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_6470396.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6470396.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6470396.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 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: 1.87, per 1000 atoms: 0.55 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 118.0 milliseconds Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 498 0.91 - 1.15: 1124 1.15 - 1.40: 600 1.40 - 1.65: 853 1.65 - 1.90: 78 Bond restraints: 3153 Sorted by residual: bond pdb=" C BGLU A 94 " pdb=" O BGLU A 94 " ideal model delta sigma weight residual 1.237 1.448 -0.211 1.19e-02 7.06e+03 3.15e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.150 0.171 1.00e-02 1.00e+04 2.93e+02 bond pdb=" CA ALA A 114 " pdb=" C ALA A 114 " ideal model delta sigma weight residual 1.523 1.739 -0.216 1.30e-02 5.92e+03 2.76e+02 bond pdb=" C LYS A 63 " pdb=" O LYS A 63 " ideal model delta sigma weight residual 1.236 1.444 -0.209 1.29e-02 6.01e+03 2.61e+02 bond pdb=" CA ALA A 14 " pdb=" C ALA A 14 " ideal model delta sigma weight residual 1.525 1.731 -0.207 1.28e-02 6.10e+03 2.61e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.01: 3319 5.01 - 10.01: 1843 10.01 - 15.02: 551 15.02 - 20.03: 59 20.03 - 25.03: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O AGLU A 96 " pdb=" C AGLU A 96 " pdb=" N AASN A 97 " ideal model delta sigma weight residual 122.07 106.39 15.68 1.03e+00 9.43e-01 2.32e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.19 135.28 -14.09 9.40e-01 1.13e+00 2.25e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH1 ARG A 28 " ideal model delta sigma weight residual 121.50 106.70 14.80 1.00e+00 1.00e+00 2.19e+02 angle pdb=" O ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 122.12 136.28 -14.16 1.06e+00 8.90e-01 1.78e+02 angle pdb=" N ILE A 9 " pdb=" CA ILE A 9 " pdb=" CB ILE A 9 " ideal model delta sigma weight residual 111.21 126.44 -15.23 1.17e+00 7.31e-01 1.69e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 16.51: 919 16.51 - 33.00: 130 33.00 - 49.49: 43 49.49 - 65.98: 16 65.98 - 82.47: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -158.79 -21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.290: 124 0.290 - 0.576: 87 0.576 - 0.862: 28 0.862 - 1.148: 3 1.148 - 1.434: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.16 -1.43 2.00e-01 2.50e+01 5.14e+01 chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -3.64 1.01 2.00e-01 2.50e+01 2.54e+01 chirality pdb=" CA BGLU A 96 " pdb=" N BGLU A 96 " pdb=" C BGLU A 96 " pdb=" CB BGLU A 96 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.11e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.074 2.00e-02 2.50e+03 5.88e-02 1.04e+02 pdb=" CG ATYR A 67 " -0.079 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.115 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.074 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.067 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.053 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.020 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.035 2.00e-02 2.50e+03 6.75e-02 1.03e+02 pdb=" CG HIS A 115 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.115 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.029 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.113 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " 0.073 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.036 2.00e-02 2.50e+03 5.67e-02 9.65e+01 pdb=" CG TYR A 141 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.022 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.078 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.067 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.086 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.093 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 1194 2.34 - 2.91: 8234 2.91 - 3.47: 10532 3.47 - 4.04: 15142 4.04 - 4.60: 21506 Nonbonded interactions: 56608 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.780 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.791 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.801 1.850 x-y,-y,-z-4/3 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.825 1.850 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.834 1.850 ... (remaining 56603 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_6470396_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= 0.2604 r_free= 0.1929 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.786796 | | target function (ml) not normalized (work): 232156.846880 | | target function (ml) not normalized (free): 11812.053274 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3035 0.2054 7.1158 4.9435| | 2: 3.57 - 2.84 1.00 2876 122 0.2419 0.1779 4.3448 4.3276| | 3: 2.84 - 2.48 1.00 2833 165 0.2346 0.1598 4.121 4.13| | 4: 2.47 - 2.25 1.00 2825 136 0.2322 0.1395 3.8283 3.8233| | 5: 2.25 - 2.09 1.00 2756 127 0.2506 0.1609 3.7892 3.8127| | 6: 2.09 - 1.97 1.00 2846 113 0.2580 0.1685 3.4757 3.4885| | 7: 1.97 - 1.87 1.00 2787 165 0.2559 0.1895 3.1299 3.2281| | 8: 1.87 - 1.79 1.00 2789 144 0.2446 0.1901 3.0508 3.1652| | 9: 1.79 - 1.72 1.00 2745 138 0.2422 0.1914 2.8966 2.9627| | 10: 1.72 - 1.66 1.00 2789 158 0.2442 0.1884 2.8094 2.8665| | 11: 1.66 - 1.61 1.00 2740 147 0.2481 0.1769 2.7303 2.7315| | 12: 1.61 - 1.56 1.00 2787 146 0.2479 0.2192 2.6119 2.7033| | 13: 1.56 - 