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_6318584.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_6318584.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6318584.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 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.79, per 1000 atoms: 0.53 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: 0.55 Conformation dependent library (CDL) restraints added in 123.4 milliseconds Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.94: 708 0.94 - 1.20: 988 1.20 - 1.47: 751 1.47 - 1.73: 691 1.73 - 1.99: 15 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 1.236 0.983 0.254 1.15e-02 7.56e+03 4.88e+02 bond pdb=" C MET A 134 " pdb=" O MET A 134 " ideal model delta sigma weight residual 1.235 0.961 0.274 1.33e-02 5.65e+03 4.26e+02 bond pdb=" C ILE A 105 " pdb=" O ILE A 105 " ideal model delta sigma weight residual 1.236 1.432 -0.196 1.01e-02 9.80e+03 3.78e+02 bond pdb=" CA TYR A 141 " pdb=" C TYR A 141 " ideal model delta sigma weight residual 1.525 1.273 0.252 1.32e-02 5.74e+03 3.64e+02 bond pdb=" C SER A 161 " pdb=" N PHE A 162 " ideal model delta sigma weight residual 1.334 1.569 -0.234 1.27e-02 6.20e+03 3.40e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.89: 3191 4.89 - 9.78: 1922 9.78 - 14.67: 560 14.67 - 19.56: 96 19.56 - 24.46: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 122.12 138.68 -16.56 1.06e+00 8.90e-01 2.44e+02 angle pdb=" O GLY A 78 " pdb=" C GLY A 78 " pdb=" N ALA A 79 " ideal model delta sigma weight residual 122.18 107.91 14.27 9.60e-01 1.09e+00 2.21e+02 angle pdb=" O BGLN A 80 " pdb=" C BGLN A 80 " pdb=" N ASN A 81 " ideal model delta sigma weight residual 122.12 137.79 -15.67 1.06e+00 8.90e-01 2.18e+02 angle pdb=" O BPRO A 66 " pdb=" C BPRO A 66 " pdb=" N BTYR A 67 " ideal model delta sigma weight residual 121.10 145.56 -24.46 1.90e+00 2.77e-01 1.66e+02 angle pdb=" O ALA A 183 " pdb=" C ALA A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 120.55 108.59 11.96 9.50e-01 1.11e+00 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 949 17.96 - 35.93: 116 35.93 - 53.89: 30 53.89 - 71.85: 14 71.85 - 89.81: 2 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 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA CYS A 106 " pdb=" C CYS A 106 " pdb=" N ALA A 107 " pdb=" CA ALA A 107 " ideal model delta harmonic sigma weight residual 180.00 155.61 24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA BLYS A 99 " pdb=" C BLYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual 180.00 158.71 21.29 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.213: 86 0.213 - 0.425: 82 0.425 - 0.637: 48 0.637 - 0.849: 21 0.849 - 1.061: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.46 1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CA ALA A 171 " pdb=" N ALA A 171 " pdb=" C ALA A 171 " pdb=" CB ALA A 171 " both_signs ideal model delta sigma weight residual False 2.48 1.49 0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CA THR A 19 " pdb=" N THR A 19 " pdb=" C THR A 19 " pdb=" CB THR A 19 " both_signs ideal model delta sigma weight residual False 2.53 3.50 -0.97 2.00e-01 2.50e+01 2.36e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.129 2.00e-02 2.50e+03 6.32e-02 1.20e+02 pdb=" CG TYR A 141 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.089 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.079 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.096 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.046 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.004 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG BTYR A 67 " -0.070 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.110 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.106 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.039 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.052 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.022 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.061 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.017 2.00e-02 2.50e+03 5.97e-02 1.07e+02 pdb=" CG PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.068 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.085 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.065 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.080 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 785 2.28 - 2.86: 7830 2.86 - 3.44: 10690 3.44 - 4.02: 15318 4.02 - 4.60: 21984 Nonbonded interactions: 56607 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.699 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.825 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.837 1.850 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.850 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H ATHR A 154 " model vdw 1.854 1.850 ... (remaining 56602 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_6318584_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= 0.2598 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787914 | | target function (ml) not normalized (work): 232249.964631 | | target function (ml) not normalized (free): 11789.298437 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2097 7.1251 4.9474| | 2: 3.57 - 2.84 1.00 2876 122 0.2439 0.1748 4.3431 4.3369| | 3: 2.84 - 2.48 1.00 2833 165 0.2332 0.1618 4.1202 4.1419| | 4: 2.47 - 2.25 1.00 2825 136 0.2337 0.1367 3.8233 3.8191| | 5: 2.25 - 2.09 1.00 2756 127 0.2450 0.1511 3.7956 3.8081| | 6: 2.09 - 1.97 1.00 2846 113 