Starting phenix.refine on Fri Dec 27 17:58:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_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.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.59, per 1000 atoms: 0.47 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: 0.51 Conformation dependent library (CDL) restraints added in 206.6 milliseconds Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 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 1.850 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.824 1.850 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.840 1.850 ... (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 nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "shake_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 = 28.236159 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 0.1581 0.1704 0.0123 0.001 0.4 3.8 0.0 0.0 0 0.125 0.1528 0.1664 0.0137 0.002 0.5 3.8 0.0 0.0 0 0.250 0.1434 0.1593 0.0159 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1381 0.1556 0.0176 0.002 0.5 2.9 0.0 0.0 0 0.750 0.1354 0.1543 0.0189 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1330 0.1524 0.0194 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1286 0.1500 0.0214 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1269 0.1494 0.0224 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1253 0.1484 0.0230 0.003 0.7 2.9 0.5 0.0 0 4.000 0.1245 0.1484 0.0238 0.004 0.7 2.9 0.5 0.0 0 5.000 0.1236 0.1470 0.0235 0.004 0.8 3.2 0.5 0.0 0 6.000 0.1237 0.1476 0.0239 0.005 0.8 3.2 0.5 0.0 0 7.000 0.1234 0.1473 0.0239 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1231 0.1475 0.0244 0.006 0.8 2.9 0.5 0.0 0 9.000 0.1229 0.1470 0.0241 0.006 0.9 3.2 0.5 0.0 0 10.000 0.1226 0.1468 0.0243 0.007 0.9 3.8 0.5 0.6 0 11.000 0.1224 0.1466 0.0242 0.007 0.9 3.2 0.5 0.6 0 12.000 0.1222 0.1469 0.0247 0.007 0.9 2.9 0.5 0.6 0 13.000 0.1223 0.1475 0.0252 0.008 1.0 3.5 0.5 0.6 0 14.118 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1224 0.1466 0.0242 0.007 0.9 3.2 0.5 0.6 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.24 14.66 2.42 3.013 19.053 2006.850 0.017 12.24 14.66 2.42 3.012 19.053 60.206 0.017 12.31 14.62 2.31 2.666 19.052 250.856 0.017 12.65 15.23 2.59 2.724 19.206 1003.425 0.016 12.51 15.45 2.94 3.301 19.624 2006.850 0.016 12.44 15.49 3.06 3.316 19.631 3010.276 0.015 12.30 15.44 3.14 3.377 19.660 4013.701 0.015 12.25 15.39 3.14 3.307 19.593 5017.126 0.015 12.15 15.35 3.19 2.966 19.386 6020.551 0.015 12.19 15.44 3.25 3.333 19.611 7023.976 0.015 12.22 15.54 3.32 3.463 19.664 8027.402 0.015 12.22 15.57 3.35 3.386 19.605 9030.827 0.015 12.23 15.66 3.43 3.600 19.702 10034.252 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 250.856 Accepted refinement result: 12.31 14.62 2.31 2.666 19.052 250.856 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.44 20.08 3.31 0 1785 Protein: 9.07 114.97 16.99 3.31 0 1519 Water: 11.46 119.44 38.22 N/A 0 258 Other: 19.71 26.60 22.05 N/A 0 8 Chain A: 9.07 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1272 20.11 - 31.15 227 31.15 - 42.18 125 42.18 - 53.22 94 53.22 - 64.25 42 64.25 - 75.29 11 75.29 - 86.33 7 86.33 - 97.36 4 97.36 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1462 r_work=0.1233 r_free=0.1465 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1465 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1462 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 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= 0.1227 r_free= 0.1462 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016742 | | target function (ls_wunit_k1) not normalized (work): 1394.593747 | | target function (ls_wunit_k1) not normalized (free): 108.967414 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1238 0.1227 0.1462 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1670 0.1671 0.1691 n_refl.: 87593 remove outliers: r(all,work,free)=0.1670 0.1671 0.1691 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1676 0.1677 0.1695 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1235 0.1224 0.1455 n_refl.: 87593 remove outliers: r(all,work,free)=0.1235 0.1224 0.1455 