1.52 1.00 2745 130 0.2530 0.1912 2.5587 2.6293| | 14: 1.52 - 1.48 1.00 2803 134 0.2542 0.1982 2.4971 2.5443| | 15: 1.48 - 1.45 1.00 2738 128 0.2535 0.2267 2.3983 2.5317| | 16: 1.45 - 1.42 1.00 2756 161 0.2617 0.2220 2.3682 2.4624| | 17: 1.42 - 1.39 1.00 2785 139 0.2643 0.2016 2.3114 2.3174| | 18: 1.39 - 1.36 1.00 2741 179 0.2642 0.2242 2.2596 2.3173| | 19: 1.36 - 1.34 1.00 2807 134 0.2716 0.2322 2.2431 2.2481| | 20: 1.34 - 1.32 1.00 2696 147 0.2625 0.2202 2.2065 2.1839| | 21: 1.32 - 1.30 1.00 2785 112 0.2699 0.2215 2.1618 2.1567| | 22: 1.29 - 1.27 1.00 2704 152 0.2763 0.2503 2.1228 2.1938| | 23: 1.27 - 1.26 1.00 2802 156 0.2782 0.2460 2.1077 2.1813| | 24: 1.26 - 1.24 1.00 2744 132 0.2766 0.2536 2.0676 2.1902| | 25: 1.24 - 1.22 1.00 2734 148 0.2847 0.2732 2.0522 2.1287| | 26: 1.22 - 1.21 1.00 2727 135 0.2872 0.2058 2.0141 2.0334| | 27: 1.21 - 1.19 1.00 2814 148 0.2967 0.2621 1.9978 1.9944| | 28: 1.19 - 1.18 1.00 2671 147 0.3034 0.2689 1.9919 1.9789| | 29: 1.18 - 1.16 1.00 2800 134 0.2983 0.2941 1.9591 2.0843| | 30: 1.16 - 1.15 1.00 2740 148 0.3011 0.2764 1.9223 1.9647| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.65 0.76 0.23 1461.79| | 2: 3.57 - 2.84 2876 122 0.81 25.75 1.27 0.23 1461.79| | 3: 2.84 - 2.48 2833 165 0.74 31.79 1.24 0.24 1211.77| | 4: 2.47 - 2.25 2825 136 0.81 25.35 1.25 0.25 562.91| | 5: 2.25 - 2.09 2756 127 0.77 29.29 1.29 0.25 562.91| | 6: 2.09 - 1.97 2846 113 0.83 22.60 1.30 0.25 307.60| | 7: 1.97 - 1.87 2787 165 0.90 16.38 1.28 0.26 89.86| | 8: 1.87 - 1.79 2789 144 0.86 20.84 1.25 0.26 89.86| | 9: 1.79 - 1.72 2745 138 0.88 18.86 1.23 0.25 56.16| | 10: 1.72 - 1.66 2789 158 0.86 20.45 1.22 0.25 49.42| | 11: 1.66 - 1.61 2740 147 0.85 21.64 1.25 0.25 47.68| | 12: 1.61 - 1.56 2787 146 0.88 18.79 1.23 0.25 30.11| | 13: 1.56 - 1.52 2745 130 0.86 20.85 1.24 0.25 30.11| | 14: 1.52 - 1.48 2803 134 0.86 20.79 1.23 0.25 26.82| | 15: 1.48 - 1.45 2738 128 0.87 20.17 1.23 0.25 20.79| | 16: 1.45 - 1.42 2756 161 0.85 21.81 1.24 0.25 20.79| | 17: 1.42 - 1.39 2785 139 0.87 20.70 1.23 0.25 17.49| | 18: 1.39 - 1.36 2741 179 0.86 21.07 1.23 0.25 15.58| | 19: 1.36 - 1.34 2807 134 0.86 21.96 1.23 0.25 15.58| | 20: 1.34 - 1.32 2696 147 0.87 20.68 1.19 0.24 12.82| | 21: 1.32 - 1.30 2785 112 0.86 21.97 1.20 0.24 12.63| | 22: 1.29 - 1.27 2704 152 0.85 22.55 1.21 0.24 12.37| | 23: 1.27 - 1.26 2802 156 0.86 22.22 1.22 0.24 11.05| | 24: 1.26 - 1.24 2744 132 0.85 22.87 1.20 0.24 11.05| | 25: 1.24 - 1.22 2734 148 0.84 23.64 1.20 0.23 10.53| | 26: 1.22 - 1.21 2727 135 0.84 24.16 1.19 0.23 9.97| | 27: 1.21 - 1.19 2814 148 0.83 25.07 1.21 0.23 9.97| | 28: 1.19 - 1.18 2671 147 0.82 25.58 1.19 0.23 9.41| | 29: 1.18 - 1.16 2800 134 0.82 25.82 1.17 0.23 9.20| | 30: 1.16 - 1.15 2740 148 0.81 27.15 1.16 0.23 9.20| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.20 max = 1461.79 mean = 212.38| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.65| |phase err.(test): min = 0.00 max = 89.65 mean = 22.45| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.236 1557 Z= 5.511 Angle : 5.297 17.365 2118 Z= 3.728 Chirality : 0.379 1.434 243 Planarity : 0.033 0.094 284 Dihedral : 14.260 82.471 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 27.03 % 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: -3.02 (0.45), residues: 224 helix: -2.90 (0.39), residues: 103 sheet: -0.84 (0.85), residues: 28 loop : -1.00 (0.52), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.021 ARG A 156 TYR 0.078 0.030 TYR A 139 PHE 0.110 0.041 PHE A 162 HIS 0.075 0.030 HIS A 126 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= 0.2604 r_free= 0.1929 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.786796 | | target function (ml) not normalized (work): 232156.846880 | | target function (ml) not normalized (free): 11812.053274 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2562 0.2605 0.1929 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2562 0.2605 0.1929 n_refl.: 87602 remove outliers: r(all,work,free)=0.1971 0.1975 0.1929 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.1994 0.2000 0.1941 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1631 0.1625 0.1748 n_refl.: 87594 remove outliers: r(all,work,free)=0.1629 0.1623 0.1748 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.87 87 5 0.3750 389.599 354.282 0.729 0.917 0.401 11.894-9.307 98.04 96 4 0.1712 616.156 590.608 1.004 0.917 0.380 9.237-7.194 100.00 213 7 0.2181 501.903 490.898 1.045 0.917 0.358 7.162-5.571 100.00 427 22 0.2191 376.650 365.014 1.021 0.918 0.296 5.546-4.326 100.00 867 58 0.1255 517.047 511.590 1.052 0.918 0.224 4.315-3.360 100.00 1859 96 0.1129 491.716 489.013 1.099 0.919 0.199 3.356-2.611 100.00 3867 181 0.1428 323.032 319.929 1.082 0.921 0.119 2.608-2.026 99.99 8198 413 0.1369 214.141 211.639 1.091 0.924 0.000 2.025-1.573 100.00 17313 902 0.1627 104.575 104.056 1.091 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2032 46.373 45.159 1.068 0.935 0.000 1.221-1.150 99.97 13689 708 0.2572 29.218 26.972 1.034 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0446 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1623 r_free=0.1748 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=0.1625 r_free=0.1749 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.518466 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1992.909061 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 0.1678 0.1805 0.0127 0.002 0.4 4.8 