Starting phenix.refine on Fri Dec 27 17:58:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6847832.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_6847832.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6847832.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.92, per 1000 atoms: 0.57 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: 0.47 Conformation dependent library (CDL) restraints added in 176.7 milliseconds Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.61 - 0.89: 371 0.89 - 1.16: 1258 1.16 - 1.44: 696 1.44 - 1.71: 812 1.71 - 1.99: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.236 1.009 0.227 1.15e-02 7.56e+03 3.90e+02 bond pdb=" C ILE A 105 " pdb=" O ILE A 105 " ideal model delta sigma weight residual 1.236 1.430 -0.194 9.90e-03 1.02e+04 3.86e+02 bond pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " ideal model delta sigma weight residual 1.326 1.535 -0.209 1.10e-02 8.26e+03 3.61e+02 bond pdb=" C ALA A 104 " pdb=" O ALA A 104 " ideal model delta sigma weight residual 1.234 1.014 0.220 1.18e-02 7.18e+03 3.47e+02 bond pdb=" C BLYS A 93 " pdb=" O BLYS A 93 " ideal model delta sigma weight residual 1.237 1.457 -0.221 1.19e-02 7.06e+03 3.43e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.45: 3029 4.45 - 8.90: 1892 8.90 - 13.35: 700 13.35 - 17.80: 132 17.80 - 22.26: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 118 " pdb=" C GLY A 118 " pdb=" N PHE A 119 " ideal model delta sigma weight residual 122.54 107.69 14.85 1.02e+00 9.61e-01 2.12e+02 angle pdb=" O ALA A 79 " pdb=" C ALA A 79 " pdb=" N AGLN A 80 " ideal model delta sigma weight residual 122.07 136.61 -14.54 1.03e+00 9.43e-01 1.99e+02 angle pdb=" O BTYR A 67 " pdb=" C BTYR A 67 " pdb=" N ASP A 68 " ideal model delta sigma weight residual 123.24 107.34 15.90 1.23e+00 6.61e-01 1.67e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.80 107.28 14.52 1.13e+00 7.83e-01 1.65e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.60 -10.37 8.10e-01 1.52e+00 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 941 17.65 - 35.29: 113 35.29 - 52.93: 45 52.93 - 70.58: 9 70.58 - 88.22: 3 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 -158.29 -21.71 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual -180.00 -159.79 -20.21 0 5.00e+00 4.00e-02 1.63e+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 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.227: 116 0.227 - 0.453: 75 0.453 - 0.678: 34 0.678 - 0.904: 14 0.904 - 1.129: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 3.56 -1.13 2.00e-01 2.50e+01 3.19e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.53 1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CA GLN A 95 " pdb=" N GLN A 95 " pdb=" C GLN A 95 " pdb=" CB GLN A 95 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.48e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.135 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.112 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.070 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.064 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.026 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG TYR A 139 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.095 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.098 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.061 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.098 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.104 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.021 2.00e-02 2.50e+03 6.54e-02 1.28e+02 pdb=" CG TYR A 141 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.122 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.077 