Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5296401.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5296401.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5296401.pdb" 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" } 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): 0.02s 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: 2.34, per 1000 atoms: 0.69 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: 0.96 Conformation dependent library (CDL) restraints added in 310.7 milliseconds Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 473 0.90 - 1.15: 1153 1.15 - 1.40: 570 1.40 - 1.65: 892 1.65 - 1.90: 65 Bond restraints: 3153 Sorted by residual: bond pdb=" C PRO A 54 " pdb=" O PRO A 54 " ideal model delta sigma weight residual 1.233 0.986 0.247 1.21e-02 6.83e+03 4.15e+02 bond pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " ideal model delta sigma weight residual 1.326 1.538 -0.212 1.10e-02 8.26e+03 3.72e+02 bond pdb=" C ARG A 48 " pdb=" O ARG A 48 " ideal model delta sigma weight residual 1.233 0.985 0.249 1.30e-02 5.92e+03 3.66e+02 bond pdb=" N VAL A 25 " pdb=" CA VAL A 25 " ideal model delta sigma weight residual 1.461 1.678 -0.217 1.19e-02 7.06e+03 3.32e+02 bond pdb=" CA THR A 154 " pdb=" C THR A 154 " ideal model delta sigma weight residual 1.523 1.305 0.218 1.25e-02 6.40e+03 3.05e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.51: 3629 5.51 - 11.02: 1759 11.02 - 16.53: 351 16.53 - 22.04: 37 22.04 - 27.56: 1 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " pdb=" CG ASN A 144 " ideal model delta sigma weight residual 112.60 126.53 -13.93 1.00e+00 1.00e+00 1.94e+02 angle pdb=" CA ALA A 103 " pdb=" C ALA A 103 " pdb=" O ALA A 103 " ideal model delta sigma weight residual 120.36 105.78 14.58 1.08e+00 8.57e-01 1.82e+02 angle pdb=" N ILE A 168 " pdb=" CA ILE A 168 " pdb=" C ILE A 168 " ideal model delta sigma weight residual 110.53 98.22 12.31 9.40e-01 1.13e+00 1.71e+02 angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" O ILE A 21 " ideal model delta sigma weight residual 118.69 127.29 -8.60 6.70e-01 2.23e+00 1.65e+02 angle pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " pdb=" CG ASP A 49 " ideal model delta sigma weight residual 112.60 125.19 -12.59 1.00e+00 1.00e+00 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 946 17.78 - 35.55: 110 35.55 - 53.33: 42 53.33 - 71.10: 12 71.10 - 88.88: 1 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 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA LYS A 62 " pdb=" C LYS A 62 " pdb=" N LYS A 63 " pdb=" CA LYS A 63 " ideal model delta harmonic sigma weight residual 180.00 158.62 21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.210: 99 0.210 - 0.419: 84 0.419 - 0.629: 41 0.629 - 0.838: 16 0.838 - 1.047: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BASN A 97 " pdb=" N BASN A 97 " pdb=" C BASN A 97 " pdb=" CB BASN A 97 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" CA GLN A 180 " pdb=" N GLN A 180 " pdb=" C GLN A 180 " pdb=" CB GLN A 180 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.27e+01 chirality pdb=" CA LEU A 10 " pdb=" N LEU A 10 " pdb=" C LEU A 10 " pdb=" CB LEU A 10 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.95e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.001 2.00e-02 2.50e+03 7.55e-02 1.71e+02 pdb=" CG TYR A 139 " -0.131 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.110 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.074 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.038 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.110 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.034 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.000 2.00e-02 2.50e+03 6.93e-02 1.44e+02 pdb=" CG BTYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.115 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.063 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.032 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.124 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.018 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.082 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.076 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " -0.072 2.00e-02 2.50e+03 7.08e-02 1.13e+02 pdb=" CG HIS A 138 " 0.062 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " -0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.108 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.096 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.065 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 800 2.29 - 2.87: 8017 2.87 - 3.45: 10551 3.45 - 4.02: 15288 4.02 - 4.60: 21979 Nonbonded interactions: 56635 