0.2532 0.1683 3.4511 3.5157| | 7: 1.97 - 1.87 1.00 2787 165 0.2521 0.1780 3.1146 3.1834| | 8: 1.87 - 1.79 1.00 2789 144 0.2486 0.2085 3.0472 3.1731| | 9: 1.79 - 1.72 1.00 2745 138 0.2413 0.1890 2.9013 2.9375| | 10: 1.72 - 1.66 1.00 2789 158 0.2430 0.2011 2.8147 2.862| | 11: 1.66 - 1.61 1.00 2740 147 0.2433 0.1866 2.7488 2.7841| | 12: 1.61 - 1.56 1.00 2787 146 0.2476 0.2165 2.6021 2.7399| | 13: 1.56 - 1.52 1.00 2745 130 0.2589 0.1887 2.5955 2.5828| | 14: 1.52 - 1.48 1.00 2803 134 0.2592 0.1866 2.5122 2.5298| | 15: 1.48 - 1.45 1.00 2738 128 0.2612 0.2257 2.4248 2.5516| | 16: 1.45 - 1.42 1.00 2756 161 0.2653 0.2124 2.3726 2.4059| | 17: 1.42 - 1.39 1.00 2785 139 0.2636 0.2052 2.3234 2.3246| | 18: 1.39 - 1.36 1.00 2741 179 0.2668 0.2046 2.2646 2.2808| | 19: 1.36 - 1.34 1.00 2807 134 0.2693 0.2400 2.2546 2.3161| | 20: 1.34 - 1.32 1.00 2696 147 0.2692 0.2176 2.1961 2.1704| | 21: 1.32 - 1.30 1.00 2785 112 0.2681 0.2253 2.1577 2.1937| | 22: 1.29 - 1.27 1.00 2704 152 0.2714 0.2561 2.1242 2.2086| | 23: 1.27 - 1.26 1.00 2802 156 0.2775 0.2289 2.0958 2.1346| | 24: 1.26 - 1.24 1.00 2744 132 0.2792 0.2671 2.0628 2.1564| | 25: 1.24 - 1.22 1.00 2734 148 0.2803 0.2588 2.0403 2.0873| | 26: 1.22 - 1.21 1.00 2727 135 0.2820 0.2422 2.0019 2.0802| | 27: 1.21 - 1.19 1.00 2814 148 0.2974 0.2634 2.0071 2.0185| | 28: 1.19 - 1.18 1.00 2671 147 0.2972 0.2708 1.9828 2.002| | 29: 1.18 - 1.16 1.00 2800 134 0.2990 0.2532 1.9542 1.9927| | 30: 1.16 - 1.15 1.00 2740 148 0.3047 0.2683 1.92 1.9127| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.63 0.76 0.23 1461.59| | 2: 3.57 - 2.84 2876 122 0.81 25.83 1.27 0.23 1461.59| | 3: 2.84 - 2.48 2833 165 0.74 31.61 1.24 0.24 1211.41| | 4: 2.47 - 2.25 2825 136 0.81 25.43 1.25 0.25 562.16| | 5: 2.25 - 2.09 2756 127 0.78 28.92 1.28 0.25 562.16| | 6: 2.09 - 1.97 2846 113 0.84 22.51 1.29 0.25 306.97| | 7: 1.97 - 1.87 2787 165 0.90 16.30 1.28 0.26 89.32| | 8: 1.87 - 1.79 2789 144 0.86 21.08 1.25 0.26 89.32| | 9: 1.79 - 1.72 2745 138 0.88 18.68 1.23 0.25 56.02| | 10: 1.72 - 1.66 2789 158 0.86 20.46 1.22 0.25 49.35| | 11: 1.66 - 1.61 2740 147 0.86 21.37 1.23 0.25 47.61| | 12: 1.61 - 1.56 2787 146 0.88 18.63 1.24 0.25 29.92| | 13: 1.56 - 1.52 2745 130 0.86 20.53 1.24 0.25 29.92| | 14: 1.52 - 1.48 2803 134 0.86 20.72 1.24 0.25 26.54| | 15: 1.48 - 1.45 2738 128 0.87 19.75 1.24 0.25 20.34| | 16: 1.45 - 1.42 2756 161 0.86 21.56 1.24 0.25 20.34| | 17: 1.42 - 1.39 2785 139 0.87 20.39 1.23 0.25 17.07| | 18: 1.39 - 1.36 2741 179 0.87 20.75 1.23 0.25 15.17| | 19: 1.36 - 1.34 2807 134 0.86 21.44 1.22 0.25 15.17| | 20: 1.34 - 1.32 2696 147 0.87 20.59 1.21 0.25 12.73| | 21: 1.32 - 1.30 2785 112 0.86 21.56 1.20 0.25 12.55| | 22: 1.29 - 1.27 2704 152 0.86 21.96 1.22 0.25 12.30| | 23: 1.27 - 1.26 2802 156 0.86 22.02 1.21 0.24 11.02| | 24: 1.26 - 1.24 2744 132 0.85 22.79 1.21 0.24 11.02| | 25: 1.24 - 1.22 2734 148 0.85 23.28 1.20 0.24 10.40| | 26: 1.22 - 1.21 2727 135 0.84 23.74 1.20 0.23 9.72| | 27: 1.21 - 1.19 2814 148 0.83 24.53 1.20 0.23 9.72| | 28: 1.19 - 1.18 2671 147 0.84 24.46 1.18 0.23 8.71| | 29: 1.18 - 1.16 2800 134 0.84 24.55 1.17 0.23 8.33| | 30: 1.16 - 1.15 2740 148 0.82 25.68 1.16 0.23 8.33| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.33 max = 1461.59 mean = 212.03| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.33| |phase err.(test): min = 0.00 max = 89.63 mean = 22.24| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.274 1557 Z= 5.356 Angle : 5.348 24.455 2118 Z= 3.727 Chirality : 0.406 1.061 243 Planarity : 0.030 0.124 284 Dihedral : 14.099 89.814 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 32.43 % 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: -2.49 (0.47), residues: 224 helix: -2.38 (0.39), residues: 108 sheet: -0.28 (0.83), residues: 30 loop : -0.84 (0.57), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.099 0.019 ARG A 27 TYR 0.102 0.042 TYR A 141 PHE 0.098 0.032 PHE A 119 HIS 0.041 0.022 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2598 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787914 | | target function (ml) not normalized (work): 232249.964631 | | target function (ml) not normalized (free): 11789.298437 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2557 0.2598 0.1926 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2557 0.2598 0.1926 n_refl.: 87602 remove outliers: r(all,work,free)=0.1968 0.1972 0.1926 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.1992 0.1997 0.1939 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1632 0.1626 0.1753 n_refl.: 87594 remove outliers: r(all,work,free)=0.1631 0.1625 0.1753 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 98.94 88 5 0.3811 386.364 359.801 0.731 0.916 0.401 11.894-9.307 98.04 96 4 0.1750 616.211 586.454 1.010 0.917 0.380 9.237-7.194 100.00 213 7 0.2127 501.948 492.395 1.045 0.917 0.334 7.162-5.571 100.00 427 22 0.2213 376.684 363.154 1.011 0.918 0.310 5.546-4.326 100.00 867 58 0.1274 517.094 510.752 1.052 0.919 0.219 4.315-3.360 100.00 1859 96 0.1136 491.760 488.167 1.096 0.920 0.199 3.356-2.611 100.00 3867 181 0.1442 323.061 320.022 1.085 0.921 0.109 2.608-2.026 99.99 8198 413 0.1340 214.160 212.103 1.091 0.923 0.000 2.025-1.573 100.00 17313 902 0.1623 104.585 103.980 1.090 0.927 0.000 1.573-1.221 100.00 36679 1900 0.2052 46.377 45.062 1.072 0.933 0.000 1.221-1.150 99.97 13689 708 0.2578 29.221 27.004 1.035 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0449 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1625 r_free=0.1753 