Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5637181.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5637181.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5637181.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 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: 1.67, per 1000 atoms: 0.49 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: 0.33 Conformation dependent library (CDL) restraints added in 137.2 milliseconds Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.93: 646 0.93 - 1.19: 1017 1.19 - 1.45: 744 1.45 - 1.71: 729 1.71 - 1.97: 17 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.235 1.440 -0.205 9.90e-03 1.02e+04 4.27e+02 bond pdb=" N AGLU A 64 " pdb=" CA AGLU A 64 " ideal model delta sigma weight residual 1.457 1.680 -0.223 1.10e-02 8.26e+03 4.12e+02 bond pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 1.450 1.231 0.219 1.16e-02 7.43e+03 3.56e+02 bond pdb=" N GLU A 18 " pdb=" CA GLU A 18 " ideal model delta sigma weight residual 1.457 1.705 -0.248 1.32e-02 5.74e+03 3.54e+02 bond pdb=" CA AGLN A 80 " pdb=" C AGLN A 80 " ideal model delta sigma weight residual 1.524 1.759 -0.236 1.27e-02 6.20e+03 3.44e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 2872 4.14 - 8.29: 1875 8.29 - 12.43: 785 12.43 - 16.57: 219 16.57 - 20.71: 26 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 135.45 -16.25 9.00e-01 1.23e+00 3.26e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH2 ARG A 28 " ideal model delta sigma weight residual 119.20 106.11 13.09 9.00e-01 1.23e+00 2.11e+02 angle pdb=" O LEU A 112 " pdb=" C LEU A 112 " pdb=" N LEU A 113 " ideal model delta sigma weight residual 122.12 137.46 -15.34 1.06e+00 8.90e-01 2.09e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.36 137.31 -15.95 1.11e+00 8.12e-01 2.07e+02 angle pdb=" O LEU A 166 " pdb=" C LEU A 166 " pdb=" N ALA A 167 " ideal model delta sigma weight residual 122.12 107.57 14.55 1.06e+00 8.90e-01 1.88e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.51: 941 16.51 - 33.00: 112 33.00 - 49.49: 38 49.49 - 65.99: 14 65.99 - 82.48: 6 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual -180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta harmonic sigma weight residual 180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.64e+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 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.201: 100 0.201 - 0.400: 61 0.400 - 0.598: 49 0.598 - 0.797: 25 0.797 - 0.995: 8 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 -1.59 -1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" CA THR A 154 " pdb=" N THR A 154 " pdb=" C THR A 154 " pdb=" CB THR A 154 " both_signs ideal model delta sigma weight residual False 2.53 3.51 -0.99 2.00e-01 2.50e+01 2.44e+01 chirality pdb=" CB VAL A 181 " pdb=" CA VAL A 181 " pdb=" CG1 VAL A 181 " pdb=" CG2 VAL A 181 " both_signs ideal model delta sigma weight residual False -2.63 -3.54 0.91 2.00e-01 2.50e+01 2.08e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.111 2.00e-02 2.50e+03 6.02e-02 1.09e+02 pdb=" CG PHE A 164 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.117 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.061 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.099 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.073 2.00e-02 2.50e+03 5.56e-02 9.28e+01 pdb=" CG PHE A 119 " 0.096 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.116 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.042 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.061 2.00e-02 2.50e+03 5.49e-02 9.04e+01 pdb=" CG ATYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.001 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.095 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 810 2.28 - 2.86: 7854 2.86 - 3.44: 10597 3.44 - 4.02: 15300 4.02 - 4.60: 22047 Nonbonded interactions: 56608 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.702 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.723 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.800 1.850 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.834 1.850 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.842 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_5637181_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= 0.2609 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788953 | | target function (ml) not normalized (work): 232336.549998 | | target function (ml) not normalized (free): 11796.004970 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2085 7.0185 4.9435| | 2: 3.57 - 2.84 1.00 2876 122 0.2446 0.1785 4.3543 4.3592| | 3: 2.84 - 2.48 1.00 2833 165 0.2373 0.1837 4.1339 4.1737| | 4: 2.47 - 2.25 1.00 2825 136 0.2362 0.1361 3.8437 3.8367| | 5: 2.25 - 2.09 1.00 2756 127 0.2489 0.1400 3.8083 3.799| | 6: 2.09 - 1.97 1.00 2846 113 0.2524 0.1821 3.469 3.572| | 7: 1.97 - 1.87 1.00 2787 165 0.2544 0.1877 3.1398 3.2458| | 8: 1.87 - 1.79 1.00 2789 144 0.2462 0.2035 3.0701 3.1957| | 9: 1.79 - 1.72 1.00 2745 138 0.2433 0.1716 2.9131 2.8922| | 10: 1.72 - 1.66 1.00 2789 158 0.2421 0.2075 2.7806 2.8685| | 11: 1.66 - 1.61 1.00 2740 147 0.2501 0.1673 2.7465 2.7088| | 12: 1.61 - 1.56 1.00 2787 146 0.2558 0.1722 2.6212 2.5251| | 13: 1.56 - 1.52 1.00 2745 130 0.2569 0.1913 2.5847 2.611| | 14: 1.52 - 1.48 1.00 2803 134 0.2586 0.2148 2.5094 2.6449| | 15: 1.48 - 1.45 1.00 2738 128 0.2534 0.1855 2.4154 2.4156| | 16: 1.45 - 