Starting phenix.refine on Sat Dec 28 21:06:33 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_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.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_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.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_8540717.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8540717.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 } 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 } } 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: 2.25, per 1000 atoms: 0.67 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: 0.59 Conformation dependent library (CDL) restraints added in 246.7 milliseconds Time building geometry restraints manager: 0.80 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 2.450 nonbonded pdb="HH22 ARG A 5 " pdb=" O AGLU A 64 " model vdw 1.844 2.450 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.851 2.450 ... (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 } 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 } } 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 = 23.768439 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 0.1211 0.1454 0.0243 0.007 0.9 1.6 0.5 0.0 0 11.884 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.54 2.43 3.013 19.076 2031.353 0.017 12.42 15.36 2.94 3.257 19.599 2031.353 0.015 Individual atomic B min max mean iso aniso Overall: 8.63 118.71 21.09 2.87 0 1785 Protein: 8.63 118.71 17.94 2.87 0 1519 Water: 11.16 114.52 39.39 N/A 0 258 Other: 23.26 36.48 29.54 N/A 0 8 Chain A: 8.63 118.71 21.09 N/A 0 1785 Histogram: Values Number of atoms 8.63 - 19.64 1210 19.64 - 30.64 225 30.64 - 41.65 165 41.65 - 52.66 100 52.66 - 63.67 55 63.67 - 74.67 16 74.67 - 85.68 7 85.68 - 96.69 4 96.69 - 107.70 0 107.70 - 118.71 3 =========================== Idealize ADP of riding H ========================== r_work=0.1242 r_free=0.1536 r_work=0.1246 r_free=0.1539 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1246 r_free = 0.1539 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1247 r_free = 0.1541 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.28 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= 0.1247 r_free= 0.1541 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015300 | | target function (ls_wunit_k1) not normalized (work): 1274.434752 | | target function (ls_wunit_k1) not normalized (free): 114.640675 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1261 0.1247 0.1541 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1705 0.1704 0.1764 n_refl.: 87592 remove outliers: r(all,work,free)=0.1705 0.1704 0.1764 n_refl.: 87592 overall B=0.12 to atoms: r(all,work,free)=0.1725 0.1724 0.1778 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1245 0.1535 n_refl.: 87592 remove outliers: r(all,work,free)=0.1259 0.1245 0.1535 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 0.3596 298.043 278.640 0.631 1.003 0.380 11.894-9.307 98.04 96 4 0.1511 479.386 467.896 0.913 1.003 0.380 9.237-7.194 100.00 213 7 0.1827 390.494 384.913 0.947 1.003 0.340 7.162-5.571 100.00 427 22 0.1716 293.044 287.980 0.923 1.003 0.258 5.546-4.326 100.00 867 58 0.0923 402.277 399.575 0.950 1.003 0.230 4.315-3.360 100.00 1859 96 0.0774 382.568 381.626 0.994 1.003 0.180 3.356-2.611 100.00 3867 181 0.1022 251.327 250.624 