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_6943566.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_6943566.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6943566.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 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: 1.47, per 1000 atoms: 0.43 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: 0.52 Conformation dependent library (CDL) restraints added in 199.2 milliseconds Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 616 0.93 - 1.20: 1079 1.20 - 1.47: 792 1.47 - 1.74: 655 1.74 - 2.01: 11 Bond restraints: 3153 Sorted by residual: bond pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 1.523 1.298 0.226 1.27e-02 6.20e+03 3.16e+02 bond pdb=" N VAL A 177 " pdb=" CA VAL A 177 " ideal model delta sigma weight residual 1.461 1.666 -0.206 1.19e-02 7.06e+03 2.99e+02 bond pdb=" CA VAL A 181 " pdb=" CB VAL A 181 " ideal model delta sigma weight residual 1.540 1.755 -0.215 1.25e-02 6.40e+03 2.96e+02 bond pdb=" N GLU A 147 " pdb=" CA GLU A 147 " ideal model delta sigma weight residual 1.455 1.248 0.207 1.21e-02 6.83e+03 2.93e+02 bond pdb=" N ASP A 60 " pdb=" CA ASP A 60 " ideal model delta sigma weight residual 1.458 1.673 -0.215 1.27e-02 6.20e+03 2.87e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.71: 3185 4.71 - 9.41: 1875 9.41 - 14.12: 592 14.12 - 18.82: 111 18.82 - 23.53: 14 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.07 115.47 5.60 3.60e-01 7.72e+00 2.42e+02 angle pdb=" OE1BGLN A 80 " pdb=" CD BGLN A 80 " pdb=" NE2BGLN A 80 " ideal model delta sigma weight residual 122.60 109.44 13.16 1.00e+00 1.00e+00 1.73e+02 angle pdb=" O MET A 17 " pdb=" C MET A 17 " pdb=" N GLU A 18 " ideal model delta sigma weight residual 122.12 135.79 -13.67 1.06e+00 8.90e-01 1.66e+02 angle pdb=" OE1 GLN A 180 " pdb=" CD GLN A 180 " pdb=" NE2 GLN A 180 " ideal model delta sigma weight residual 122.60 109.83 12.77 1.00e+00 1.00e+00 1.63e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.90 134.09 -13.19 1.07e+00 8.73e-01 1.52e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 960 17.65 - 35.30: 98 35.30 - 52.95: 41 52.95 - 70.59: 8 70.59 - 88.24: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ILE A 9 " pdb=" C ILE A 9 " pdb=" N LEU A 10 " pdb=" CA LEU A 10 " ideal model delta harmonic sigma weight residual -180.00 -158.95 -21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 122 0.248 - 0.495: 81 0.495 - 0.742: 30 0.742 - 0.989: 9 0.989 - 1.237: 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 -1.35 -1.24 2.00e-01 2.50e+01 3.82e+01 chirality pdb=" CA BLYS A 93 " pdb=" N BLYS A 93 " pdb=" C BLYS A 93 " pdb=" CB BLYS A 93 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CG ALEU A 153 " pdb=" CB ALEU A 153 " pdb=" CD1ALEU A 153 " pdb=" CD2ALEU A 153 " both_signs ideal model delta sigma weight residual False -2.59 -3.56 0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.017 2.00e-02 2.50e+03 6.32e-02 1.20e+02 pdb=" CG TYR A 141 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.121 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.071 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.080 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.092 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.016 2.00e-02 2.50e+03 6.74e-02 1.02e+02 pdb=" CG HIS A 115 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.103 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.053 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.125 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.057 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.012 2.00e-02 2.50e+03 5.62e-02 9.46e+01 pdb=" CG PHE A 162 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.105 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.077 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.032 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.049 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.040 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.091 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.015 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.050 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 854 2.29 - 2.87: 7943 2.87 - 3.45: 10608 3.45 - 4.02: 15268 4.02 - 4.60: 21947 Nonbonded interactions: 56620 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.715 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.785 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.800 2.270 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.825 2.100 nonbonded pdb="HH22 ARG A 5 " pdb=" O AGLU A 64 " model vdw 1.843 1.850 ... (remaining 56615 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_6943566_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= 0.2607 r_free= 0.1912 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790819 | | target function (ml) not normalized (work): 232491.997603 | | target function (ml) not normalized (free): 11807.322548 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3015 0.2024 7.0679 4.9435| | 2: 3.57 - 2.84 1.00 2876 122 0.2437 0.1700 4.3454 4.3336| | 3: 2.84 - 2.48 1.00 2833 165 0.2335 0.1716 4.1262 4.1555| | 4: 2.47 - 2.25 1.00 2825 136 0.2308 0.1465 3.8347 3.8388| | 5: 2.25 - 2.09 1.00 2756 127 0.2493 0.1621 3.797 3.8273| | 6: 2.09 - 1.97 1.00 2846 113 0.2524 0.1796 3.4617 3.5726| | 7: 1.97 - 1.87 1.00 2787 165 0.2554 0.1716 3.1375 3.1501| | 8: 1.87 - 1.79 1.00 2789 144 0.2463 0.1852 3.0547 3.1512| | 9: 1.79 - 1.72 1.00 2745 138 0.2446 0.1754 2.9036 2.896| | 10: 1.72 - 1.66 1.00 2789 