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 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1625 r_free=0.1753 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.571042 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2021.193992 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 0.1684 0.1794 0.0110 0.002 0.5 3.8 0.0 0.0 0 0.125 0.1543 0.1671 0.0128 0.002 0.5 3.5 0.0 0.0 0 0.250 0.1422 0.1574 0.0152 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1383 0.1552 0.0169 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1364 0.1547 0.0183 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1345 0.1529 0.0185 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1297 0.1504 0.0208 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1256 0.1468 0.0212 0.003 0.7 3.2 0.5 0.0 0 3.000 0.1254 0.1475 0.0221 0.003 0.7 2.6 0.5 0.0 0 4.000 0.1253 0.1481 0.0228 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1240 0.1466 0.0226 0.004 0.8 4.2 0.5 0.0 0 6.000 0.1236 0.1466 0.0230 0.005 0.8 3.2 0.5 0.0 0 7.000 0.1230 0.1459 0.0229 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1230 0.1464 0.0234 0.006 0.9 2.9 0.5 0.0 0 9.000 0.1226 0.1455 0.0229 0.006 0.9 3.5 0.5 0.6 0 10.000 0.1224 0.1460 0.0236 0.007 0.9 2.6 0.5 0.6 0 11.000 0.1224 0.1460 0.0235 0.007 0.9 3.5 0.5 0.6 0 12.000 0.1222 0.1464 0.0242 0.008 1.0 3.5 0.5 0.6 0 13.786 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1226 0.1455 0.0229 0.006 0.9 3.5 0.5 0.6 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.55 2.29 3.013 19.055 2021.194 0.017 12.26 14.55 2.28 2.988 19.055 60.636 0.017 12.33 14.53 2.20 2.669 19.054 252.649 0.017 12.67 15.20 2.53 2.747 19.227 1010.597 0.016 12.60 15.46 2.86 3.466 19.727 2021.194 0.016 12.48 15.41 2.94 3.432 19.704 3031.791 0.015 12.35 15.38 3.03 3.386 19.666 4042.388 0.015 12.23 15.25 3.02 3.269 19.586 5052.985 0.015 12.26 15.34 3.07 3.402 19.653 6063.582 0.015 12.22 15.37 3.16 3.477 19.698 7074.179 0.015 12.21 15.40 3.20 3.540 19.718 8084.776 0.015 12.13 15.30 3.17 3.438 19.650 9095.373 0.015 12.13 15.34 3.21 3.525 19.683 10105.970 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: 252.649 Accepted refinement result: 12.33 14.53 2.20 2.669 19.054 252.649 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.43 20.08 3.31 0 1785 Protein: 9.06 114.99 16.99 3.32 0 1519 Water: 11.45 119.43 38.22 N/A 0 258 Other: 19.70 26.59 22.05 N/A 0 8 Chain A: 9.06 119.43 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1272 20.10 - 31.14 227 31.14 - 42.17 125 42.17 - 53.21 94 53.21 - 64.25 42 64.25 - 75.29 11 75.29 - 86.32 7 86.32 - 97.36 4 97.36 - 108.40 1 108.40 - 119.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1453 r_work=0.1234 r_free=0.1456 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1456 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 = 0.1226 r_free = 0.1451 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 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= 0.1226 r_free= 0.1451 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016709 | | target function (ls_wunit_k1) not normalized (work): 1391.787002 | | target function (ls_wunit_k1) not normalized (free): 107.577173 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1237 0.1226 0.1451 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1671 0.1673 0.1688 n_refl.: 87592 remove outliers: r(all,work,free)=0.1671 0.1673 0.1688 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1678 0.1679 0.1693 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1236 0.1225 0.1448 n_refl.: 87592 remove outliers: r(all,work,free)=0.1236 0.1225 0.1448 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 96.88 88 5 0.3570 303.896 285.022 0.660 1.002 0.395 11.894-9.307 98.04 96 4 0.1583 484.683 471.927 0.931 1.003 0.366 9.237-7.194 100.00 213 7 0.1889 394.808 389.580 0.961 1.003 0.324 7.162-5.571 100.00 427 22 0.1840 296.282 290.011 0.932 1.003 0.263 5.546-4.326 100.00 867 58 0.1006 406.722 403.482 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0865 386.795 385.700 1.009 1.002 0.190 3.356-2.611 100.00 3867 181 0.1170 254.104 252.968 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1019 168.448 167.737 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1111 82.261 82.463 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1452 36.478 35.981 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2256 22.984 21.465 0.980 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0558 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1448 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=0.1227 r_free=0.1448 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1448 | n_water=258 | time (s): 1.840 (total time: 1.840) Filter (dist) r_work=0.1234 r_free=0.1448 | n_water=251 | time (s): 22.200 (total time: 24.040) Filter (q & B) r_work=0.1236 r_free=0.1448 | n_water=248 | time (s): 2.400 (total time: 26.440) Compute maps r_work=0.1236 r_free=0.1448 | n_water=248 | time (s): 1.310 (total time: 27.750) Filter (map) r_work=0.1254 r_free=0.1455 | n_water=226 | time (s): 2.390 (total time: 30.140) Find peaks r_work=0.1254 r_free=0.1455 | n_water=226 | time (s): 0.590 (total time: 30.730) Add new water r_work=0.1399 r_free=0.1618 | n_water=431 | time (s): 3.040 (total time: 33.770) Refine new water occ: r_work=0.1305 r_free=0.1475 adp: r_work=0.1227 r_free=0.1425 occ: r_work=0.1238 r_free=0.1412 adp: r_work=0.1206 r_free=0.1401 occ: r_work=0.1208 r_free=0.1392 adp: r_work=0.1199 r_free=0.1393 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1393 r_work=0.1199 r_free=0.1393 | n_water=431 | time (s): 60.350 (total time: 94.120) Filter (q & B) r_work=0.1203 r_free=0.1393 | n_water=417 | time (s): 3.030 (total time: 97.150) Filter (dist only) r_work=0.1203 r_free=0.1392 | n_water=416 | time (s): 34.260 (total time: 131.