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 0.3507 301.779 280.990 0.646 1.003 0.375 11.894-9.307 99.02 97 4 0.1616 483.433 471.281 0.923 1.003 0.371 9.237-7.194 100.00 213 7 0.1856 395.389 390.090 0.962 1.004 0.350 7.162-5.571 100.00 427 22 0.1836 296.717 290.864 0.934 1.004 0.264 5.546-4.326 100.00 867 58 0.1003 407.320 404.309 0.966 1.003 0.240 4.315-3.360 100.00 1859 96 0.0873 387.364 386.191 1.006 1.003 0.170 3.356-2.611 100.00 3867 181 0.1171 254.478 253.322 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1018 168.696 167.968 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1108 82.382 82.585 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1449 36.532 36.040 1.019 0.996 0.000 1.221-1.150 99.97 13689 708 0.2246 23.017 21.506 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0518 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1455 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=0.1225 r_free=0.1456 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1456 | n_water=258 | time (s): 2.100 (total time: 2.100) Filter (dist) r_work=0.1234 r_free=0.1455 | n_water=250 | time (s): 23.210 (total time: 25.310) Filter (q & B) r_work=0.1236 r_free=0.1454 | n_water=247 | time (s): 2.430 (total time: 27.740) Compute maps r_work=0.1236 r_free=0.1454 | n_water=247 | time (s): 1.220 (total time: 28.960) Filter (map) r_work=0.1254 r_free=0.1462 | n_water=225 | time (s): 3.100 (total time: 32.060) Find peaks r_work=0.1254 r_free=0.1462 | n_water=225 | time (s): 0.480 (total time: 32.540) Add new water r_work=0.1406 r_free=0.1647 | n_water=437 | time (s): 2.540 (total time: 35.080) Refine new water occ: r_work=0.1310 r_free=0.1507 adp: r_work=0.1227 r_free=0.1446 occ: r_work=0.1241 r_free=0.1433 adp: r_work=0.1205 r_free=0.1417 occ: r_work=0.1208 r_free=0.1403 adp: r_work=0.1198 r_free=0.1401 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1401 r_work=0.1198 r_free=0.1401 | n_water=437 | time (s): 60.350 (total time: 95.430) Filter (q & B) r_work=0.1202 r_free=0.1405 | n_water=420 | time (s): 2.870 (total time: 98.300) Filter (dist only) r_work=0.1202 r_free=0.1403 | n_water=419 | time (s): 36.010 (total time: 134.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.891116 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1496.006136 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 0.1666 0.1770 0.0104 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1532 0.1656 0.0124 0.001 0.4 6.1 0.0 0.0 0 0.250 0.1406 0.1555 0.0149 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1354 0.1510 0.0156 0.002 0.5 5.1 0.0 0.0 0 0.750 0.1333 0.1507 0.0173 0.002 0.5 4.2 0.0 0.0 0 1.000 0.1311 0.1492 0.0181 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1253 0.1455 0.0202 0.002 0.6 3.8 0.5 0.0 0 2.000 0.1228 0.1441 0.0213 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1213 0.1431 0.0218 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1212 0.1433 0.0221 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1206 0.1429 0.0223 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1203 0.1428 0.0225 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1198 0.1424 0.0226 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1197 0.1424 0.0228 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1192 0.1425 0.0233 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1193 0.1425 0.0232 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1192 0.1425 0.0233 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1191 0.1424 0.0233 0.008 0.9 4.5 0.5 0.6 0 13.946 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1424 0.0226 0.005 0.8 4.5 0.5 0.0 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 14.24 2.26 3.773 21.791 1496.006 0.016 11.98 14.24 2.26 3.773 21.791 44.880 0.016 11.98 14.24 2.26 3.773 21.791 187.001 0.016 12.26 14.79 2.53 3.568 21.837 748.003 0.016 12.20 15.05 2.86 3.485 22.179 1496.006 0.015 12.06 15.00 2.94 3.515 21.916 2244.009 0.015 11.92 14.89 2.97 3.501 21.949 2992.012 0.014 11.86 14.92 3.06 3.488 22.005 3740.015 0.014 11.77 14.83 3.05 3.503 21.985 4488.018 0.014 11.79 14.87 3.08 3.519 22.115 5236.021 0.014 11.78 14.93 3.14 3.532 22.114 