158 0.2502 0.1967 2.8083 2.8997| | 11: 1.66 - 1.61 1.00 2740 147 0.2484 0.1777 2.7276 2.73| | 12: 1.61 - 1.56 1.00 2787 146 0.2515 0.1901 2.6284 2.6441| | 13: 1.56 - 1.52 1.00 2745 130 0.2518 0.1763 2.5501 2.5632| | 14: 1.52 - 1.48 1.00 2803 134 0.2591 0.1900 2.5064 2.5198| | 15: 1.48 - 1.45 1.00 2738 128 0.2572 0.2096 2.4249 2.5084| | 16: 1.45 - 1.42 1.00 2756 161 0.2662 0.2251 2.382 2.466| | 17: 1.42 - 1.39 1.00 2785 139 0.2619 0.2081 2.3273 2.3777| | 18: 1.39 - 1.36 1.00 2741 179 0.2675 0.2223 2.2832 2.3244| | 19: 1.36 - 1.34 1.00 2807 134 0.2647 0.2590 2.2525 2.3722| | 20: 1.34 - 1.32 1.00 2696 147 0.2760 0.2166 2.2069 2.2044| | 21: 1.32 - 1.30 1.00 2785 112 0.2786 0.2041 2.178 2.1094| | 22: 1.29 - 1.27 1.00 2704 152 0.2738 0.2471 2.1406 2.1995| | 23: 1.27 - 1.26 1.00 2802 156 0.2810 0.2546 2.1017 2.2271| | 24: 1.26 - 1.24 1.00 2744 132 0.2811 0.2412 2.0764 2.1122| | 25: 1.24 - 1.22 1.00 2734 148 0.2884 0.2595 2.04 2.1034| | 26: 1.22 - 1.21 1.00 2727 135 0.2855 0.2383 2.0108 2.1362| | 27: 1.21 - 1.19 1.00 2814 148 0.2987 0.2547 2.0047 1.9638| | 28: 1.19 - 1.18 1.00 2671 147 0.3064 0.2775 1.9947 1.9901| | 29: 1.18 - 1.16 1.00 2800 134 0.3008 0.2611 1.9658 2.0176| | 30: 1.16 - 1.15 1.00 2740 148 0.3078 0.2841 1.9292 1.9564| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.70 0.76 0.23 1483.75| | 2: 3.57 - 2.84 2876 122 0.80 26.08 1.27 0.23 1483.75| | 3: 2.84 - 2.48 2833 165 0.74 31.97 1.24 0.24 1230.42| | 4: 2.47 - 2.25 2825 136 0.81 25.51 1.25 0.25 572.98| | 5: 2.25 - 2.09 2756 127 0.77 29.39 1.29 0.25 572.98| | 6: 2.09 - 1.97 2846 113 0.83 22.78 1.29 0.25 313.06| | 7: 1.97 - 1.87 2787 165 0.90 16.64 1.28 0.26 91.38| | 8: 1.87 - 1.79 2789 144 0.86 21.16 1.25 0.26 91.38| | 9: 1.79 - 1.72 2745 138 0.88 18.20 1.23 0.25 53.96| | 10: 1.72 - 1.66 2789 158 0.87 19.99 1.24 0.25 46.46| | 11: 1.66 - 1.61 2740 147 0.86 20.88 1.24 0.25 44.79| | 12: 1.61 - 1.56 2787 146 0.89 17.88 1.23 0.25 27.84| | 13: 1.56 - 1.52 2745 130 0.87 19.74 1.23 0.25 27.84| | 14: 1.52 - 1.48 2803 134 0.87 20.08 1.24 0.25 25.04| | 15: 1.48 - 1.45 2738 128 0.87 19.75 1.22 0.25 19.93| | 16: 1.45 - 1.42 2756 161 0.86 21.06 1.23 0.25 19.93| | 17: 1.42 - 1.39 2785 139 0.87 20.37 1.22 0.25 17.17| | 18: 1.39 - 1.36 2741 179 0.86 21.01 1.23 0.25 15.57| | 19: 1.36 - 1.34 2807 134 0.86 21.61 1.21 0.25 15.57| | 20: 1.34 - 1.32 2696 147 0.87 21.14 1.22 0.25 13.21| | 21: 1.32 - 1.30 2785 112 0.86 22.21 1.21 0.25 13.04| | 22: 1.29 - 1.27 2704 152 0.86 22.31 1.21 0.25 12.74| | 23: 1.27 - 1.26 2802 156 0.85 22.36 1.22 0.24 11.24| | 24: 1.26 - 1.24 2744 132 0.85 22.97 1.21 0.24 11.24| | 25: 1.24 - 1.22 2734 148 0.84 23.78 1.21 0.24 10.62| | 26: 1.22 - 1.21 2727 135 0.84 23.86 1.20 0.24 9.93| | 27: 1.21 - 1.19 2814 148 0.83 24.63 1.21 0.24 9.93| | 28: 1.19 - 1.18 2671 147 0.83 24.88 1.20 0.23 9.04| | 29: 1.18 - 1.16 2800 134 0.83 24.93 1.18 0.23 8.70| | 30: 1.16 - 1.15 2740 148 0.81 26.49 1.16 0.23 8.70| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.70 max = 1483.75 mean = 214.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 22.41| |phase err.(test): min = 0.00 max = 89.60 mean = 22.15| |-----------------------------------------------------------------------------| ----------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 0.249 1557 Z= 5.539 Angle : 5.281 19.516 2118 Z= 3.691 Chirality : 0.371 1.237 243 Planarity : 0.032 0.103 284 Dihedral : 13.797 88.242 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 27.57 % 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: -2.61 (0.47), residues: 224 helix: -2.85 (0.32), residues: 108 sheet: -1.43 (0.67), residues: 40 loop : 0.44 (0.70), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.107 0.030 ARG A 145 TYR 0.088 0.047 TYR A 141 PHE 0.120 0.035 PHE A 164 HIS 0.065 0.032 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2607 r_free= 0.1912 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790819 | | target function (ml) not normalized (work): 232491.997603 | | target function (ml) not normalized (free): 11807.322548 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2565 0.2607 0.1913 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2565 0.2607 0.1913 n_refl.: 87602 remove outliers: r(all,work,free)=0.1973 0.1978 0.1913 n_refl.: 87594 overall B=0.17 to atoms: r(all,work,free)=0.1995 0.2000 0.1925 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1639 0.1634 0.1749 n_refl.: 87594 remove outliers: r(all,work,free)=0.1639 0.1633 0.1749 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.87 87 5 0.3836 382.322 354.267 0.663 1.001 0.397 11.894-9.307 99.02 97 4 0.1852 614.119 592.856 0.930 1.003 0.375 9.237-7.194 100.00 213 7 0.2159 502.274 492.138 0.958 1.003 0.344 7.162-5.571 100.00 427 22 0.2168 376.928 365.139 0.935 1.003 0.320 5.546-4.326 100.00 867 58 0.1265 517.430 511.608 0.960 1.003 0.219 4.315-3.360 100.00 1859 96 0.1142 492.079 488.652 1.005 1.003 0.199 3.356-2.611 100.00 3867 181 0.1426 323.271 319.876 0.997 1.002 0.029 2.608-2.026 99.99 8198 413 0.1351 214.299 212.020 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1643 104.652 104.009 1.014 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2066 46.407 45.084 1.002 0.996 0.000 1.221-1.150 99.97 13689 708 0.2594 29.240 26.983 0.979 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0401 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1633 r_free=0.1749 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1635 r_free=0.1753 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 32.569073 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2004.155187 