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0976 166.607 166.030 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1216 81.362 81.525 1.017 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1655 36.079 35.547 1.006 0.999 0.000 1.221-1.150 99.97 13689 708 0.2365 22.732 21.249 0.970 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0471 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1245 r_free=0.1535 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1246 r_free=0.1536 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1246 r_free=0.1536 | n_water=258 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1255 r_free=0.1535 | n_water=252 | time (s): 25.660 (total time: 28.060) Filter (q & B) r_work=0.1258 r_free=0.1534 | n_water=249 | time (s): 3.790 (total time: 31.850) Compute maps r_work=0.1258 r_free=0.1534 | n_water=249 | time (s): 1.860 (total time: 33.710) Filter (map) r_work=0.1274 r_free=0.1538 | n_water=236 | time (s): 3.840 (total time: 37.550) Find peaks r_work=0.1274 r_free=0.1538 | n_water=236 | time (s): 0.710 (total time: 38.260) Add new water r_work=0.1429 r_free=0.1681 | n_water=447 | time (s): 3.800 (total time: 42.060) Refine new water occ: r_work=0.1342 r_free=0.1575 adp: r_work=0.1261 r_free=0.1508 occ: r_work=0.1274 r_free=0.1519 adp: r_work=0.1239 r_free=0.1490 occ: r_work=0.1243 r_free=0.1492 adp: r_work=0.1233 r_free=0.1488 ADP+occupancy (water only), MIN, final r_work=0.1233 r_free=0.1488 r_work=0.1233 r_free=0.1488 | n_water=447 | time (s): 77.700 (total time: 119.760) Filter (q & B) r_work=0.1238 r_free=0.1492 | n_water=429 | time (s): 3.790 (total time: 123.550) Filter (dist only) r_work=0.1238 r_free=0.1491 | n_water=428 | time (s): 43.480 (total time: 167.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.267607 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1549.021668 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 0.1230 0.1513 0.0283 0.007 0.9 2.6 0.5 0.0 0 13.134 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 15.13 2.83 3.801 23.261 1549.022 0.015 11.97 14.75 2.78 4.290 23.061 1549.022 0.015 Individual atomic B min max mean iso aniso Overall: 8.83 113.83 23.23 2.61 192 1763 Protein: 8.83 113.83 17.67 2.62 0 1519 Water: 11.15 74.42 42.92 N/A 192 236 Other: 22.47 33.19 26.80 N/A 0 8 Chain A: 8.83 113.83 20.40 N/A 0 1763 Chain S: 15.22 74.42 49.29 N/A 192 0 Histogram: Values Number of atoms 8.83 - 19.33 1209 19.33 - 29.83 244 29.83 - 40.33 185 40.33 - 50.83 136 50.83 - 61.33 115 61.33 - 71.83 52 71.83 - 82.33 8 82.33 - 92.83 3 92.83 - 103.33 1 103.33 - 113.83 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1476 r_work=0.1197 r_free=0.1475 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1475 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1479 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.22 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= 0.1198 r_free= 0.1479 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013939 | | target function (ls_wunit_k1) not normalized (work): 1161.085008 | | target function (ls_wunit_k1) not normalized (free): 104.803538 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1198 0.1479 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1607 0.1602 0.1733 n_refl.: 87591 remove outliers: r(all,work,free)=0.1607 0.1602 0.1733 n_refl.: 87591 overall B=0.03 to atoms: r(all,work,free)=0.1612 