chain A: 9.12 115.21 19.64 N/A 0 1762 Chain S: 12.54 59.99 35.63 N/A 238 0 Histogram: Values Number of atoms 9.12 - 19.73 1265 19.73 - 30.34 300 30.34 - 40.94 213 40.94 - 51.55 142 51.55 - 62.16 55 62.16 - 72.77 13 72.77 - 83.38 6 83.38 - 93.99 4 93.99 - 104.60 0 104.60 - 115.21 2 =========================== Idealize ADP of riding H ========================== r_work=0.1118 r_free=0.1288 r_work=0.1118 r_free=0.1288 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1118 r_free = 0.1288 target_work(ml) = 3.597 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1116 r_free = 0.1288 target_work(ml) = 3.596 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1116 r_free= 0.1288 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.596421 | | target function (ml) not normalized (work): 299509.942953 | | target function (ml) not normalized (free): 15790.576348 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1301 0.1340 5.6242 5.5927| | 2: 3.57 - 2.84 1.00 2888 124 0.1026 0.1404 5.1373 5.213| | 3: 2.83 - 2.48 1.00 2820 163 0.1087 0.1176 4.9313 4.9587| | 4: 2.47 - 2.25 1.00 2825 136 0.0888 0.1024 4.6171 4.661| | 5: 2.25 - 2.09 1.00 2756 127 0.0857 0.0983 4.5644 4.6258| | 6: 2.09 - 1.97 1.00 2846 113 0.0851 0.1001 4.2579 4.3446| | 7: 1.97 - 1.87 1.00 2787 165 0.0875 0.1086 3.971 4.0802| | 8: 1.87 - 1.79 1.00 2789 144 0.0907 0.1127 3.8802 3.9981| | 9: 1.79 - 1.72 1.00 2745 138 0.0852 0.1179 3.632 3.8241| | 10: 1.72 - 1.66 1.00 2831 160 0.0911 0.1159 3.5581 3.6902| | 11: 1.66 - 1.61 1.00 2712 147 0.0853 0.1022 3.4861 3.5674| | 12: 1.61 - 1.56 1.00 2773 144 0.0892 0.1143 3.3199 3.4521| | 13: 1.56 - 1.52 1.00 2745 130 0.0941 0.1046 3.3016 3.4027| | 14: 1.52 - 1.48 1.00 2803 134 0.0973 0.1084 3.2326 3.3336| | 15: 1.48 - 1.45 1.00 2738 128 0.0994 0.1227 3.1474 3.2622| | 16: 1.45 - 1.42 1.00 2756 161 0.1052 0.1238 3.1315 3.232| | 17: 1.42 - 1.39 1.00 2785 139 0.1131 0.1306 3.1118 3.2269| | 18: 1.39 - 1.36 1.00 2741 179 0.1193 0.1329 3.0996 3.2369| | 19: 1.36 - 1.34 1.00 2807 134 0.1260 0.1547 3.1092 3.2653| | 20: 1.34 - 1.32 1.00 2696 147 0.1358 0.1470 3.1062 3.1587| | 21: 1.32 - 1.30 1.00 2785 112 0.1464 0.1507 3.1108 3.1007| | 22: 1.29 - 1.27 1.00 2704 152 0.1556 0.1973 3.1201 3.2903| | 23: 1.27 - 1.26 1.00 2802 156 0.1643 0.1797 3.1299 3.2029| | 24: 1.26 - 1.24 1.00 2744 132 0.1707 0.1835 3.125 3.2283| | 25: 1.24 - 1.22 1.00 2733 148 0.1875 0.2150 3.1393 3.2567| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1759 3.1457 3.2| | 27: 1.21 - 1.19 1.00 2814 148 0.2070 0.2158 3.1691 3.1581| | 28: 1.19 - 1.18 1.00 2671 147 0.2201 0.2296 3.1649 3.1728| | 29: 1.18 - 1.16 1.00 2800 134 0.2260 0.2377 3.1458 3.2286| | 30: 1.16 - 1.15 1.00 2739 148 0.2444 0.2440 3.141 3.1635| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2918 171 0.95 8.28 1.00 0.97 5578.79| | 2: 3.57 - 2.84 2888 124 0.93 12.34 1.01 0.97 5578.79| | 3: 2.83 - 2.48 2820 163 0.90 16.33 0.99 0.97 4662.66| | 4: 2.47 - 2.25 2825 136 0.92 13.29 1.00 0.98 2300.26| | 5: 2.25 - 2.09 2756 127 0.90 15.43 1.01 0.98 2300.26| | 6: 2.09 - 1.97 2846 113 0.93 12.25 1.02 0.97 1332.27| | 7: 1.97 - 1.87 2787 165 0.95 9.25 1.02 0.97 506.71| | 8: 1.87 - 1.79 2789 144 0.93 12.63 1.00 0.97 506.71| | 9: 1.79 - 1.72 