0.0 0.0 0 0.125 0.1498 0.1650 0.0151 0.001 0.5 3.8 0.0 0.0 0 0.250 0.1438 0.1608 0.0170 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1364 0.1552 0.0188 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1326 0.1525 0.0199 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1365 0.1564 0.0199 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1283 0.1504 0.0221 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1266 0.1493 0.0227 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1250 0.1481 0.0230 0.004 0.7 3.5 0.5 0.0 0 4.000 0.1242 0.1470 0.0228 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1236 0.1466 0.0230 0.005 0.8 3.8 0.5 0.0 0 6.000 0.1234 0.1463 0.0229 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1231 0.1464 0.0233 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1230 0.1464 0.0234 0.006 0.9 3.2 0.5 0.0 0 9.000 0.1226 0.1459 0.0233 0.006 0.9 3.2 0.5 0.0 0 10.000 0.1226 0.1464 0.0238 0.007 0.9 3.2 0.5 0.0 0 11.000 0.1222 0.1457 0.0236 0.007 0.9 3.2 0.5 0.0 0 12.000 0.1220 0.1463 0.0243 0.008 1.0 3.5 0.5 0.6 0 13.759 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1222 0.1457 0.0236 0.007 0.9 3.2 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.22 14.57 2.36 3.013 19.052 1992.909 0.017 12.22 14.57 2.35 2.995 19.052 59.787 0.017 12.29 14.54 2.25 2.666 19.052 249.114 0.017 12.63 15.19 2.56 2.740 19.222 996.455 0.016 12.52 15.38 2.87 3.353 19.655 1992.909 0.015 12.33 15.28 2.96 3.154 19.549 2989.364 0.015 12.33 15.42 3.10 3.459 19.707 3985.818 0.015 12.29 15.42 3.14 3.415 19.669 4982.273 0.015 12.20 15.41 3.20 3.422 19.675 5978.727 0.015 12.16 15.39 3.23 3.400 19.653 6975.182 0.015 12.20 15.51 3.31 3.549 19.715 7971.636 0.015 12.22 15.60 3.39 3.500 19.677 8968.091 0.014 12.17 15.57 3.40 3.635 19.739 9964.545 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: 249.114 Accepted refinement result: 12.29 14.54 2.25 2.666 19.052 249.114 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.44 20.08 3.31 0 1785 Protein: 9.08 114.97 16.99 3.31 0 1519 Water: 11.44 119.44 38.22 N/A 0 258 Other: 19.72 26.59 22.05 N/A 0 8 Chain A: 9.08 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.15 227 31.15 - 42.19 125 42.19 - 53.22 94 53.22 - 64.26 42 64.26 - 75.30 11 75.30 - 86.33 7 86.33 - 97.37 4 97.37 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1229 r_free=0.1454 r_work=0.1230 r_free=0.1458 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1458 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 = 0.1225 r_free = 0.1451 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1225 r_free= 0.1451 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016625 | | target function (ls_wunit_k1) not normalized (work): 1384.775230 | | target function (ls_wunit_k1) not normalized (free): 108.789787 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1236 0.1225 0.1451 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1666 0.1667 0.1686 n_refl.: 87591 remove outliers: r(all,work,free)=0.1666 0.1667 0.1686 n_refl.: 87591 overall B=0.04 to atoms: r(all,work,free)=0.1673 0.1674 0.1690 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1235 0.1224 0.1446 n_refl.: 87591 remove outliers: r(all,work,free)=0.1235 0.1224 0.1446 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 94.79 86 5 0.3458 303.913 284.962 0.642 1.003 0.375 11.894-9.307 98.04 96 4 0.1600 484.690 472.150 0.927 1.003 0.371 9.237-7.194 100.00 213 7 0.1896 394.814 389.222 0.963 1.003 0.350 7.162-5.571 100.00 427 22 0.1838 296.286 290.230 0.938 1.003 0.259 5.546-4.326 100.00 867 58 0.1008 406.728 403.647 0.962 1.003 0.204 4.315-3.360 100.00 1859 96 0.0866 386.801 385.811 1.009 1.003 0.180 3.356-2.611 100.00 3867 181 0.1167 254.108 252.963 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1017 168.450 167.753 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1110 82.262 82.452 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1450 36.479 35.986 1.019 0.996 0.000 1.221-1.150 99.97 13689 708 0.2253 22.984 21.468 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0553 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1446 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=0.1224 r_free=0.1446 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1446 | n_water=258 | time (s): 2.020 (total time: 2.020) Filter (dist) r_work=0.1234 r_free=0.1445 | n_water=251 | time (s): 23.050 (total time: 25.070) Filter (q & B) r_work=0.1236 r_free=0.1445 | n_water=248 | time (s): 3.380 (total time: 28.450) Compute maps r_work=0.1236 r_free=0.1445 | n_water=248 | time (s): 1.410 (total time: 29.860) Filter (map) r_work=0.1249 r_free=0.1451 | n_water=228 | time (s): 2.530 (total time: 32.390) Find peaks r_work=0.1249 r_free=0.1451 | n_water=228 | time (s): 0.650 (total time: 33.040) Add new water r_work=0.1385 r_free=0.1626 | n_water=427 | time (s): 2.850 (total time: 35.890) Refine new water occ: r_work=0.1295 r_free=0.1479 adp: r_work=0.1223 r_free=0.1433 occ: r_work=0.1234 r_free=0.1417 adp: r_work=0.1204 r_free=0.1406 occ: r_work=0.1206 r_free=0.1389 adp: r_work=0.1196 r_free=0.1390 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1390 r_work=0.1196 r_free=0.1390 | n_water=427 | time (s): 66.090 (total time: 101.980) Filter (q & B) r_work=0.1199 r_free=0.1399 | n_water=409 | time (s): 3.110 (total time: 105.090) Filter (dist only) r_work=0.1200 r_free=0.1396 | n_water=408 | time (s): 33.480 (total time: 138.