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.715 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.735 2.270 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.776 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.824 2.450 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.840 2.450 ... (remaining 56630 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_5296401_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= 0.2612 r_free= 0.1954 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793120 | | target function (ml) not normalized (work): 232683.677301 | | target function (ml) not normalized (free): 11844.089987 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3016 0.2074 7.0089 4.9418| | 2: 3.57 - 2.84 1.00 2876 122 0.2461 0.1947 4.3585 4.363| | 3: 2.84 - 2.48 1.00 2833 165 0.2403 0.1608 4.1358 4.1588| | 4: 2.47 - 2.25 1.00 2825 136 0.2319 0.1443 3.8364 3.8262| | 5: 2.25 - 2.09 1.00 2756 127 0.2465 0.1662 3.8027 3.8335| | 6: 2.09 - 1.97 1.00 2846 113 0.2546 0.1736 3.4664 3.534| | 7: 1.97 - 1.87 1.00 2787 165 0.2530 0.1730 3.1311 3.1572| | 8: 1.87 - 1.79 1.00 2789 144 0.2441 0.1671 3.055 3.1075| | 9: 1.79 - 1.72 1.00 2745 138 0.2435 0.1904 2.9031 2.9776| | 10: 1.72 - 1.66 1.00 2789 158 0.2392 0.2053 2.8058 2.8762| | 11: 1.66 - 1.61 1.00 2740 147 0.2507 0.1961 2.7587 2.7627| | 12: 1.61 - 1.56 1.00 2787 146 0.2567 0.1916 2.6403 2.66| | 13: 1.56 - 1.52 1.00 2745 130 0.2573 0.1919 2.5833 2.6252| | 14: 1.52 - 1.48 1.00 2803 134 0.2581 0.1953 2.5222 2.5446| | 15: 1.48 - 1.45 1.00 2738 128 0.2559 0.2292 2.4353 2.5814| | 16: 1.45 - 1.42 1.00 2756 161 0.2650 0.2226 2.385 2.4564| | 17: 1.42 - 1.39 1.00 2785 139 0.2688 0.2178 2.3417 2.3554| | 18: 1.39 - 1.36 1.00 2741 179 0.2672 0.2338 2.2808 2.3828| | 19: 1.36 - 1.34 1.00 2807 134 0.2699 0.2325 2.2453 2.2826| | 20: 1.34 - 1.32 1.00 2696 147 0.2715 0.2254 2.2098 2.1798| | 21: 1.32 - 1.30 1.00 2785 112 0.2709 0.2272 2.1573 2.1796| | 22: 1.29 - 1.27 1.00 2704 152 0.2701 0.2616 2.1228 2.2549| | 23: 1.27 - 1.26 1.00 2802 156 0.2837 0.2384 2.1245 2.1335| | 24: 1.26 - 1.24 1.00 2744 132 0.2765 0.2501 2.0673 2.1181| | 25: 1.24 - 1.22 1.00 2734 148 0.2878 0.2558 2.0488 2.096| | 26: 1.22 - 1.21 1.00 2727 135 0.2894 0.2262 2.0133 2.09| | 27: 1.21 - 1.19 1.00 2814 148 0.2964 0.2794 2.0041 2.04| | 28: 1.19 - 1.18 1.00 2671 147 0.3015 0.2678 1.989 1.9908| | 29: 1.18 - 1.16 1.00 2800 134 0.3027 0.2906 1.9782 2.0893| | 30: 1.16 - 1.15 1.00 2740 148 0.3070 0.2872 1.9288 1.9677| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.99 0.76 0.23 1501.66| | 2: 3.57 - 2.84 2876 122 0.80 26.25 1.28 0.23 1501.66| | 3: 2.84 - 2.48 2833 165 0.74 32.36 1.25 0.23 1244.15| | 4: 2.47 - 2.25 2825 136 0.81 25.58 1.25 0.25 575.88| | 5: 2.25 - 2.09 2756 127 0.77 29.34 1.28 0.25 575.88| | 6: 2.09 - 1.97 2846 113 0.83 22.64 1.29 0.25 313.31| | 7: 1.97 - 1.87 2787 165 0.90 16.51 1.28 0.26 89.38| | 8: 1.87 - 1.79 2789 144 0.86 20.86 1.25 0.26 89.38| | 9: 1.79 - 1.72 2745 138 0.88 18.56 1.24 0.25 55.29| | 10: 1.72 - 1.66 2789 158 0.86 20.53 1.22 0.25 48.46| | 11: 1.66 - 1.61 2740 147 0.86 21.39 1.24 0.25 46.83| | 12: 1.61 - 1.56 2787 146 0.88 18.74 1.24 0.25 30.28| | 13: 1.56 - 1.52 2745 130 0.87 20.55 1.24 0.25 30.28| | 14: 1.52 - 1.48 2803 134 0.86 20.96 1.23 0.25 27.17| | 15: 1.48 - 1.45 2738 128 0.87 20.49 1.22 0.25 21.47| | 16: 1.45 - 1.42 2756 161 0.86 21.77 1.24 0.25 21.47| | 17: 1.42 - 1.39 2785 139 0.86 21.07 1.23 0.25 18.22| | 18: 1.39 - 1.36 2741 179 0.86 21.49 1.23 0.25 16.34| | 19: 1.36 - 1.34 2807 134 0.85 22.76 1.22 0.25 16.34| | 20: 1.34 - 1.32 2696 147 0.86 21.24 1.21 0.25 13.28| | 21: 1.32 - 1.30 2785 112 0.85 22.26 1.20 0.25 13.06| | 22: 1.29 - 1.27 2704 152 0.85 22.59 1.21 0.24 12.76| | 23: 1.27 - 1.26 2802 156 0.85 22.42 1.22 0.24 11.20| | 24: 1.26 - 1.24 2744 132 0.85 22.83 1.20 0.24 11.20| | 25: 1.24 - 1.22 2734 148 0.84 23.83 1.21 0.24 10.73| | 26: 1.22 - 1.21 2727 135 0.84 24.35 1.21 0.23 10.21| | 27: 1.21 - 1.19 2814 148 0.83 25.16 1.20 0.23 10.21| | 28: 1.19 - 1.18 2671 147 0.82 26.04 1.19 0.23 9.74| | 29: 1.18 - 1.16 2800 134 0.82 26.28 1.17 0.23 9.56| | 30: 1.16 - 1.15 2740 148 0.80 28.11 1.15 0.23 9.56| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.56 max = 1501.66 mean = 217.46| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.94 mean = 22.87| |phase err.