1.42 1.00 2756 161 0.2649 0.2345 2.3709 2.4837| | 17: 1.42 - 1.39 1.00 2785 139 0.2693 0.1967 2.3333 2.317| | 18: 1.39 - 1.36 1.00 2741 179 0.2641 0.2254 2.2725 2.3773| | 19: 1.36 - 1.34 1.00 2807 134 0.2652 0.2393 2.255 2.3312| | 20: 1.34 - 1.32 1.00 2696 147 0.2706 0.2384 2.2192 2.2768| | 21: 1.32 - 1.30 1.00 2785 112 0.2739 0.2185 2.1638 2.1137| | 22: 1.29 - 1.27 1.00 2704 152 0.2738 0.2482 2.1313 2.1944| | 23: 1.27 - 1.26 1.00 2802 156 0.2763 0.2421 2.0892 2.1544| | 24: 1.26 - 1.24 1.00 2744 132 0.2760 0.2551 2.0674 2.1624| | 25: 1.24 - 1.22 1.00 2734 148 0.2892 0.2472 2.0492 2.0178| | 26: 1.22 - 1.21 1.00 2727 135 0.2832 0.2333 2.0016 2.0759| | 27: 1.21 - 1.19 1.00 2814 148 0.2956 0.2482 2.0116 1.9428| | 28: 1.19 - 1.18 1.00 2671 147 0.2898 0.2882 1.9663 2.0145| | 29: 1.18 - 1.16 1.00 2800 134 0.2993 0.2556 1.9562 1.9457| | 30: 1.16 - 1.15 1.00 2740 148 0.3032 0.3011 1.9181 1.9908| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.94 0.76 0.23 1498.37| | 2: 3.57 - 2.84 2876 122 0.80 26.26 1.27 0.23 1498.37| | 3: 2.84 - 2.48 2833 165 0.74 32.26 1.25 0.23 1243.65| | 4: 2.47 - 2.25 2825 136 0.81 25.84 1.26 0.25 582.61| | 5: 2.25 - 2.09 2756 127 0.77 29.57 1.28 0.25 582.61| | 6: 2.09 - 1.97 2846 113 0.83 22.91 1.28 0.25 319.88| | 7: 1.97 - 1.87 2787 165 0.89 17.09 1.28 0.26 95.81| | 8: 1.87 - 1.79 2789 144 0.85 21.70 1.25 0.26 95.81| | 9: 1.79 - 1.72 2745 138 0.88 18.56 1.23 0.26 55.40| | 10: 1.72 - 1.66 2789 158 0.86 20.26 1.23 0.25 47.30| | 11: 1.66 - 1.61 2740 147 0.86 21.03 1.24 0.25 45.53| | 12: 1.61 - 1.56 2787 146 0.89 17.78 1.24 0.25 27.57| | 13: 1.56 - 1.52 2745 130 0.87 19.64 1.23 0.25 27.57| | 14: 1.52 - 1.48 2803 134 0.87 19.98 1.23 0.25 25.00| | 15: 1.48 - 1.45 2738 128 0.87 19.71 1.23 0.25 20.30| | 16: 1.45 - 1.42 2756 161 0.86 21.47 1.25 0.25 20.30| | 17: 1.42 - 1.39 2785 139 0.86 21.00 1.24 0.25 17.67| | 18: 1.39 - 1.36 2741 179 0.86 21.49 1.22 0.25 16.15| | 19: 1.36 - 1.34 2807 134 0.85 22.24 1.22 0.25 16.15| | 20: 1.34 - 1.32 2696 147 0.87 21.09 1.21 0.25 13.49| | 21: 1.32 - 1.30 2785 112 0.85 22.51 1.21 0.25 13.31| | 22: 1.29 - 1.27 2704 152 0.85 22.87 1.21 0.24 12.95| | 23: 1.27 - 1.26 2802 156 0.86 22.15 1.22 0.24 11.13| | 24: 1.26 - 1.24 2744 132 0.85 22.74 1.20 0.24 11.13| | 25: 1.24 - 1.22 2734 148 0.84 23.71 1.22 0.24 10.49| | 26: 1.22 - 1.21 2727 135 0.84 23.78 1.20 0.23 9.78| | 27: 1.21 - 1.19 2814 148 0.84 24.39 1.19 0.23 9.78| | 28: 1.19 - 1.18 2671 147 0.83 25.15 1.18 0.23 9.23| | 29: 1.18 - 1.16 2800 134 0.82 25.93 1.17 0.22 9.03| | 30: 1.16 - 1.15 2740 148 0.80 27.41 1.16 0.22 9.03| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.03 max = 1498.37 mean = 217.81| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.94 mean = 22.65| |phase err.(test): min = 0.00 max = 89.50 mean = 22.65| |-----------------------------------------------------------------------------| ----------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 0.249 1557 Z= 5.616 Angle : 5.384 16.340 2118 Z= 3.824 Chirality : 0.383 0.995 243 Planarity : 0.032 0.146 284 Dihedral : 14.086 82.483 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 39.46 % 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: -2.51 (0.48), residues: 224 helix: -2.56 (0.38), residues: 108 sheet: -0.55 (0.92), residues: 28 loop : -0.48 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.021 ARG A 98 TYR 0.141 0.047 TYR A 141 PHE 0.093 0.041 PHE A 119 HIS 0.072 0.035 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788953 | | target function (ml) not normalized (work): 232336.549998 | | target function (ml) not normalized (free): 11796.004970 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2568 0.2610 0.1940 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2568 0.2610 0.1940 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1986 0.1940 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.2003 0.2008 0.1953 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1648 0.1642 0.1773 n_refl.: 87594 remove outliers: r(all,work,free)=0.1648 0.1641 0.1773 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 0.3837 386.471 355.721 0.661 1.002 0.401 11.894-9.307 99.02 97 4 0.1885 613.891 593.624 0.930 1.003 0.380 9.237-7.194 100.00 213 7 0.2141 502.087 491.204 0.963 1.003 0.360 7.162-5.571 100.00 427 22 0.2221 376.788 364.696 0.932 1.003 0.330 5.546-4.326 100.00 867 58 0.1282 517.237 511.722 0.963 1.003 0.240 4.315-3.360 100.00 1859 96 0.1151 491.896 487.903 1.003 1.003 0.179 3.356-2.611 100.00 3867 181 0.1447 323.150 319.821 0.998 1.003 0.043 2.608-2.026 99.99 8198 413 0.1375 214.219 212.074 1.008 1.002 0.000 2.025-1.573 100.00 17313 902 0.1645 104.614 103.735 1.010 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2059 46.390 45.119 1.003 0.998 0.000 1.221-1.150 99.97 13689 708 0.2554 29.229 27.052 0.975 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0421 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1641 r_free=0.1773 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1641 r_free=0.1773 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.399543 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2007.740291 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 0.1719 0.1849 0.0129 0.001 0.4 5.1 0.0 0.0 0 0.125 0.1580 0.1728 0.0148 0.002 0.4 4.2 0.0 0.0 0 0.250 0.1443 0.1618 0.0175 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1387 0.1583 0.0196 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1344 