5984.025 0.014 11.76 14.89 3.13 3.552 22.155 6732.028 0.014 11.74 14.91 3.17 3.585 22.212 7480.031 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.880 Accepted refinement result: 11.98 14.24 2.26 3.773 21.791 44.880 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.00 22.22 3.31 194 1752 Protein: 9.11 115.00 17.02 3.31 0 1519 Water: 11.49 76.69 41.05 N/A 194 225 Other: 19.75 26.63 22.08 N/A 0 8 Chain A: 9.11 115.00 19.44 N/A 0 1752 Chain S: 16.37 60.00 47.30 N/A 194 0 Histogram: Values Number of atoms 9.11 - 19.70 1257 19.70 - 30.29 248 30.29 - 40.88 161 40.88 - 51.47 133 51.47 - 62.05 124 62.05 - 72.64 12 72.64 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1424 r_work=0.1198 r_free=0.1424 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1424 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1419 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1196 r_free= 0.1419 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015414 | | target function (ls_wunit_k1) not normalized (work): 1283.908697 | | target function (ls_wunit_k1) not normalized (free): 102.414976 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1196 0.1419 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1586 0.1585 0.1636 n_refl.: 87592 remove outliers: r(all,work,free)=0.1586 0.1585 0.1636 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1588 0.1587 0.1637 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1192 0.1414 n_refl.: 87592 remove outliers: r(all,work,free)=0.1202 0.1191 0.1414 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3334 297.678 274.491 0.597 1.003 0.354 11.894-9.307 99.02 97 4 0.1607 483.433 475.689 0.916 1.003 0.350 9.237-7.194 100.00 213 7 0.1720 395.389 395.197 0.982 1.003 0.264 7.162-5.571 100.00 427 22 0.1651 296.717 291.717 0.932 1.003 0.230 5.546-4.326 100.00 867 58 0.0896 407.320 404.020 0.960 1.003 0.220 4.315-3.360 100.00 1859 96 0.0796 387.364 386.418 1.005 1.003 0.170 3.356-2.611 100.00 3867 181 0.1087 254.478 253.391 1.010 1.002 0.140 2.608-2.026 99.99 8198 413 0.1014 168.696 168.089 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1108 82.382 82.586 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1447 36.532 36.070 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 23.017 21.525 0.987 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0172 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1414 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1414 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1414 | n_water=419 | time (s): 2.130 (total time: 2.130) Filter (dist) r_work=0.1191 r_free=0.1415 | n_water=417 | time (s): 33.100 (total time: 35.230) Filter (q & B) r_work=0.1191 r_free=0.1415 | n_water=417 | time (s): 0.910 (total time: 36.140) Compute maps r_work=0.1191 r_free=0.1415 | n_water=417 | time (s): 1.700 (total time: 37.840) Filter (map) r_work=0.1238 r_free=0.1404 | n_water=281 | time (s): 2.780 (total time: 40.620) Find peaks r_work=0.1238 r_free=0.1404 | n_water=281 | time (s): 0.470 (total time: 41.090) Add new water r_work=0.1351 r_free=0.1524 | n_water=464 | time (s): 2.510 (total time: 43.600) Refine new water occ: r_work=0.1257 r_free=0.1436 adp: r_work=0.1259 r_free=0.1438 occ: r_work=0.1237 r_free=0.1415 adp: r_work=0.1236 r_free=0.1417 occ: r_work=0.1221 r_free=0.1396 adp: r_work=0.1216 r_free=0.1397 ADP+occupancy (water only), MIN, final r_work=0.1216 r_free=0.1397 r_work=0.1216 r_free=0.1397 | n_water=464 | time (s): 212.090 (total time: 255.690) Filter (q & B) r_work=0.1221 r_free=0.1402 | n_water=430 | time (s): 2.690 (total time: 258.380) Filter (dist only) r_work=0.1222 r_free=0.1401 | n_water=429 | time (s): 37.460 (total time: 295.