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.469279 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1478.189242 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 0.1574 0.1698 0.0124 0.001 0.4 6.7 0.0 0.0 0 0.125 0.1512 0.1645 0.0133 0.001 0.4 5.8 0.0 0.0 0 0.250 0.1407 0.1565 0.0158 0.002 0.4 4.8 0.0 0.0 0 0.500 0.1354 0.1527 0.0173 0.002 0.5 4.5 0.0 0.0 0 0.750 0.1325 0.1507 0.0182 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1322 0.1505 0.0183 0.002 0.5 4.2 0.0 0.0 0 1.000 0.1258 0.1462 0.0204 0.002 0.6 4.2 0.5 0.0 0 2.000 0.1235 0.1444 0.0209 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1221 0.1426 0.0205 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1215 0.1421 0.0206 0.004 0.7 5.1 0.5 0.0 0 5.000 0.1211 0.1419 0.0208 0.004 0.7 5.1 0.5 0.0 0 6.000 0.1205 0.1408 0.0203 0.005 0.8 5.1 0.5 0.0 0 7.000 0.1199 0.1405 0.0206 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1199 0.1409 0.0209 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1193 0.1400 0.0207 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1194 0.1410 0.0216 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1191 0.1400 0.0209 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1188 0.1407 0.0219 0.008 0.9 4.8 0.5 0.0 0 13.735 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1400 0.0209 0.007 0.9 4.5 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 14.00 2.09 3.773 21.672 1478.189 0.016 11.91 14.00 2.09 3.773 21.672 44.346 0.016 11.91 14.00 2.09 3.773 21.672 184.774 0.016 12.07 14.42 2.35 3.641 21.669 739.095 0.016 12.11 14.77 2.66 3.567 21.737 1478.189 0.015 11.97 14.76 2.80 3.477 22.024 2217.284 0.015 11.86 14.71 2.85 3.500 21.868 2956.378 0.014 11.79 14.68 2.89 3.546 21.809 3695.473 0.014 11.74 14.65 2.91 3.521 21.969 4434.568 0.014 11.75 14.76 3.01 3.555 22.019 5173.662 0.014 11.71 14.72 3.01 3.567 22.001 5912.757 0.014 11.72 14.81 3.09 3.607 22.123 6651.852 0.014 11.68 14.76 3.08 3.600 22.026 7390.946 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: 184.774 Accepted refinement result: 11.91 14.00 2.09 3.773 21.672 184.774 0.016 Individual atomic B min max mean iso aniso Overall: 9.12 115.00 22.00 3.31 180 1755 Protein: 9.12 115.00 17.02 3.31 0 1519 Water: 11.48 76.68 40.52 N/A 180 228 Other: 19.75 26.63 22.09 N/A 0 8 Chain A: 9.12 115.00 19.49 N/A 0 1755 Chain S: 12.59 60.00 46.41 N/A 180 0 Histogram: Values Number of atoms 9.12 - 19.71 1262 19.71 - 30.30 243 30.30 - 40.88 165 40.88 - 51.47 128 51.47 - 62.06 114 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1400 r_work=0.1191 r_free=0.1400 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1400 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 = 0.1195 r_free = 0.1412 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1195 r_free= 0.1412 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015456 | | target function (ls_wunit_k1) not normalized (work): 1287.429363 | | target function (ls_wunit_k1) not normalized (free): 102.498218 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1195 0.1412 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1592 0.1592 0.1625 n_refl.: 87590 remove outliers: r(all,work,free)=0.1592 0.1592 0.1625 n_refl.: 87590 overall B=0.01 to atoms: r(all,work,free)=0.1594 0.1594 0.1626 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1192 0.1405 n_refl.: 87590 remove outliers: r(all,work,free)=0.1201 0.1191 0.1405 n_refl.: 87587 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3266 299.859 276.222 0.590 1.003 0.350 11.894-9.307 98.04 96 4 0.1583 484.690 473.235 0.919 1.003 0.337 9.237-7.194 100.00 213 7 0.1744 394.814 392.096 0.979 1.003 0.300 7.162-5.571 100.00 427 22 0.1630 296.286 291.865 0.938 1.003 0.220 5.546-4.326 100.00 867 58 0.0917 406.728 403.783 0.959 1.003 0.200 4.315-3.360 100.00 1859 96 0.0794 386.801 386.124 1.005 1.002 0.190 3.356-2.611 100.00 3867 181 0.1090 254.108 253.322 1.010 1.002 0.057 2.608-2.026 99.99 8198 413 0.1018 168.450 167.878 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1104 82.262 82.470 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.479 36.014 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2252 22.984 21.501 0.986 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0163 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1405 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1405 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1405 | n_water=408 | time (s): 1.760 (total time: 1.760) Filter (dist) r_work=0.1190 r_free=0.1399 | n_water=404 | time (s): 34.420 (total time: 36.180) Filter (q & B) r_work=0.1190 r_free=0.1399 | n_water=404 | time (s): 0.910 (total time: 37.090) Compute maps r_work=0.1190 r_free=0.1399 | n_water=404 | time (s): 1.650 (total time: 38.740) Filter (map) r_work=0.1227 r_free=0.1386 | n_water=283 | time (s): 3.470 (total time: 42.210) Find peaks r_work=0.1227 r_free=0.1386 | n_water=283 | time (s): 0.650 (total time: 42.860) Add new water r_work=0.1342 r_free=0.1505 | n_water=459 | time (s): 3.360 (total time: 46.220) Refine new water occ: r_work=0.1245 r_free=0.1417 adp: r_work=0.1247 r_free=0.1418 occ: r_work=0.1223 r_free=0.1396 adp: r_work=0.1223 r_free=0.1397 occ: r_work=0.1206 r_free=0.1380 adp: r_work=0.1202 r_free=0.1378 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1378 r_work=0.1202 r_free=0.1378 | n_water=459 | time (s): 187.660 (total time: 233.880) Filter (q & B) r_work=0.1206 r_free=0.1389 | n_water=426 | time (s): 2.680 (total time: 236.560) Filter (dist only) r_work=0.1206 r_free=0.1388 | n_water=424 | time (s): 35.420 (total time: 271.