0.1545 0.0202 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1352 0.1558 0.0205 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1291 0.1508 0.0218 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1269 0.1499 0.0230 0.003 0.6 3.8 0.5 0.0 0 3.000 0.1254 0.1488 0.0234 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1250 0.1484 0.0234 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1241 0.1477 0.0237 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1237 0.1479 0.0242 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1231 0.1473 0.0241 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1229 0.1471 0.0242 0.006 0.9 4.2 0.5 0.0 0 9.000 0.1228 0.1478 0.0249 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1226 0.1471 0.0245 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1226 0.1477 0.0251 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1223 0.1477 0.0253 0.008 1.0 3.5 0.5 0.6 0 13.200 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1471 0.0242 0.006 0.9 4.2 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.71 2.42 3.013 19.042 2007.740 0.018 12.29 14.71 2.41 3.007 19.042 60.232 0.018 12.36 14.70 2.34 2.665 19.042 250.968 0.018 12.72 15.36 2.65 2.738 19.209 1003.870 0.017 12.58 15.50 2.91 3.241 19.571 2007.740 0.016 12.49 15.56 3.06 3.309 19.618 3011.610 0.016 12.38 15.50 3.12 3.328 19.615 4015.481 0.015 12.34 15.53 3.19 3.345 19.607 5019.351 0.015 12.21 15.43 3.22 3.292 19.587 6023.221 0.015 12.22 15.49 3.27 3.409 19.639 7027.091 0.015 12.22 15.51 3.28 3.305 19.575 8030.961 0.015 12.20 15.53 3.34 3.454 19.649 9034.831 0.015 12.18 15.53 3.34 3.442 19.629 10038.701 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: 250.968 Accepted refinement result: 12.36 14.70 2.34 2.665 19.042 250.968 0.018 Individual atomic B min max mean iso aniso Overall: 9.05 119.42 20.07 3.30 0 1785 Protein: 9.05 114.94 16.98 3.31 0 1519 Water: 11.46 119.42 38.21 N/A 0 258 Other: 19.68 26.59 22.04 N/A 0 8 Chain A: 9.05 119.42 20.07 N/A 0 1785 Histogram: Values Number of atoms 9.05 - 20.08 1272 20.08 - 31.12 227 31.12 - 42.16 125 42.16 - 53.19 94 53.19 - 64.23 42 64.23 - 75.27 11 75.27 - 86.31 7 86.31 - 97.34 4 97.34 - 108.38 1 108.38 - 119.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1470 r_work=0.1238 r_free=0.1474 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1474 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1464 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1230 r_free= 0.1464 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017024 | | target function (ls_wunit_k1) not normalized (work): 1418.049346 | | target function (ls_wunit_k1) not normalized (free): 108.443703 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1242 0.1230 0.1464 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1672 0.1673 0.1689 n_refl.: 87593 remove outliers: r(all,work,free)=0.1672 0.1673 0.1689 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1679 0.1681 0.1694 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1238 0.1227 0.1454 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 94.79 86 5 0.3511 298.290 282.099 0.650 1.002 0.380 11.894-9.307 99.02 97 4 0.1648 483.361 471.766 0.923 1.003 0.371 9.237-7.194 100.00 213 7 0.1949 395.330 388.622 0.963 1.003 0.324 7.162-5.571 100.00 427 22 0.1835 296.673 290.715 0.936 1.003 0.269 5.546-4.326 100.00 867 58 0.1007 407.259 404.268 0.962 1.003 0.209 4.315-3.360 100.00 1859 96 0.0876 387.306 386.227 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1173 254.440 253.300 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1019 168.670 167.955 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1108 82.370 82.564 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1452 36.526 36.032 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 23.014 21.491 0.979 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0606 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1454 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=0.1229 r_free=0.1456 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1229 r_free=0.1456 | n_water=258 | time (s): 1.640 (total time: 1.640) Filter (dist) r_work=0.1237 r_free=0.1454 | n_water=250 | time (s): 21.420 (total time: 23.060) Filter (q & B) r_work=0.1239 r_free=0.1454 | n_water=247 | time (s): 2.510 (total time: 25.570) Compute maps r_work=0.1239 r_free=0.1454 | n_water=247 | time (s): 1.080 (total time: 26.650) Filter (map) r_work=0.1261 r_free=0.1453 | n_water=224 | time (s): 2.580 (total time: 29.230) Find peaks r_work=0.1261 r_free=0.1453 | n_water=224 | time (s): 0.500 (total time: 29.730) Add new water r_work=0.1404 r_free=0.1636 | n_water=426 | time (s): 2.190 (total time: 31.920) Refine new water occ: r_work=0.1309 r_free=0.1488 adp: r_work=0.1230 r_free=0.1439 occ: r_work=0.1242 r_free=0.1418 adp: r_work=0.1208 r_free=0.1405 occ: r_work=0.1210 r_free=0.1392 adp: r_work=0.1202 r_free=0.1391 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1391 r_work=0.1202 r_free=0.1391 | n_water=426 | time (s): 62.520 (total time: 94.440) Filter (q & B) r_work=0.1205 r_free=0.1391 | n_water=413 | time (s): 2.500 (total time: 96.940) Filter (dist only) r_work=0.1205 r_free=0.1391 | n_water=412 | time (s): 36.100 (total time: 133.