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.108 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.048 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.082 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 619 2.25 - 2.84: 7586 2.84 - 3.42: 10750 3.42 - 4.01: 15382 4.01 - 4.60: 22268 Nonbonded interactions: 56605 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.662 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.798 1.850 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.821 1.850 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.838 1.850 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.865 1.850 ... (remaining 56600 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_6847832_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= 0.2603 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789943 | | target function (ml) not normalized (work): 232418.969773 | | target function (ml) not normalized (free): 11838.504851 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3034 0.2077 7.0875 4.9372| | 2: 3.57 - 2.84 1.00 2876 122 0.2446 0.1672 4.3449 4.3155| | 3: 2.84 - 2.48 1.00 2833 165 0.2342 0.1819 4.1244 4.1679| | 4: 2.47 - 2.25 1.00 2825 136 0.2317 0.1417 3.8257 3.8175| | 5: 2.25 - 2.09 1.00 2756 127 0.2461 0.1550 3.7874 3.8036| | 6: 2.09 - 1.97 1.00 2846 113 0.2514 0.1716 3.4542 3.5266| | 7: 1.97 - 1.87 1.00 2787 165 0.2547 0.1659 3.1239 3.1095| | 8: 1.87 - 1.79 1.00 2789 144 0.2475 0.1863 3.0478 3.1129| | 9: 1.79 - 1.72 1.00 2745 138 0.2402 0.1940 2.8787 3.0135| | 10: 1.72 - 1.66 1.00 2789 158 0.2436 0.2045 2.8149 2.9135| | 11: 1.66 - 1.61 1.00 2740 147 0.2511 0.1831 2.752 2.7503| | 12: 1.61 - 1.56 1.00 2787 146 0.2525 0.1993 2.6358 2.6764| | 13: 1.56 - 1.52 1.00 2745 130 0.2544 0.1923 2.56 2.6722| | 14: 1.52 - 1.48 1.00 2803 134 0.2504 0.2041 2.4985 2.5724| | 15: 1.48 - 1.45 1.00 2738 128 0.2630 0.2073 2.419 2.4842| | 16: 1.45 - 1.42 1.00 2756 161 0.2617 0.2102 2.3884 2.4317| | 17: 1.42 - 1.39 1.00 2785 139 0.2665 0.2469 2.3258 2.4371| | 18: 1.39 - 1.36 1.00 2741 179 0.2643 0.2363 2.2905 2.4019| | 19: 1.36 - 1.34 1.00 2807 134 0.2608 0.2342 2.2504 2.3712| | 20: 1.34 - 1.32 1.00 2696 147 0.2711 0.2341 2.2031 2.2296| | 21: 1.32 - 1.30 1.00 2785 112 0.2695 0.2103 2.1552 2.1362| | 22: 1.29 - 1.27 1.00 2704 152 0.2694 0.2452 2.1285 2.1698| | 23: 1.27 - 1.26 1.00 2802 156 0.2743 0.2342 2.0969 2.1437| | 24: 1.26 - 1.24 1.00 2744 132 0.2770 0.2628 2.0649 2.1743| | 25: 1.24 - 1.22 1.00 2734 148 0.2868 0.2492 2.0429 2.041| | 26: 1.22 - 1.21 1.00 2727 135 0.2886 0.2471 2.0234 2.1134| | 27: 1.21 - 1.19 1.00 2814 148 0.3008 0.2605 2.0219 2.0054| | 28: 1.19 - 1.18 1.00 2671 147 0.3051 0.2843 1.9988 2.0419| | 29: 1.18 - 1.16 1.00 2800 134 0.3006 0.2767 1.9659 2.0496| | 30: 1.16 - 1.15 1.00 2740 148 0.3045 0.2692 1.9301 1.9021| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.69 0.76 0.23 1457.91| | 2: 3.57 - 2.84 2876 122 0.80 25.99 1.27 0.23 1457.91| | 3: 2.84 - 2.48 2833 165 0.74 31.68 1.24 0.24 1208.53| | 4: 2.47 - 2.25 2825 136 0.81 25.36 1.25 0.25 561.36| | 5: 2.25 - 2.09 2756 127 0.77 29.05 1.28 0.25 561.36| | 6: 2.09 - 1.97 2846 113 0.84 22.31 1.29 0.25 306.72| | 7: 1.97 - 1.87 2787 165 0.90 16.40 1.29 0.26 89.55| | 8: 1.87 - 1.79 2789 144 0.86 20.75 1.26 0.26 89.55| | 9: 1.79 - 1.72 2745 138 0.88 18.61 1.23 0.26 55.98| | 10: 1.72 - 1.66 2789 158 0.86 20.33 1.23 0.25 49.26| | 11: 1.66 - 1.61 2740 147 0.85 21.68 1.24 0.25 47.57| | 12: 1.61 - 1.56 2787 146 0.88 18.69 1.23 0.25 30.49| | 13: 1.56 - 1.52 2745 130 0.86 20.86 1.24 0.25 30.49| | 14: 1.52 - 1.48 2803 134 0.86 20.96 1.22 0.25 27.42| | 15: 1.48 - 1.45 2738 128 0.86 21.08 1.24 0.25 21.81| | 16: 1.45 - 1.42 2756 161 0.85 22.04 1.23 0.25 21.81| | 