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.814042 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.608159 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1238 0.1355 0.0118 0.002 0.6 5.1 0.5 0.0 0 0.091 0.1194 0.1326 0.0132 0.003 0.7 3.8 0.5 0.0 0 0.272 0.1177 0.1316 0.0140 0.004 0.8 3.5 0.5 0.0 0 0.544 0.1170 0.1314 0.0144 0.005 0.9 3.5 0.5 0.0 0 0.816 0.1165 0.1313 0.0148 0.006 1.0 3.5 0.5 0.0 0 1.088 0.1163 0.1315 0.0152 0.007 1.0 3.5 0.5 0.0 0 1.361 0.1161 0.1310 0.0149 0.007 1.1 3.8 0.5 0.0 0 1.633 0.1159 0.1314 0.0155 0.008 1.1 3.8 0.5 0.0 0 1.905 0.1169 0.1315 0.0146 0.005 0.9 2.9 0.5 0.0 0 0.907 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1161 0.1310 0.0149 0.007 1.1 3.8 0.5 0.0 0 1.633 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.61 13.10 1.49 3.776 21.195 49.608 3.621 11.61 13.10 1.49 3.776 21.195 1.488 3.621 11.61 13.10 1.49 3.766 21.195 6.201 3.620 11.64 13.21 1.57 3.713 21.179 24.804 3.614 11.63 13.30 1.66 3.739 21.148 49.608 3.613 11.53 13.23 1.70 3.764 21.143 74.412 3.605 11.53 13.26 1.73 3.775 21.124 99.216 3.603 11.50 13.25 1.75 3.792 21.120 124.020 3.601 11.50 13.28 1.78 3.809 21.103 148.824 3.601 11.47 13.23 1.76 3.815 21.102 173.629 3.598 11.45 13.21 1.76 3.826 21.102 198.433 3.596 11.44 13.21 1.77 3.836 21.099 223.237 3.596 11.41 13.17 1.76 3.833 21.108 248.041 3.594 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.488 Accepted refinement result: 11.61 13.10 1.49 3.776 21.195 1.488 3.621 Individual atomic B min max mean iso aniso Overall: 9.13 115.01 21.12 3.31 201 1750 Protein: 9.13 115.01 17.03 3.31 0 1519 Water: 11.49 76.69 35.72 N/A 201 223 Other: 19.76 26.64 22.10 N/A 0 8 Chain A: 9.13 115.01 19.42 N/A 0 1750 Chain S: 12.60 60.01 35.84 N/A 201 0 Histogram: Values Number of atoms 9.13 - 19.72 1266 19.72 - 30.31 282 30.31 - 40.89 204 40.89 - 51.48 125 51.48 - 62.07 51 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1161 r_free=0.1310 r_work=0.1161 r_free=0.1310 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1161 r_free = 0.1310 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1149 r_free = 0.1301 target_work(ml) = 3.612 | | 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.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1149 r_free= 0.1301 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.611994 | | target function (ml) not normalized (work): 300846.610109 | | target function (ml) not normalized (free): 15831.334895 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1156 0.1149 0.1301 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1483 0.1484 0.1503 n_refl.: 87587 remove outliers: r(all,work,free)=0.1483 0.1484 0.1503 n_refl.: 87587 overall B=-0.00 to atoms: r(all,work,free)=0.1483 0.1483 0.1502 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1151 0.1144 0.1289 n_refl.: 87587 remove outliers: r(all,work,free)=0.1148 0.1141 0.1289 n_refl.: 87579 ======================== 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 0.3769 296.606 262.538 0.494 1.001 0.312 11.894-9.307 96.08 94 4 0.2144 477.997 468.794 0.889 1.002 0.300 9.237-7.194 98.18 209 7 0.2248 386.290 385.154 0.952 1.002 0.199 7.162-5.571 100.00 427 22 0.2142 296.286 285.461 0.921 1.003 0.170 5.546-4.326 100.00 867 58 0.1138 406.728 402.004 0.962 1.003 0.145 4.315-3.360 100.00 1859 96 0.0926 386.801 384.542 1.002 1.002 0.114 3.356-2.611 100.00 3867 181 0.1118 254.108 252.190 1.009 1.002 0.043 2.608-2.026 99.99 8198 413 0.0938 168.450 167.598 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0899 82.262 82.572 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.479 36.061 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.984 21.525 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0106 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1141 r_free=0.1289 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1141 r_free=0.1288 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1141 r_free=0.1288 | n_water=424 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1144 r_free=0.1290 | n_water=421 | time (s): 42.970 (total time: 45.480) Filter (q & B) r_work=0.1144 r_free=0.1290 | n_water=420 | time (s): 4.010 (total time: 49.490) Compute maps r_work=0.1144 r_free=0.1290 | n_water=420 | time (s): 1.860 (total time: 51.350) Filter (map) r_work=0.1171 r_free=0.1289 | n_water=325 | time (s): 3.800 (total time: 55.150) Find peaks r_work=0.1171 r_free=0.1289 | n_water=325 | time (s): 0.720 (total time: 55.870) Add new water r_work=0.1236 r_free=0.1353 | n_water=488 | time (s): 3.830 (total time: 59.700) Refine new water occ: r_work=0.1159 r_free=0.1286 adp: r_work=0.1160 r_free=0.1289 occ: r_work=0.1145 r_free=0.1274 adp: r_work=0.1144 r_free=0.1275 occ: r_work=0.1134 r_free=0.1266 adp: r_work=0.1130 r_free=0.1265 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1265 r_work=0.1130 r_free=0.1265 | n_water=488 | time (s): 197.900 (total time: 257.600) Filter (q & B) r_work=0.1140 r_free=0.1271 | n_water=443 | time (s): 4.090 (total time: 261.690) Filter (dist only) r_work=0.1140 r_free=0.1272 | n_water=441 | time (s): 46.390 (total time: 308.