0.1607 0.1736 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1195 0.1470 n_refl.: 87591 remove outliers: r(all,work,free)=0.1206 0.1193 0.1470 n_refl.: 87587 ======================== 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 0.3297 290.762 272.580 0.613 0.937 0.350 11.894-9.307 98.04 96 4 0.1608 479.386 476.778 0.984 0.938 0.330 9.237-7.194 100.00 213 7 0.1678 390.494 389.325 1.044 0.938 0.260 7.162-5.571 100.00 427 22 0.1506 293.044 289.561 1.003 0.938 0.234 5.546-4.326 100.00 867 58 0.0830 402.277 399.841 1.022 0.939 0.220 4.315-3.360 100.00 1859 96 0.0699 382.568 381.663 1.068 0.939 0.200 3.356-2.611 100.00 3867 181 0.0954 251.327 250.595 1.077 0.940 0.140 2.608-2.026 99.99 8198 413 0.0963 166.607 166.204 1.083 0.941 0.000 2.025-1.573 100.00 17313 902 0.1170 81.362 81.548 1.089 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1609 36.079 35.594 1.073 0.947 0.000 1.221-1.150 99.97 13689 708 0.2334 22.732 21.301 1.027 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0498 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1470 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=0.1193 r_free=0.1470 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1470 | n_water=428 | time (s): 1.990 (total time: 1.990) Filter (dist) r_work=0.1193 r_free=0.1470 | n_water=426 | time (s): 40.240 (total time: 42.230) Filter (q & B) r_work=0.1193 r_free=0.1470 | n_water=426 | time (s): 0.910 (total time: 43.140) Compute maps r_work=0.1193 r_free=0.1470 | n_water=426 | time (s): 1.250 (total time: 44.390) Filter (map) r_work=0.1236 r_free=0.1465 | n_water=288 | time (s): 2.950 (total time: 47.340) Find peaks r_work=0.1236 r_free=0.1465 | n_water=288 | time (s): 0.710 (total time: 48.050) Add new water r_work=0.1371 r_free=0.1600 | n_water=484 | time (s): 3.540 (total time: 51.590) Refine new water occ: r_work=0.1267 r_free=0.1513 adp: r_work=0.1268 r_free=0.1515 occ: r_work=0.1243 r_free=0.1486 adp: r_work=0.1240 r_free=0.1486 occ: r_work=0.1226 r_free=0.1466 adp: r_work=0.1218 r_free=0.1464 ADP+occupancy (water only), MIN, final r_work=0.1218 r_free=0.1464 r_work=0.1218 r_free=0.1464 | n_water=484 | time (s): 193.720 (total time: 245.310) Filter (q & B) r_work=0.1222 r_free=0.1468 | n_water=449 | time (s): 3.800 (total time: 249.110) Filter (dist only) r_work=0.1222 r_free=0.1466 | n_water=448 | time (s): 37.240 (total time: 286.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.047483 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.524307 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 0.1222 0.1433 0.0212 0.006 0.9 1.6 0.5 0.0 0 1.024 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.22 14.33 2.12 3.621 22.157 47.524 3.718 12.09 13.89 1.79 4.063 21.979 47.524 3.648 Individual atomic B min max mean iso aniso Overall: 9.23 109.45 21.80 2.33 214 1761 Protein: 9.23 109.45 17.27 2.33 0 1519 Water: 11.51 71.13 37.10 N/A 214 234 Other: 18.73 29.52 24.47 N/A 0 8 Chain A: 9.23 109.45 19.97 N/A 0 1761 Chain S: 14.81 66.12 36.83 N/A 214 0 Histogram: Values Number of atoms 9.23 - 19.25 1232 19.25 - 29.27 271 29.27 - 39.30 214 39.30 - 49.32 144 49.32 - 59.34 81 59.34 - 69.36 19 69.36 - 79.39 8 79.39 - 89.41 3 89.41 - 99.43 1 99.43 - 109.