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.799555 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.878493 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 0.1251 0.1367 0.0117 0.002 0.6 4.5 0.5 0.0 0 0.090 0.1198 0.1330 0.0132 0.003 0.7 3.5 0.5 0.0 0 0.270 0.1183 0.1321 0.0138 0.004 0.8 2.9 0.5 0.0 0 0.540 0.1175 0.1319 0.0144 0.005 0.9 2.9 0.5 0.0 0 0.810 0.1171 0.1317 0.0146 0.006 1.0 2.9 0.5 0.0 0 1.080 0.1168 0.1317 0.0148 0.007 1.0 2.9 0.5 0.0 0 1.350 0.1165 0.1317 0.0151 0.007 1.1 3.5 0.5 0.0 0 1.620 0.1164 0.1318 0.0154 0.008 1.1 3.5 0.5 0.0 0 1.890 0.1175 0.1319 0.0145 0.005 0.9 2.6 0.5 0.0 0 0.900 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1168 0.1317 0.0148 0.007 1.0 2.9 0.5 0.0 0 1.350 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.68 13.17 1.48 3.776 21.209 42.878 3.626 11.68 13.17 1.48 3.776 21.209 1.286 3.626 11.68 13.17 1.48 3.776 21.209 5.360 3.626 11.72 13.24 1.52 3.708 21.199 21.439 3.620 11.78 13.41 1.63 3.728 21.166 42.878 3.623 11.70 13.38 1.67 3.752 21.153 64.318 3.617 11.66 13.34 1.68 3.765 21.148 85.757 3.612 11.62 13.32 1.70 3.775 21.140 107.196 3.609 11.59 13.29 1.70 3.787 21.139 128.635 3.607 11.58 13.32 1.73 3.803 21.128 150.075 3.606 11.56 13.30 1.74 3.811 21.123 171.514 3.605 11.56 13.30 1.75 3.821 21.120 192.953 3.604 11.57 13.34 1.77 3.833 21.113 214.392 3.604 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.360 Accepted refinement result: 11.68 13.17 1.48 3.776 21.209 5.360 3.626 Individual atomic B min max mean iso aniso Overall: 9.12 115.01 21.14 3.31 207 1749 Protein: 9.12 115.01 17.03 3.31 0 1519 Water: 11.50 76.70 35.68 N/A 207 222 Other: 19.76 26.64 22.09 N/A 0 8 Chain A: 9.12 115.01 19.41 N/A 0 1749 Chain S: 16.17 60.01 35.79 N/A 207 0 Histogram: Values Number of atoms 9.12 - 19.71 1261 19.71 - 30.30 289 30.30 - 40.89 210 40.89 - 51.48 118 51.48 - 62.07 55 62.07 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1168 r_free=0.1317 r_work=0.1168 r_free=0.1317 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1168 r_free = 0.1317 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1162 r_free = 0.1319 target_work(ml) = 3.620 | | 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.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1162 r_free= 0.1319 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.620291 | | target function (ml) not normalized (work): 301544.917940 | | target function (ml) not normalized (free): 15863.948115 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1170 0.1162 0.1319 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1495 0.1493 0.1547 n_refl.: 87589 remove outliers: r(all,work,free)=0.1495 0.1493 0.1547 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1495 0.1493 0.1546 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1165 0.1157 0.1314 n_refl.: 87589 remove outliers: r(all,work,free)=0.1162 0.1154 0.1314 n_refl.: 87581 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3810 288.850 266.541 0.493 1.000 0.320 11.894-9.307 97.06 95 4 0.2179 476.759 465.117 0.877 1.001 0.320 9.237-7.194 98.18 209 7 0.2353 386.852 386.457 0.953 1.001 0.200 7.162-5.571 100.00 427 22 0.2188 296.717 284.412 0.918 1.001 0.170 5.546-4.326 100.00 867 58 0.1117 407.320 402.430 0.962 1.002 0.160 4.315-3.360 100.00 1859 96 0.0952 387.364 384.402 1.005 1.002 0.150 3.356-2.611 100.00 3867 181 0.1150 254.478 252.462 1.008 1.002 0.048 2.608-2.026 99.99 8198 413 0.0949 168.696 167.854 1.022 1.001 0.000 2.025-1.573 100.00 17313 902 0.0904 82.382 82.675 1.033 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1263 36.532 36.088 1.023 1.001 0.000 1.221-1.150 99.97 13689 708 0.2166 23.017 21.457 0.980 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0021 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1154 r_free=0.1314 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=0.1154 r_free=0.1314 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1154 r_free=0.1314 | n_water=429 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1154 r_free=0.1315 | n_water=427 | time (s): 47.020 (total time: 49.580) Filter (q & B) r_work=0.1154 r_free=0.1314 | n_water=426 | time (s): 3.970 (total time: 53.550) Compute maps r_work=0.1154 r_free=0.1314 | n_water=426 | time (s): 1.870 (total time: 55.420) Filter (map) r_work=0.1175 r_free=0.1309 | n_water=317 | time (s): 3.990 (total time: 59.410) Find peaks r_work=0.1175 r_free=0.1309 | n_water=317 | time (s): 0.730 (total time: 60.140) Add new water r_work=0.1248 r_free=0.1385 | n_water=491 | time (s): 3.870 (total time: 64.010) Refine new water occ: r_work=0.1173 r_free=0.1326 adp: r_work=0.1174 r_free=0.1328 occ: r_work=0.1158 r_free=0.1311 adp: r_work=0.1157 r_free=0.1312 occ: r_work=0.1146 r_free=0.1299 adp: r_work=0.1143 r_free=0.1300 ADP+occupancy (water only), MIN, final r_work=0.1143 r_free=0.1300 r_work=0.1143 r_free=0.1300 | n_water=491 | time (s): 253.010 (total time: 317.020) Filter (q & B) r_work=0.1151 r_free=0.1307 | n_water=447 | time (s): 3.900 (total time: 320.920) Filter (dist only) r_work=0.1157 r_free=0.1304 | n_water=445 | time (s): 46.710 (total time: 367.