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.787430 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1492.918408 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 0.1655 0.1769 0.0114 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1547 0.1673 0.0126 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1402 0.1554 0.0151 0.001 0.4 6.1 0.0 0.0 0 0.500 0.1335 0.1503 0.0168 0.002 0.5 5.8 0.0 0.0 0 0.750 0.1312 0.1487 0.0175 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1323 0.1498 0.0175 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1261 0.1460 0.0200 0.002 0.5 4.8 0.5 0.0 0 2.000 0.1231 0.1442 0.0211 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1217 0.1427 0.0210 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1211 0.1424 0.0212 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1206 0.1417 0.0211 0.005 0.7 4.5 0.5 0.0 0 6.000 0.1200 0.1411 0.0211 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1198 0.1412 0.0214 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1195 0.1412 0.0218 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1195 0.1415 0.0220 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1193 0.1411 0.0218 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1193 0.1413 0.0220 0.007 0.9 5.4 0.5 0.6 0 12.000 0.1188 0.1416 0.0228 0.008 0.9 4.5 0.5 0.6 0 13.894 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1200 0.1411 0.0211 0.005 0.8 4.2 0.5 0.0 0 7.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 14.11 2.11 3.776 21.787 1492.918 0.016 12.00 14.11 2.11 3.776 21.787 44.788 0.016 12.00 14.11 2.11 3.775 21.787 186.615 0.016 12.18 14.54 2.36 3.619 21.800 746.459 0.016 12.11 14.74 2.63 3.527 21.875 1492.918 0.015 12.06 14.93 2.87 3.509 21.932 2239.378 0.015 11.98 14.81 2.83 3.468 22.181 2985.837 0.014 11.88 14.79 2.91 3.481 22.216 3732.296 0.014 11.75 14.65 2.90 3.462 22.175 4478.755 0.014 11.78 14.71 2.93 3.509 22.167 5225.214 0.014 11.78 14.82 3.04 3.548 22.242 5971.674 0.014 11.80 14.86 3.06 3.559 22.208 6718.133 0.014 11.73 14.74 3.01 3.564 22.207 7464.592 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: 44.788 Accepted refinement result: 12.00 14.11 2.11 3.776 21.787 44.788 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 22.21 3.31 190 1753 Protein: 9.10 115.03 17.03 3.32 0 1519 Water: 10.38 76.69 41.12 N/A 190 226 Other: 19.74 26.63 22.09 N/A 0 8 Chain A: 9.10 115.03 19.46 N/A 0 1753 Chain S: 10.38 60.00 47.51 N/A 190 0 Histogram: Values Number of atoms 9.10 - 19.69 1258 19.69 - 30.29 244 30.29 - 40.88 160 40.88 - 51.47 136 51.47 - 62.06 122 62.06 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1411 r_work=0.1200 r_free=0.1411 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1411 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 = 0.1200 r_free = 0.1407 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.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1200 r_free= 0.1407 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015308 | | target function (ls_wunit_k1) not normalized (work): 1275.070244 | | target function (ls_wunit_k1) not normalized (free): 98.727819 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1200 0.1407 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1598 0.1596 0.1660 n_refl.: 87592 remove outliers: r(all,work,free)=0.1598 0.1596 0.1660 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1599 0.1598 0.1661 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1197 0.1405 n_refl.: 87592 remove outliers: r(all,work,free)=0.1206 0.1196 0.1405 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3350 299.932 276.572 0.605 1.003 0.360 11.894-9.307 98.04 96 4 0.1599 484.683 477.012 0.931 1.003 0.324 9.237-7.194 100.00 213 7 0.1762 394.808 393.298 0.980 1.003 0.269 7.162-5.571 100.00 427 22 0.1644 296.282 292.120 0.936 1.003 0.229 5.546-4.326 100.00 867 58 0.0908 406.722 404.108 0.961 1.003 0.210 4.315-3.360 100.00 1859 96 0.0795 386.795 385.880 1.004 1.003 0.190 3.356-2.611 100.00 3867 181 0.1101 254.104 252.969 1.009 1.002 0.130 2.608-2.026 99.99 8198 413 0.1014 168.448 167.911 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1109 82.261 82.446 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1454 36.478 35.999 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2257 22.984 21.497 0.988 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0166 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1405 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1405 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1405 | n_water=416 | time (s): 1.540 (total time: 1.540) Filter (dist) r_work=0.1196 r_free=0.1405 | n_water=414 | time (s): 34.940 (total time: 36.480) Filter (q & B) r_work=0.1196 r_free=0.1405 | n_water=414 | time (s): 1.140 (total time: 37.620) Compute maps r_work=0.1196 r_free=0.1405 | n_water=414 | time (s): 1.420 (total time: 39.040) Filter (map) r_work=0.1240 r_free=0.1408 | n_water=277 | time (s): 3.330 (total time: 42.370) Find peaks r_work=0.1240 r_free=0.1408 | n_water=277 | time (s): 0.630 (total time: 43.000) Add new water r_work=0.1360 r_free=0.1523 | n_water=459 | time (s): 3.270 (total time: 46.270) Refine new water occ: r_work=0.1264 r_free=0.1423 adp: r_work=0.1265 r_free=0.1427 occ: r_work=0.1241 r_free=0.1400 adp: r_work=0.1240 r_free=0.1404 occ: r_work=0.1223 r_free=0.1384 adp: r_work=0.1218 r_free=0.1384 ADP+occupancy (water only), MIN, final r_work=0.1218 r_free=0.1384 r_work=0.1218 r_free=0.1384 | n_water=459 | time (s): 196.010 (total time: 242.280) Filter (q & B) r_work=0.1223 r_free=0.1383 | n_water=431 | time (s): 2.550 (total time: 244.830) Filter (dist only) r_work=0.1223 r_free=0.1382 | n_water=430 | time (s): 35.410 (total time: 280.