17: 1.42 - 1.39 2785 139 0.86 21.62 1.23 0.25 18.68| | 18: 1.39 - 1.36 2741 179 0.86 21.74 1.22 0.25 16.87| | 19: 1.36 - 1.34 2807 134 0.85 22.65 1.21 0.25 16.87| | 20: 1.34 - 1.32 2696 147 0.86 21.68 1.21 0.25 13.81| | 21: 1.32 - 1.30 2785 112 0.85 22.67 1.21 0.25 13.60| | 22: 1.29 - 1.27 2704 152 0.85 22.85 1.21 0.24 13.24| | 23: 1.27 - 1.26 2802 156 0.85 22.60 1.21 0.24 11.40| | 24: 1.26 - 1.24 2744 132 0.84 23.50 1.21 0.24 11.40| | 25: 1.24 - 1.22 2734 148 0.84 24.26 1.20 0.24 10.76| | 26: 1.22 - 1.21 2727 135 0.84 24.22 1.20 0.23 10.04| | 27: 1.21 - 1.19 2814 148 0.83 24.99 1.21 0.23 10.04| | 28: 1.19 - 1.18 2671 147 0.82 25.56 1.19 0.23 9.33| | 29: 1.18 - 1.16 2800 134 0.82 25.90 1.16 0.22 9.06| | 30: 1.16 - 1.15 2740 148 0.81 27.15 1.14 0.22 9.06| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.06 max = 1457.91 mean = 212.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.86| |phase err.(test): min = 0.00 max = 89.91 mean = 22.91| |-----------------------------------------------------------------------------| ----------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 0.227 1557 Z= 5.392 Angle : 5.351 17.239 2118 Z= 3.755 Chirality : 0.369 1.129 243 Planarity : 0.030 0.111 284 Dihedral : 14.223 88.220 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.32 % Favored : 95.14 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 29.73 % 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: -2.74 (0.47), residues: 224 helix: -3.19 (0.35), residues: 102 sheet: -0.39 (0.96), residues: 28 loop : -0.30 (0.55), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.084 0.015 ARG A 98 TYR 0.099 0.044 TYR A 141 PHE 0.104 0.043 PHE A 119 HIS 0.067 0.025 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= 0.2603 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789943 | | target function (ml) not normalized (work): 232418.969773 | | target function (ml) not normalized (free): 11838.504851 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2562 0.2603 0.1940 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2562 0.2603 0.1940 n_refl.: 87602 remove outliers: r(all,work,free)=0.1971 0.1975 0.1940 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.1998 0.2002 0.1955 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1634 0.1627 0.1763 n_refl.: 87594 remove outliers: r(all,work,free)=0.1633 0.1626 0.1763 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3857 386.214 358.750 0.669 1.002 0.407 11.894-9.307 99.02 97 4 0.1820 613.482 590.998 0.925 1.003 0.385 9.237-7.194 100.00 213 7 0.2118 501.753 490.824 0.947 1.004 0.349 7.162-5.571 100.00 427 22 0.2154 376.538 364.866 0.928 1.004 0.288 5.546-4.326 100.00 867 58 0.1289 516.893 512.052 0.962 1.004 0.234 4.315-3.360 100.00 1859 96 0.1144 491.569 487.594 1.006 1.003 0.209 3.356-2.611 100.00 3867 181 0.1436 322.936 319.686 0.995 1.002 0.057 2.608-2.026 99.99 8198 413 0.1339 214.077 211.864 1.005 1.001 0.000 2.025-1.573 100.00 17313 902 0.1627 104.544 104.017 1.015 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2044 46.359 44.992 1.004 0.994 0.000 1.221-1.150 99.97 13689 708 0.2624 29.209 26.902 0.977 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0493 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1626 r_free=0.1763 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 180 GLN Total number of N/Q/H flips: 1 r_work=0.1628 r_free=0.1764 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.293659 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1997.902904 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 0.1748 0.1862 0.0114 0.002 0.4 4.8 0.0 0.0 0 0.125 0.1581 0.1719 0.0138 0.001 0.4 4.5 0.0 0.0 0 0.250 0.1460 0.1625 0.0166 0.002 0.4 3.8 0.0 