(test): min = 0.00 max = 89.96 mean = 22.73| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.257 1557 Z= 5.612 Angle : 5.206 18.205 2118 Z= 3.695 Chirality : 0.361 1.047 243 Planarity : 0.031 0.078 284 Dihedral : 13.883 88.878 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.62 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 30.81 % 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: -3.24 (0.44), residues: 224 helix: -2.80 (0.35), residues: 109 sheet: -0.82 (0.72), residues: 38 loop : -1.43 (0.59), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.115 0.026 ARG A 156 TYR 0.123 0.052 TYR A 141 PHE 0.067 0.030 PHE A 164 HIS 0.051 0.026 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2612 r_free= 0.1954 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793120 | | target function (ml) not normalized (work): 232683.677301 | | target function (ml) not normalized (free): 11844.089987 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2571 0.2613 0.1954 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2571 0.2613 0.1954 n_refl.: 87602 remove outliers: r(all,work,free)=0.1984 0.1988 0.1954 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2008 0.2012 0.1968 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1650 0.1644 0.1776 n_refl.: 87594 remove outliers: r(all,work,free)=0.1650 0.1643 0.1776 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3780 386.377 357.622 0.667 1.002 0.401 11.894-9.307 99.02 97 4 0.1774 613.742 594.433 0.934 1.003 0.380 9.237-7.194 100.00 213 7 0.2125 501.965 491.757 0.956 1.003 0.354 7.162-5.571 100.00 427 22 0.2196 376.697 362.736 0.923 1.003 0.293 5.546-4.326 100.00 867 58 0.1275 517.112 510.727 0.968 1.003 0.259 4.315-3.360 100.00 1859 96 0.1129 491.777 487.351 1.003 1.002 0.148 3.356-2.611 100.00 3867 181 0.1476 323.072 319.653 1.000 1.002 0.109 2.608-2.026 99.99 8198 413 0.1354 214.167 212.059 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1652 104.588 103.899 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2074 46.379 45.066 1.003 0.996 0.000 1.221-1.150 99.97 13689 708 0.2603 29.222 26.942 0.976 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0445 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1643 r_free=0.1776 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1643 r_free=0.1776 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.302946 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2006.850394 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 0.1466 0.0255 0.007 1.0 1.0 0.5 0.0 0 13.151 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.66 2.55 3.013 19.053 2006.850 0.017 12.39 15.39 3.00 3.163 19.528 2006.850 0.016 Individual atomic B min max mean iso aniso Overall: 8.53 118.25 20.98 2.87 0 1785 Protein: 8.53 118.25 17.84 2.87 0 1519 Water: 11.05 114.49 39.22 N/A 0 258 Other: 23.14 36.05 28.99 N/A 0 8 Chain A: 8.53 118.25 20.98 N/A 0 1785 Histogram: Values Number of atoms 8.53 - 19.50 1205 19.50 - 30.47 232 30.47 - 41.44 162 41.44 - 52.42 102 52.42 - 63.39 55 63.39 - 74.36 16 74.36 - 85.33 6 85.33 - 96.30 4 96.30 - 107.27 0 107.27 - 118.25 3 =========================== Idealize ADP of riding H ========================== r_work=0.1240 r_free=0.1539 r_work=0.1244 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1244 r_free = 0.1544 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 = 0.1243 r_free = 0.1545 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1243 r_free= 0.1545 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015319 | | target function (ls_wunit_k1) not normalized (work): 1276.005205 | | target function (ls_wunit_k1) not normalized (free): 114.670559 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1257 0.1243 0.1545 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1696 0.1694 0.1764 n_refl.: 87593 remove outliers: r(all,work,free)=0.1696 0.1694 0.1764 n_refl.: 87593 overall B=0.17 to atoms: r(all,work,free)=0.1724 0.1723 0.1784 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1255 0.1240 0.1538 n_refl.: 87593 remove outliers: r(all,work,free)=0.1254 0.1240 0.1538 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3580 299.159 279.038 0.691 0.924 0.380 11.894-9.307 99.02 97 4 0.1582 479.236 467.054 0.983 0.924 0.380 9.237-7.194 100.00 213 7 0.1822 391.956 386.610 1.025 0.925 0.340 7.162-5.571 100.00 427 22 0.1733 294.141 288.626 0.992 0.925 0.254 5.546-4.326 100.00 867 58 0.0919 403.783 401.095 1.027 0.926 0.230 4.315-3.360 100.00 1859 96 0.0775 384.001 382.991 1.071 0.927 0.169 3.356-2.611 100.00 3867 181 0.1018 252.269 251.572 1.075 0.929 0.109 2.608-2.026 99.99 8198 413 0.0973 167.231 166.625 1.081 0.933 0.000 2.025-1.573 100.00 17313 902 0.1205 81.667 81.847 1.082 0.938 0.000 1.573-1.221 100.00 36679 1900 0.1645 36.214 35.684 1.058 0.947 0.000 1.221-1.150 99.97 13689 708 0.2356 22.818 21.351 1.012 0.955 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0394 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1240 r_free=0.1538 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=0.1241 r_free=0.1539 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1241 