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.749225 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.587899 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 0.1243 0.1346 0.0103 0.002 0.6 4.2 0.5 0.0 0 0.087 0.1197 0.1312 0.0115 0.003 0.7 3.5 0.5 0.0 0 0.262 0.1182 0.1302 0.0119 0.004 0.8 2.9 0.5 0.0 0 0.525 0.1173 0.1295 0.0122 0.005 0.9 3.2 0.5 0.0 0 0.787 0.1169 0.1294 0.0125 0.006 1.0 3.2 0.5 0.0 0 1.050 0.1167 0.1294 0.0126 0.007 1.0 3.2 0.5 0.0 0 1.312 0.1164 0.1295 0.0131 0.007 1.0 3.8 0.5 0.0 0 1.574 0.1163 0.1295 0.0132 0.008 1.1 3.8 0.5 0.0 0 1.837 0.1172 0.1300 0.0128 0.005 0.9 3.5 0.5 0.0 0 0.875 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1167 0.1294 0.0126 0.007 1.0 3.2 0.5 0.0 0 1.312 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.67 12.94 1.26 3.779 21.215 46.588 3.620 11.67 12.94 1.26 3.779 21.215 1.398 3.620 11.68 12.94 1.26 3.769 21.215 5.823 3.620 11.73 13.04 1.31 3.711 21.201 23.294 3.615 11.71 13.10 1.39 3.737 21.176 46.588 3.614 11.65 13.09 1.43 3.755 21.163 69.882 3.608 11.62 13.09 1.47 3.762 21.157 93.176 3.604 11.56 13.02 1.45 3.776 21.158 116.470 3.600 11.56 13.06 1.51 3.794 21.140 139.764 3.599 11.54 13.06 1.52 3.805 21.133 163.058 3.598 11.53 13.06 1.53 3.816 21.130 186.352 3.597 11.52 13.06 1.53 3.824 21.127 209.646 3.596 11.52 13.06 1.54 3.832 21.125 232.939 3.595 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.398 Accepted refinement result: 11.67 12.94 1.26 3.779 21.215 1.398 3.620 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.15 3.31 208 1749 Protein: 9.11 115.04 17.04 3.32 0 1519 Water: 10.39 76.70 35.66 N/A 208 222 Other: 19.75 26.64 22.10 N/A 0 8 Chain A: 9.11 115.04 19.39 N/A 0 1749 Chain S: 10.39 60.01 35.90 N/A 208 0 Histogram: Values Number of atoms 9.11 - 19.70 1264 19.70 - 30.30 286 30.30 - 40.89 202 40.89 - 51.48 129 51.48 - 62.07 53 62.07 - 72.67 12 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1167 r_free=0.1294 r_work=0.1167 r_free=0.1294 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1167 r_free = 0.1294 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1158 r_free = 0.1299 target_work(ml) = 3.614 | | 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.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1158 r_free= 0.1299 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.613680 | | target function (ml) not normalized (work): 300994.282267 | | target function (ml) not normalized (free): 15825.727090 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1165 0.1158 0.1299 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1507 0.1508 0.1520 n_refl.: 87589 remove outliers: r(all,work,free)=0.1507 0.1508 0.1520 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1507 0.1508 0.1519 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1160 0.1153 0.1299 n_refl.: 87589 remove outliers: r(all,work,free)=0.1157 0.1149 0.1299 n_refl.: 87581 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3791 299.452 264.621 0.495 1.000 0.324 11.894-9.307 97.06 95 4 0.2187 484.829 466.142 0.880 1.002 0.320 9.237-7.194 97.73 208 7 0.2312 387.368 385.831 0.947 1.002 0.240 7.162-5.571 100.00 427 22 0.2192 296.282 285.477 0.915 1.002 0.178 5.546-4.326 100.00 867 58 0.1118 406.722 403.148 0.962 1.002 0.149 4.315-3.360 100.00 1859 96 0.0953 386.795 384.303 1.004 1.002 0.133 3.356-2.611 100.00 3867 181 0.1143 254.104 251.909 1.009 1.002 0.090 2.608-2.026 99.99 8198 413 0.0934 168.448 167.693 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0904 82.261 82.563 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1259 36.478 36.059 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 22.984 21.519 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0121 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1149 r_free=0.1299 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=0.1299 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1149 r_free=0.1299 | n_water=430 | time (s): 2.270 (total time: 2.270) Filter (dist) r_work=0.1149 r_free=0.1298 | n_water=427 | time (s): 43.030 (total time: 45.300) Filter (q & B) r_work=0.1150 r_free=0.1299 | n_water=424 | time (s): 3.610 (total time: 48.910) Compute maps r_work=0.1150 r_free=0.1299 | n_water=424 | time (s): 1.780 (total time: 50.690) Filter (map) r_work=0.1170 r_free=0.1277 | n_water=323 | time (s): 3.760 (total time: 54.450) Find peaks r_work=0.1170 r_free=0.1277 | n_water=323 | time (s): 0.680 (total time: 55.130) Add new water r_work=0.1241 r_free=0.1364 | n_water=488 | time (s): 3.690 (total time: 58.820) Refine new water occ: r_work=0.1172 r_free=0.1308 adp: r_work=0.1172 r_free=0.1310 occ: r_work=0.1157 r_free=0.1298 adp: r_work=0.1155 r_free=0.1298 occ: r_work=0.1144 r_free=0.1291 adp: r_work=0.1140 r_free=0.1290 ADP+occupancy (water only), MIN, final r_work=0.1140 r_free=0.1290 r_work=0.1140 r_free=0.1290 | n_water=488 | time (s): 234.300 (total time: 293.120) Filter (q & B) r_work=0.1148 r_free=0.1295 | n_water=452 | time (s): 3.770 (total time: 296.890) Filter (dist only) r_work=0.1148 r_free=0.1294 | n_water=451 | time (s): 44.350 (total time: 341.