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 0.1629 0.1746 0.0117 0.002 0.5 4.2 0.0 0.0 0 0.125 0.1516 0.1649 0.0133 0.001 0.5 3.2 0.0 0.0 0 0.250 0.1444 0.1594 0.0150 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1370 0.1537 0.0167 0.002 0.5 2.9 0.0 0.0 0 0.750 0.1353 0.1530 0.0178 0.002 0.5 2.6 0.0 0.0 0 1.000 0.1340 0.1519 0.0179 0.002 0.5 2.6 0.0 0.0 0 1.000 0.1290 0.1497 0.0207 0.002 0.6 2.6 0.5 0.0 0 2.000 0.1266 0.1487 0.0221 0.003 0.7 2.9 0.5 0.0 0 3.000 0.1266 0.1495 0.0229 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1249 0.1480 0.0230 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1243 0.1475 0.0232 0.005 0.8 3.2 0.5 0.0 0 6.000 0.1237 0.1472 0.0234 0.005 0.8 3.2 0.5 0.0 0 7.000 0.1234 0.1470 0.0236 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1233 0.1472 0.0239 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1230 0.1466 0.0236 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1227 0.1467 0.0239 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1226 0.1464 0.0238 0.007 0.9 3.2 0.5 0.0 0 12.000 0.1225 0.1462 0.0238 0.007 1.0 3.2 0.5 0.0 0 13.000 0.1224 0.1466 0.0243 0.008 1.0 3.2 0.5 0.0 0 14.000 0.1221 0.1462 0.0241 0.008 1.0 3.5 0.5 0.0 0 15.000 0.1221 0.1469 0.0248 0.009 1.0 3.5 0.5 0.0 0 16.285 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1221 0.1462 0.0241 0.008 1.0 3.5 0.5 0.0 0 15.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 14.62 2.41 3.013 19.033 2004.155 0.017 12.21 14.61 2.40 2.989 19.032 60.125 0.017 12.27 14.59 2.31 2.681 19.033 250.519 0.017 12.61 15.21 2.60 2.731 19.207 1002.078 0.016 12.49 15.40 2.91 3.251 19.569 2004.155 0.016 12.38 15.38 3.00 3.375 19.654 3006.233 0.015 12.27 15.32 3.06 3.360 19.639 4008.310 0.015 12.19 15.29 3.10 3.279 19.591 5010.388 0.015 12.20 15.33 3.13 3.352 19.617 6012.466 0.015 12.19 15.37 3.18 3.408 19.639 7014.543 0.015 12.09 15.27 3.18 3.406 19.635 8016.621 0.015 12.14 15.41 3.27 3.345 19.583 9018.698 0.015 12.13 15.42 3.30 3.413 19.614 10020.776 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: 250.519 Accepted refinement result: 12.27 14.59 2.31 2.681 19.033 250.519 0.017 Individual atomic B min max mean iso aniso Overall: 9.05 119.42 20.06 3.34 0 1785 Protein: 9.05 115.09 16.97 3.34 0 1519 Water: 11.46 119.42 38.20 N/A 0 258 Other: 19.67 26.56 22.01 N/A 0 8 Chain A: 9.05 119.42 20.06 N/A 0 1785 Histogram: Values Number of atoms 9.05 - 20.09 1272 20.09 - 31.12 227 31.12 - 42.16 125 42.16 - 53.20 95 53.20 - 64.24 41 64.24 - 75.27 11 75.27 - 86.31 7 86.31 - 97.35 4 97.35 - 108.39 1 108.39 - 119.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1227 r_free=0.1459 r_work=0.1229 r_free=0.1461 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1229 r_free = 0.1461 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 = 0.1222 r_free = 0.1457 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1222 r_free= 0.1457 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016622 | | target function (ls_wunit_k1) not normalized (work): 1384.565672 | | target function (ls_wunit_k1) not normalized (free): 108.355594 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1222 0.1457 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1664 0.1665 0.1689 n_refl.: 87592 remove outliers: r(all,work,free)=0.1664 0.1665 0.1689 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1671 0.1672 0.1694 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1231 0.1220 0.1451 n_refl.: 87592 remove outliers: r(all,work,free)=0.1231 0.1220 0.1451 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3539 300.971 278.655 0.654 1.002 0.388 11.894-9.307 99.02 97 4 0.1659 483.446 471.323 0.924 1.003 0.364 9.237-7.194 100.00 213 7 0.1853 395.399 390.718 0.964 1.003 0.329 7.162-5.571 100.00 427 22 0.1804 296.725 290.889 0.938 1.003 0.268 5.546-4.326 100.00 867 58 0.0996 407.331 404.177 0.962 1.003 0.204 4.315-3.360 100.00 1859 96 0.0864 387.374 386.256 1.008 1.002 0.180 3.356-2.611 100.00 3867 181 0.1172 254.485 253.337 1.009 1.002 0.090 2.608-2.026 99.99 8198 413 0.1018 168.700 167.986 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1102 82.384 82.597 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1441 36.533 36.043 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2245 23.018 21.501 0.979 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0618 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1220 r_free=0.1451 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 144 ASN Total number of N/Q/H flips: 1 r_work=0.1219 r_free=0.1450 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1219 r_free=0.1450 | n_water=258 | time (s): 1.710 (total time: 1.710) Filter (dist) r_work=0.1227 r_free=0.1448 | n_water=252 | time (s): 22.670 (total time: 24.380) Filter (q & B) r_work=0.1230 r_free=0.1446 | n_water=249 | time (s): 2.500 (total time: 26.880) Compute maps r_work=0.1230 r_free=0.1446 | n_water=249 | time (s): 1.250 (total time: 28.130) Filter (map) r_work=0.1246 r_free=0.1458 | n_water=225 | time (s): 3.210 (total time: 31.340) Find peaks r_work=0.1246 r_free=0.1458 | n_water=225 | time (s): 0.550 (total time: 31.890) Add new water r_work=0.1392 r_free=0.1618 | n_water=429 | time (s): 2.770 (total time: 34.660) Refine new water occ: r_work=0.1297 r_free=0.1486 adp: r_work=0.1218 r_free=0.1433 occ: r_work=0.1229 r_free=0.1417 adp: r_work=0.1197 r_free=0.1407 occ: r_work=0.1199 r_free=0.1391 adp: r_work=0.1189 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1394 r_work=0.1189 r_free=0.1394 | n_water=429 | time (s): 49.250 (total time: 83.910) Filter (q & B) r_work=0.1192 r_free=0.1398 | n_water=416 | time (s): 2.750 (total time: 86.660) Filter (dist only) r_work=0.1192 r_free=0.1396 | n_water=415 | time (s): 36.180 (total time: 122.