0.0 0 0.500 0.1396 0.1588 0.0192 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1362 0.1562 0.0200 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1359 0.1565 0.0205 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1306 0.1526 0.0220 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1275 0.1502 0.0226 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1260 0.1486 0.0226 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1249 0.1479 0.0229 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1245 0.1475 0.0230 0.004 0.8 4.2 0.5 0.0 0 6.000 0.1240 0.1474 0.0233 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1236 0.1469 0.0233 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1232 0.1468 0.0236 0.006 0.9 3.5 0.5 0.0 0 9.000 0.1232 0.1476 0.0245 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1229 0.1474 0.0244 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1227 0.1476 0.0249 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1224 0.1480 0.0256 0.007 1.0 3.8 0.5 0.6 0 13.147 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1232 0.1468 0.0236 0.006 0.9 3.5 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.68 2.36 3.013 19.074 1997.903 0.017 12.32 14.68 2.36 3.003 19.074 59.937 0.017 12.38 14.64 2.27 2.668 19.073 249.738 0.017 12.76 15.39 2.63 2.963 19.403 998.951 0.016 12.57 15.46 2.89 3.377 19.679 1997.903 0.016 12.47 15.45 2.98 3.336 19.652 2996.854 0.015 12.42 15.49 3.07 3.460 19.702 3995.806 0.015 12.30 15.40 3.10 3.342 19.635 4994.757 0.015 12.20 15.34 3.14 3.365 19.651 5993.709 0.015 12.25 15.45 3.20 3.360 19.637 6992.660 0.015 12.21 15.44 3.24 3.360 19.622 7991.612 0.015 12.18 15.44 3.25 3.574 19.732 8990.563 0.015 12.13 15.39 3.26 3.475 19.670 9989.515 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: 249.738 Accepted refinement result: 12.38 14.64 2.27 2.668 19.073 249.738 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.46 20.10 3.31 0 1785 Protein: 9.08 115.01 17.01 3.32 0 1519 Water: 11.48 119.46 38.24 N/A 0 258 Other: 19.74 26.61 22.07 N/A 0 8 Chain A: 9.08 119.46 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.16 227 31.16 - 42.20 125 42.20 - 53.23 94 53.23 - 64.27 42 64.27 - 75.31 11 75.31 - 86.35 7 86.35 - 97.38 4 97.38 - 108.42 1 108.42 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1464 r_work=0.1239 r_free=0.1468 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1468 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 = 0.1233 r_free = 0.1459 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1233 r_free= 0.1459 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016808 | | target function (ls_wunit_k1) not normalized (work): 1400.069394 | | target function (ls_wunit_k1) not normalized (free): 109.243440 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1244 0.1233 0.1459 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1679 0.1681 0.1694 n_refl.: 87593 remove outliers: r(all,work,free)=0.1679 0.1681 0.1694 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1685 0.1686 0.1698 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1242 0.1231 0.1452 n_refl.: 87593 remove outliers: r(all,work,free)=0.1242 0.1231 0.1452 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3508 303.456 283.957 0.669 1.002 0.395 11.894-9.307 99.02 97 4 0.1637 482.025 470.138 0.925 1.003 0.384 9.237-7.194 100.00 213 7 0.1893 394.237 389.821 0.962 1.003 0.319 7.162-5.571 100.00 427 22 0.1794 295.853 290.376 0.937 1.003 0.253 5.546-4.326 100.00 867 58 0.1000 406.133 403.271 0.963 1.003 0.204 4.315-3.360 100.00 1859 96 0.0873 386.235 385.291 1.009 1.002 0.190 3.356-2.611 100.00 3867 181 0.1181 253.737 252.522 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1027 