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1389 r_work=0.1210 r_free=0.1390 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1390 target_work(ml) = 3.648 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1390 target_work(ml) = 3.646 | | 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.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1206 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.646355 | | target function (ml) not normalized (work): 303708.562818 | | target function (ml) not normalized (free): 16041.450354 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1206 0.1390 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1535 0.1534 0.1591 n_refl.: 87587 remove outliers: r(all,work,free)=0.1535 0.1534 0.1591 n_refl.: 87587 overall B=-0.01 to atoms: r(all,work,free)=0.1534 0.1532 0.1590 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1198 0.1379 n_refl.: 87587 remove outliers: r(all,work,free)=0.1204 0.1195 0.1379 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 88.54 80 5 0.3892 282.716 258.912 0.452 1.000 0.291 11.894-9.307 96.08 94 4 0.2539 472.766 457.589 0.849 1.002 0.270 9.237-7.194 99.09 211 7 0.2391 385.052 383.933 0.948 1.002 0.160 7.162-5.571 100.00 427 22 0.2010 293.044 283.955 0.914 1.002 0.160 5.546-4.326 100.00 867 58 0.1091 402.277 398.023 0.950 1.002 0.160 4.315-3.360 100.00 1859 96 0.0907 382.568 379.952 0.993 1.002 0.160 3.356-2.611 100.00 3867 181 0.1147 251.327 249.490 1.000 1.002 0.130 2.608-2.026 99.99 8198 413 0.1045 166.607 165.645 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1019 81.362 81.497 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1294 36.079 35.664 1.019 0.999 0.000 1.221-1.150 99.97 13689 708 0.2126 22.732 21.355 0.977 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0270 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1379 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1379 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1379 | n_water=448 | time (s): 2.240 (total time: 2.240) Filter (dist) r_work=0.1195 r_free=0.1379 | n_water=448 | time (s): 37.720 (total time: 39.960) Filter (q & B) r_work=0.1195 r_free=0.1379 | n_water=448 | time (s): 0.820 (total time: 40.780) Compute maps r_work=0.1195 r_free=0.1379 | n_water=448 | time (s): 1.370 (total time: 42.150) Filter (map) r_work=0.1214 r_free=0.1371 | n_water=328 | time (s): 3.550 (total time: 45.700) Find peaks r_work=0.1214 r_free=0.1371 | n_water=328 | time (s): 0.640 (total time: 46.340) Add new water r_work=0.1275 r_free=0.1410 | n_water=482 | time (s): 2.520 (total time: 48.860) Refine new water occ: r_work=0.1209 r_free=0.1361 adp: r_work=0.1209 r_free=0.1362 occ: r_work=0.1195 r_free=0.1360 adp: r_work=0.1193 r_free=0.1358 occ: r_work=0.1186 r_free=0.1362 adp: r_work=0.1183 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1357 r_work=0.1183 r_free=0.1357 | n_water=482 | time (s): 201.580 (total time: 250.440) Filter (q & B) r_work=0.1188 r_free=0.1362 | n_water=444 | time (s): 3.610 (total time: 254.050) Filter (dist only) r_work=0.1188 r_free=0.1361 | n_water=443 | time (s): 35.840 (total time: 289.