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.784861 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.373598 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 0.1342 0.0120 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1181 0.1318 0.0137 0.003 0.8 3.5 0.5 0.0 0 0.268 0.1168 0.1313 0.0145 0.004 0.9 3.5 0.5 0.0 0 0.535 0.1161 0.1308 0.0147 0.006 1.0 3.5 0.5 0.0 0 0.803 0.1157 0.1307 0.0150 0.006 1.0 4.2 0.5 0.0 0 1.071 0.1155 0.1310 0.0155 0.007 1.0 3.5 0.5 0.0 0 1.339 0.1153 0.1310 0.0158 0.008 1.1 3.5 0.5 0.0 0 1.606 0.1151 0.1312 0.0161 0.009 1.1 3.5 0.5 0.0 0 1.874 0.1160 0.1315 0.0156 0.006 1.0 3.8 0.5 0.0 0 0.892 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1157 0.1307 0.0150 0.006 1.0 4.2 0.5 0.0 0 1.071 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 13.07 1.50 3.777 21.197 43.374 3.616 11.57 13.07 1.50 3.777 21.197 1.301 3.616 11.57 13.07 1.50 3.777 21.197 5.422 3.616 11.61 13.13 1.53 3.709 21.188 21.687 3.611 11.66 13.28 1.62 3.727 21.161 43.374 3.614 11.60 13.26 1.66 3.748 21.150 65.060 3.609 11.53 13.19 1.67 3.764 21.148 86.747 3.603 11.51 13.19 1.69 3.772 21.144 108.434 3.601 11.47 13.16 1.69 3.781 21.144 130.121 3.599 11.48 13.22 1.74 3.796 21.132 151.808 3.599 11.46 13.20 1.74 3.805 21.130 173.494 3.597 11.46 13.20 1.75 3.815 21.126 195.181 3.597 11.44 13.19 1.75 3.820 21.127 216.868 3.596 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.422 Accepted refinement result: 11.57 13.07 1.50 3.777 21.197 5.422 3.616 Individual atomic B min max mean iso aniso Overall: 9.12 115.01 21.12 3.31 225 1747 Protein: 9.12 115.01 17.03 3.31 0 1519 Water: 11.50 76.70 35.07 N/A 225 220 Other: 19.76 26.64 22.09 N/A 0 8 Chain A: 9.12 115.01 19.40 N/A 0 1747 Chain S: 16.17 60.01 34.48 N/A 225 0 Histogram: Values Number of atoms 9.12 - 19.71 1263 19.71 - 30.30 299 30.30 - 40.88 218 40.88 - 51.47 118 51.47 - 62.06 51 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1157 r_free=0.1307 r_work=0.1157 r_free=0.1307 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1157 r_free = 0.1307 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1152 r_free = 0.1302 target_work(ml) = 3.614 | | 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.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1152 r_free= 0.1302 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.613691 | | target function (ml) not normalized (work): 300966.292293 | | target function (ml) not normalized (free): 15839.206543 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1160 0.1152 0.1302 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1481 0.1479 0.1530 n_refl.: 87581 remove outliers: r(all,work,free)=0.1481 0.1479 0.1530 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1480 0.1478 0.1530 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1158 0.1151 0.1303 n_refl.: 87581 remove outliers: r(all,work,free)=0.1156 0.1148 0.1303 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 0.3768 288.866 252.422 0.435 1.000 0.275 11.894-9.307 94.12 92 4 0.2440 474.173 454.183 0.853 1.002 0.257 9.237-7.194 98.18 209 7 0.2458 386.852 378.656 0.920 1.002 0.170 7.162-5.571 100.00 427 22 0.2170 296.717 285.466 0.911 1.003 0.150 5.546-4.326 100.00 867 58 0.1154 407.320 402.896 0.964 1.003 0.135 4.315-3.360 100.00 1859 96 0.0944 387.364 384.966 1.005 1.002 0.130 3.356-2.611 100.00 3867 181 0.1135 254.478 252.685 1.011 1.002 0.060 2.608-2.026 99.99 8198 413 0.0931 168.696 168.078 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0895 82.382 82.747 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1257 36.532 36.143 1.029 0.996 0.000 1.221-1.150 99.97 13689 708 0.2171 23.017 