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.749452 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.075221 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 0.1200 0.1313 0.0113 0.002 0.6 4.2 0.5 0.0 0 0.087 0.1164 0.1289 0.0125 0.003 0.7 3.2 0.5 0.0 0 0.262 0.1149 0.1279 0.0131 0.005 0.9 3.5 0.5 0.0 0 0.525 0.1143 0.1276 0.0133 0.005 0.9 3.5 0.5 0.0 0 0.787 0.1139 0.1276 0.0136 0.006 1.0 3.2 0.5 0.0 0 1.050 0.1137 0.1281 0.0144 0.007 1.0 3.8 0.5 0.0 0 1.312 0.1135 0.1276 0.0141 0.008 1.1 3.5 0.5 0.0 0 1.575 0.1133 0.1275 0.0142 0.008 1.1 3.5 0.5 0.0 0 1.837 0.1141 0.1275 0.0134 0.006 1.0 3.5 0.5 0.0 0 0.875 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1133 0.1275 0.0142 0.008 1.1 3.5 0.5 0.0 0 1.837 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.33 12.75 1.42 3.777 21.235 48.075 3.604 11.33 12.75 1.42 3.777 21.235 1.442 3.604 11.34 12.75 1.41 3.766 21.235 6.009 3.604 11.35 12.83 1.47 3.715 21.226 24.038 3.598 11.40 12.97 1.57 3.740 21.193 48.075 3.600 11.33 12.92 1.59 3.760 21.185 72.113 3.594 11.28 12.89 1.60 3.773 21.182 96.150 3.590 11.27 12.89 1.63 3.785 21.176 120.188 3.588 11.27 12.94 1.67 3.803 21.159 144.226 3.588 11.24 12.90 1.66 3.814 21.158 168.263 3.586 11.23 12.92 1.68 3.825 21.156 192.301 3.585 11.22 12.90 1.68 3.832 21.156 216.338 3.584 11.20 12.87 1.67 3.834 21.155 240.376 3.582 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.442 Accepted refinement result: 11.33 12.75 1.42 3.777 21.235 1.442 3.604 Individual atomic B min max mean iso aniso Overall: 9.12 115.01 21.19 3.31 221 1747 Protein: 9.12 115.01 17.03 3.31 0 1519 Water: 11.49 76.69 35.51 N/A 221 220 Other: 19.76 26.63 22.09 N/A 0 8 Chain A: 9.12 115.01 19.40 N/A 0 1747 Chain S: 12.60 60.01 35.38 N/A 221 0 Histogram: Values Number of atoms 9.12 - 19.71 1266 19.71 - 30.30 291 30.30 - 40.89 208 40.89 - 51.48 131 51.48 - 62.07 49 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=0.1133 r_free=0.1275 r_work=0.1133 r_free=0.1275 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1133 r_free = 0.1275 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1128 r_free = 0.1274 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1128 r_free= 0.1274 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601424 | | target function (ml) not normalized (work): 299937.434277 | | target function (ml) not normalized (free): 15801.087035 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1128 0.1274 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1453 0.1454 0.1475 n_refl.: 87579 remove outliers: r(all,work,free)=0.1453 0.1454 0.1475 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1453 0.1453 0.1475 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1134 0.1127 0.1272 n_refl.: 87579 remove outliers: r(all,work,free)=0.1132 0.1125 0.1272 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3930 293.217 257.414 0.466 1.001 0.309 11.894-9.307 94.12 92 4 0.2189 481.753 462.440 0.870 1.002 0.301 9.237-7.194 98.18 209 7 0.2334 386.290 380.983 0.928 1.002 0.160 7.162-5.571 100.00 427 22 0.2112 296.286 285.705 0.914 1.003 0.134 5.546-4.326 100.00 867 58 0.1110 406.728 402.463 0.962 1.003 0.120 4.315-3.360 100.00 1859 96 0.0901 386.801 384.744 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1103 254.108 252.387 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0910 168.450 167.832 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0885 82.262 82.630 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.479 36.095 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.984 21.542 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0136 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1125 r_free=0.1272 After: r_work=0.1127 r_free=0.1272 ================================== NQH flips ================================== r_work=0.1127 r_free=0.1272 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=0.1127 r_free=0.1272 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1127 r_free=0.1272 | n_water=441 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1127 r_free=0.1272 | n_water=441 | time (s): 41.980 (total time: 44.470) Filter (q & B) r_work=0.1127 r_free=0.1272 | n_water=441 | time (s): 1.380 (total time: 45.850) Compute maps r_work=0.1127 r_free=0.1272 | n_water=441 | time (s): 1.890 (total time: 47.740) Filter (map) r_work=0.1168 r_free=0.1308 | n_water=347 | time (s): 4.070 (total time: 51.810) Find peaks r_work=0.1168 r_free=0.1308 | n_water=347 | time (s): 0.700 (total time: 52.510) Add new water r_work=0.1215 r_free=0.1366 | n_water=491 | time (s): 3.810 (total time: 56.320) Refine new water occ: r_work=0.1145 r_free=0.1286 adp: r_work=0.1145 r_free=0.1289 occ: r_work=0.1134 r_free=0.1273 adp: r_work=0.1133 r_free=0.1276 occ: r_work=0.1125 r_free=0.1260 adp: r_work=0.1123 r_free=0.1262 ADP+occupancy (water only), MIN, final r_work=0.1123 r_free=0.1262 r_work=0.1123 r_free=0.1262 | n_water=491 | time (s): 233.250 (total time: 289.570) Filter (q & B) r_work=0.1131 r_free=0.1268 | n_water=445 | time (s): 3.910 (total time: 293.480) Filter (dist only) r_work=0.1131 r_free=0.1268 | n_water=443 | time (s): 47.400 (total time: 340.