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.872927 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.552313 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 0.1193 0.1367 0.0174 0.006 0.9 1.9 0.5 0.0 0 0.936 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.67 1.74 3.435 21.590 49.552 3.636 11.76 13.56 1.80 3.852 21.456 49.552 3.619 Individual atomic B min max mean iso aniso Overall: 9.23 105.72 21.34 2.18 211 1759 Protein: 9.23 105.72 16.95 2.18 0 1519 Water: 11.42 69.59 36.38 N/A 211 232 Other: 18.41 26.54 22.36 N/A 0 8 Chain A: 9.23 105.72 19.58 N/A 0 1759 Chain S: 14.83 60.23 36.07 N/A 211 0 Histogram: Values Number of atoms 9.23 - 18.87 1225 18.87 - 28.52 282 28.52 - 38.17 201 38.17 - 47.82 149 47.82 - 57.47 74 57.47 - 67.12 25 67.12 - 76.77 9 76.77 - 86.42 2 86.42 - 96.07 1 96.07 - 105.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1176 r_free=0.1356 r_work=0.1176 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1176 r_free = 0.1356 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1172 r_free = 0.1353 target_work(ml) = 3.617 | | 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.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1172 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.617243 | | target function (ml) not normalized (work): 301258.476639 | | target function (ml) not normalized (free): 15914.912773 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1181 0.1172 0.1353 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1497 0.1496 0.1546 n_refl.: 87580 remove outliers: r(all,work,free)=0.1497 0.1496 0.1546 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1495 0.1495 0.1545 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1182 0.1173 0.1356 n_refl.: 87580 remove outliers: r(all,work,free)=0.1180 0.1171 0.1356 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.4077 285.290 248.130 0.430 1.000 0.305 11.894-9.307 95.10 93 4 0.2411 476.651 455.612 0.840 1.002 0.249 9.237-7.194 97.73 208 7 0.2400 383.135 377.342 0.923 1.002 0.174 7.162-5.571 100.00 427 22 0.2101 293.044 283.298 0.909 1.002 0.150 5.546-4.326 100.00 867 58 0.1107 402.277 398.681 0.951 1.002 0.150 4.315-3.360 100.00 1859 96 0.0922 382.568 379.871 0.994 1.002 0.140 3.356-2.611 100.00 3867 181 0.1145 251.327 249.573 1.001 1.002 0.057 2.608-2.026 99.99 8198 413 0.1012 166.607 165.819 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0966 81.362 81.661 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.079 35.713 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2126 22.732 21.366 0.978 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0246 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1171 r_free=0.1356 After: r_work=0.1172 r_free=0.1355 ================================== NQH flips ================================== r_work=0.1172 r_free=0.1355 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=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1172 r_free=0.1355 | n_water=443 | time (s): 1.890 (total time: 1.890) Filter (dist) r_work=0.1172 r_free=0.1356 | n_water=442 | time (s): 38.610 (total time: 40.500) Filter (q & B) r_work=0.1172 r_free=0.1356 | n_water=441 | time (s): 2.840 (total time: 43.340) Compute maps r_work=0.1172 r_free=0.1356 | n_water=441 | time (s): 1.400 (total time: 44.740) Filter (map) r_work=0.1195 r_free=0.1370 | n_water=334 | time (s): 3.080 (total time: 47.820) Find peaks r_work=0.1195 r_free=0.1370 | n_water=334 | time (s): 0.690 (total time: 48.510) Add new water r_work=0.1248 r_free=0.1419 | n_water=484 | time (s): 3.490 (total time: 52.000) Refine new water occ: r_work=0.1189 r_free=0.1367 adp: r_work=0.1189 r_free=0.1369 occ: r_work=0.1177 r_free=0.1357 adp: r_work=0.1176 r_free=0.1358 occ: r_work=0.1168 r_free=0.1354 adp: r_work=0.1165 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1165 r_free=0.1352 r_work=0.1165 r_free=0.1352 | n_water=484 | time (s): 169.580 (total time: 221.580) Filter (q & B) r_work=0.1172 r_free=0.1350 | n_water=442 | time (s): 2.790 (total time: 224.370) Filter (dist only) r_work=0.1172 r_free=0.1348 | n_water=441 | time (s): 39.320 (total time: 263.