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.154910 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1508.605042 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 0.1713 0.1823 0.0110 0.002 0.4 8.0 0.0 0.0 0 0.125 0.1525 0.1661 0.0136 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1387 0.1549 0.0162 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1360 0.1531 0.0171 0.002 0.5 5.1 0.0 0.0 0 0.750 0.1305 0.1491 0.0185 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1315 0.1499 0.0184 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1245 0.1456 0.0210 0.002 0.6 4.2 0.5 0.0 0 2.000 0.1230 0.1444 0.0214 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1218 0.1435 0.0217 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1210 0.1431 0.0222 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1197 0.1416 0.0219 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1190 0.1410 0.0220 0.005 0.8 5.1 0.5 0.0 0 7.000 0.1192 0.1417 0.0225 0.005 0.8 5.1 0.5 0.0 0 8.000 0.1194 0.1420 0.0227 0.006 0.8 4.5 0.5 0.0 0 9.000 0.1190 0.1411 0.0221 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1190 0.1419 0.0229 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1187 0.1412 0.0226 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1186 0.1412 0.0226 0.007 0.9 4.5 0.5 0.0 0 13.000 0.1185 0.1414 0.0229 0.008 1.0 5.4 0.5 0.6 0 14.077 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1410 0.0220 0.005 0.8 5.1 0.5 0.0 0 7.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 14.10 2.20 3.784 21.727 1508.605 0.016 11.90 14.10 2.20 3.784 21.727 45.258 0.016 11.90 14.10 2.20 3.784 21.727 188.576 0.016 12.16 14.65 2.48 3.566 21.772 754.303 0.015 12.05 14.75 2.70 3.527 21.807 1508.605 0.015 11.99 14.87 2.89 3.490 21.869 2262.908 0.014 11.80 14.62 2.81 3.447 21.999 3017.210 0.014 11.80 14.69 2.89 3.473 22.022 3771.513 0.014 11.68 14.67 2.99 3.517 21.871 4525.815 0.014 11.74 14.66 2.92 3.509 22.029 5280.118 0.014 11.72 14.82 3.09 3.555 22.151 6034.420 0.014 11.69 14.83 3.14 3.559 22.114 6788.723 0.014 11.70 14.88 3.18 3.600 22.169 7543.025 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: 45.258 Accepted refinement result: 11.90 14.10 2.20 3.784 21.727 45.258 0.016 Individual atomic B min max mean iso aniso Overall: 9.09 115.13 22.11 3.34 190 1752 Protein: 9.09 115.13 17.01 3.34 0 1519 Water: 11.50 76.68 40.80 N/A 190 225 Other: 19.71 26.60 22.05 N/A 0 8 Chain A: 9.09 115.13 19.43 N/A 0 1752 Chain S: 11.72 60.00 46.83 N/A 190 0 Histogram: Values Number of atoms 9.09 - 19.69 1260 19.69 - 30.30 248 30.30 - 40.90 164 40.90 - 51.51 126 51.51 - 62.11 121 62.11 - 72.72 12 72.72 - 83.32 5 83.32 - 93.92 4 93.92 - 104.53 0 104.53 - 115.13 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1410 r_work=0.1190 r_free=0.1410 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1410 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1401 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1189 r_free= 0.1401 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015053 | | target function (ls_wunit_k1) not normalized (work): 1253.822500 | | target function (ls_wunit_k1) not normalized (free): 99.778540 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1189 0.1401 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1588 0.1588 0.1630 n_refl.: 87592 remove outliers: r(all,work,free)=0.1588 0.1588 0.1630 n_refl.: 87592 overall B=0.02 to atoms: r(all,work,free)=0.1591 0.1591 0.1632 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1186 0.1396 n_refl.: 87592 remove outliers: r(all,work,free)=0.1195 0.1185 0.1396 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 0.3308 300.333 276.658 0.603 1.003 0.360 11.894-9.307 99.02 97 4 0.1650 483.446 476.655 0.925 1.004 0.320 9.237-7.194 100.00 213 7 0.1806 395.399 393.741 0.980 1.004 0.290 7.162-5.571 100.00 427 22 0.1600 296.725 293.102 0.936 1.003 0.250 5.546-4.326 100.00 867 58 0.0882 407.331 404.480 0.959 1.003 0.205 4.315-3.360 100.00 1859 96 0.0798 387.374 386.119 1.004 1.003 0.200 3.356-2.611 100.00 3867 181 0.1079 254.485 253.415 1.009 1.002 0.120 2.608-2.026 99.99 8198 413 0.0999 168.700 168.140 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1101 82.384 82.597 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1446 36.533 36.058 1.023 0.996 0.000 1.221-1.150 99.97 13689 708 0.2252 23.018 21.526 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=0.0264 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1396 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=0.1185 r_free=0.1396 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1396 | n_water=415 | time (s): 1.720 (total time: 1.720) Filter (dist) r_work=0.1187 r_free=0.1398 | n_water=412 | time (s): 38.410 (total time: 40.130) Filter (q & B) r_work=0.1187 r_free=0.1398 | n_water=412 | time (s): 0.870 (total time: 41.000) Compute maps r_work=0.1187 r_free=0.1398 | n_water=412 | time (s): 1.310 (total time: 42.310) Filter (map) r_work=0.1232 r_free=0.1390 | n_water=287 | time (s): 3.240 (total time: 45.550) Find peaks r_work=0.1232 r_free=0.1390 | n_water=287 | time (s): 0.690 (total time: 46.240) Add new water r_work=0.1345 r_free=0.1488 | n_water=450 | time (s): 3.240 (total time: 49.480) Refine new water occ: r_work=0.1252 r_free=0.1405 adp: r_work=0.1253 r_free=0.1407 occ: r_work=0.1230 r_free=0.1387 adp: r_work=0.1228 r_free=0.1385 occ: r_work=0.1214 r_free=0.1379 adp: r_work=0.1208 r_free=0.1373 ADP+occupancy (water only), MIN, final r_work=0.1208 r_free=0.1373 r_work=0.1208 r_free=0.1373 | n_water=450 | time (s): 219.680 (total time: 269.160) Filter (q & B) r_work=0.1210 r_free=0.1376 | n_water=432 | time (s): 3.170 (total time: 272.330) Filter (dist only) r_work=0.1210 r_free=0.1374 | n_water=431 | time (s): 35.240 (total time: 307.