r_free=0.1539 | n_water=258 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1250 r_free=0.1539 | n_water=252 | time (s): 26.100 (total time: 28.520) Filter (q & B) r_work=0.1254 r_free=0.1538 | n_water=249 | time (s): 3.570 (total time: 32.090) Compute maps r_work=0.1254 r_free=0.1538 | n_water=249 | time (s): 1.800 (total time: 33.890) Filter (map) r_work=0.1266 r_free=0.1545 | n_water=237 | time (s): 3.860 (total time: 37.750) Find peaks r_work=0.1266 r_free=0.1545 | n_water=237 | time (s): 0.690 (total time: 38.440) Add new water r_work=0.1417 r_free=0.1704 | n_water=447 | time (s): 3.690 (total time: 42.130) Refine new water occ: r_work=0.1332 r_free=0.1573 adp: r_work=0.1254 r_free=0.1522 occ: r_work=0.1267 r_free=0.1512 adp: r_work=0.1233 r_free=0.1499 occ: r_work=0.1237 r_free=0.1488 adp: r_work=0.1227 r_free=0.1488 ADP+occupancy (water only), MIN, final r_work=0.1227 r_free=0.1488 r_work=0.1227 r_free=0.1488 | n_water=447 | time (s): 123.600 (total time: 165.730) Filter (q & B) r_work=0.1234 r_free=0.1492 | n_water=427 | time (s): 3.770 (total time: 169.500) Filter (dist only) r_work=0.1234 r_free=0.1492 | n_water=427 | time (s): 39.480 (total time: 208.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.722299 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1501.106595 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 0.1228 0.1510 0.0282 0.007 0.9 1.9 0.5 0.0 0 12.361 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 15.10 2.82 3.780 23.174 1501.107 0.015 12.01 14.85 2.84 4.208 22.983 1501.107 0.015 Individual atomic B min max mean iso aniso Overall: 8.90 113.42 23.17 2.60 190 1764 Protein: 8.90 113.42 17.64 2.61 0 1519 Water: 11.05 77.17 42.75 N/A 190 237 Other: 24.65 35.73 29.41 N/A 0 8 Chain A: 8.90 113.42 20.37 N/A 0 1764 Chain S: 17.78 77.17 49.23 N/A 190 0 Histogram: Values Number of atoms 8.90 - 19.35 1212 19.35 - 29.80 246 29.80 - 40.26 176 40.26 - 50.71 146 50.71 - 61.16 105 61.16 - 71.61 55 71.61 - 82.06 8 82.06 - 92.52 3 92.52 - 102.97 1 102.97 - 113.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1485 r_work=0.1201 r_free=0.1485 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1485 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 = 0.1200 r_free = 0.1488 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1200 r_free= 0.1488 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013997 | | target function (ls_wunit_k1) not normalized (work): 1165.934012 | | target function (ls_wunit_k1) not normalized (free): 106.557418 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1200 0.1488 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1611 0.1608 0.1713 n_refl.: 87592 remove outliers: r(all,work,free)=0.1611 0.1608 0.1713 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1617 0.1613 0.1716 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1198 0.1485 n_refl.: 87592 remove outliers: r(all,work,free)=0.1211 0.1197 0.1485 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3404 297.718 272.300 0.597 1.001 0.370 11.894-9.307 99.02 97 4 0.1568 479.236 474.786 0.916 1.001 0.370 9.237-7.194 100.00 213 7 0.1705 391.956 391.073 0.979 1.002 0.290 7.162-5.571 100.00 427 22 0.1534 294.141 290.682 0.935 1.002 0.235 5.546-4.326 100.00 867 58 0.0825 403.783 401.549 0.959 1.002 0.214 4.315-3.360 100.00 1859 96 0.0703 384.001 382.911 1.001 1.002 0.200 3.356-2.611 100.00 3867 181 0.0954 252.269 251.606 1.009 1.002 0.067 2.608-2.026 99.99 8198 413 0.0963 167.231 166.856 1.017 1.002 0.000 2.025-1.573 100.00 17313 902 0.1182 81.667 81.895 1.026 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1611 36.214 35.701 1.015 1.002 0.000 1.221-1.150 99.97 13689 708 0.2336 22.818 21.260 0.970 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0554 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1485 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=0.1197 r_free=0.1485 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1485 | n_water=427 | time (s): 1.560 (total time: 1.560) Filter (dist) r_work=0.1199 r_free=0.1484 | n_water=424 | time (s): 36.670 (total time: 38.230) Filter (q & B) r_work=0.1199 r_free=0.1484 | n_water=424 | time (s): 1.440 (total time: 39.670) Compute maps r_work=0.1199 r_free=0.1484 | n_water=424 | time (s): 1.820 (total time: 41.490) Filter (map) r_work=0.1235 r_free=0.1488 | n_water=294 | time (s): 3.440 (total time: 44.930) Find peaks r_work=0.1235 r_free=0.1488 | n_water=294 | time (s): 0.670 (total time: 45.600) Add new water r_work=0.1364 r_free=0.1612 | n_water=486 | time (s): 2.880 (total time: 48.480) Refine new water occ: r_work=0.1266 r_free=0.1529 adp: r_work=0.1266 r_free=0.1530 occ: r_work=0.1245 r_free=0.1505 adp: r_work=0.1242 r_free=0.1506 occ: r_work=0.1229 r_free=0.1490 adp: r_work=0.1222 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1222 r_free=0.1487 r_work=0.1222 r_free=0.1487 | n_water=486 | time (s): 152.410 (total time: 200.890) Filter (q & B) r_work=0.1227 r_free=0.1487 | n_water=449 | time (s): 3.350 (total time: 204.240) Filter (dist only) r_work=0.1227 r_free=0.1485 | n_water=448 | time (s): 37.360 (total time: 241.