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.762005 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.849993 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 0.1209 0.1341 0.0132 0.002 0.6 4.8 0.5 0.0 0 0.088 0.1170 0.1313 0.0144 0.003 0.7 3.2 0.5 0.0 0 0.264 0.1156 0.1304 0.0147 0.005 0.9 3.5 0.5 0.0 0 0.529 0.1150 0.1301 0.0151 0.006 0.9 3.5 0.5 0.0 0 0.793 0.1146 0.1302 0.0157 0.006 1.0 3.8 0.5 0.0 0 1.057 0.1143 0.1300 0.0157 0.007 1.1 3.8 0.5 0.0 0 1.322 0.1141 0.1297 0.0157 0.008 1.1 3.8 0.5 0.0 0 1.586 0.1139 0.1298 0.0159 0.009 1.1 3.8 0.5 0.0 0 1.850 0.1148 0.1302 0.0154 0.006 1.0 3.2 0.5 0.0 0 0.881 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1141 0.1297 0.0157 0.008 1.1 3.8 0.5 0.0 0 1.586 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.41 12.97 1.57 3.780 21.251 36.850 3.607 11.41 12.97 1.57 3.780 21.251 1.105 3.607 11.41 12.97 1.57 3.780 21.251 4.606 3.607 11.44 13.01 1.57 3.710 21.245 18.425 3.603 11.55 13.17 1.62 3.720 21.219 36.850 3.608 11.48 13.16 1.68 3.736 21.206 55.275 3.602 11.41 13.10 1.70 3.761 21.201 73.700 3.596 11.36 13.07 1.71 3.772 21.199 92.125 3.593 11.35 13.06 1.71 3.779 21.193 110.550 3.590 11.33 13.06 1.73 3.788 21.189 128.975 3.589 11.31 13.03 1.73 3.793 21.191 147.400 3.587 11.30 13.04 1.74 3.807 21.181 165.825 3.587 11.30 13.06 1.76 3.818 21.176 184.250 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.105 Accepted refinement result: 11.41 12.97 1.57 3.780 21.251 1.105 3.607 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.22 3.31 229 1749 Protein: 9.11 115.03 17.03 3.32 0 1519 Water: 10.39 76.70 35.29 N/A 229 222 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.11 115.03 19.39 N/A 0 1749 Chain S: 10.39 60.01 35.16 N/A 229 0 Histogram: Values Number of atoms 9.11 - 19.70 1262 19.70 - 30.29 298 30.29 - 40.88 214 40.88 - 51.48 132 51.48 - 62.07 49 62.07 - 72.66 12 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1141 r_free=0.1297 r_work=0.1141 r_free=0.1297 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1141 r_free = 0.1297 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1134 r_free = 0.1293 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1134 r_free= 0.1293 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604208 | | target function (ml) not normalized (work): 300176.454957 | | target function (ml) not normalized (free): 15813.199263 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1142 0.1134 0.1293 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1455 0.1453 0.1513 n_refl.: 87581 remove outliers: r(all,work,free)=0.1455 0.1453 0.1513 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1454 0.1452 0.1512 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1141 0.1133 0.1295 n_refl.: 87581 remove outliers: r(all,work,free)=0.1138 0.1130 0.1295 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 0.3842 293.213 264.051 0.474 0.999 0.304 11.894-9.307 95.10 93 4 0.2330 488.948 467.989 0.872 1.002 0.300 9.237-7.194 97.73 208 7 0.2356 387.368 379.774 0.926 1.002 0.170 7.162-5.571 100.00 427 22 0.2141 296.282 285.954 0.912 1.002 0.140 5.546-4.326 100.00 867 58 0.1118 406.722 402.530 0.964 1.002 0.120 4.315-3.360 100.00 1859 96 0.0916 386.795 384.913 1.004 1.002 0.110 3.356-2.611 100.00 3867 181 0.1117 254.104 252.167 1.010 1.002 0.029 2.608-2.026 99.99 8198 413 0.0911 168.448 167.876 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0883 82.261 82.616 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.478 36.086 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.984 21.533 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0144 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1130 r_free=0.1295 After: r_work=0.1132 r_free=0.1295 ================================== NQH flips ================================== r_work=0.1132 r_free=0.1295 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=0.1132 r_free=0.1295 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1132 r_free=0.1295 | n_water=451 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1132 r_free=0.1295 | n_water=451 | time (s): 42.530 (total time: 44.910) Filter (q & B) r_work=0.1132 r_free=0.1295 | n_water=450 | time (s): 3.930 (total time: 48.840) Compute maps r_work=0.1132 r_free=0.1295 | n_water=450 | time (s): 1.720 (total time: 50.560) Filter (map) r_work=0.1156 r_free=0.1284 | n_water=352 | time (s): 3.850 (total time: 54.410) Find peaks r_work=0.1156 r_free=0.1284 | n_water=352 | time (s): 0.690 (total time: 55.100) Add new water r_work=0.1205 r_free=0.1351 | n_water=505 | time (s): 3.710 (total time: 58.810) Refine new water occ: r_work=0.1149 r_free=0.1300 adp: r_work=0.1149 r_free=0.1301 occ: r_work=0.1138 r_free=0.1291 adp: r_work=0.1137 r_free=0.1291 occ: r_work=0.1130 r_free=0.1287 adp: r_work=0.1127 r_free=0.1285 ADP+occupancy (water only), MIN, final r_work=0.1127 r_free=0.1285 r_work=0.1127 r_free=0.1285 | n_water=505 | time (s): 237.630 (total time: 296.440) Filter (q & B) r_work=0.1134 r_free=0.1300 | n_water=461 | time (s): 4.020 (total time: 300.460) Filter (dist only) r_work=0.1134 r_free=0.1298 | n_water=460 | time (s): 47.740 (total time: 348.