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.438896 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1485.184156 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 0.1725 0.1826 0.0101 0.001 0.4 8.6 0.0 0.0 0 0.125 0.1545 0.1665 0.0120 0.001 0.4 7.4 0.0 0.0 0 0.250 0.1436 0.1574 0.0139 0.001 0.4 7.7 0.0 0.0 0 0.500 0.1363 0.1519 0.0157 0.001 0.4 6.1 0.0 0.0 0 0.750 0.1320 0.1490 0.0170 0.002 0.5 6.1 0.0 0.0 0 1.000 0.1336 0.1503 0.0168 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1264 0.1464 0.0200 0.002 0.5 5.8 0.5 0.0 0 2.000 0.1232 0.1438 0.0206 0.003 0.6 6.1 0.5 0.0 0 3.000 0.1221 0.1437 0.0216 0.003 0.7 6.4 0.5 0.0 0 4.000 0.1213 0.1434 0.0221 0.004 0.7 6.4 0.5 0.0 0 5.000 0.1210 0.1428 0.0218 0.004 0.7 6.1 0.5 0.0 0 6.000 0.1203 0.1428 0.0225 0.005 0.8 6.4 0.5 0.0 0 7.000 0.1199 0.1427 0.0228 0.005 0.8 6.1 0.5 0.0 0 8.000 0.1197 0.1419 0.0223 0.006 0.8 5.8 0.5 0.0 0 9.000 0.1196 0.1427 0.0231 0.006 0.9 6.1 0.5 0.0 0 10.000 0.1193 0.1429 0.0236 0.007 0.9 6.7 0.5 0.0 0 11.000 0.1189 0.1420 0.0231 0.007 0.9 6.7 0.5 0.0 0 12.000 0.1189 0.1427 0.0238 0.008 0.9 6.7 0.5 0.0 0 13.000 0.1187 0.1429 0.0242 0.008 1.0 7.0 0.5 0.0 0 14.219 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1419 0.0223 0.006 0.8 5.8 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 14.19 2.23 3.771 21.734 1485.184 0.016 11.97 14.19 2.23 3.771 21.734 44.556 0.016 11.97 14.19 2.23 3.771 21.734 185.648 0.016 12.16 14.64 2.47 3.614 21.748 742.592 0.016 12.15 14.96 2.81 3.547 21.814 1485.184 0.015 11.99 14.89 2.90 3.443 22.013 2227.776 0.015 11.88 14.86 2.98 3.505 21.888 2970.368 0.014 11.85 14.76 2.91 3.478 22.053 3712.960 0.014 11.84 14.89 3.05 3.500 22.138 4455.552 0.014 11.81 14.90 3.09 3.529 22.154 5198.145 0.014 11.79 14.90 3.11 3.542 22.158 5940.737 0.014 11.72 14.85 3.13 3.548 22.187 6683.329 0.014 11.77 14.97 3.21 3.583 22.171 7425.921 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: 44.556 Accepted refinement result: 11.97 14.19 2.23 3.771 21.734 44.556 0.016 Individual atomic B min max mean iso aniso Overall: 9.08 114.98 22.12 3.30 188 1751 Protein: 9.08 114.98 17.02 3.31 0 1519 Water: 11.50 76.68 40.93 N/A 188 224 Other: 19.72 26.63 22.08 N/A 0 8 Chain A: 9.08 114.98 19.43 N/A 0 1751 Chain S: 14.49 60.00 47.18 N/A 188 0 Histogram: Values Number of atoms 9.08 - 19.67 1260 19.67 - 30.26 242 30.26 - 40.85 165 40.85 - 51.44 132 51.44 - 62.03 117 62.03 - 72.62 12 72.62 - 83.21 5 83.21 - 93.80 4 93.80 - 104.39 0 104.39 - 114.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1419 r_work=0.1197 r_free=0.1419 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1419 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 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.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1197 r_free= 0.1412 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015249 | | target function (ls_wunit_k1) not normalized (work): 1270.140561 | | target function (ls_wunit_k1) not normalized (free): 103.159456 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1197 0.1412 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1586 0.1583 0.1675 n_refl.: 87591 remove outliers: r(all,work,free)=0.1586 0.1583 0.1675 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1589 0.1586 0.1677 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1195 0.1408 n_refl.: 87591 remove outliers: r(all,work,free)=0.1204 0.1194 0.1408 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3364 300.281 272.663 0.587 1.002 0.350 11.894-9.307 99.02 97 4 0.1578 483.361 479.169 0.919 1.003 0.330 9.237-7.194 100.00 213 7 0.1751 395.330 394.526 0.985 1.003 0.280 7.162-5.571 100.00 427 22 0.1587 296.673 292.133 0.932 1.003 0.229 5.546-4.326 100.00 867 58 0.0881 407.259 404.367 0.960 1.003 0.205 4.315-3.360 100.00 1859 96 0.0802 387.306 386.269 1.005 1.002 0.200 3.356-2.611 100.00 3867 181 0.1107 254.440 253.454 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1021 168.670 168.131 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1104 82.370 82.596 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1449 36.526 36.067 1.024 0.996 0.000 1.221-1.150 99.97 13689 708 0.2256 23.014 21.524 0.986 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0209 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1408 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1195 r_free=0.1409 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1409 | n_water=412 | time (s): 1.890 (total time: 1.890) Filter (dist) r_work=0.1195 r_free=0.1412 | n_water=409 | time (s): 32.080 (total time: 33.970) Filter (q & B) r_work=0.1195 r_free=0.1412 | n_water=409 | time (s): 0.780 (total time: 34.750) Compute maps r_work=0.1195 r_free=0.1412 | n_water=409 | time (s): 1.540 (total time: 36.290) Filter (map) r_work=0.1230 r_free=0.1403 | n_water=278 | time (s): 3.060 (total time: 39.350) Find peaks r_work=0.1230 r_free=0.1403 | n_water=278 | time (s): 0.690 (total time: 40.040) Add new water r_work=0.1351 r_free=0.1543 | n_water=457 | time (s): 2.760 (total time: 42.800) Refine new water occ: r_work=0.1263 r_free=0.1457 adp: r_work=0.1265 r_free=0.1459 occ: r_work=0.1240 r_free=0.1432 adp: r_work=0.1240 r_free=0.1432 occ: r_work=0.1221 r_free=0.1411 adp: r_work=0.1217 r_free=0.1407 ADP+occupancy (water only), MIN, final r_work=0.1217 r_free=0.1407 r_work=0.1217 r_free=0.1407 | n_water=457 | time (s): 234.000 (total time: 276.800) Filter (q & B) r_work=0.1222 r_free=0.1408 | n_water=423 | time (s): 3.590 (total time: 280.390) Filter (dist only) r_work=0.1222 r_free=0.1407 | n_water=422 | time (s): 34.990 (total time: 315.