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.986539 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.238072 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 0.1190 0.1368 0.0178 0.007 1.0 4.2 0.5 0.0 0 0.993 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.68 1.78 3.303 21.172 49.238 3.625 11.96 13.70 1.74 3.514 21.094 49.238 3.618 Individual atomic B min max mean iso aniso Overall: 9.28 101.78 21.06 2.05 210 1758 Protein: 9.28 101.78 16.77 2.05 0 1519 Water: 11.44 68.63 35.81 N/A 210 231 Other: 18.50 25.90 22.15 N/A 0 8 Chain A: 9.28 101.78 19.37 N/A 0 1758 Chain S: 14.63 60.17 35.24 N/A 210 0 Histogram: Values Number of atoms 9.28 - 18.53 1222 18.53 - 27.78 280 27.78 - 37.03 202 37.03 - 46.28 148 46.28 - 55.53 72 55.53 - 64.78 27 64.78 - 74.03 12 74.03 - 83.28 2 83.28 - 92.53 1 92.53 - 101.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1370 r_work=0.1196 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1370 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1366 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1192 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.616968 | | target function (ml) not normalized (work): 301217.450384 | | target function (ml) not normalized (free): 15937.533135 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1397 0.1398 5.6452 5.6444| | 2: 3.57 - 2.84 1.00 2888 124 0.1121 0.1455 5.2034 5.2799| | 3: 2.83 - 2.48 1.00 2820 163 0.1217 0.1258 5.0076 5.0369| | 4: 2.47 - 2.25 1.00 2825 136 0.1035 0.1171 4.7117 4.7582| | 5: 2.25 - 2.09 1.00 2756 127 0.0989 0.1102 4.6513 4.7091| | 6: 2.09 - 1.97 1.00 2846 113 0.0972 0.1206 4.3544 4.4888| | 7: 1.97 - 1.87 1.00 2787 165 0.0991 0.1201 4.0766 4.1805| | 8: 1.87 - 1.79 1.00 2789 144 0.1026 0.1250 3.9916 4.0844| | 9: 1.79 - 1.72 1.00 2745 138 0.0961 0.1291 3.7196 3.9082| | 10: 1.72 - 1.66 1.00 2831 160 0.1000 0.1285 3.6344 3.7887| | 11: 1.66 - 1.61 1.00 2712 147 0.0969 0.1108 3.5705 3.6105| | 12: 1.61 - 1.56 1.00 2773 144 0.0908 0.1149 3.338 3.4801| | 13: 1.56 - 1.52 1.00 2745 130 0.0974 0.1065 3.3328 3.4326| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1117 3.2531 3.3248| | 15: 1.48 - 1.45 1.00 2738 128 0.1006 0.1345 3.1597 3.3099| | 16: 1.45 - 1.42 1.00 2756 161 0.1061 0.1235 3.1424 3.2367| | 17: 1.42 - 1.39 1.00 2785 139 0.1117 0.1271 3.1086 3.2038| | 18: 1.39 - 1.36 1.00 2741 179 0.1142 0.1388 3.0767 3.259| | 19: 1.36 - 1.34 1.00 2807 134 0.1205 0.1632 3.0834 3.2793| | 20: 1.34 - 1.32 1.00 2696 147 0.1315 0.1484 3.0812 3.1282| | 21: 1.32 - 1.30 1.00 2785 112 0.1409 0.1614 3.0801 3.1578| | 22: 1.29 - 1.27 1.00 2704 152 0.1464 0.1900 3.0795 3.2862| | 23: 1.27 - 1.26 1.00 2802 156 0.1567 0.1871 3.0963 3.2123| | 24: 1.26 - 1.24 1.00 2744 132 0.1622 0.1772 3.0888 3.1967| | 25: 1.24 - 1.22 1.00 2733 148 0.1788 0.2336 3.1045 3.2903| | 26: 1.22 - 1.21 1.00 2727 135 0.1855 0.1785 3.1191 3.2| | 27: 1.21 - 1.19 1.00 2814 148 0.2004 0.2093 3.1365 3.1403| | 28: 1.19 - 1.18 1.00 2671 147 