2745 138 0.94 10.00 0.98 0.97 287.61| | 10: 1.72 - 1.66 2831 160 0.94 11.11 0.98 0.97 243.73| | 11: 1.66 - 1.61 2712 147 0.94 11.71 0.98 0.97 233.50| | 12: 1.61 - 1.56 2773 144 0.95 8.89 0.99 0.97 137.02| | 13: 1.56 - 1.52 2745 130 0.95 10.33 1.03 0.97 137.02| | 14: 1.52 - 1.48 2803 134 0.94 10.76 1.02 0.98 123.04| | 15: 1.48 - 1.45 2738 128 0.95 9.91 1.02 0.98 97.44| | 16: 1.45 - 1.42 2756 161 0.94 11.11 1.02 0.98 97.44| | 17: 1.42 - 1.39 2785 139 0.95 10.89 1.01 0.98 88.78| | 18: 1.39 - 1.36 2741 179 0.94 11.52 1.01 0.98 83.78| | 19: 1.36 - 1.34 2807 134 0.94 11.85 1.00 0.98 83.78| | 20: 1.34 - 1.32 2696 147 0.94 12.15 0.98 0.96 79.88| | 21: 1.32 - 1.30 2785 112 0.94 13.11 0.98 0.96 79.61| | 22: 1.29 - 1.27 2704 152 0.93 13.68 0.98 0.96 80.02| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.97 0.94 82.10| | 24: 1.26 - 1.24 2744 132 0.92 14.88 0.96 0.94 82.10| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.94 84.02| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.02 0.93 86.15| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.15| | 28: 1.19 - 1.18 2671 147 0.88 20.38 1.01 0.93 89.70| | 29: 1.18 - 1.16 2800 134 0.88 20.46 0.99 0.92 91.03| | 30: 1.16 - 1.15 2739 148 0.86 22.01 0.98 0.92 91.03| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.61 max = 5578.79 mean = 864.73| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.95 mean = 13.40| |phase err.(test): min = 0.00 max = 89.69 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1124 0.1116 0.1288 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1427 0.1424 0.1513 n_refl.: 87576 remove outliers: r(all,work,free)=0.1427 0.1424 0.1513 n_refl.: 87576 overall B=-0.00 to atoms: r(all,work,free)=0.1426 0.1423 0.1513 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1124 0.1116 0.1290 n_refl.: 87576 remove outliers: r(all,work,free)=0.1123 0.1115 0.1290 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3982 288.098 251.563 0.441 1.001 0.291 11.894-9.307 93.14 91 4 0.2478 472.345 464.255 0.879 1.002 0.218 9.237-7.194 98.18 209 7 0.2223 385.824 381.691 0.932 1.002 0.170 7.162-5.571 100.00 427 22 0.2073 295.928 286.054 0.912 1.002 0.125 5.546-4.326 100.00 867 58 0.1090 406.237 401.886 0.966 1.002 0.116 4.315-3.360 100.00 1859 96 0.0887 386.334 384.127 1.001 1.002 0.110 3.356-2.611 100.00 3867 181 0.1080 253.801 251.858 1.010 1.001 0.019 2.608-2.026 99.99 8198 413 0.0902 168.247 167.581 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0876 82.163 82.475 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1245 36.434 36.024 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.956 21.492 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0125 ================= 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 : 0.2599 0.1899 0.082 5.387 8.8 119.3 19.9 258 0.000 1_bss: 0.1627 0.1719 0.082 5.387 9.1 119.5 20.1 258 0.000 1_settarget: 0.1627 0.1719 0.082 5.387 9.1 119.5 20.1 258 0.000 1_nqh: 0.1627 0.1719 0.082 5.387 9.1 119.5 20.1 258 0.000 1_weight: 0.1627 0.1719 0.082 5.387 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1206 0.1448 0.007 0.949 9.1 119.5 20.1 258 0.129 1_adp: 0.1213 0.1446 0.007 0.949 9.1 119.5 20.1 258 0.129 1_regHadp: 0.1215 0.1450 0.007 