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.721365 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.588421 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 0.1221 0.1325 0.0104 0.004 0.7 5.8 0.0 0.0 0 0.086 0.1167 0.1291 0.0124 0.004 0.8 5.4 0.0 0.0 0 0.258 0.1151 0.1281 0.0130 0.005 0.9 4.8 0.5 0.0 0 0.516 0.1145 0.1278 0.0133 0.006 1.0 4.5 0.5 0.0 0 0.775 0.1137 0.1271 0.0134 0.006 1.1 4.5 0.5 0.0 0 1.033 0.1134 0.1269 0.0135 0.007 1.1 4.5 0.5 0.0 0 1.291 0.1132 0.1268 0.0136 0.008 1.1 4.2 0.5 0.0 0 1.549 0.1131 0.1268 0.0137 0.008 1.2 4.2 0.5 0.0 0 1.807 0.1140 0.1273 0.0133 0.006 1.0 4.5 0.5 0.0 0 0.861 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1131 0.1268 0.0137 0.008 1.2 4.2 0.5 0.0 0 1.807 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 12.68 1.37 3.777 21.196 39.588 3.602 11.31 12.68 1.37 3.777 21.196 1.188 3.602 11.31 12.68 1.37 3.777 21.196 4.949 3.602 11.34 12.74 1.40 3.710 21.187 19.794 3.597 11.45 12.93 1.48 3.714 21.159 39.588 3.603 11.34 12.87 1.53 3.749 21.147 59.383 3.595 11.27 12.82 1.55 3.765 21.145 79.177 3.590 11.26 12.81 1.56 3.776 21.141 98.971 3.588 11.23 12.80 1.57 3.784 21.140 118.765 3.586 11.23 12.83 1.60 3.797 21.131 138.559 3.585 11.23 12.85 1.63 3.813 21.124 158.354 3.585 11.22 12.85 1.63 3.822 21.121 178.148 3.584 11.19 12.81 1.62 3.823 21.123 197.942 3.582 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.188 Accepted refinement result: 11.31 12.68 1.37 3.777 21.196 1.188 3.602 Individual atomic B min max mean iso aniso Overall: 9.12 115.00 21.12 3.31 225 1745 Protein: 9.12 115.00 17.02 3.31 0 1519 Water: 11.48 76.69 35.16 N/A 225 218 Other: 19.75 26.63 22.09 N/A 0 8 Chain A: 9.12 115.00 19.37 N/A 0 1745 Chain S: 12.59 60.00 34.69 N/A 225 0 Histogram: Values Number of atoms 9.12 - 19.71 1267 19.71 - 30.30 292 30.30 - 40.88 217 40.88 - 51.47 127 51.47 - 62.06 44 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1268 r_work=0.1131 r_free=0.1268 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1268 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1126 r_free = 0.1260 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1126 r_free= 0.1260 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.598981 | | target function (ml) not normalized (work): 299723.131435 | | target function (ml) not normalized (free): 15773.332254 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1302 0.1259 5.6465 5.5556| | 2: 3.57 - 2.84 1.00 2888 124 0.1063 0.1302 5.1326 5.1814| | 3: 2.83 - 2.48 1.00 2820 163 0.1098 0.1199 4.9134 4.9498| | 4: 2.47 - 2.25 1.00 2825 136 0.0891 0.0994 4.5993 4.647| | 5: 2.25 - 2.09 1.00 2756 127 0.0857 0.0925 4.541 4.5885| | 6: 2.09 - 1.97 1.00 2846 113 0.0849 0.1050 4.2494 4.3419| | 7: 1.97 - 1.87 1.00 2787 165 0.0886 0.1075 3.9768 4.0627| | 8: 1.87 - 1.79 1.00 2789 144 0.0930 0.1119 3.8906 4.0008| | 9: 1.79 - 1.72 1.00 2745 138 0.0881 0.1148 3.6458 3.8081| | 10: 1.72 - 1.66 1.00 2831 160 0.0921 0.1186 3.5617 3.71| | 11: 1.66 - 1.61 1.00 2712 147 0.0873 0.1055 3.4959 3.5679| | 12: 1.61 - 1.56 1.00 2773 144 0.0904 0.1169 3.3282 3.475| | 13: 1.56 - 1.52 1.00 2745 130 0.0942 0.1012 3.3083 3.3827| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1081 3.2432 3.3333| | 15: 1.48 - 1.45 1.00 2738 128 0.1004 0.1216 3.1558 3.2546| | 16: 1.45 - 1.42 1.00 2756 161 0.1058 0.1240 3.1385 3.2422| | 17: 1.42 - 1.39 1.00 2785 139 0.1139 0.1296 3.119 3.2262| | 18: 1.39 - 1.36 1.00 2741 179 0.1198 0.1330 3.1048 3.2422| | 19: 1.36 - 1.34 1.00 2807 134 0.1266 0.1556 3.1129 3.2606| | 20: 1.34 - 1.32 1.00 2696 147 0.1366 0.1457 3.111 3.1518| | 21: 1.32 - 1.30 1.00 2785 112 0.1477 0.1509 3.1151 3.1008| | 22: 1.29 - 1.27 1.00 2704 152 0.1558 0.1985 3.1205 3.296| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1799 3.1321 3.2001| | 24: 1.26 - 1.24 1.00 2744 132 0.1708 0.1829 3.1269 3.2263| | 25: 1.24 - 1.22 1.00 2733 148 0.1879 0.2131 3.1424 3.2551| | 26: 1.22 - 1.21 1.00 2727 135 0.1907 0.1772 3.1485 3.2044| | 27: 1.21 - 1.19 1.00 2814 148 0.2072 0.2157 3.1716 3.1627| | 28: 1.19 - 1.18 1.00 2671 147 0.2199 0.2283 3.1657 3.1712| | 29: 1.18 - 1.16 1.00 2800 134 0.2268 0.2399 3.1485 3.2327| | 30: 1.16 - 1.15 1.00 2739 148 0.2444 0.2457 3.1424 3.1691| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2918 171 0.95 7.86 1.00 0.97 5156.61| | 2: 3.57 - 2.84 2888 124 0.93 11.72 1.01 0.97 5156.61| | 3: 2.83 - 2.48 2820 163 0.90 15.56 0.99 0.97 4318.56| | 4: 2.47 - 2.25 2825 136 0.92 12.77 1.00 0.98 2157.48| | 5: 2.25 - 2.09 2756 127 0.91 14.89 1.01 0.98 2157.48| | 6: 2.09 - 1.97 2846 113 0.93 11.91 1.02 0.98 1265.73| | 7: 1.97 - 1.87 2787 165 0.95 9.21 1.02 0.97 505.18| | 8: 1.87 - 1.79 2789 144 0.93 12.53 0.99 0.97 505.18| | 9: 1.79 - 1.72 2745 138 0.94 10.03 0.98 0.97 287.89| | 10: 1.72 - 1.66 2831 160 0.94 11.14 0.98 0.97 244.37| | 11: 1.66 - 1.61 2712 147 0.93 11.73 0.98 0.97 234.13| | 12: 1.61 - 1.56 2773 144 0.95 8.93 0.99 0.97 137.59| | 13: 1.56 - 1.52 2745 130 0.95 10.41 1.02 0.97 137.59| | 14: 1.52 - 1.48 2803 134 0.94 10.76 1.02 0.98 123.39| | 15: 1.48 - 1.45 2738 128 0.95 9.87 1.02 0.98 97.38| | 16: 1.45 - 1.42 2756 161 0.94 11.06 1.02 0.98 97.38| | 17: 1.42 - 1.39 2785 139 0.95 10.90 1.01 0.98 88.68| | 18: 1.39 - 1.36 2741 179 0.94 11.52 1.01 0.98 83.65| | 19: 1.36 - 1.34 2807 134 0.94 11.85 0.99 0.98 83.65| | 20: 1.34 - 1.32 2696 147 0.94 12.09 0.98 0.97 79.70| | 21: 1.32 - 1.30 2785 112 0.94 13.06 0.98 0.96 79.42| | 22: 1.29 - 1.27 2704 152 0.93 13.60 0.98 0.96 79.86| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.97 0.94 82.06| | 24: 1.26 - 1.24 2744 132 0.93 14.83 0.96 0.94 82.06| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 84.09| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.02 0.93 86.34| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 86.34| | 28: 1.19 - 1.18 2671 147 0.88 20.41 1.01 0.93 90.16| | 29: 1.18 - 1.16 2800 134 0.88 20.53 0.99 0.92 91.60| | 30: 1.16 - 1.15 2739 148 0.86 22.04 0.98 0.92 91.60| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.42 max = 5156.61 mean = 811.