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.761023 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.305449 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 0.1223 0.1359 0.0135 0.004 0.7 4.8 0.0 0.0 0 0.088 0.1168 0.1322 0.0154 0.004 0.8 4.5 0.0 0.0 0 0.264 0.1155 0.1313 0.0158 0.005 0.9 4.5 0.5 0.0 0 0.528 0.1144 0.1305 0.0161 0.006 1.0 4.2 0.5 0.0 0 0.792 0.1138 0.1300 0.0162 0.007 1.1 4.2 0.5 0.0 0 1.057 0.1136 0.1298 0.0163 0.007 1.1 3.8 0.5 0.0 0 1.321 0.1134 0.1298 0.0164 0.008 1.1 3.8 0.5 0.0 0 1.585 0.1134 0.1298 0.0164 0.008 1.1 3.8 0.5 0.0 0 1.849 0.1142 0.1303 0.0161 0.006 1.0 4.2 0.5 0.0 0 0.881 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1134 0.1298 0.0164 0.008 1.1 3.8 0.5 0.0 0 1.585 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.34 12.98 1.64 3.780 21.243 37.305 3.605 11.34 12.98 1.64 3.780 21.243 1.119 3.605 11.34 12.98 1.64 3.780 21.243 4.663 3.605 11.38 13.02 1.65 3.711 21.236 18.653 3.601 11.48 13.19 1.71 3.724 21.209 37.305 3.607 11.40 13.17 1.77 3.747 21.196 55.958 3.601 11.33 13.13 1.80 3.766 21.193 74.611 3.595 11.31 13.13 1.82 3.775 21.188 93.264 3.593 11.27 13.08 1.81 3.784 21.189 111.916 3.589 11.26 13.07 1.81 3.791 21.187 130.569 3.588 11.25 13.09 1.83 3.803 21.180 149.222 3.588 11.24 13.09 1.84 3.812 21.178 167.875 3.587 11.24 13.09 1.85 3.824 21.166 186.527 3.586 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.119 Accepted refinement result: 11.34 12.98 1.64 3.780 21.243 1.119 3.605 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 21.21 3.31 238 1749 Protein: 9.10 115.03 17.03 3.32 0 1519 Water: 10.38 76.69 35.00 N/A 238 222 Other: 19.74 26.63 22.09 N/A 0 8 Chain A: 9.10 115.03 19.39 N/A 0 1749 Chain S: 10.38 60.00 34.60 N/A 238 0 Histogram: Values Number of atoms 9.10 - 19.69 1263 19.69 - 30.29 303 30.29 - 40.88 223 40.88 - 51.47 126 51.47 - 62.06 49 62.06 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1134 r_free=0.1298 r_work=0.1134 r_free=0.1298 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1134 r_free = 0.1298 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1131 r_free = 0.1297 target_work(ml) = 3.604 | | 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= 0.1131 r_free= 0.1297 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604323 | | target function (ml) not normalized (work): 300167.986973 | | target function (ml) not normalized (free): 15818.266055 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1353 0.1387 5.65 5.6303| | 2: 3.57 - 2.84 1.00 2888 124 0.1048 0.1365 5.167 5.2186| | 3: 2.83 - 2.48 1.00 2820 163 0.1091 0.1262 4.95 4.9928| | 4: 2.47 - 2.25 1.00 2825 136 0.0890 0.0952 4.6336 4.6594| | 5: 2.25 - 2.09 1.00 2756 127 0.0859 0.0956 4.583 4.6332| | 6: 2.09 - 1.97 1.00 2846 113 0.0851 0.0998 4.268 4.3567| | 7: 1.97 - 1.87 1.00 2787 165 0.0887 0.1138 3.9799 4.1011| | 8: 1.87 - 1.79 1.00 2789 144 0.0914 0.1112 3.885 3.9938| | 9: 1.79 - 1.72 1.00 2745 138 0.0872 0.1198 3.6431 3.8407| | 10: 1.72 - 1.66 1.00 2831 160 0.0918 0.1164 3.5628 3.6993| | 11: 1.66 - 1.61 1.00 2712 147 0.0867 0.0996 3.4945 3.5549| | 12: 1.61 - 1.56 1.00 2773 144 0.0905 0.1131 3.327 3.4541| | 13: 1.56 - 1.52 1.00 2745 130 0.0942 0.1052 3.305 3.4066| | 14: 1.52 - 1.48 1.00 2803 134 0.0977 0.1047 3.2357 3.3197| | 15: 1.48 - 1.45 1.00 2738 128 0.0999 0.1243 3.1509 3.2738| | 16: 1.45 - 1.42 1.00 2756 161 0.1056 0.1249 3.134 3.2427| | 17: 1.42 - 1.39 1.00 2785 139 0.1136 0.1313 3.1171 3.2346| | 18: 1.39 - 1.36 1.00 2741 179 0.1197 0.1343 3.1053 3.2379| | 19: 1.36 - 1.34 1.00 2807 134 0.1266 0.1558 3.1159 3.2661| | 20: 1.34 - 1.32 1.00 2696 147 0.1371 0.1444 3.1132 3.1528| | 21: 1.32 - 1.30 1.00 2785 112 0.1472 0.1510 3.115 3.1046| | 22: 1.29 - 1.27 1.00 2704 152 0.1559 0.1982 3.1239 3.2922| | 23: 1.27 - 1.26 1.00 2802 156 0.1649 0.1801 3.1342 3.2071| | 24: 1.26 - 1.24 1.00 2744 132 0.1706 0.1843 3.1271 3.2315| | 25: 1.24 - 1.22 1.00 2733 148 0.1883 0.2137 3.1433 3.2538| | 26: 1.22 - 1.21 1.00 2727 135 0.1909 0.1775 3.1494 3.2065| | 27: 1.21 - 1.19 1.00 2814 148 0.2077 0.2179 3.1727 3.1664| | 28: 1.19 - 1.18 1.00 2671 147 0.2201 0.2306 3.1669 3.1778| | 29: 1.18 - 1.16 1.00 2800 134 0.2263 0.2384 3.1486 3.2327| | 30: 1.16 - 1.15 1.00 2739 148 0.2447 0.2460 3.1434 3.1689| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.72 1.00 0.97 5911.35| | 2: 3.57 - 2.84 2888 124 0.92 12.78 1.01 0.97 5911.35| | 3: 2.83 - 2.48 2820 163 0.89 16.82 0.99 0.97 4934.00| | 4: 2.47 - 2.25 2825 136 0.92 13.66 1.00 0.98 2413.71| | 5: 2.25 - 2.09 2756 127 0.90 15.82 1.01 0.98 2413.71| | 6: 2.09 - 1.97 2846 113 0.92 12.47 1.02 0.98 1385.77| | 7: 1.97 - 1.87 2787 165 0.95 9.28 1.02 0.97 509.07| | 8: 1.87 - 1.79 2789 144 0.93 12.63 0.99 0.97 509.07| | 9: 1.79 - 1.72 2745 138 0.94 10.02 0.98 0.97 288.90| | 10: 1.72 - 1.66 2831 160 0.94 11.13 0.98 0.97 244.81| | 11: 1.66 - 1.61 2712 147 0.94 11.70 0.98 0.97 234.44| | 12: 1.61 - 1.56 2773 144 0.96 8.85 0.99 0.97 136.66| | 13: 1.56 - 1.52 2745 130 0.95 10.37 1.03 0.97 136.66| | 14: 1.52 - 1.48 2803 134 0.94 10.74 1.02 0.98 122.80| | 15: 1.48 - 1.45 2738 128 0.95 9.87 1.02 0.98 97.42| | 16: 1.45 - 1.42 2756 161 0.94 11.09 1.02 0.98 97.42| | 17: 1.42 - 1.39 2785 139 0.95 10.90 1.01 0.98 88.92| | 18: 1.39 - 1.36 2741 179 0.94 11.51 1.01 0.98 84.00| | 19: 1.36 - 1.34 2807 134 0.94 11.86 0.99 0.98 84.00| | 20: 1.34 - 1.32 2696 147 0.94 12.16 0.98 0.96 80.21| | 21: 1.32 - 1.30 2785 112 0.94 13.08 0.98 0.96 79.95| | 22: 1.29 - 1.27 2704 152 0.93 13.69 0.98 0.96 80.38| | 23: 1.27 - 1.26 2802 156 0.92 14.86 0.97 0.94 82.58| | 24: 1.26 - 1.24 2744 132 0.92 14.91 0.96 0.94 82.58| | 25: 1.24 - 1.22 2733 148 0.91 16.40 0.96 0.94 84.63| | 26: 1.22 - 1.21 2727 135 0.90 18.17 1.02 0.93 86.90| | 27: 1.21 - 1.19 2814 148 0.89 18.83 1.02 0.93 86.90| | 28: 1.19 - 1.18 2671 147 0.88 20.48 1.01 0.93 90.75| | 29: 1.18 - 1.16 2800 134 0.88 20.60 0.99 0.92 92.20| | 30: 1.16 - 1.15 2739 148 0.86 22.15 0.98 0.92 92.20| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.95 max = 5911.35 mean = 907.03| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.91 mean = 13.50| |phase err.