0.949 9.1 119.5 20.1 258 0.129 1_occ: 0.1207 0.1444 0.007 0.949 9.1 119.5 20.1 258 0.129 2_bss: 0.1204 0.1435 0.007 0.949 9.1 119.5 20.1 258 0.129 2_settarget: 0.1204 0.1435 0.007 0.949 9.1 119.5 20.1 258 0.129 2_updatecdl: 0.1204 0.1435 0.007 0.955 9.1 119.5 20.1 258 0.129 2_nqh: 0.1206 0.1436 0.007 0.955 9.1 119.5 20.1 258 0.132 2_sol: 0.1177 0.1382 0.007 0.955 9.1 115.2 22.3 424 n/a 2_weight: 0.1177 0.1382 0.007 0.955 9.1 115.2 22.3 424 n/a 2_xyzrec: 0.1178 0.1404 0.006 0.847 9.1 115.2 22.3 424 n/a 2_adp: 0.1178 0.1404 0.006 0.847 9.1 115.2 22.3 424 n/a 2_regHadp: 0.1178 0.1404 0.006 0.847 9.1 115.2 22.3 424 n/a 2_occ: 0.1177 0.1405 0.006 0.847 9.1 115.2 22.3 424 n/a 3_bss: 0.1172 0.1400 0.006 0.847 9.1 115.2 22.3 424 n/a 3_settarget: 0.1172 0.1400 0.006 0.847 9.1 115.2 22.3 424 n/a 3_updatecdl: 0.1172 0.1400 0.006 0.847 9.1 115.2 22.3 424 n/a 3_nqh: 0.1172 0.1400 0.006 0.847 9.1 115.2 22.3 424 n/a 3_sol: 0.1193 0.1387 0.006 0.847 9.1 115.2 21.5 450 n/a 3_weight: 0.1193 0.1387 0.006 0.847 9.1 115.2 21.5 450 n/a 3_xyzrec: 0.1153 0.1316 0.006 0.943 9.1 115.2 21.5 450 n/a 3_adp: 0.1153 0.1316 0.006 0.943 9.1 115.2 21.5 450 n/a 3_regHadp: 0.1153 0.1316 0.006 0.943 9.1 115.2 21.5 450 n/a 3_occ: 0.1144 0.1308 0.006 0.943 9.1 115.2 21.5 450 n/a 4_bss: 0.1135 0.1296 0.006 0.943 9.1 115.2 21.5 450 n/a 4_settarget: 0.1135 0.1296 0.006 0.943 9.1 115.2 21.5 450 n/a 4_updatecdl: 0.1135 0.1296 0.006 0.945 9.1 115.2 21.5 450 n/a 4_nqh: 0.1135 0.1296 0.006 0.945 9.1 115.2 21.5 450 n/a 4_sol: 0.1135 0.1290 0.006 0.945 9.1 115.2 21.4 460 n/a 4_weight: 0.1135 0.1290 0.006 0.945 9.1 115.2 21.4 460 n/a 4_xyzrec: 0.1121 0.1288 0.008 1.128 9.1 115.2 21.4 460 n/a 4_adp: 0.1121 0.1288 0.008 1.128 9.1 115.2 21.4 460 n/a 4_regHadp: 0.1121 0.1288 0.008 1.128 9.1 115.2 21.4 460 n/a 4_occ: 0.1117 0.1286 0.008 1.128 9.1 115.2 21.4 460 n/a 5_bss: 0.1114 0.1290 0.008 1.128 9.1 115.2 21.4 460 n/a 5_settarget: 0.1114 0.1290 0.008 1.128 9.1 115.2 21.4 460 n/a 5_updatecdl: 0.1114 0.1290 0.008 1.129 9.1 115.2 21.4 460 n/a 5_setrh: 0.1116 0.1289 0.008 1.129 9.1 115.2 21.4 460 n/a 5_nqh: 0.1116 0.1289 0.008 1.129 9.1 115.2 21.4 460 n/a 5_sol: 0.1117 0.1288 0.008 1.129 9.1 115.2 21.5 473 n/a 5_weight: 0.1117 0.1288 0.008 1.129 9.1 115.2 21.5 473 n/a 5_xyzrec: 0.1118 0.1288 0.008 1.129 9.1 115.2 21.5 473 n/a 5_adp: 0.1118 0.1288 0.008 1.129 9.1 115.2 21.5 473 n/a 5_regHadp: 0.1118 0.1288 0.008 1.129 9.1 115.2 21.5 473 n/a 5_occ: 0.1116 0.1288 0.008 1.129 9.1 115.2 21.5 473 n/a end: 0.1115 0.1290 0.008 1.129 9.1 115.2 21.5 473 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8540717_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8540717_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6300 Refinement macro-cycles (run) : 12016.0500 Write final files (write_after_run_outputs) : 95.0900 Total : 12114.7700 Total CPU time: 3.37 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 21:37:44 PST -0800 (1735364264.88 s) Start R-work = 0.1627, R-free = 0.1719 Final R-work = 0.1115, R-free = 0.1290 =============================================================================== Job complete usr+sys time: 12295.92 seconds wall clock time: 222 minutes 14.71 seconds (13334.71 seconds total)