21.564 0.991 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0150 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1148 r_free=0.1303 After: r_work=0.1149 r_free=0.1303 ================================== NQH flips ================================== r_work=0.1149 r_free=0.1303 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1149 r_free=0.1303 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1149 r_free=0.1303 | n_water=445 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1149 r_free=0.1303 | n_water=444 | time (s): 46.640 (total time: 49.090) Filter (q & B) r_work=0.1149 r_free=0.1303 | n_water=444 | time (s): 1.410 (total time: 50.500) Compute maps r_work=0.1149 r_free=0.1303 | n_water=444 | time (s): 1.880 (total time: 52.380) Filter (map) r_work=0.1174 r_free=0.1316 | n_water=342 | time (s): 4.100 (total time: 56.480) Find peaks r_work=0.1174 r_free=0.1316 | n_water=342 | time (s): 0.690 (total time: 57.170) Add new water r_work=0.1222 r_free=0.1371 | n_water=481 | time (s): 3.860 (total time: 61.030) Refine new water occ: r_work=0.1168 r_free=0.1313 adp: r_work=0.1169 r_free=0.1316 occ: r_work=0.1157 r_free=0.1303 adp: r_work=0.1156 r_free=0.1305 occ: r_work=0.1148 r_free=0.1297 adp: r_work=0.1146 r_free=0.1298 ADP+occupancy (water only), MIN, final r_work=0.1146 r_free=0.1298 r_work=0.1146 r_free=0.1298 | n_water=481 | time (s): 321.450 (total time: 382.480) Filter (q & B) r_work=0.1152 r_free=0.1310 | n_water=449 | time (s): 4.010 (total time: 386.490) Filter (dist only) r_work=0.1152 r_free=0.1309 | n_water=447 | time (s): 47.200 (total time: 433.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.807545 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.132791 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 0.1237 0.1359 0.0123 0.003 0.7 5.8 0.0 0.0 0 0.090 0.1188 0.1330 0.0141 0.004 0.8 5.8 0.0 0.0 0 0.271 0.1166 0.1316 0.0150 0.005 0.9 5.8 0.5 0.0 0 0.542 0.1155 0.1310 0.0155 0.006 1.0 6.1 0.5 0.0 0 0.813 0.1152 0.1309 0.0157 0.006 1.0 6.1 0.5 0.0 0 1.085 0.1151 0.1309 0.0158 0.007 1.0 6.1 0.5 0.0 0 1.356 0.1150 0.1309 0.0159 0.007 1.0 6.1 0.5 0.0 0 1.627 0.1149 0.1309 0.0160 0.008 1.1 5.8 0.5 0.0 0 1.898 0.1153 0.1309 0.0156 0.006 1.0 6.1 0.5 0.0 0 0.904 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1149 0.1309 0.0160 0.008 1.1 5.8 0.5 0.0 0 1.898 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.49 13.09 1.60 3.777 21.154 41.133 3.611 11.49 13.09 1.60 3.777 21.154 1.234 3.611 11.49 13.09 1.59 3.776 21.154 5.142 3.611 11.52 13.13 1.61 3.710 21.149 20.566 3.606 11.62 13.31 1.70 3.722 21.120 41.133 3.612 11.53 13.28 1.75 3.744 21.110 61.699 3.605 11.47 13.25 1.78 3.761 21.105 82.266 3.600 11.43 13.20 1.77 3.768 21.107 102.832 3.597 11.42 13.22 1.80 3.779 21.102 123.398 3.595 11.39 13.21 1.82 3.787 21.102 143.965 3.594 11.40 13.24 1.84 3.804 21.087 164.531 3.594 11.38 13.22 1.85 3.811 21.088 185.098 3.593 11.38 13.22 1.85 3.820 21.086 205.664 3.592 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.142 Accepted refinement result: 11.49 13.09 1.59 3.776 21.154 5.142 3.611 Individual atomic B min max mean iso aniso Overall: 9.11 115.00 21.05 3.30 229 1745 Protein: 9.11 115.00 17.02 3.31 0 1519 Water: 11.50 76.69 34.70 N/A 229 218 Other: 19.75 26.63 22.09 N/A 0 8 Chain A: 9.11 115.00 19.36 N/A 0 1745 Chain S: 14.92 60.00 33.92 N/A 229 0 Histogram: Values Number of atoms 9.11 - 19.70 1263 19.70 - 30.29 307 30.29 - 40.88 218 40.88 - 51.47 117 51.47 - 62.05 46 62.05 - 72.64 12 72.64 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1149 r_free=0.1309 r_work=0.1149 r_free=0.1309 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1149 r_free = 0.1309 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1308 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1145 r_free= 0.1308 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.609469 | | target function (ml) not normalized (work): 300592.947681 | | target function (ml) not normalized (free): 15827.161085 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1363 0.1388 5.665 5.6129| | 2: 3.57 - 2.84 1.00 2888 124 0.1085 0.1455 5.1795 5.2471| | 3: 2.83 - 2.48 1.00 