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.809647 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.655124 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 0.1242 0.1381 0.0139 0.002 0.6 4.8 0.5 0.0 0 0.090 0.1199 0.1345 0.0146 0.003 0.7 3.5 0.5 0.0 0 0.271 0.1183 0.1334 0.0150 0.004 0.8 3.2 0.5 0.0 0 0.543 0.1176 0.1328 0.0153 0.005 0.9 3.2 0.5 0.0 0 0.814 0.1172 0.1327 0.0155 0.006 1.0 3.2 0.5 0.0 0 1.086 0.1169 0.1326 0.0157 0.007 1.0 3.5 0.5 0.0 0 1.357 0.1166 0.1324 0.0158 0.007 1.1 3.5 0.5 0.0 0 1.629 0.1165 0.1324 0.0159 0.008 1.1 4.2 0.5 0.0 0 1.900 0.1175 0.1330 0.0156 0.005 0.9 3.2 0.5 0.0 0 0.905 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1165 0.1324 0.0159 0.008 1.1 4.2 0.5 0.0 0 1.900 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.65 13.24 1.59 3.774 21.217 46.655 3.623 11.65 13.24 1.59 3.774 21.217 1.400 3.623 11.66 13.24 1.58 3.763 21.217 5.832 3.622 11.72 13.36 1.64 3.710 21.200 23.328 3.619 11.73 13.43 1.70 3.731 21.167 46.655 3.617 11.64 13.37 1.74 3.759 21.160 69.983 3.611 11.60 13.35 1.75 3.773 21.152 93.310 3.607 11.57 13.34 1.77 3.786 21.144 116.638 3.604 11.56 13.36 1.80 3.802 21.134 139.965 3.603 11.55 13.38 1.83 3.819 21.122 163.293 3.603 11.53 13.36 1.83 3.826 21.118 186.620 3.600 11.51 13.32 1.81 3.832 21.116 209.948 3.599 11.51 13.33 1.83 3.841 21.114 233.276 3.598 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.400 Accepted refinement result: 11.65 13.24 1.59 3.774 21.217 1.400 3.623 Individual atomic B min max mean iso aniso Overall: 9.10 114.99 21.16 3.30 203 1746 Protein: 9.10 114.99 17.03 3.31 0 1519 Water: 11.52 76.70 36.01 N/A 203 219 Other: 19.73 26.64 22.09 N/A 0 8 Chain A: 9.10 114.99 19.35 N/A 0 1746 Chain S: 14.50 60.01 36.73 N/A 203 0 Histogram: Values Number of atoms 9.10 - 19.69 1260 19.69 - 30.28 283 30.28 - 40.87 201 40.87 - 51.46 126 51.46 - 62.04 56 62.04 - 72.63 12 72.63 - 83.22 5 83.22 - 93.81 4 93.81 - 104.40 0 104.40 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1165 r_free=0.1324 r_work=0.1165 r_free=0.1324 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1165 r_free = 0.1324 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1157 r_free = 0.1317 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1157 r_free= 0.1317 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.615445 | | target function (ml) not normalized (work): 301144.895355 | | target function (ml) not normalized (free): 15848.634656 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1165 0.1157 0.1317 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1501 0.1498 0.1568 n_refl.: 87590 remove outliers: r(all,work,free)=0.1501 0.1498 0.1568 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1500 0.1497 0.1567 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1162 0.1154 0.1317 n_refl.: 87590 remove outliers: r(all,work,free)=0.1159 0.1151 0.1317 n_refl.: 87584 ======================== 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 0.3799 294.363 271.198 0.497 1.000 0.298 11.894-9.307 98.04 96 4 0.2329 483.486 466.282 0.875 1.001 0.283 9.237-7.194 98.64 210 7 0.2295 387.803 386.609 0.959 1.002 0.209 7.162-5.571 100.00 427 22 0.2046 296.673 286.548 0.919 1.002 0.170 5.546-4.326 100.00 867 58 0.1108 407.259 402.246 0.966 1.002 0.160 4.315-3.360 100.00 1859 96 0.0962 387.306 384.562 1.006 1.002 0.160 3.356-2.611 100.00 3867 181 0.1166 254.440 252.362 1.007 1.001 0.053 2.608-2.026 99.99 8198 413 0.0938 168.670 167.889 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0903 82.370 82.647 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.526 36.113 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2164 23.014 21.556 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0162 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1151 r_free=0.1317 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=0.1151 r_free=0.1317 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1151 r_free=0.1317 | n_water=422 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1151 r_free=0.1319 | n_water=419 | time (s): 46.260 (total time: 48.740) Filter (q & B) r_work=0.1151 r_free=0.1319 | n_water=418 | time (s): 3.810 (total time: 52.550) Compute maps r_work=0.1151 r_free=0.1319 | n_water=418 | time (s): 1.820 (total time: 54.370) Filter (map) r_work=0.1169 r_free=0.1298 | n_water=318 | time (s): 3.940 (total time: 58.310) Find peaks r_work=0.1169 r_free=0.1298 | n_water=318 | time (s): 0.700 (total time: 59.010) Add new water r_work=0.1248 r_free=0.1385 | n_water=491 | time (s): 3.770 (total time: 62.780) Refine new water occ: r_work=0.1173 r_free=0.1323 adp: r_work=0.1173 r_free=0.1325 occ: r_work=0.1158 r_free=0.1313 adp: r_work=0.1156 r_free=0.1313 occ: r_work=0.1145 r_free=0.1306 adp: r_work=0.1141 r_free=0.1303 ADP+occupancy (water only), MIN, final r_work=0.1141 r_free=0.1303 r_work=0.1141 r_free=0.1303 | n_water=491 | time (s): 217.730 (total time: 280.510) Filter (q & B) r_work=0.1146 r_free=0.1305 | n_water=453 | time (s): 3.950 (total time: 284.460) Filter (dist only) r_work=0.1147 r_free=0.1305 | n_water=451 | time (s): 47.380 (total time: 331.