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.056567 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.859731 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 0.1452 0.0222 0.006 0.9 1.6 0.5 0.0 0 1.028 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 14.52 2.22 3.612 22.094 49.860 3.725 12.16 14.10 1.94 4.129 21.901 49.860 3.656 Individual atomic B min max mean iso aniso Overall: 9.30 108.69 21.67 2.32 213 1762 Protein: 9.30 108.69 17.19 2.32 0 1519 Water: 11.51 71.14 36.79 N/A 213 235 Other: 20.06 31.28 25.68 N/A 0 8 Chain A: 9.30 108.69 19.89 N/A 0 1762 Chain S: 14.86 67.35 36.38 N/A 213 0 Histogram: Values Number of atoms 9.30 - 19.24 1236 19.24 - 29.18 278 29.18 - 39.12 206 39.12 - 49.06 142 49.06 - 59.00 77 59.00 - 68.94 22 68.94 - 78.87 8 78.87 - 88.81 3 88.81 - 98.75 1 98.75 - 108.69 2 =========================== Idealize ADP of riding H ========================== r_work=0.1216 r_free=0.1410 r_work=0.1217 r_free=0.1412 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1217 r_free = 0.1412 target_work(ml) = 3.656 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1211 r_free = 0.1408 target_work(ml) = 3.653 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1211 r_free= 0.1408 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.653150 | | target function (ml) not normalized (work): 304285.454308 | | target function (ml) not normalized (free): 16068.735495 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1211 0.1408 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1543 0.1541 0.1600 n_refl.: 87590 remove outliers: r(all,work,free)=0.1543 0.1541 0.1600 n_refl.: 87590 overall B=-0.02 to atoms: r(all,work,free)=0.1539 0.1538 0.1598 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1199 0.1374 n_refl.: 87590 remove outliers: r(all,work,free)=0.1203 0.1194 0.1374 n_refl.: 87577 ======================== 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 0.3829 288.486 263.636 0.474 1.000 0.302 11.894-9.307 95.10 93 4 0.2309 476.530 454.150 0.852 1.001 0.283 9.237-7.194 97.73 208 7 0.2274 384.569 386.110 0.951 1.002 0.180 7.162-5.571 100.00 427 22 0.2034 294.141 284.436 0.912 1.002 0.167 5.546-4.326 100.00 867 58 0.1107 403.783 399.150 0.954 1.002 0.160 4.315-3.360 100.00 1859 96 0.0923 384.001 381.443 0.994 1.002 0.157 3.356-2.611 100.00 3867 181 0.1156 252.269 250.148 0.999 1.002 0.150 2.608-2.026 99.99 8198 413 0.1047 167.231 166.329 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.1015 81.667 81.818 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1286 36.214 35.796 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2129 22.818 21.442 0.982 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0050 b_overall=-0.0465 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1374 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1195 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1376 | n_water=448 | time (s): 1.540 (total time: 1.540) Filter (dist) r_work=0.1194 r_free=0.1377 | n_water=447 | time (s): 36.850 (total time: 38.390) Filter (q & B) r_work=0.1194 r_free=0.1377 | n_water=447 | time (s): 0.970 (total time: 39.360) Compute maps r_work=0.1194 r_free=0.1377 | n_water=447 | time (s): 1.790 (total time: 41.150) Filter (map) r_work=0.1214 r_free=0.1375 | n_water=317 | time (s): 2.920 (total time: 44.070) Find peaks r_work=0.1214 r_free=0.1375 | n_water=317 | time (s): 0.540 (total time: 44.610) Add new water r_work=0.1282 r_free=0.1430 | n_water=480 | time (s): 2.750 (total time: 47.360) Refine new water occ: r_work=0.1211 r_free=0.1360 adp: r_work=0.1211 r_free=0.1361 occ: r_work=0.1195 r_free=0.1349 adp: r_work=0.1194 r_free=0.1349 occ: r_work=0.1185 r_free=0.1347 adp: r_work=0.1182 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1344 r_work=0.1182 r_free=0.1344 | n_water=480 | time (s): 153.340 (total time: 200.700) Filter (q & B) r_work=0.1190 r_free=0.1350 | n_water=440 | time (s): 3.150 (total time: 203.850) Filter (dist only) r_work=0.1190 r_free=0.1349 | n_water=439 | time (s): 38.540 (total time: 242.