2820 163 0.1124 0.1253 4.9622 5.0078| | 4: 2.47 - 2.25 1.00 2825 136 0.0908 0.1004 4.6419 4.6778| | 5: 2.25 - 2.09 1.00 2756 127 0.0877 0.0950 4.5899 4.6426| | 6: 2.09 - 1.97 1.00 2846 113 0.0863 0.1026 4.2786 4.3707| | 7: 1.97 - 1.87 1.00 2787 165 0.0889 0.1117 3.986 4.0925| | 8: 1.87 - 1.79 1.00 2789 144 0.0921 0.1108 3.8943 3.9996| | 9: 1.79 - 1.72 1.00 2745 138 0.0876 0.1155 3.6499 3.8088| | 10: 1.72 - 1.66 1.00 2831 160 0.0927 0.1160 3.57 3.7001| | 11: 1.66 - 1.61 1.00 2712 147 0.0877 0.1066 3.4992 3.5883| | 12: 1.61 - 1.56 1.00 2773 144 0.0909 0.1138 3.3362 3.4606| | 13: 1.56 - 1.52 1.00 2745 130 0.0952 0.1055 3.3144 3.4131| | 14: 1.52 - 1.48 1.00 2803 134 0.0984 0.1032 3.2458 3.3177| | 15: 1.48 - 1.45 1.00 2738 128 0.1007 0.1228 3.1573 3.2632| | 16: 1.45 - 1.42 1.00 2756 161 0.1054 0.1257 3.1378 3.246| | 17: 1.42 - 1.39 1.00 2785 139 0.1140 0.1308 3.1219 3.2385| | 18: 1.39 - 1.36 1.00 2741 179 0.1195 0.1319 3.1062 3.2405| | 19: 1.36 - 1.34 1.00 2807 134 0.1265 0.1543 3.1162 3.2603| | 20: 1.34 - 1.32 1.00 2696 147 0.1365 0.1465 3.113 3.1566| | 21: 1.32 - 1.30 1.00 2785 112 0.1474 0.1523 3.1166 3.1197| | 22: 1.29 - 1.27 1.00 2704 152 0.1566 0.1973 3.1264 3.2915| | 23: 1.27 - 1.26 1.00 2802 156 0.1649 0.1784 3.1351 3.2017| | 24: 1.26 - 1.24 1.00 2744 132 0.1707 0.1823 3.128 3.228| | 25: 1.24 - 1.22 1.00 2733 148 0.1879 0.2178 3.1439 3.2682| | 26: 1.22 - 1.21 1.00 2727 135 0.1908 0.1765 3.1493 3.2033| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2163 3.1728 3.1607| | 28: 1.19 - 1.18 1.00 2671 147 0.2205 0.2289 3.1682 3.1712| | 29: 1.18 - 1.16 1.00 2800 134 0.2266 0.2376 3.149 3.2284| | 30: 1.16 - 1.15 1.00 2739 148 0.2444 0.2440 3.1444 3.1651| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2917 171 0.95 8.72 1.00 0.97 5928.81| | 2: 3.57 - 2.84 2888 124 0.92 12.77 1.01 0.97 5928.81| | 3: 2.83 - 2.48 2820 163 0.89 16.70 0.99 0.97 4949.49| | 4: 2.47 - 2.25 2825 136 0.92 13.65 1.00 0.98 2424.14| | 5: 2.25 - 2.09 2756 127 0.90 15.79 1.01 0.98 2424.14| | 6: 2.09 - 1.97 2846 113 0.92 12.50 1.02 0.98 1393.91| | 7: 1.97 - 1.87 2787 165 0.95 9.35 1.02 0.98 515.27| | 8: 1.87 - 1.79 2789 144 0.93 12.66 1.00 0.98 515.27| | 9: 1.79 - 1.72 2745 138 0.94 10.09 0.98 0.97 291.08| | 10: 1.72 - 1.66 2831 160 0.94 11.14 0.98 0.97 246.18| | 11: 1.66 - 1.61 2712 147 0.93 11.78 0.98 0.97 235.93| | 12: 1.61 - 1.56 2773 144 0.95 8.92 0.99 0.97 139.22| | 13: 1.56 - 1.52 2745 130 0.95 10.49 1.03 0.97 139.22| | 14: 1.52 - 1.48 2803 134 0.94 10.82 1.02 0.98 124.85| | 15: 1.48 - 1.45 2738 128 0.95 9.98 1.02 0.98 98.53| | 16: 1.45 - 1.42 2756 161 0.94 11.11 1.02 0.98 98.53| | 17: 1.42 - 1.39 2785 139 0.95 10.96 1.01 0.98 89.72| | 18: 1.39 - 1.36 2741 179 0.94 11.56 1.01 0.98 84.62| | 19: 1.36 - 1.34 2807 134 0.94 11.92 0.99 0.98 84.62| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.97 80.42| | 21: 1.32 - 1.30 2785 112 0.94 13.15 0.98 0.96 80.13| | 22: 1.29 - 1.27 2704 152 0.93 13.67 0.98 0.96 80.51| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.97 0.94 82.41| | 24: 1.26 - 1.24 2744 132 0.92 14.87 0.96 0.94 82.41| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 84.28| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.02 0.93 86.35| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.02 0.93 86.35| | 28: 1.19 - 1.18 2671 147 0.88 20.35 1.01 0.93 89.82| | 29: 1.18 - 1.16 2800 134 0.88 20.43 0.99 0.93 91.12| | 30: 1.16 - 1.15 2739 148 0.86 21.95 0.98 0.93 91.12| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 80.13 max = 5928.81 mean = 910.51| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.95 mean = 13.50| |phase err.(test): min = 0.00 max = 89.81 mean = 13.