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.694235 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 53.023670 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 0.1233 0.1351 0.0119 0.002 0.6 4.8 0.5 0.0 0 0.085 0.1185 0.1315 0.0129 0.003 0.7 3.5 0.5 0.0 0 0.254 0.1170 0.1303 0.0133 0.004 0.8 3.2 0.5 0.0 0 0.508 0.1161 0.1297 0.0136 0.005 0.9 3.5 0.5 0.0 0 0.762 0.1157 0.1299 0.0142 0.006 1.0 3.5 0.5 0.0 0 1.017 0.1155 0.1298 0.0144 0.007 1.0 3.8 0.5 0.0 0 1.271 0.1152 0.1298 0.0146 0.007 1.0 4.5 0.5 0.0 0 1.525 0.1149 0.1298 0.0148 0.008 1.1 4.5 0.5 0.0 0 1.779 0.1160 0.1298 0.0137 0.005 0.9 3.8 0.5 0.0 0 0.847 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1161 0.1297 0.0136 0.005 0.9 3.5 0.5 0.0 0 0.762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.61 12.97 1.36 3.788 21.267 53.024 3.621 11.61 12.97 1.36 3.788 21.267 1.591 3.621 11.62 12.97 1.36 3.778 21.267 6.628 3.620 11.66 13.08 1.42 3.718 21.250 26.512 3.616 11.62 13.11 1.50 3.744 21.226 53.024 3.613 11.57 13.11 1.54 3.760 21.214 79.536 3.607 11.54 13.10 1.56 3.771 21.207 106.047 3.604 11.51 13.10 1.58 3.788 21.198 132.559 3.602 11.48 13.07 1.59 3.799 21.194 159.071 3.599 11.46 13.07 1.61 3.809 21.192 185.583 3.598 11.47 13.08 1.61 3.824 21.179 212.095 3.598 11.46 13.07 1.61 3.829 21.178 238.607 3.597 11.44 13.06 1.62 3.837 21.179 265.118 3.596 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.591 Accepted refinement result: 11.61 12.97 1.36 3.788 21.267 1.591 3.621 Individual atomic B min max mean iso aniso Overall: 9.11 115.15 21.25 3.34 211 1747 Protein: 9.11 115.15 17.03 3.34 0 1519 Water: 11.51 76.70 36.14 N/A 211 220 Other: 19.73 26.61 22.07 N/A 0 8 Chain A: 9.11 115.15 19.36 N/A 0 1747 Chain S: 11.74 60.02 36.90 N/A 211 0 Histogram: Values Number of atoms 9.11 - 19.71 1263 19.71 - 30.32 283 30.32 - 40.92 201 40.92 - 51.52 127 51.52 - 62.13 61 62.13 - 72.73 12 72.73 - 83.34 5 83.34 - 93.94 4 93.94 - 104.55 0 104.55 - 115.15 2 =========================== Idealize ADP of riding H ========================== r_work=0.1161 r_free=0.1297 r_work=0.1161 r_free=0.1297 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1161 r_free = 0.1297 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1157 r_free = 0.1301 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.18 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= 0.1301 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.615821 | | target function (ml) not normalized (work): 301176.182170 | | target function (ml) not normalized (free): 15826.796482 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1164 0.1157 0.1301 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1508 0.1508 0.1536 n_refl.: 87590 remove outliers: r(all,work,free)=0.1508 0.1508 0.1536 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1507 0.1507 0.1536 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1160 0.1153 0.1296 n_refl.: 87590 remove outliers: r(all,work,free)=0.1156 0.1149 0.1296 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 0.3683 291.987 264.931 0.516 1.000 0.330 11.894-9.307 97.06 95 4 0.2125 483.670 465.744 0.889 1.002 0.284 9.237-7.194 97.73 208 7 0.2215 387.948 387.001 0.960 1.002 0.240 7.162-5.571 100.00 427 22 0.2119 296.725 286.032 0.920 1.003 0.194 5.546-4.326 100.00 867 58 0.1108 407.331 403.245 0.964 1.003 0.175 4.315-3.360 100.00 1859 96 0.0935 387.374 385.005 1.005 1.002 0.170 3.356-2.611 100.00 3867 181 0.1145 254.485 252.594 1.008 1.002 0.043 2.608-2.026 99.99 8198 413 0.0942 168.700 167.962 1.022 1.001 0.000 2.025-1.573 100.00 17313 902 0.0912 82.384 82.679 1.034 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1268 36.533 36.115 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 23.018 21.553 0.989 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0047 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1149 r_free=0.1296 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1149 r_free=0.1296 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1149 r_free=0.1296 | n_water=431 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1151 r_free=0.1298 | n_water=428 | time (s): 44.100 (total time: 46.440) Filter (q & B) r_work=0.1151 r_free=0.1300 | n_water=426 | time (s): 3.520 (total time: 49.960) Compute maps r_work=0.1151 r_free=0.1300 | n_water=426 | time (s): 1.750 (total time: 51.710) Filter (map) r_work=0.1169 r_free=0.1288 | n_water=327 | time (s): 3.750 (total time: 55.460) Find peaks r_work=0.1169 r_free=0.1288 | n_water=327 | time (s): 0.690 (total time: 56.150) Add new water r_work=0.1247 r_free=0.1374 | n_water=490 | time (s): 3.570 (total time: 59.720) Refine new water occ: r_work=0.1176 r_free=0.1312 adp: r_work=0.1177 r_free=0.1314 occ: r_work=0.1160 r_free=0.1296 adp: r_work=0.1159 r_free=0.1297 occ: r_work=0.1148 r_free=0.1282 adp: r_work=0.1144 r_free=0.1281 ADP+occupancy (water only), MIN, final r_work=0.1144 r_free=0.1281 r_work=0.1144 r_free=0.1281 | n_water=490 | time (s): 281.340 (total time: 341.060) Filter (q & B) r_work=0.1150 r_free=0.1293 | n_water=458 | time (s): 4.250 (total time: 345.310) Filter (dist only) r_work=0.1157 r_free=0.1291 | n_water=456 | time (s): 47.590 (total time: 392.