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.765273 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.128604 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 0.1210 0.1339 0.0129 0.002 0.6 4.2 0.5 0.0 0 0.088 0.1175 0.1318 0.0143 0.003 0.7 3.2 0.5 0.0 0 0.265 0.1158 0.1309 0.0150 0.005 0.9 4.2 0.5 0.0 0 0.530 0.1154 0.1309 0.0155 0.005 0.9 3.5 0.5 0.0 0 0.794 0.1150 0.1308 0.0158 0.006 1.0 3.5 0.5 0.0 0 1.059 0.1147 0.1310 0.0163 0.007 1.0 3.5 0.5 0.0 0 1.324 0.1145 0.1308 0.0163 0.008 1.1 3.5 0.5 0.0 0 1.589 0.1143 0.1307 0.0164 0.008 1.1 3.5 0.5 0.0 0 1.854 0.1152 0.1311 0.0158 0.006 1.0 3.5 0.5 0.0 0 0.883 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1143 0.1307 0.0164 0.008 1.1 3.5 0.5 0.0 0 1.854 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.43 13.07 1.64 3.776 21.231 48.129 3.610 11.43 13.07 1.64 3.776 21.231 1.444 3.610 11.44 13.07 1.63 3.765 21.231 6.016 3.609 11.46 13.13 1.67 3.715 21.222 24.064 3.605 11.46 13.20 1.74 3.739 21.199 48.129 3.604 11.43 13.25 1.81 3.762 21.181 72.193 3.601 11.41 13.25 1.83 3.773 21.175 96.257 3.599 11.37 13.23 1.86 3.788 21.167 120.322 3.595 11.35 13.22 1.87 3.803 21.164 144.386 3.594 11.33 13.21 1.88 3.815 21.158 168.450 3.592 11.32 13.21 1.88 3.827 21.153 192.514 3.591 11.31 13.20 1.89 3.835 21.151 216.579 3.590 11.30 13.19 1.89 3.839 21.153 240.643 3.589 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.444 Accepted refinement result: 11.43 13.07 1.64 3.776 21.231 1.444 3.610 Individual atomic B min max mean iso aniso Overall: 9.09 114.99 21.19 3.30 233 1745 Protein: 9.09 114.99 17.02 3.31 0 1519 Water: 11.51 76.69 35.20 N/A 233 218 Other: 19.73 26.64 22.09 N/A 0 8 Chain A: 9.09 114.99 19.34 N/A 0 1745 Chain S: 14.49 60.01 35.05 N/A 233 0 Histogram: Values Number of atoms 9.09 - 19.68 1263 19.68 - 30.27 298 30.27 - 40.86 221 40.86 - 51.45 120 51.45 - 62.04 53 62.04 - 72.63 12 72.63 - 83.22 5 83.22 - 93.81 4 93.81 - 104.40 0 104.40 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1143 r_free=0.1307 r_work=0.1143 r_free=0.1307 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1307 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1138 r_free = 0.1308 target_work(ml) = 3.607 | | 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.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1138 r_free= 0.1308 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607343 | | target function (ml) not normalized (work): 300448.391489 | | target function (ml) not normalized (free): 15836.842321 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1146 0.1138 0.1308 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1468 0.1467 0.1522 n_refl.: 87584 remove outliers: r(all,work,free)=0.1468 0.1467 0.1522 n_refl.: 87584 overall B=-0.00 to atoms: r(all,work,free)=0.1468 0.1467 0.1522 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1145 0.1137 0.1306 n_refl.: 87584 remove outliers: r(all,work,free)=0.1144 0.1135 0.1306 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4086 290.969 250.857 0.446 0.999 0.310 11.894-9.307 97.06 95 4 0.2438 487.389 469.975 0.859 1.001 0.310 9.237-7.194 98.18 209 7 0.2322 386.795 381.940 0.937 1.001 0.189 7.162-5.571 100.00 427 22 0.2133 296.673 286.136 0.919 1.001 0.160 5.546-4.326 100.00 867 58 0.1091 407.259 402.602 0.964 1.001 0.130 4.315-3.360 100.00 1859 96 0.0935 387.306 384.928 1.003 1.002 0.130 3.356-2.611 100.00 3867 181 0.1125 254.440 252.598 1.009 1.002 0.034 2.608-2.026 99.99 8198 413 0.0921 168.670 168.069 1.024 1.002 0.000 2.025-1.573 100.00 17313 902 0.0882 82.370 82.736 1.033 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.526 36.129 1.023 1.001 0.000 1.221-1.150 99.97 13689 708 0.2166 23.014 21.482 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=-0.0032 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1135 r_free=0.1306 After: r_work=0.1137 r_free=0.1306 ================================== NQH flips ================================== r_work=0.1137 r_free=0.1306 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=0.1137 r_free=0.1306 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1306 | n_water=451 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1137 r_free=0.1303 | n_water=450 | time (s): 48.160 (total time: 50.620) Filter (q & B) r_work=0.1137 r_free=0.1303 | n_water=450 | time (s): 1.400 (total time: 52.020) Compute maps r_work=0.1137 r_free=0.1303 | n_water=450 | time (s): 1.740 (total time: 53.760) Filter (map) r_work=0.1170 r_free=0.1333 | n_water=346 | time (s): 4.050 (total time: 57.810) Find peaks r_work=0.1170 r_free=0.1333 | n_water=346 | time (s): 0.680 (total time: 58.490) Add new water r_work=0.1218 r_free=0.1384 | n_water=482 | time (s): 3.590 (total time: 62.080) Refine new water occ: r_work=0.1156 r_free=0.1317 adp: r_work=0.1156 r_free=0.1319 occ: r_work=0.1145 r_free=0.1304 adp: r_work=0.1145 r_free=0.1307 occ: r_work=0.1137 r_free=0.1292 adp: r_work=0.1135 r_free=0.1294 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1294 r_work=0.1135 r_free=0.1294 | n_water=482 | time (s): 298.240 (total time: 360.320) Filter (q & B) r_work=0.1141 r_free=0.1298 | n_water=444 | time (s): 3.950 (total time: 364.270) Filter (dist only) r_work=0.1141 r_free=0.1297 | n_water=441 | time (s): 45.780 (total time: 410.