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1153 0.1145 0.1308 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1460 0.1458 0.1525 n_refl.: 87575 remove outliers: r(all,work,free)=0.1460 0.1458 0.1525 n_refl.: 87575 overall B=-0.00 to atoms: r(all,work,free)=0.1460 0.1457 0.1524 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1153 0.1145 0.1308 n_refl.: 87575 remove outliers: r(all,work,free)=0.1152 0.1144 0.1308 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 0.3929 288.866 253.512 0.441 1.000 0.284 11.894-9.307 93.14 91 4 0.2509 467.782 456.518 0.852 1.001 0.214 9.237-7.194 97.73 208 7 0.2403 386.371 378.676 0.913 1.002 0.166 7.162-5.571 100.00 427 22 0.2169 296.717 285.653 0.908 1.002 0.150 5.546-4.326 100.00 867 58 0.1155 407.320 402.438 0.963 1.002 0.120 4.315-3.360 100.00 1859 96 0.0948 387.364 384.905 1.005 1.002 0.120 3.356-2.611 100.00 3867 181 0.1124 254.478 252.619 1.011 1.002 0.040 2.608-2.026 99.99 8198 413 0.0922 168.696 167.982 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0894 82.382 82.703 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.532 36.125 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 23.017 21.552 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0121 ================= 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: 0.1224 0.1466 0.007 0.925 9.0 119.5 20.1 258 0.128 1_adp: 0.1231 0.1462 0.007 0.925 9.1 119.4 20.1 258 0.128 1_regHadp: 0.1233 0.1465 0.007 0.925 9.1 119.4 20.1 258 0.128 1_occ: 0.1227 0.1462 0.007 0.925 9.1 119.4 20.1 258 0.128 2_bss: 0.1224 0.1455 0.007 0.925 9.1 119.5 20.1 258 0.128 2_settarget: 0.1224 0.1455 0.007 0.925 9.1 119.5 20.1 258 0.128 2_updatecdl: 0.1224 0.1455 0.007 0.943 9.1 119.5 20.1 258 0.128 2_nqh: 0.1225 0.1456 0.007 0.943 9.1 119.5 20.1 258 0.131 2_sol: 0.1202 0.1403 0.007 0.943 9.1 115.0 22.2 419 n/a 2_weight: 0.1202 0.1403 0.007 0.943 9.1 115.0 22.2 419 n/a 2_xyzrec: 0.1198 0.1424 0.005 0.801 9.1 115.0 22.2 419 n/a 2_adp: 0.1198 0.1424 0.005 0.801 9.1 115.0 22.2 419 n/a 2_regHadp: 0.1198 0.1424 0.005 0.801 9.1 115.0 22.2 419 n/a 2_occ: 0.1196 0.1419 0.005 0.801 9.1 115.0 22.2 419 n/a 3_bss: 0.1191 0.1414 0.005 0.801 9.1 115.0 22.2 419 n/a 3_settarget: 0.1191 0.1414 0.005 0.801 9.1 115.0 22.2 419 n/a 3_updatecdl: 0.1191 0.1414 0.005 0.800 9.1 115.0 22.2 419 n/a 3_nqh: 0.1191 0.1414 0.005 0.800 9.1 115.0 22.2 419 n/a 3_sol: 0.1222 0.1401 0.005 0.800 9.1 115.0 21.1 429 n/a 3_weight: 0.1222 0.1401 0.005 0.800 9.1 115.0 21.1 429 n/a 3_xyzrec: 0.1168 0.1317 0.007 1.012 9.1 115.0 21.1 429 n/a 3_adp: 0.1168 0.1317 0.007 1.012 9.1 115.0 21.1 429 n/a 3_regHadp: 0.1168 0.1317 0.007 1.012 9.1 115.0 21.1 429 n/a 3_occ: 0.1162 0.1319 0.007 1.012 9.1 115.0 21.1 429 n/a 4_bss: 0.1154 0.1314 0.007 1.012 9.1 115.0 21.1 429 n/a 4_settarget: 0.1154 0.1314 0.007 1.012 9.1 115.0 21.1 429 n/a 4_updatecdl: 0.1154 0.1314 0.007 1.016 9.1 115.0 21.1 429 n/a 4_nqh: 0.1154 0.1314 0.007 1.016 9.1 115.0 21.1 429 n/a 4_sol: 0.1157 0.1304 0.007 1.016 9.1 115.0 21.1 445 n/a 4_weight: 0.1157 0.1304 0.007 1.016 9.1 115.0 21.1 445 n/a 4_xyzrec: 0.1157 0.1307 0.006 1.008 9.1 115.0 21.1 445 n/a 4_adp: 0.1157 0.1307 0.006 1.008 9.1 115.0 21.1 445 n/a 4_regHadp: 0.1157 0.1307 0.006 1.008 9.1 115.0 21.1 445 n/a 4_occ: 0.1152 0.1302 0.006 1.008 9.1 115.0 21.1 445 n/a 5_bss: 0.1148 0.1303 0.006 1.008 9.1 115.0 21.1 445 n/a 5_settarget: 0.1148 0.1303 0.006 1.008 9.1 115.0 21.1 445 n/a 5_updatecdl: 0.1148 0.1303 0.006 1.007 9.1 115.0 21.1 445 n/a 5_setrh: 0.1149 0.1303 0.006 1.007 9.1 115.0 21.1 445 n/a 5_nqh: 0.1149 0.1303 0.006 1.007 9.1 115.0 21.1 445 n/a 5_sol: 0.1152 0.1309 0.006 1.007 9.1 115.0 21.0 447 n/a 5_weight: 0.1152 0.1309 0.006 1.007 9.1 115.0 21.0 447 n/a 5_xyzrec: 0.1149 0.1309 0.008 1.074 9.1 115.0 21.0 447 n/a 5_adp: 0.1149 0.1309 0.008 1.074 9.1 115.0 21.0 447 n/a 5_regHadp: 0.1149 0.1309 0.008 1.074 9.1 115.0 21.0 447 n/a 5_occ: 0.1145 0.1308 0.008 1.074 9.1 115.0 21.0 447 n/a end: 0.1144 0.1308 0.008 1.074 9.1 115.0 21.0 447 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5296401_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5296401_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1700 Refinement macro-cycles (run) : 13945.0100 Write final files (write_after_run_outputs) : 93.3600 Total : 14041.5400 Total CPU time: 3.91 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:13:50 PST -0800 (1735366430.50 s) Start R-work = 0.1643, R-free = 0.1776 Final R-work = 0.1144, R-free = 0.1308 =============================================================================== Job complete usr+sys time: 14222.98 seconds wall clock time: 257 minutes 59.63 seconds (15479.63 seconds total)