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.800957 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.553901 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1211 0.1335 0.0124 0.002 0.6 4.8 0.5 0.0 0 0.090 0.1172 0.1306 0.0134 0.003 0.8 3.5 0.5 0.0 0 0.270 0.1159 0.1301 0.0143 0.005 0.9 3.8 0.5 0.0 0 0.540 0.1153 0.1295 0.0142 0.006 1.0 4.2 0.5 0.0 0 0.810 0.1148 0.1296 0.0148 0.007 1.0 4.2 0.5 0.0 0 1.081 0.1146 0.1297 0.0151 0.007 1.1 3.8 0.5 0.0 0 1.351 0.1144 0.1296 0.0152 0.008 1.1 4.2 0.5 0.0 0 1.621 0.1143 0.1297 0.0154 0.009 1.1 4.2 0.5 0.0 0 1.891 0.1151 0.1300 0.0149 0.006 1.0 3.8 0.5 0.0 0 0.900 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1153 0.1295 0.0142 0.006 1.0 4.2 0.5 0.0 0 0.810 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.53 12.95 1.42 3.790 21.267 41.554 3.614 11.53 12.95 1.42 3.790 21.267 1.247 3.614 11.53 12.95 1.42 3.790 21.267 5.194 3.614 11.56 13.01 1.44 3.716 21.260 20.777 3.609 11.65 13.16 1.51 3.724 21.236 41.554 3.613 11.56 13.12 1.56 3.748 21.224 62.331 3.606 11.50 13.08 1.58 3.766 21.222 83.108 3.602 11.47 13.07 1.59 3.775 21.218 103.885 3.599 11.45 13.04 1.60 3.784 21.217 124.662 3.597 11.42 13.02 1.60 3.788 21.218 145.439 3.595 11.44 13.09 1.64 3.808 21.198 166.216 3.595 11.41 13.05 1.64 3.814 21.197 186.993 3.593 11.42 13.06 1.65 3.823 21.196 207.770 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: 5.194 Accepted refinement result: 11.53 12.95 1.42 3.790 21.267 5.194 3.614 Individual atomic B min max mean iso aniso Overall: 9.10 115.15 21.25 3.34 238 1745 Protein: 9.10 115.15 17.02 3.34 0 1519 Water: 11.51 76.70 35.33 N/A 238 218 Other: 19.73 26.61 22.07 N/A 0 8 Chain A: 9.10 115.15 19.36 N/A 0 1745 Chain S: 11.74 60.01 35.16 N/A 238 0 Histogram: Values Number of atoms 9.10 - 19.71 1265 19.71 - 30.31 302 30.31 - 40.92 215 40.92 - 51.52 125 51.52 - 62.13 53 62.13 - 72.73 12 72.73 - 83.34 5 83.34 - 93.94 4 93.94 - 104.54 0 104.54 - 115.15 2 =========================== Idealize ADP of riding H ========================== r_work=0.1153 r_free=0.1295 r_work=0.1153 r_free=0.1295 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1295 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1147 r_free = 0.1293 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.15 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= 0.1147 r_free= 0.1293 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.611260 | | target function (ml) not normalized (work): 300756.603001 | | target function (ml) not normalized (free): 15831.736663 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1154 0.1147 0.1293 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1467 0.1467 0.1495 n_refl.: 87579 remove outliers: r(all,work,free)=0.1467 0.1467 0.1495 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1466 0.1466 0.1494 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1152 0.1145 0.1291 n_refl.: 87579 remove outliers: r(all,work,free)=0.1151 0.1143 0.1291 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 0.3988 288.533 258.930 0.455 1.000 0.298 11.894-9.307 96.08 94 4 0.2310 476.802 470.825 0.880 1.002 0.290 9.237-7.194 97.27 207 7 0.2333 387.470 381.790 0.931 1.002 0.176 7.162-5.571 100.00 427 22 0.2137 296.725 287.047 0.911 1.002 0.155 5.546-4.326 100.00 867 58 0.1137 407.331 402.536 0.964 1.003 0.140 4.315-3.360 100.00 1859 96 0.0934 387.374 385.231 1.004 1.002 0.130 3.356-2.611 100.00 3867 181 0.1128 254.485 252.669 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0932 168.700 167.936 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0896 82.384 82.698 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1257 36.533 36.132 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 23.018 21.565 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=-0.0155 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1143 r_free=0.1291 After: r_work=0.1144 r_free=0.1291 ================================== NQH flips ================================== r_work=0.1144 r_free=0.1291 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=0.1144 r_free=0.1291 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1144 r_free=0.1291 | n_water=456 | time (s): 2.610 (total time: 2.610) Filter (dist) r_work=0.1144 r_free=0.1293 | n_water=455 | time (s): 48.380 (total time: 50.990) Filter (q & B) r_work=0.1144 r_free=0.1291 | n_water=454 | time (s): 3.920 (total time: 54.910) Compute maps r_work=0.1144 r_free=0.1291 | n_water=454 | time (s): 1.800 (total time: 56.710) Filter (map) r_work=0.1166 r_free=0.1288 | n_water=359 | time (s): 3.990 (total time: 60.700) Find peaks r_work=0.1166 r_free=0.1288 | n_water=359 | time (s): 0.720 (total time: 61.420) Add new water r_work=0.1215 r_free=0.1341 | n_water=495 | time (s): 3.750 (total time: 65.170) Refine new water occ: r_work=0.1164 r_free=0.1288 adp: r_work=0.1164 r_free=0.1289 occ: r_work=0.1154 r_free=0.1275 adp: r_work=0.1153 r_free=0.1275 occ: r_work=0.1147 r_free=0.1263 adp: r_work=0.1143 r_free=0.1263 ADP+occupancy (water only), MIN, final r_work=0.1143 r_free=0.1263 r_work=0.1143 r_free=0.1263 | n_water=495 | time (s): 231.910 (total time: 297.080) Filter (q & B) r_work=0.1150 r_free=0.1277 | n_water=453 | time (s): 4.100 (total time: 301.180) Filter (dist only) r_work=0.1150 r_free=0.1275 | n_water=451 | time (s): 48.540 (total time: 349.