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.037127 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.933370 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 0.1189 0.1356 0.0167 0.006 1.0 1.6 0.5 0.0 0 1.019 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.56 1.67 3.413 21.470 46.933 3.635 11.76 13.41 1.66 3.720 21.377 46.933 3.620 Individual atomic B min max mean iso aniso Overall: 9.29 105.25 21.29 2.16 205 1761 Protein: 9.29 105.25 16.96 2.16 0 1519 Water: 11.49 69.91 36.21 N/A 205 234 Other: 19.84 28.68 24.46 N/A 0 8 Chain A: 9.29 105.25 19.61 N/A 0 1761 Chain S: 13.67 59.21 35.70 N/A 205 0 Histogram: Values Number of atoms 9.29 - 18.88 1229 18.88 - 28.48 279 28.48 - 38.08 208 38.08 - 47.67 129 47.67 - 57.27 78 57.27 - 66.87 29 66.87 - 76.46 9 76.46 - 86.06 2 86.06 - 95.66 1 95.66 - 105.25 2 =========================== Idealize ADP of riding H ========================== r_work=0.1176 r_free=0.1341 r_work=0.1176 r_free=0.1342 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1176 r_free = 0.1342 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1173 r_free = 0.1341 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1173 r_free= 0.1341 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.618840 | | target function (ml) not normalized (work): 301380.622711 | | target function (ml) not normalized (free): 15919.288614 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1181 0.1173 0.1341 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1502 0.1502 0.1535 n_refl.: 87577 remove outliers: r(all,work,free)=0.1502 0.1502 0.1535 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1499 0.1499 0.1533 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1181 0.1172 0.1344 n_refl.: 87577 remove outliers: r(all,work,free)=0.1179 0.1170 0.1344 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3812 286.358 254.022 0.458 0.998 0.322 11.894-9.307 93.14 91 4 0.2148 481.145 448.719 0.841 1.001 0.310 9.237-7.194 97.73 208 7 0.2407 384.569 378.052 0.920 1.001 0.130 7.162-5.571 100.00 427 22 0.2176 294.141 283.881 0.904 1.001 0.135 5.546-4.326 100.00 867 58 0.1111 403.783 399.640 0.954 1.001 0.140 4.315-3.360 100.00 1859 96 0.0934 384.001 381.528 0.993 1.001 0.140 3.356-2.611 100.00 3867 181 0.1144 252.269 250.569 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.1009 167.231 166.488 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0972 81.667 81.991 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1241 36.214 35.852 1.020 1.001 0.000 1.221-1.150 99.97 13689 708 0.2119 22.818 21.406 0.975 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0389 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1170 r_free=0.1344 After: r_work=0.1171 r_free=0.1344 ================================== NQH flips ================================== r_work=0.1171 r_free=0.1344 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=0.1171 r_free=0.1344 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1171 r_free=0.1344 | n_water=439 | time (s): 1.610 (total time: 1.610) Filter (dist) r_work=0.1171 r_free=0.1342 | n_water=438 | time (s): 37.630 (total time: 39.240) Filter (q & B) r_work=0.1171 r_free=0.1342 | n_water=438 | time (s): 0.880 (total time: 40.120) Compute maps r_work=0.1171 r_free=0.1342 | n_water=438 | time (s): 1.190 (total time: 41.310) Filter (map) r_work=0.1193 r_free=0.1364 | n_water=337 | time (s): 3.360 (total time: 44.670) Find peaks r_work=0.1193 r_free=0.1364 | n_water=337 | time (s): 0.650 (total time: 45.320) Add new water r_work=0.1243 r_free=0.1408 | n_water=491 | time (s): 2.590 (total time: 47.910) Refine new water occ: r_work=0.1184 r_free=0.1342 adp: r_work=0.1184 r_free=0.1346 occ: r_work=0.1173 r_free=0.1329 adp: r_work=0.1171 r_free=0.1334 occ: r_work=0.1165 r_free=0.1323 adp: r_work=0.1161 r_free=0.1325 ADP+occupancy (water only), MIN, final r_work=0.1161 r_free=0.1325 r_work=0.1161 r_free=0.1325 | n_water=491 | time (s): 187.110 (total time: 235.020) Filter (q & B) r_work=0.1169 r_free=0.1331 | n_water=454 | time (s): 2.770 (total time: 237.790) Filter (dist only) r_work=0.1169 r_free=0.1330 | n_water=453 | time (s): 37.150 (total time: 274.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.936000 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 52.552169 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 0.1198 0.1351 0.0153 0.007 1.0 4.5 0.5 0.0 0 0.968 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.51 1.53 3.297 21.233 52.552 3.628 11.99 13.54 1.56 3.619 21.137 52.552 3.620 Individual atomic B min max mean iso aniso Overall: 9.29 101.16 21.12 2.04 221 1759 Protein: 9.29 101.16 16.69 2.05 0 1519 Water: 11.56 68.56 35.91 N/A 221 232 Other: 19.96 27.95 23.99 N/A 0 8 Chain A: 9.29 101.16 19.29 N/A 0 1759 Chain S: 14.34 59.74 35.64 N/A 221 0 Histogram: Values Number of atoms 9.29 - 18.47 1226 18.47 - 27.66 269 27.66 - 36.85 216 36.85 - 46.04 140 46.04 - 55.22 86 55.22 - 64.41 28 64.41 - 73.60 10 73.60 - 82.78 2 82.78 - 91.97 1 91.97 - 101.