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.94 mean = 13.29| |phase err.(test): min = 0.00 max = 87.61 mean = 13.24| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1133 0.1126 0.1260 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1452 0.1452 0.1465 n_refl.: 87576 remove outliers: r(all,work,free)=0.1452 0.1452 0.1465 n_refl.: 87576 overall B=-0.00 to atoms: r(all,work,free)=0.1451 0.1452 0.1465 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1134 0.1127 0.1261 n_refl.: 87576 remove outliers: r(all,work,free)=0.1132 0.1126 0.1261 n_refl.: 87572 ======================== 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 0.3839 288.446 257.977 0.452 1.001 0.279 11.894-9.307 91.18 89 4 0.2157 476.047 463.272 0.872 1.002 0.231 9.237-7.194 98.18 209 7 0.2355 386.290 379.158 0.921 1.002 0.168 7.162-5.571 100.00 427 22 0.2122 296.286 285.998 0.914 1.002 0.133 5.546-4.326 100.00 867 58 0.1105 406.728 402.336 0.962 1.002 0.106 4.315-3.360 100.00 1859 96 0.0898 386.801 384.822 1.002 1.002 0.090 3.356-2.611 100.00 3867 181 0.1108 254.108 252.311 1.011 1.002 0.029 2.608-2.026 99.99 8198 413 0.0903 168.450 167.835 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0892 82.262 82.608 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.479 36.082 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 22.984 21.529 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0075 ================= 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 : 0.2604 0.1929 0.083 5.297 8.8 119.3 19.9 258 0.000 1_bss: 0.1623 0.1748 0.083 5.297 9.0 119.5 20.1 258 0.000 1_settarget: 0.1623 0.1748 0.083 5.297 9.0 119.5 20.1 258 0.000 1_nqh: 0.1625 0.1749 0.083 5.297 9.0 119.5 20.1 258 0.003 1_weight: 0.1625 0.1749 0.083 5.297 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1222 0.1457 0.007 0.929 9.0 119.5 20.1 258 0.136 1_adp: 0.1229 0.1454 0.007 0.929 9.1 119.4 20.1 258 0.136 1_regHadp: 0.1230 0.1458 0.007 0.929 9.1 119.4 20.1 258 0.136 1_occ: 0.1225 0.1451 0.007 0.929 9.1 119.4 20.1 258 0.136 2_bss: 0.1224 0.1446 0.007 0.929 9.1 119.5 20.1 258 0.136 2_settarget: 0.1224 0.1446 0.007 0.929 9.1 119.5 20.1 258 0.136 2_updatecdl: 0.1224 0.1446 0.007 0.932 9.1 119.5 20.1 258 0.136 2_nqh: 0.1224 0.1446 0.007 0.932 9.1 119.5 20.1 258 0.136 2_sol: 0.1200 0.1396 0.007 0.932 9.1 115.0 22.0 408 n/a 2_weight: 0.1200 0.1396 0.007 0.932 9.1 115.0 22.0 408 n/a 2_xyzrec: 0.1191 0.1400 0.007 0.907 9.1 115.0 22.0 408 n/a 2_adp: 0.1191 0.1400 0.007 0.907 9.1 115.0 22.0 408 n/a 2_regHadp: 0.1191 0.1400 0.007 0.907 9.1 115.0 22.0 408 n/a 2_occ: 0.1195 0.1412 0.007 0.907 9.1 115.0 22.0 408 n/a 3_bss: 0.1191 0.1405 0.007 0.907 9.1 115.0 22.0 408 n/a 3_settarget: 0.1191 0.1405 0.007 0.907 9.1 115.0 22.0 408 n/a 3_updatecdl: 0.1191 0.1405 0.007 0.903 9.1 115.0 22.0 408 n/a 3_nqh: 0.1191 0.1405 0.007 0.903 9.1 115.0 22.0 408 n/a 3_sol: 0.1206 0.1388 0.007 0.903 9.1 115.0 21.1 424 n/a 3_weight: 0.1206 0.1388 0.007 0.903 9.1 115.0 21.1 424 n/a 3_xyzrec: 0.1161 0.1310 0.007 1.059 9.1 115.0 21.1 424 n/a 3_adp: 0.1161 0.1310 0.007 1.059 9.1 115.0 21.1 424 n/a 3_regHadp: 0.1161 0.1310 0.007 1.059 9.1 115.0 21.1 424 n/a 3_occ: 0.1149 0.1301 0.007 1.059 9.1 115.0 21.1 424 n/a 4_bss: 0.1141 0.1289 0.007 1.059 9.1 115.0 21.1 424 n/a 4_settarget: 0.1141 0.1289 0.007 1.059 9.1 115.0 21.1 424 n/a 4_updatecdl: 0.1141 0.1289 0.007 1.061 9.1 115.0 21.1 424 n/a 4_nqh: 0.1141 0.1288 0.007 1.061 9.1 115.0 21.1 424 n/a 4_sol: 0.1140 0.1272 0.007 1.061 9.1 115.0 21.2 441 n/a 4_weight: 0.1140 0.1272 0.007 1.061 9.1 115.0 21.2 441 n/a 4_xyzrec: 0.1133 0.1275 0.008 1.125 9.1 115.0 21.2 441 n/a 4_adp: 0.1133 0.1275 0.008 1.125 9.1 115.0 21.2 441 n/a 4_regHadp: 0.1133 0.1275 0.008 1.125 9.1 115.0 21.2 441 n/a 4_occ: 0.1128 0.1274 0.008 1.125 9.1 115.0 21.2 441 n/a 5_bss: 0.1125 0.1272 0.008 1.125 9.1 115.0 21.2 441 n/a 5_settarget: 0.1125 0.1272 0.008 1.125 9.1 115.0 21.2 441 n/a 5_updatecdl: 0.1125 0.1272 0.008 1.129 9.1 115.0 21.2 441 n/a 5_setrh: 0.1127 0.1272 0.008 1.129 9.1 115.0 21.2 441 n/a 5_nqh: 0.1127 0.1272 0.008 1.129 9.1 115.0 21.2 441 n/a 5_sol: 0.1131 0.1268 0.008 1.129 9.1 115.0 21.1 443 n/a 5_weight: 0.1131 0.1268 0.008 1.129 9.1 115.0 21.1 443 n/a 5_xyzrec: 0.1131 0.1268 0.008 1.152 9.1 115.0 21.1 443 n/a 5_adp: 0.1131 0.1268 0.008 1.152 9.1 115.0 21.1 443 n/a 5_regHadp: 0.1131 0.1268 0.008 1.152 9.1 115.0 21.1 443 n/a 5_occ: 0.1126 0.1260 0.008 1.152 9.1 115.0 21.1 443 n/a end: 0.1126 0.1261 0.008 1.152 9.1 115.0 21.1 443 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6470396_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6470396_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.5900 Refinement macro-cycles (run) : 14354.6900 Write final files (write_after_run_outputs) : 70.6700 Total : 14428.9500 Total CPU time: 4.02 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:20:04 PST -0800 (1735366804.57 s) Start R-work = 0.1623, R-free = 0.1748 Final R-work = 0.1126, R-free = 0.1261 =============================================================================== Job complete usr+sys time: 14569.29 seconds wall clock time: 263 minutes 34.70 seconds (15814.70 seconds total)