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.721292 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.921242 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 0.1320 0.0100 0.003 0.7 5.4 0.0 0.0 0 0.086 0.1179 0.1293 0.0114 0.004 0.8 5.1 0.0 0.0 0 0.258 0.1156 0.1277 0.0120 0.005 0.9 4.5 0.5 0.0 0 0.516 0.1151 0.1274 0.0124 0.006 1.0 4.5 0.5 0.0 0 0.775 0.1149 0.1274 0.0124 0.006 1.0 4.5 0.5 0.0 0 1.033 0.1147 0.1273 0.0125 0.007 1.0 4.5 0.5 0.0 0 1.291 0.1146 0.1272 0.0126 0.007 1.0 4.5 0.5 0.0 0 1.549 0.1143 0.1271 0.0128 0.009 1.1 4.2 0.5 0.0 0 1.807 0.1150 0.1274 0.0124 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 0.1143 0.1271 0.0128 0.009 1.1 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 11.43 12.71 1.28 3.789 21.224 41.921 3.603 11.43 12.71 1.28 3.789 21.224 1.258 3.603 11.43 12.71 1.27 3.789 21.224 5.240 3.603 11.47 12.77 1.30 3.716 21.217 20.961 3.598 11.51 12.87 1.36 3.737 21.198 41.921 3.602 11.45 12.88 1.43 3.748 21.183 62.882 3.596 11.39 12.83 1.44 3.767 21.181 83.842 3.591 11.37 12.83 1.46 3.774 21.178 104.803 3.589 11.36 12.83 1.47 3.784 21.172 125.764 3.587 11.33 12.80 1.47 3.792 21.175 146.724 3.585 11.33 12.81 1.49 3.804 21.164 167.685 3.585 11.32 12.81 1.50 3.814 21.161 188.646 3.584 11.30 12.80 1.50 3.821 21.161 209.606 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.240 Accepted refinement result: 11.43 12.71 1.27 3.789 21.224 5.240 3.603 Individual atomic B min max mean iso aniso Overall: 9.10 115.14 21.18 3.33 233 1745 Protein: 9.10 115.14 17.02 3.34 0 1519 Water: 11.51 76.69 35.18 N/A 233 218 Other: 19.72 26.60 22.06 N/A 0 8 Chain A: 9.10 115.14 19.35 N/A 0 1745 Chain S: 11.73 60.01 34.88 N/A 233 0 Histogram: Values Number of atoms 9.10 - 19.70 1265 19.70 - 30.31 302 30.31 - 40.91 207 40.91 - 51.51 134 51.51 - 62.12 47 62.12 - 72.72 12 72.72 - 83.33 5 83.33 - 93.93 4 93.93 - 104.53 0 104.53 - 115.14 2 =========================== Idealize ADP of riding H ========================== r_work=0.1143 r_free=0.1271 r_work=0.1143 r_free=0.1271 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1271 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1269 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1140 r_free= 0.1269 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601525 | | target function (ml) not normalized (work): 299934.985309 | | target function (ml) not normalized (free): 15792.594212 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1351 0.1259 5.683 5.5566| | 2: 3.57 - 2.84 1.00 2888 124 0.1087 0.1305 5.1528 5.1868| | 3: 2.83 - 2.48 1.00 2820 163 0.1116 0.1241 4.9246 4.9632| | 4: 2.47 - 2.25 1.00 2825 136 0.0907 0.1015 4.606 4.6437| | 5: 2.25 - 2.09 1.00 2756 127 0.0877 0.0994 4.5508 4.6054| | 6: 2.09 - 1.97 1.00 2846 113 0.0863 0.1007 4.2553 4.3447| | 7: 1.97 - 1.87 1.00 2787 165 0.0886 0.1116 3.9772 4.0926| | 8: 1.87 - 1.79 1.00 2789 144 0.0923 0.1082 3.8849 3.9868| | 9: 1.79 - 1.72 1.00 2745 138 0.0863 0.1171 3.6395 3.8278| | 10: 1.72 - 1.66 1.00 2831 160 0.0917 0.1155 3.5622 3.69| | 11: 1.66 - 1.61 1.00 2712 147 0.0862 0.1026 3.4917 3.5705| | 12: 1.61 - 1.56 1.00 2773 144 0.0904 0.1171 3.3322 3.4801| | 13: 1.56 - 1.52 1.00 2745 130 0.0946 0.1052 3.3084 3.4049| | 14: 1.52 - 1.48 1.00 2803 134 0.0983 0.1037 3.2411 3.3215| | 15: 1.48 - 1.45 1.00 2738 128 0.1002 0.1240 3.1552 3.2679| | 16: 1.45 - 1.42 1.00 2756 161 0.1047 0.1265 3.1318 3.2522| | 17: 1.42 - 1.39 1.00 2785 139 0.1138 0.1297 3.1203 3.2433| | 18: 1.39 - 1.36 1.00 2741 179 0.1192 0.1324 3.1043 3.2392| | 19: 1.36 - 1.34 1.00 2807 134 0.1260 0.1563 3.1132 3.2698| | 20: 1.34 - 1.32 1.00 2696 147 0.1358 0.1474 3.1109 3.1591| | 21: 1.32 - 1.30 1.00 2785 112 0.1465 0.1520 3.1136 3.111| | 22: 1.29 - 1.27 1.00 2704 152 0.1559 0.1974 3.1241 3.2929| | 23: 1.27 - 1.26 1.00 2802 156 0.1641 0.1780 3.1328 3.2025| | 24: 1.26 - 1.24 1.00 2744 132 0.1704 0.1837 3.1278 3.2297| | 25: 1.24 - 1.22 1.00 2733 148 0.1872 0.2146 3.1424 3.2642| | 26: 1.22 - 1.21 1.00 2727 135 0.1898 0.1756 3.1468 3.2012| | 27: 1.21 - 1.19 1.00 2814 148 0.2068 0.2163 3.1703 3.1614| | 28: 1.19 - 1.18 1.00 2671 147 0.2202 0.2294 3.1667 3.1744| | 29: 1.18 - 1.16 1.00 2800 134 0.2261 0.2377 3.1483 3.2288| | 30: 1.16 - 1.15 1.00 2739 148 0.2440 0.2442 3.1434 3.1674| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7.82 1.00 0.97 5233.64| | 2: 3.57 - 2.84 2888 124 0.93 11.86 1.01 0.97 5233.64| | 3: 2.83 - 2.48 2820 163 0.90 15.66 0.99 0.97 4379.76| | 4: 2.47 - 2.25 2825 136 0.92 12.82 1.00 0.98 2177.90| | 5: 2.25 - 2.09 2756 127 0.91 14.86 1.01 0.98 2177.90| | 6: 2.09 - 1.97 2846 113 0.93 11.94 1.02 0.98 1272.37| | 7: 1.97 - 1.87 2787 165 0.95 9.16 1.02 0.98 500.07| | 8: 1.87 - 1.79 2789 144 0.93 12.44 1.00 0.98 500.07| | 9: 1.79 - 1.72 2745 138 0.94 9.97 0.98 0.98 286.21| | 10: 1.72 - 1.66 2831 160 0.94 11.08 0.98 0.97 243.38| | 11: 1.66 - 1.61 2712 147 0.94 11.67 0.98 0.97 233.33| | 12: 1.61 - 1.56 2773 144 0.95 8.91 0.99 0.97 138.54| | 13: 1.56 - 1.52 2745 130 0.95 10.43 1.03 0.97 138.54| | 14: 1.52 - 1.48 2803 134 0.94 10.81 1.02 0.98 124.46| | 15: 1.48 - 1.45 2738 128 0.95 9.95 1.02 0.98 98.66| | 16: 1.45 - 1.42 2756 161 0.94 11.14 1.02 0.98 98.66| | 17: 1.42 - 1.39 2785 139 0.95 10.99 1.01 0.98 90.00| | 18: 1.39 - 1.36 2741 179 0.94 11.57 1.01 0.98 84.98| | 19: 1.36 - 1.34 2807 134 0.94 11.96 1.00 0.98 84.98| | 20: 1.34 - 1.32 2696 147 0.94 12.14 0.98 0.97 80.68| | 21: 1.32 - 1.30 2785 112 0.94 13.17 0.98 0.97 80.38| | 22: 1.29 - 1.27 2704 152 0.93 13.69 0.98 0.96 80.74| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.97 0.95 82.58| | 24: 1.26 - 1.24 2744 132 0.92 14.87 0.96 0.95 82.58| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 84.44| | 26: 1.22 - 1.21 2727 135 0.90 18.06 1.03 0.93 86.50| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.02 0.93 86.50| | 28: 1.19 - 1.18 2671 147 0.88 20.38 1.01 0.93 90.13| | 29: 1.18 - 1.16 2800 134 0.88 20.45 0.99 0.93 91.50| | 30: 1.16 - 1.15 2739 148 0.86 21.97 0.98 0.93 91.50| |alpha: min = 0.93 max = 0.98 mean = 0.97| |beta: min = 80.38 max = 5233.64 mean = 820.87| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.30| |phase err.