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1354 r_work=0.1199 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1355 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1353 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87573 (all), 4.91 % free)------------| | | | r_work= 0.1197 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.619204 | | target function (ml) not normalized (work): 301396.454613 | | target function (ml) not normalized (free): 15930.487852 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2915 171 0.1427 0.1361 5.7053 5.6133| | 2: 3.57 - 2.84 1.00 2888 124 0.1118 0.1424 5.1907 5.2466| | 3: 2.83 - 2.48 1.00 2820 163 0.1235 0.1217 4.9935 5.0058| | 4: 2.47 - 2.25 1.00 2825 136 0.1031 0.1192 4.6991 4.7609| | 5: 2.25 - 2.09 1.00 2756 127 0.0990 0.1119 4.636 4.7138| | 6: 2.09 - 1.97 1.00 2846 113 0.0973 0.1168 4.3467 4.4814| | 7: 1.97 - 1.87 1.00 2787 165 0.0999 0.1187 4.0834 4.1604| | 8: 1.87 - 1.79 1.00 2789 144 0.1025 0.1297 3.9933 4.1017| | 9: 1.79 - 1.72 1.00 2745 138 0.0957 0.1285 3.7191 3.8989| | 10: 1.72 - 1.66 1.00 2831 160 0.0998 0.1249 3.6358 3.7611| | 11: 1.66 - 1.61 1.00 2712 147 0.0953 0.1121 3.5702 3.629| | 12: 1.61 - 1.56 1.00 2773 144 0.0922 0.1177 3.3509 3.4846| | 13: 1.56 - 1.52 1.00 2745 130 0.0972 0.1081 3.3388 3.4481| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1133 3.2587 3.3358| | 15: 1.48 - 1.45 1.00 2738 128 0.0995 0.1341 3.1597 3.3354| | 16: 1.45 - 1.42 1.00 2756 161 0.1057 0.1240 3.1456 3.223| | 17: 1.42 - 1.39 1.00 2785 139 0.1108 0.1290 3.1104 3.2275| | 18: 1.39 - 1.36 1.00 2741 179 0.1142 0.1410 3.0792 3.2751| | 19: 1.36 - 1.34 1.00 2807 134 0.1205 0.1566 3.0873 3.249| | 20: 1.34 - 1.32 1.00 2696 147 0.1314 0.1509 3.0839 3.1411| | 21: 1.32 - 1.30 1.00 2785 112 0.1410 0.1637 3.0841 3.1652| | 22: 1.29 - 1.27 1.00 2704 152 0.1467 0.1882 3.0812 3.2799| | 23: 1.27 - 1.26 1.00 2802 156 0.1561 0.1860 3.0969 3.2103| | 24: 1.26 - 1.24 1.00 2744 132 0.1608 0.1767 3.0886 3.1947| | 25: 1.24 - 1.22 1.00 2733 148 0.1780 0.2286 3.1054 3.2837| | 26: 1.22 - 1.21 1.00 2727 135 0.1855 0.1801 3.1225 3.2016| | 27: 1.21 - 1.19 1.00 2814 148 0.2002 0.2117 3.1403 3.1545| | 28: 1.19 - 1.18 1.00 2671 147 0.2143 0.2340 3.1404 3.1723| | 29: 1.18 - 1.16 1.00 2800 134 0.2205 0.2353 3.1243 3.2191| | 30: 1.16 - 1.15 1.00 2739 148 0.2367 0.2464 3.1128 3.162| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2915 171 0.95 8.77 1.00 0.97 5981.02| | 2: 3.57 - 2.84 2888 124 0.92 12.92 1.01 0.97 5981.02| | 3: 2.83 - 2.48 2820 163 0.89 17.13 0.99 0.97 5021.90| | 4: 2.47 - 2.25 2825 136 0.91 14.30 1.00 0.98 2548.63| | 5: 2.25 - 2.09 2756 127 0.90 16.53 1.01 0.98 2548.63| | 6: 2.09 - 1.97 2846 113 0.92 13.52 1.02 0.97 1512.85| | 7: 1.97 - 1.87 2787 165 0.94 10.87 1.02 0.97 629.48| | 8: 1.87 - 1.79 2789 144 0.91 14.44 1.00 0.97 629.48| | 9: 1.79 - 1.72 2745 138 0.93 11.57 0.98 0.97 344.43| | 10: 1.72 - 1.66 2831 160 0.93 12.45 0.98 0.97 287.35| | 11: 1.66 - 1.61 2712 147 0.93 13.05 0.98 0.97 274.19| | 12: 1.61 - 1.56 2773 144 0.95 9.70 0.99 0.97 150.11| | 13: 1.56 - 1.52 2745 130 0.94 11.24 1.02 0.97 150.11| | 14: 1.52 - 1.48 2803 134 0.94 11.38 1.02 0.97 133.57| | 15: 1.48 - 1.45 2738 128 0.95 10.40 1.01 0.98 103.28| | 16: 1.45 - 1.42 2756 161 0.94 11.58 1.02 0.98 103.28| | 17: 1.42 - 1.39 2785 139 0.94 11.41 1.01 0.98 92.99| | 18: 1.39 - 1.36 2741 179 0.94 11.65 1.01 0.98 87.03| | 19: 1.36 - 1.34 2807 134 0.94 12.25 1.00 0.98 87.03| | 20: 1.34 - 1.32 2696 147 0.94 12.38 0.99 0.97 81.88| | 21: 1.32 - 1.30 2785 112 0.94 13.29 0.98 0.97 81.52| | 22: 1.29 - 1.27 2704 152 0.93 13.82 0.98 0.96 81.72| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.98 0.95 82.73| | 24: 1.26 - 1.24 2744 132 0.92 14.93 0.97 0.95 82.73| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 84.36| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.03 0.93 86.18| | 27: 1.21 - 1.19 2814 148 0.89 18.72 1.02 0.93 86.18| | 28: 1.19 - 1.18 2671 147 0.88 20.25 1.01 0.93 89.60| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.93 90.89| | 30: 1.16 - 1.15 2739 148 0.86 21.97 0.98 0.93 90.89| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 81.52 max = 5981.02 mean = 942.66| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 13.99| |phase err.