0.2139 0.2337 3.1351 3.1659| | 29: 1.18 - 1.16 1.00 2800 134 0.2213 0.2355 3.1229 3.2172| | 30: 1.16 - 1.15 1.00 2739 148 0.2374 0.2498 3.1124 3.1618| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2917 171 0.95 9.23 1.00 0.97 6364.78| | 2: 3.57 - 2.84 2888 124 0.92 13.48 1.01 0.97 6364.78| | 3: 2.83 - 2.48 2820 163 0.88 17.65 0.99 0.97 5333.91| | 4: 2.47 - 2.25 2825 136 0.91 14.72 1.00 0.98 2675.60| | 5: 2.25 - 2.09 2756 127 0.89 16.97 1.01 0.98 2675.60| | 6: 2.09 - 1.97 2846 113 0.92 13.73 1.02 0.97 1569.96| | 7: 1.97 - 1.87 2787 165 0.94 10.87 1.02 0.97 626.99| | 8: 1.87 - 1.79 2789 144 0.91 14.45 1.00 0.97 626.99| | 9: 1.79 - 1.72 2745 138 0.93 11.46 0.98 0.97 341.55| | 10: 1.72 - 1.66 2831 160 0.93 12.37 0.98 0.97 284.39| | 11: 1.66 - 1.61 2712 147 0.93 12.99 0.98 0.97 271.24| | 12: 1.61 - 1.56 2773 144 0.95 9.61 0.99 0.97 147.29| | 13: 1.56 - 1.52 2745 130 0.94 11.16 1.02 0.97 147.29| | 14: 1.52 - 1.48 2803 134 0.94 11.33 1.02 0.97 131.20| | 15: 1.48 - 1.45 2738 128 0.95 10.32 1.01 0.98 101.72| | 16: 1.45 - 1.42 2756 161 0.94 11.48 1.02 0.98 101.72| | 17: 1.42 - 1.39 2785 139 0.94 11.36 1.01 0.98 91.79| | 18: 1.39 - 1.36 2741 179 0.94 11.62 1.01 0.98 86.04| | 19: 1.36 - 1.34 2807 134 0.94 12.17 1.00 0.98 86.04| | 20: 1.34 - 1.32 2696 147 0.94 12.39 0.99 0.96 81.54| | 21: 1.32 - 1.30 2785 112 0.94 13.32 0.98 0.96 81.23| | 22: 1.29 - 1.27 2704 152 0.93 13.84 0.98 0.96 81.45| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.95 82.55| | 24: 1.26 - 1.24 2744 132 0.92 14.97 0.97 0.95 82.55| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.94 84.17| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.02 0.93 85.95| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 85.95| | 28: 1.19 - 1.18 2671 147 0.88 20.26 1.01 0.93 89.26| | 29: 1.18 - 1.16 2800 134 0.88 20.60 0.99 0.92 90.50| | 30: 1.16 - 1.15 2739 148 0.86 21.97 0.98 0.92 90.50| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.23 max = 6364.78 mean = 989.52| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.06| |phase err.(test): min = 0.00 max = 89.61 mean = 14.19| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1192 0.1366 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1516 0.1514 0.1576 n_refl.: 87575 remove outliers: r(all,work,free)=0.1516 0.1514 0.1576 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1514 0.1513 0.1575 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1192 0.1367 n_refl.: 87575 remove outliers: r(all,work,free)=0.1200 0.1191 0.1367 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 0.4070 285.290 252.417 0.432 1.001 0.283 11.894-9.307 95.10 93 4 0.2480 476.651 456.947 0.839 1.002 0.204 9.237-7.194 97.27 207 7 0.2454 382.662 377.389 0.913 1.002 0.150 7.162-5.571 100.00 427 22 0.2195 293.044 282.542 0.903 1.002 0.133 5.546-4.326 100.00 867 58 0.1178 402.277 398.249 0.951 1.002 0.130 4.315-3.360 100.00 1859 96 0.0976 382.568 379.789 0.994 1.002 0.130 3.356-2.611 100.00 3867 181 0.1186 251.327 249.301 1.001 1.002 0.110 2.608-2.026 99.99 8198 413 0.1041 166.607 165.743 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0976 81.362 81.623 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1221 36.079 35.714 1.021 0.996 0.000 1.221-1.150 99.97 13689 708 0.2111 22.732 21.368 0.979 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0223 ================= 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: 