(test): min = 0.00 max = 89.92 mean = 13.52| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1131 0.1297 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1440 0.1439 0.1496 n_refl.: 87576 remove outliers: r(all,work,free)=0.1440 0.1439 0.1496 n_refl.: 87576 overall B=0.00 to atoms: r(all,work,free)=0.1441 0.1439 0.1497 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1139 0.1131 0.1298 n_refl.: 87576 remove outliers: r(all,work,free)=0.1139 0.1131 0.1298 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4059 293.213 252.087 0.446 0.999 0.310 11.894-9.307 94.12 92 4 0.2347 482.010 468.781 0.877 1.001 0.232 9.237-7.194 97.73 208 7 0.2344 387.368 379.546 0.924 1.001 0.160 7.162-5.571 100.00 427 22 0.2155 296.282 285.683 0.907 1.001 0.120 5.546-4.326 100.00 867 58 0.1151 406.722 401.840 0.962 1.002 0.110 4.315-3.360 100.00 1859 96 0.0924 386.795 384.786 1.003 1.002 0.100 3.356-2.611 100.00 3867 181 0.1095 254.104 252.328 1.009 1.002 0.040 2.608-2.026 99.99 8198 413 0.0902 168.448 167.864 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0888 82.261 82.598 1.032 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.478 36.039 1.023 1.000 0.000 1.221-1.150 99.97 13689 708 0.2171 22.984 21.417 0.979 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0059 ================= 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 : 0.2598 0.1926 0.081 5.348 8.8 119.3 19.9 258 0.000 1_bss: 0.1625 0.1753 0.081 5.348 9.0 119.5 20.1 258 0.000 1_settarget: 0.1625 0.1753 0.081 5.348 9.0 119.5 20.1 258 0.000 1_nqh: 0.1625 0.1753 0.081 5.348 9.0 119.5 20.1 258 0.003 1_weight: 0.1625 0.1753 0.081 5.348 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1226 0.1455 0.006 0.886 9.0 119.5 20.1 258 0.129 1_adp: 0.1233 0.1453 0.006 0.886 9.1 119.4 20.1 258 0.129 1_regHadp: 0.1234 0.1456 0.006 0.886 9.1 119.4 20.1 258 0.129 1_occ: 0.1226 0.1451 0.006 0.886 9.1 119.4 20.1 258 0.129 2_bss: 0.1225 0.1448 0.006 0.886 9.1 119.5 20.1 258 0.129 2_settarget: 0.1225 0.1448 0.006 0.886 9.1 119.5 20.1 258 0.129 2_updatecdl: 0.1225 0.1448 0.006 0.894 9.1 119.5 20.1 258 0.129 2_nqh: 0.1227 0.1448 0.006 0.894 9.1 119.5 20.1 258 0.132 2_sol: 0.1203 0.1392 0.006 0.894 9.1 115.0 22.2 416 n/a 2_weight: 0.1203 0.1392 0.006 0.894 9.1 115.0 22.2 416 n/a 2_xyzrec: 0.1200 0.1411 0.005 0.764 9.1 115.0 22.2 416 n/a 2_adp: 0.1200 0.1411 0.005 0.764 9.1 115.0 22.2 416 n/a 2_regHadp: 0.1200 0.1411 0.005 0.764 9.1 115.0 22.2 416 n/a 2_occ: 0.1200 0.1407 0.005 0.764 9.1 115.0 22.2 416 n/a 3_bss: 0.1196 0.1405 0.005 0.764 9.1 115.0 22.2 416 n/a 3_settarget: 0.1196 0.1405 0.005 0.764 9.1 115.0 22.2 416 n/a 3_updatecdl: 0.1196 0.1405 0.005 0.768 9.1 115.0 22.2 416 n/a 3_nqh: 0.1196 0.1405 0.005 0.768 9.1 115.0 22.2 416 n/a 3_sol: 0.1223 0.1382 0.005 0.768 9.1 115.0 21.1 430 n/a 3_weight: 0.1223 0.1382 0.005 0.768 9.1 115.0 21.1 430 n/a 3_xyzrec: 0.1167 0.1294 0.007 1.015 9.1 115.0 21.1 430 n/a 3_adp: 0.1167 0.1294 0.007 1.015 9.1 115.0 21.1 430 n/a 3_regHadp: 0.1167 0.1294 0.007 1.015 9.1 115.0 21.1 430 n/a 3_occ: 0.1158 0.1299 0.007 1.015 9.1 115.0 21.1 430 n/a 4_bss: 0.1149 0.1299 0.007 1.015 9.1 115.0 21.1 430 n/a 4_settarget: 0.1149 0.1299 0.007 1.015 9.1 115.0 21.1 430 n/a 4_updatecdl: 0.1149 0.1299 0.007 1.017 9.1 115.0 21.1 430 n/a 4_nqh: 0.1149 0.1299 0.007 1.017 9.1 115.0 21.1 430 n/a 4_sol: 0.1148 0.1294 0.007 1.017 9.1 115.0 21.2 451 n/a 4_weight: 0.1148 0.1294 0.007 1.017 9.1 115.0 21.2 451 n/a 4_xyzrec: 0.1141 0.1297 0.008 1.089 9.1 115.0 21.2 451 n/a 4_adp: 0.1141 0.1297 0.008 1.089 9.1 115.0 21.2 451 n/a 4_regHadp: 0.1141 0.1297 0.008 1.089 9.1 115.0 21.2 451 n/a 4_occ: 0.1134 0.1293 0.008 1.089 9.1 115.0 21.2 451 n/a 5_bss: 0.1130 0.1295 0.008 1.089 9.1 115.0 21.2 451 n/a 5_settarget: 0.1130 0.1295 0.008 1.089 9.1 115.0 21.2 451 n/a 5_updatecdl: 0.1130 0.1295 0.008 1.091 9.1 115.0 21.2 451 n/a 5_setrh: 0.1132 0.1295 0.008 1.091 9.1 115.0 21.2 451 n/a 5_nqh: 0.1132 0.1295 0.008 1.091 9.1 115.0 21.2 451 n/a 5_sol: 0.1134 0.1298 0.008 1.091 9.1 115.0 21.2 460 n/a 5_weight: 0.1134 0.1298 0.008 1.091 9.1 115.0 21.2 460 n/a 5_xyzrec: 0.1134 0.1298 0.008 1.106 9.1 115.0 21.2 460 n/a 5_adp: 0.1134 0.1298 0.008 1.106 9.1 115.0 21.2 460 n/a 5_regHadp: 0.1134 0.1298 0.008 1.106 9.1 115.0 21.2 460 n/a 5_occ: 0.1131 0.1297 0.008 1.106 9.1 115.0 21.2 460 n/a end: 0.1131 0.1298 0.008 1.106 9.1 115.0 21.2 460 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6318584_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6318584_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1700 Refinement macro-cycles (run) : 13378.0400 Write final files (write_after_run_outputs) : 97.6600 Total : 13478.8700 Total CPU time: 3.75 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:07:24 PST -0800 (1735366045.00 s) Start R-work = 0.1625, R-free = 0.1753 Final R-work = 0.1131, R-free = 0.1298 =============================================================================== Job complete usr+sys time: 13658.85 seconds wall clock time: 251 minutes 34.06 seconds (15094.06 seconds total)