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.765689 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.239199 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1220 0.1346 0.0126 0.004 0.7 6.4 0.0 0.0 0 0.088 0.1176 0.1317 0.0141 0.004 0.8 6.7 0.0 0.0 0 0.265 0.1161 0.1307 0.0147 0.005 0.9 6.4 0.5 0.0 0 0.530 0.1152 0.1302 0.0149 0.006 1.0 6.1 0.5 0.0 0 0.795 0.1147 0.1298 0.0151 0.006 1.1 5.8 0.5 0.0 0 1.059 0.1144 0.1297 0.0152 0.007 1.1 6.1 0.5 0.0 0 1.324 0.1142 0.1296 0.0154 0.008 1.1 5.8 0.5 0.0 0 1.589 0.1141 0.1296 0.0155 0.008 1.1 5.8 0.5 0.0 0 1.854 0.1150 0.1300 0.0150 0.006 1.0 6.1 0.5 0.0 0 0.883 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1141 0.1296 0.0155 0.008 1.1 5.8 0.5 0.0 0 1.854 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.41 12.96 1.55 3.775 21.152 42.239 3.609 11.41 12.96 1.55 3.775 21.152 1.267 3.609 11.41 12.96 1.55 3.775 21.152 5.280 3.609 11.43 13.00 1.56 3.712 21.143 21.120 3.604 11.53 13.19 1.66 3.729 21.111 42.239 3.609 11.44 13.15 1.71 3.753 21.101 63.359 3.603 11.37 13.09 1.73 3.767 21.101 84.478 3.597 11.34 13.07 1.73 3.775 21.100 105.598 3.595 11.35 13.14 1.78 3.796 21.083 126.718 3.595 11.32 13.10 1.78 3.803 21.085 147.837 3.593 11.32 13.12 1.80 3.819 21.073 168.957 3.592 11.31 13.11 1.81 3.829 21.071 190.076 3.591 11.30 13.10 1.80 3.834 21.071 211.196 3.590 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.267 Accepted refinement result: 11.41 12.96 1.55 3.775 21.152 1.267 3.609 Individual atomic B min max mean iso aniso Overall: 9.09 114.98 21.05 3.30 224 1744 Protein: 9.09 114.98 17.02 3.31 0 1519 Water: 11.51 76.69 34.89 N/A 224 217 Other: 19.73 26.63 22.09 N/A 0 8 Chain A: 9.09 114.98 19.34 N/A 0 1744 Chain S: 14.49 60.01 34.35 N/A 224 0 Histogram: Values Number of atoms 9.09 - 19.68 1263 19.68 - 30.27 297 30.27 - 40.86 215 40.86 - 51.45 124 51.45 - 62.04 46 62.04 - 72.63 12 72.63 - 83.22 5 83.22 - 93.81 4 93.81 - 104.40 0 104.40 - 114.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.1141 r_free=0.1296 r_work=0.1141 r_free=0.1296 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1141 r_free = 0.1296 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1138 r_free = 0.1293 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1138 r_free= 0.1293 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607799 | | target function (ml) not normalized (work): 300471.966189 | | target function (ml) not normalized (free): 15824.284008 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2922 171 0.1356 0.1356 5.6734 5.6153| | 2: 3.57 - 2.84 1.00 2888 124 0.1076 0.1400 5.1775 5.2475| | 3: 2.83 - 2.48 1.00 2820 163 0.1112 0.1234 4.9565 4.9995| | 4: 2.47 - 2.25 1.00 2825 136 0.0891 0.0977 4.6372 4.6561| | 5: 2.25 - 2.09 1.00 2756 127 0.0860 0.0963 4.587 4.6377| | 6: 2.09 - 1.97 1.00 2846 113 0.0864 0.1035 4.2791 4.3819| | 7: 1.97 - 1.87 1.00 2787 165 0.0880 0.1103 3.983 4.098| | 8: 1.87 - 1.79 1.00 2789 144 0.0917 0.1105 3.8945 3.9953| | 9: 1.79 - 1.72 1.00 2745 138 0.0875 0.1178 3.648 3.8271| | 10: 1.72 - 1.66 1.00 2831 160 0.0923 0.1183 3.565 3.6992| | 11: 1.66 - 1.61 1.00 2712 147 0.0869 0.1023 3.496 3.564| | 12: 1.61 - 1.56 1.00 2773 144 0.0898 0.1161 3.3261 3.4755| | 13: 1.56 - 1.52 1.00 2745 130 0.0949 0.1049 3.3099 3.4089| | 14: 1.52 - 1.48 1.00 2803 134 0.0980 0.1034 3.2423 3.3099| | 15: 1.48 - 1.45 1.00 2738 128 0.1000 0.1230 3.1527 3.2703| | 16: 1.45 - 1.42 1.00 2756 161 0.1053 0.1233 3.137 3.2397| | 17: 1.42 - 1.39 1.00 2785 139 0.1139 0.1307 3.1203 3.2315| | 18: 1.39 - 1.36 1.00 2741 179 0.1192 0.1337 3.1043 3.2484| | 19: 1.36 - 1.34 1.00 2807 134 0.1260 0.1576 3.113 3.2753| | 20: 1.34 - 1.32 1.00 2696 147 0.1369 0.1457 3.1138 3.1564| | 21: 1.32 - 1.30 1.00 2785 112 0.1471 0.1528 3.1143 3.1138| | 22: 1.29 - 1.27 1.00 2704 152 0.1559 0.1958 3.1223 3.2918| | 23: 1.27 - 1.26 1.00 2802 156 0.1644 0.1802 3.1321 3.2015| | 24: 1.26 - 1.24 1.00 2744 132 0.1712 0.1823 3.1283 3.2187| | 25: 1.24 - 1.22 1.00 2733 148 0.1885 0.2148 3.1442 3.2661| | 26: 1.22 - 1.21 1.00 2727 135 0.1913 0.1785 3.1515 3.2055| | 27: 1.21 - 1.19 1.00 2814 148 0.2078 0.2153 3.1743 3.1622| | 28: 1.19 - 1.18 1.00 2671 147 0.2202 0.2272 3.1681 3.1686| | 29: 1.18 - 1.16 1.00 2800 134 0.2268 0.2379 3.1495 3.2294| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2448 3.1441 3.1673| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2922 171 0.95 8.81 1.00 0.97 5922.85| | 2: 3.57 - 2.84 2888 124 0.92 12.81 1.01 0.97 5922.85| | 3: 2.83 - 2.48 2820 163 0.89 16.82 0.99 0.97 4945.83| | 4: 2.47 - 2.25 2825 136 0.92 13.65 1.00 0.98 2426.43| | 5: 2.25 - 2.09 2756 127 0.90 15.85 1.01 0.98 2426.43| | 6: 2.09 - 1.97 2846 113 0.92 12.47 1.02 0.98 1397.11| | 7: 1.97 - 1.87 2787 165 0.95 9.38 1.02 0.98 519.25| | 8: 1.87 - 1.79 2789 144 0.93 12.73 0.99 0.98 519.25| | 9: 1.79 - 1.72 2745 138 0.94 10.10 0.98 0.97 292.28| | 10: 1.72 - 1.66 2831 160 0.94 11.18 0.98 0.97 246.83| | 11: 1.66 - 1.61 2712 147 0.93 11.83 0.98 0.97 236.43| | 12: 1.61 - 1.56 2773 144 0.95 8.93 0.99 0.97 138.33| | 13: 1.56 - 1.52 2745 130 0.94 10.49 1.03 0.97 138.33| | 14: 1.52 - 1.48 2803 134 0.94 10.75 1.02 0.98 124.06| | 15: 1.48 - 1.45 2738 128 0.95 9.97 1.02 0.98 97.94| | 16: 1.45 - 1.42 2756 161 0.94 11.08 1.02 0.98 97.94| | 17: 1.42 - 1.39 2785 139 0.95 10.97 1.01 0.98 89.43| | 18: 1.39 - 1.36 2741 179 0.94 11.54 1.01 0.98 84.51| | 19: 1.36 - 1.34 2807 134 0.94 11.89 1.00 0.98 84.51| | 20: 1.34 - 1.32 2696 147 0.94 12.17 0.98 0.97 80.43| | 21: 1.32 - 1.30 2785 112 0.94 13.12 0.98 0.96 80.14| | 22: 1.29 - 1.27 2704 152 0.93 13.68 0.98 0.96 80.52| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.97 0.95 82.47| | 24: 1.26 - 1.24 2744 132 0.92 14.87 0.96 0.95 82.47| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 84.30| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.03 0.93 86.33| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.03 0.93 86.33| | 28: 1.19 - 1.18 2671 147 0.88 20.34 1.01 0.93 89.80| | 29: 1.18 - 1.16 2800 134 0.88 20.44 0.99 0.93 91.11| | 30: 1.16 - 1.15 2739 148 0.86 21.94 0.98 0.93 91.11| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 80.14 max = 5922.85 mean = 910.74| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.51| |phase err.