0.1211 0.1454 0.007 0.937 9.1 119.5 20.1 258 0.125 1_adp: 0.1242 0.1536 0.007 0.937 8.6 118.7 21.1 258 0.125 1_regHadp: 0.1246 0.1539 0.007 0.937 8.6 118.7 21.1 258 0.125 1_occ: 0.1247 0.1541 0.007 0.937 8.6 118.7 21.1 258 0.125 2_bss: 0.1245 0.1535 0.007 0.937 8.7 118.8 21.2 258 0.125 2_settarget: 0.1245 0.1535 0.007 0.937 8.7 118.8 21.2 258 0.125 2_updatecdl: 0.1245 0.1535 0.007 0.944 8.7 118.8 21.2 258 0.125 2_nqh: 0.1246 0.1536 0.007 0.944 8.7 118.8 21.2 258 0.128 2_sol: 0.1238 0.1491 0.007 0.944 8.7 118.8 23.6 428 n/a 2_weight: 0.1238 0.1491 0.007 0.944 8.7 118.8 23.6 428 n/a 2_xyzrec: 0.1230 0.1513 0.007 0.888 8.7 118.8 23.6 428 n/a 2_adp: 0.1197 0.1476 0.007 0.888 8.8 113.8 23.2 428 n/a 2_regHadp: 0.1197 0.1475 0.007 0.888 8.8 113.8 23.2 428 n/a 2_occ: 0.1198 0.1479 0.007 0.888 8.8 113.8 23.2 428 n/a 3_bss: 0.1193 0.1470 0.007 0.888 8.9 113.9 23.3 428 n/a 3_settarget: 0.1193 0.1470 0.007 0.888 8.9 113.9 23.3 428 n/a 3_updatecdl: 0.1193 0.1470 0.007 0.889 8.9 113.9 23.3 428 n/a 3_nqh: 0.1193 0.1470 0.007 0.889 8.9 113.9 23.3 428 n/a 3_sol: 0.1222 0.1466 0.007 0.889 8.9 113.9 22.1 448 n/a 3_weight: 0.1222 0.1466 0.007 0.889 8.9 113.9 22.1 448 n/a 3_xyzrec: 0.1222 0.1433 0.006 0.923 8.9 113.9 22.1 448 n/a 3_adp: 0.1209 0.1389 0.006 0.923 9.2 109.5 21.8 448 n/a 3_regHadp: 0.1210 0.1390 0.006 0.923 9.2 109.5 21.8 448 n/a 3_occ: 0.1206 0.1390 0.006 0.923 9.2 109.5 21.8 448 n/a 4_bss: 0.1195 0.1379 0.006 0.923 9.2 109.4 21.8 448 n/a 4_settarget: 0.1195 0.1379 0.006 0.923 9.2 109.4 21.8 448 n/a 4_updatecdl: 0.1195 0.1379 0.006 0.922 9.2 109.4 21.8 448 n/a 4_nqh: 0.1195 0.1379 0.006 0.922 9.2 109.4 21.8 448 n/a 4_sol: 0.1188 0.1361 0.006 0.922 9.2 109.4 21.6 443 n/a 4_weight: 0.1188 0.1361 0.006 0.922 9.2 109.4 21.6 443 n/a 4_xyzrec: 0.1193 0.1367 0.006 0.944 9.2 109.4 21.6 443 n/a 4_adp: 0.1176 0.1356 0.006 0.944 9.2 105.7 21.3 443 n/a 4_regHadp: 0.1176 0.1356 0.006 0.944 9.2 105.7 21.3 443 n/a 4_occ: 0.1172 0.1353 0.006 0.944 9.2 105.7 21.3 443 n/a 5_bss: 0.1171 0.1356 0.006 0.944 9.2 105.7 21.3 443 n/a 5_settarget: 0.1171 0.1356 0.006 0.944 9.2 105.7 21.3 443 n/a 5_updatecdl: 0.1171 0.1356 0.006 0.945 9.2 105.7 21.3 443 n/a 5_setrh: 0.1172 0.1355 0.006 0.945 9.2 105.7 21.3 443 n/a 5_nqh: 0.1172 0.1355 0.006 0.945 9.2 105.7 21.3 443 n/a 5_sol: 0.1172 0.1348 0.006 0.945 9.2 105.7 21.2 441 n/a 5_weight: 0.1172 0.1348 0.006 0.945 9.2 105.7 21.2 441 n/a 5_xyzrec: 0.1190 0.1368 0.007 1.046 9.2 105.7 21.2 441 n/a 5_adp: 0.1196 0.1370 0.007 1.046 9.3 101.8 21.1 441 n/a 5_regHadp: 0.1196 0.1370 0.007 1.046 9.3 101.8 21.1 441 n/a 5_occ: 0.1192 0.1366 0.007 1.046 9.3 101.8 21.1 441 n/a end: 0.1191 0.1367 0.007 1.046 9.3 101.8 21.1 441 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8540717_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8540717_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7900 Refinement macro-cycles (run) : 3488.1900 Write final files (write_after_run_outputs) : 68.7800 Total : 3561.7600 Total CPU time: 59.98 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:46 PST -0800 (1735452706.13 s) Start R-work = 0.1627, R-free = 0.1719 Final R-work = 0.1191, R-free = 0.1367 =============================================================================== Job complete usr+sys time: 3696.14 seconds wall clock time: 66 minutes 56.42 seconds (4016.42 seconds total)