(test): min = 0.00 max = 89.75 mean = 13.31| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1146 0.1140 0.1269 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1461 0.1462 0.1473 n_refl.: 87576 remove outliers: r(all,work,free)=0.1461 0.1462 0.1473 n_refl.: 87576 overall B=-0.00 to atoms: r(all,work,free)=0.1460 0.1461 0.1473 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1146 0.1140 0.1270 n_refl.: 87576 remove outliers: r(all,work,free)=0.1145 0.1138 0.1270 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 86.46 78 5 0.4180 286.301 248.752 0.444 0.999 0.299 11.894-9.307 94.12 92 4 0.2307 474.460 461.303 0.864 1.002 0.220 9.237-7.194 97.27 207 7 0.2367 387.470 380.718 0.927 1.002 0.160 7.162-5.571 100.00 427 22 0.2130 296.725 286.744 0.907 1.002 0.150 5.546-4.326 100.00 867 58 0.1148 407.331 402.161 0.963 1.003 0.134 4.315-3.360 100.00 1859 96 0.0930 387.374 385.306 1.004 1.002 0.120 3.356-2.611 100.00 3867 181 0.1130 254.485 252.680 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0921 168.700 168.022 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0889 82.384 82.723 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.533 36.140 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 23.018 21.567 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=-0.0123 ================= 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 : 0.2607 0.1912 0.083 5.281 8.8 119.3 19.9 258 0.000 1_bss: 0.1633 0.1749 0.083 5.281 9.0 119.5 20.1 258 0.000 1_settarget: 0.1633 0.1749 0.083 5.281 9.0 119.5 20.1 258 0.000 1_nqh: 0.1635 0.1753 0.083 5.281 9.0 119.5 20.1 258 0.006 1_weight: 0.1635 0.1753 0.083 5.281 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1221 0.1462 0.008 1.006 9.0 119.5 20.1 258 0.134 1_adp: 0.1227 0.1459 0.008 1.006 9.0 119.4 20.1 258 0.134 1_regHadp: 0.1229 0.1461 0.008 1.006 9.0 119.4 20.1 258 0.134 1_occ: 0.1222 0.1457 0.008 1.006 9.0 119.4 20.1 258 0.134 2_bss: 0.1220 0.1451 0.008 1.006 9.1 119.5 20.1 258 0.134 2_settarget: 0.1220 0.1451 0.008 1.006 9.1 119.5 20.1 258 0.134 2_updatecdl: 0.1220 0.1451 0.008 1.004 9.1 119.5 20.1 258 0.134 2_nqh: 0.1219 0.1450 0.008 1.004 9.1 119.5 20.1 258 0.131 2_sol: 0.1192 0.1396 0.008 1.004 9.1 115.1 22.1 415 n/a 2_weight: 0.1192 0.1396 0.008 1.004 9.1 115.1 22.1 415 n/a 2_xyzrec: 0.1190 0.1410 0.005 0.794 9.1 115.1 22.1 415 n/a 2_adp: 0.1190 0.1410 0.005 0.794 9.1 115.1 22.1 415 n/a 2_regHadp: 0.1190 0.1410 0.005 0.794 9.1 115.1 22.1 415 n/a 2_occ: 0.1189 0.1401 0.005 0.794 9.1 115.1 22.1 415 n/a 3_bss: 0.1185 0.1396 0.005 0.794 9.1 115.2 22.1 415 n/a 3_settarget: 0.1185 0.1396 0.005 0.794 9.1 115.2 22.1 415 n/a 3_updatecdl: 0.1185 0.1396 0.005 0.795 9.1 115.2 22.1 415 n/a 3_nqh: 0.1185 0.1396 0.005 0.795 9.1 115.2 22.1 415 n/a 3_sol: 0.1210 0.1374 0.005 0.795 9.1 115.2 21.3 431 n/a 3_weight: 0.1210 0.1374 0.005 0.795 9.1 115.2 21.3 431 n/a 3_xyzrec: 0.1161 0.1297 0.005 0.910 9.1 115.2 21.3 431 n/a 3_adp: 0.1161 0.1297 0.005 0.910 9.1 115.2 21.3 431 n/a 3_regHadp: 0.1161 0.1297 0.005 0.910 9.1 115.2 21.3 431 n/a 3_occ: 0.1157 0.1301 0.005 0.910 9.1 115.2 21.3 431 n/a 4_bss: 0.1149 0.1296 0.005 0.910 9.1 115.1 21.3 431 n/a 4_settarget: 0.1149 0.1296 0.005 0.910 9.1 115.1 21.3 431 n/a 4_updatecdl: 0.1149 0.1296 0.005 0.910 9.1 115.1 21.3 431 n/a 4_nqh: 0.1149 0.1296 0.005 0.910 9.1 115.1 21.3 431 n/a 4_sol: 0.1157 0.1291 0.005 0.910 9.1 115.1 21.3 456 n/a 4_weight: 0.1157 0.1291 0.005 0.910 9.1 115.1 21.3 456 n/a 4_xyzrec: 0.1153 0.1295 0.006 0.956 9.1 115.1 21.3 456 n/a 4_adp: 0.1153 0.1295 0.006 0.956 9.1 115.1 21.3 456 n/a 4_regHadp: 0.1153 0.1295 0.006 0.956 9.1 115.1 21.3 456 n/a 4_occ: 0.1147 0.1293 0.006 0.956 9.1 115.1 21.3 456 n/a 5_bss: 0.1143 0.1291 0.006 0.956 9.1 115.1 21.2 456 n/a 5_settarget: 0.1143 0.1291 0.006 0.956 9.1 115.1 21.2 456 n/a 5_updatecdl: 0.1143 0.1291 0.006 0.957 9.1 115.1 21.2 456 n/a 5_setrh: 0.1144 0.1291 0.006 0.957 9.1 115.1 21.2 456 n/a 5_nqh: 0.1144 0.1291 0.006 0.957 9.1 115.1 21.2 456 n/a 5_sol: 0.1150 0.1275 0.006 0.957 9.1 115.1 21.2 451 n/a 5_weight: 0.1150 0.1275 0.006 0.957 9.1 115.1 21.2 451 n/a 5_xyzrec: 0.1143 0.1271 0.009 1.113 9.1 115.1 21.2 451 n/a 5_adp: 0.1143 0.1271 0.009 1.113 9.1 115.1 21.2 451 n/a 5_regHadp: 0.1143 0.1271 0.009 1.113 9.1 115.1 21.2 451 n/a 5_occ: 0.1140 0.1269 0.009 1.113 9.1 115.1 21.2 451 n/a end: 0.1138 0.1270 0.009 1.113 9.1 115.1 21.2 451 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6943566_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6943566_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4600 Refinement macro-cycles (run) : 14201.5800 Write final files (write_after_run_outputs) : 81.2900 Total : 14286.3300 Total CPU time: 3.98 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:18:09 PST -0800 (1735366689.46 s) Start R-work = 0.1633, R-free = 0.1749 Final R-work = 0.1138, R-free = 0.1270 =============================================================================== Job complete usr+sys time: 14434.71 seconds wall clock time: 261 minutes 46.91 seconds (15706.91 seconds total)