(test): min = 0.00 max = 88.78 mean = 13.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1146 0.1138 0.1293 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1463 0.1463 0.1496 n_refl.: 87580 remove outliers: r(all,work,free)=0.1463 0.1463 0.1496 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1462 0.1462 0.1495 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1145 0.1138 0.1296 n_refl.: 87580 remove outliers: r(all,work,free)=0.1144 0.1136 0.1296 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 0.4148 286.217 254.753 0.426 0.999 0.260 11.894-9.307 94.12 92 4 0.2441 476.887 461.413 0.856 1.001 0.247 9.237-7.194 98.18 209 7 0.2430 386.795 379.510 0.925 1.001 0.173 7.162-5.571 100.00 427 22 0.2155 296.673 285.600 0.911 1.002 0.143 5.546-4.326 100.00 867 58 0.1139 407.259 402.217 0.966 1.002 0.125 4.315-3.360 100.00 1859 96 0.0930 387.306 384.936 1.004 1.002 0.120 3.356-2.611 100.00 3867 181 0.1115 254.440 252.483 1.011 1.002 0.029 2.608-2.026 99.99 8198 413 0.0910 168.670 168.041 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0888 82.370 82.703 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.526 36.132 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2168 23.014 21.559 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0161 ================= 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 : 0.2609 0.1940 0.084 5.384 8.8 119.3 19.9 258 0.000 1_bss: 0.1641 0.1773 0.084 5.384 9.0 119.5 20.1 258 0.000 1_settarget: 0.1641 0.1773 0.084 5.384 9.0 119.5 20.1 258 0.000 1_nqh: 0.1641 0.1773 0.084 5.384 9.0 119.5 20.1 258 0.000 1_weight: 0.1641 0.1773 0.084 5.384 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1229 0.1471 0.006 0.861 9.0 119.5 20.1 258 0.130 1_adp: 0.1236 0.1470 0.006 0.861 9.0 119.4 20.1 258 0.130 1_regHadp: 0.1238 0.1474 0.006 0.861 9.0 119.4 20.1 258 0.130 1_occ: 0.1230 0.1464 0.006 0.861 9.0 119.4 20.1 258 0.130 2_bss: 0.1227 0.1454 0.006 0.861 9.1 119.5 20.1 258 0.130 2_settarget: 0.1227 0.1454 0.006 0.861 9.1 119.5 20.1 258 0.130 2_updatecdl: 0.1227 0.1454 0.006 0.872 9.1 119.5 20.1 258 0.130 2_nqh: 0.1229 0.1456 0.006 0.872 9.1 119.5 20.1 258 0.133 2_sol: 0.1205 0.1391 0.006 0.872 9.1 115.0 22.1 412 n/a 2_weight: 0.1205 0.1391 0.006 0.872 9.1 115.0 22.1 412 n/a 2_xyzrec: 0.1197 0.1419 0.006 0.828 9.1 115.0 22.1 412 n/a 2_adp: 0.1197 0.1419 0.006 0.828 9.1 115.0 22.1 412 n/a 2_regHadp: 0.1197 0.1419 0.006 0.828 9.1 115.0 22.1 412 n/a 2_occ: 0.1197 0.1412 0.006 0.828 9.1 115.0 22.1 412 n/a 3_bss: 0.1194 0.1408 0.006 0.828 9.1 115.0 22.1 412 n/a 3_settarget: 0.1194 0.1408 0.006 0.828 9.1 115.0 22.1 412 n/a 3_updatecdl: 0.1194 0.1408 0.006 0.830 9.1 115.0 22.1 412 n/a 3_nqh: 0.1195 0.1409 0.006 0.830 9.1 115.0 22.1 412 n/a 3_sol: 0.1222 0.1407 0.006 0.830 9.1 115.0 21.2 422 n/a 3_weight: 0.1222 0.1407 0.006 0.830 9.1 115.0 21.2 422 n/a 3_xyzrec: 0.1165 0.1324 0.008 1.089 9.1 115.0 21.2 422 n/a 3_adp: 0.1165 0.1324 0.008 1.089 9.1 115.0 21.2 422 n/a 3_regHadp: 0.1165 0.1324 0.008 1.089 9.1 115.0 21.2 422 n/a 3_occ: 0.1157 0.1317 0.008 1.089 9.1 115.0 21.2 422 n/a 4_bss: 0.1151 0.1317 0.008 1.089 9.1 115.0 21.2 422 n/a 4_settarget: 0.1151 0.1317 0.008 1.089 9.1 115.0 21.2 422 n/a 4_updatecdl: 0.1151 0.1317 0.008 1.090 9.1 115.0 21.2 422 n/a 4_nqh: 0.1151 0.1317 0.008 1.090 9.1 115.0 21.2 422 n/a 4_sol: 0.1147 0.1305 0.008 1.090 9.1 115.0 21.2 451 n/a 4_weight: 0.1147 0.1305 0.008 1.090 9.1 115.0 21.2 451 n/a 4_xyzrec: 0.1143 0.1307 0.008 1.123 9.1 115.0 21.2 451 n/a 4_adp: 0.1143 0.1307 0.008 1.123 9.1 115.0 21.2 451 n/a 4_regHadp: 0.1143 0.1307 0.008 1.123 9.1 115.0 21.2 451 n/a 4_occ: 0.1138 0.1308 0.008 1.123 9.1 115.0 21.2 451 n/a 5_bss: 0.1135 0.1306 0.008 1.123 9.1 115.0 21.2 451 n/a 5_settarget: 0.1135 0.1306 0.008 1.123 9.1 115.0 21.2 451 n/a 5_updatecdl: 0.1135 0.1306 0.008 1.121 9.1 115.0 21.2 451 n/a 5_setrh: 0.1137 0.1306 0.008 1.121 9.1 115.0 21.2 451 n/a 5_nqh: 0.1137 0.1306 0.008 1.121 9.1 115.0 21.2 451 n/a 5_sol: 0.1141 0.1297 0.008 1.121 9.1 115.0 21.0 441 n/a 5_weight: 0.1141 0.1297 0.008 1.121 9.1 115.0 21.0 441 n/a 5_xyzrec: 0.1141 0.1296 0.008 1.140 9.1 115.0 21.0 441 n/a 5_adp: 0.1141 0.1296 0.008 1.140 9.1 115.0 21.0 441 n/a 5_regHadp: 0.1141 0.1296 0.008 1.140 9.1 115.0 21.0 441 n/a 5_occ: 0.1138 0.1293 0.008 1.140 9.1 115.0 21.0 441 n/a end: 0.1136 0.1296 0.008 1.140 9.1 115.0 21.0 441 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5637181_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5637181_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4600 Refinement macro-cycles (run) : 13593.9500 Write final files (write_after_run_outputs) : 90.6200 Total : 13688.0300 Total CPU time: 3.81 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:10:20 PST -0800 (1735366220.32 s) Start R-work = 0.1641, R-free = 0.1773 Final R-work = 0.1136, R-free = 0.1296 =============================================================================== Job complete usr+sys time: 13862.14 seconds wall clock time: 254 minutes 24.41 seconds (15264.41 seconds total)