(test): min = 0.00 max = 89.52 mean = 14.10| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1197 0.1353 n_refl.: 87573 re-set all scales: r(all,work,free)=0.1511 0.1509 0.1560 n_refl.: 87573 remove outliers: r(all,work,free)=0.1511 0.1509 0.1560 n_refl.: 87573 overall B=-0.01 to atoms: r(all,work,free)=0.1508 0.1507 0.1558 n_refl.: 87573 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1197 0.1355 n_refl.: 87573 remove outliers: r(all,work,free)=0.1205 0.1197 0.1355 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.4019 286.358 251.708 0.434 0.999 0.308 11.894-9.307 93.14 91 4 0.2372 481.145 459.879 0.863 1.001 0.236 9.237-7.194 97.73 208 7 0.2534 384.569 375.519 0.908 1.001 0.147 7.162-5.571 100.00 427 22 0.2299 294.141 282.768 0.896 1.001 0.120 5.546-4.326 100.00 867 58 0.1201 403.783 399.094 0.953 1.001 0.120 4.315-3.360 100.00 1859 96 0.0998 384.001 381.600 0.995 1.001 0.118 3.356-2.611 100.00 3867 181 0.1188 252.269 250.263 1.000 1.001 0.053 2.608-2.026 99.99 8198 413 0.1044 167.231 166.252 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0977 81.667 81.899 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1218 36.214 35.845 1.021 0.999 0.000 1.221-1.150 99.97 13689 708 0.2110 22.818 21.421 0.976 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0381 ================= 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 : 0.2612 0.1954 0.084 5.206 8.8 119.3 19.9 258 0.000 1_bss: 0.1643 0.1776 0.084 5.206 9.0 119.5 20.1 258 0.000 1_settarget: 0.1643 0.1776 0.084 5.206 9.0 119.5 20.1 258 0.000 1_nqh: 0.1643 0.1776 0.084 5.206 9.0 119.5 20.1 258 0.000 1_weight: 0.1643 0.1776 0.084 5.206 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1211 0.1466 0.007 0.954 9.0 119.5 20.1 258 0.122 1_adp: 0.1240 0.1539 0.007 0.954 8.5 118.2 21.0 258 0.122 1_regHadp: 0.1244 0.1544 0.007 0.954 8.5 118.2 21.0 258 0.122 1_occ: 0.1243 0.1545 0.007 0.954 8.5 118.2 21.0 258 0.122 2_bss: 0.1240 0.1538 0.007 0.954 8.7 118.4 21.2 258 0.122 2_settarget: 0.1240 0.1538 0.007 0.954 8.7 118.4 21.2 258 0.122 2_updatecdl: 0.1240 0.1538 0.007 0.970 8.7 118.4 21.2 258 0.122 2_nqh: 0.1241 0.1539 0.007 0.970 8.7 118.4 21.2 258 0.125 2_sol: 0.1234 0.1492 0.007 0.970 8.7 118.4 23.5 427 n/a 2_weight: 0.1234 0.1492 0.007 0.970 8.7 118.4 23.5 427 n/a 2_xyzrec: 0.1228 0.1510 0.007 0.875 8.7 118.4 23.5 427 n/a 2_adp: 0.1201 0.1485 0.007 0.875 8.9 113.4 23.2 427 n/a 2_regHadp: 0.1201 0.1485 0.007 0.875 8.9 113.4 23.2 427 n/a 2_occ: 0.1200 0.1488 0.007 0.875 8.9 113.4 23.2 427 n/a 3_bss: 0.1197 0.1485 0.007 0.875 8.9 113.5 23.2 427 n/a 3_settarget: 0.1197 0.1485 0.007 0.875 8.9 113.5 23.2 427 n/a 3_updatecdl: 0.1197 0.1485 0.007 0.876 8.9 113.5 23.2 427 n/a 3_nqh: 0.1197 0.1485 0.007 0.876 8.9 113.5 23.2 427 n/a 3_sol: 0.1227 0.1485 0.007 0.876 8.9 113.5 22.0 448 n/a 3_weight: 0.1227 0.1485 0.007 0.876 8.9 113.5 22.0 448 n/a 3_xyzrec: 0.1230 0.1452 0.006 0.918 8.9 113.5 22.0 448 n/a 3_adp: 0.1216 0.1410 0.006 0.918 9.3 108.7 21.7 448 n/a 3_regHadp: 0.1217 0.1412 0.006 0.918 9.3 108.7 21.7 448 n/a 3_occ: 0.1211 0.1408 0.006 0.918 9.3 108.7 21.7 448 n/a 4_bss: 0.1194 0.1374 0.006 0.918 9.3 108.7 21.6 448 n/a 4_settarget: 0.1194 0.1374 0.006 0.918 9.3 108.7 21.6 448 n/a 4_updatecdl: 0.1194 0.1374 0.006 0.917 9.3 108.7 21.6 448 n/a 4_nqh: 0.1195 0.1376 0.006 0.917 9.3 108.7 21.6 448 n/a 4_sol: 0.1190 0.1349 0.006 0.917 9.3 108.7 21.5 439 n/a 4_weight: 0.1190 0.1349 0.006 0.917 9.3 108.7 21.5 439 n/a 4_xyzrec: 0.1189 0.1356 0.006 0.959 9.3 108.7 21.5 439 n/a 4_adp: 0.1176 0.1341 0.006 0.959 9.3 105.3 21.3 439 n/a 4_regHadp: 0.1176 0.1342 0.006 0.959 9.3 105.3 21.3 439 n/a 4_occ: 0.1173 0.1341 0.006 0.959 9.3 105.3 21.3 439 n/a 5_bss: 0.1170 0.1344 0.006 0.959 9.3 105.2 21.3 439 n/a 5_settarget: 0.1170 0.1344 0.006 0.959 9.3 105.2 21.3 439 n/a 5_updatecdl: 0.1170 0.1344 0.006 0.959 9.3 105.2 21.3 439 n/a 5_setrh: 0.1171 0.1344 0.006 0.959 9.3 105.2 21.3 439 n/a 5_nqh: 0.1171 0.1344 0.006 0.959 9.3 105.2 21.3 439 n/a 5_sol: 0.1169 0.1330 0.006 0.959 9.3 105.2 21.3 453 n/a 5_weight: 0.1169 0.1330 0.006 0.959 9.3 105.2 21.3 453 n/a 5_xyzrec: 0.1198 0.1351 0.007 1.043 9.3 105.2 21.3 453 n/a 5_adp: 0.1199 0.1354 0.007 1.043 9.3 101.2 21.1 453 n/a 5_regHadp: 0.1199 0.1355 0.007 1.043 9.3 101.2 21.1 453 n/a 5_occ: 0.1197 0.1353 0.007 1.043 9.3 101.2 21.1 453 n/a end: 0.1197 0.1355 0.007 1.043 9.3 101.1 21.1 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5296401_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5296401_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.6900 Refinement macro-cycles (run) : 3332.8100 Write final files (write_after_run_outputs) : 75.8000 Total : 3413.3000 Total CPU time: 57.51 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:09:18 PST -0800 (1735452558.09 s) Start R-work = 0.1643, R-free = 0.1776 Final R-work = 0.1197, R-free = 0.1355 =============================================================================== Job complete usr+sys time: 3566.74 seconds wall clock time: 64 minutes 47.64 seconds (3887.64 seconds total)