168.204 167.447 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1119 82.142 82.334 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1455 36.425 35.930 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 22.950 21.438 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0445 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1452 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** A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1230 r_free=0.1451 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1451 | n_water=258 | time (s): 1.900 (total time: 1.900) Filter (dist) r_work=0.1238 r_free=0.1451 | n_water=252 | time (s): 22.430 (total time: 24.330) Filter (q & B) r_work=0.1241 r_free=0.1451 | n_water=249 | time (s): 3.370 (total time: 27.700) Compute maps r_work=0.1241 r_free=0.1451 | n_water=249 | time (s): 1.450 (total time: 29.150) Filter (map) r_work=0.1274 r_free=0.1470 | n_water=219 | time (s): 2.670 (total time: 31.820) Find peaks r_work=0.1274 r_free=0.1470 | n_water=219 | time (s): 0.470 (total time: 32.290) Add new water r_work=0.1421 r_free=0.1625 | n_water=421 | time (s): 2.870 (total time: 35.160) Refine new water occ: r_work=0.1311 r_free=0.1495 adp: r_work=0.1230 r_free=0.1431 occ: r_work=0.1242 r_free=0.1423 adp: r_work=0.1209 r_free=0.1405 occ: r_work=0.1211 r_free=0.1397 adp: r_work=0.1202 r_free=0.1393 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1393 r_work=0.1202 r_free=0.1393 | n_water=421 | time (s): 89.420 (total time: 124.580) Filter (q & B) r_work=0.1205 r_free=0.1394 | n_water=409 | time (s): 2.680 (total time: 127.260) Filter (dist only) r_work=0.1205 r_free=0.1393 | n_water=408 | time (s): 34.160 (total time: 161.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.775845 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1493.108288 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 0.1660 0.1761 0.0101 0.001 0.4 8.6 0.0 0.0 0 0.125 0.1522 0.1644 0.0123 0.001 0.4 8.3 0.0 0.0 0 0.250 0.1389 0.1536 0.0146 0.001 0.4 7.7 0.0 0.0 0 0.500 0.1356 0.1510 0.0155 0.001 0.4 6.1 0.0 0.0 0 0.750 0.1318 0.1481 0.0163 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1311 0.1476 0.0165 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1254 0.1438 0.0184 0.002 0.5 5.1 0.5 0.0 0 2.000 0.1229 0.1422 0.0194 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1215 0.1410 0.0195 0.003 0.7 5.1 0.5 0.0 0 4.000 0.1204 0.1404 0.0200 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1201 0.1413 0.0211 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1197 0.1408 0.0211 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1194 0.1409 0.0215 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1191 0.1409 0.0218 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1187 0.1411 0.0224 0.006 0.9 5.1 0.5 0.0 0 10.000 0.1184 0.1409 0.0224 0.007 0.9 5.8 0.5 0.0 0 11.000 0.1182 0.1414 0.0232 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1180 0.1412 0.0232 0.007 0.9 5.4 0.5 0.0 0 13.000 0.1178 0.1415 0.0236 0.008 0.9 4.8 0.5 0.0 0 14.388 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1204 0.1404 0.0200 0.004 0.7 4.2 0.5 0.0 0 5.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 14.04 2.00 3.777 21.745 1493.108 0.016 12.04 14.04 2.00 3.777 21.745 44.793 0.016 12.04 14.04 2.00 3.777 21.745 186.639 0.016 12.25 14.52 2.27 3.626 21.749 746.554 0.015 12.23 14.85 2.63 3.537 21.819 1493.108 0.015 12.12 14.87 2.75 3.455 22.126 2239.662 0.014 11.99 14.87 2.88 3.498 21.899 2986.217 0.014 11.91 14.69 2.78 3.476 22.099 3732.771 0.014 11.87 14.71 2.83 3.495 22.117 4479.325 0.014 11.84 14.73 2.89 3.502 22.006 5225.879 0.014 11.84 14.77 2.93 3.529 22.116 5972.433 0.014 11.83 14.81 2.99 3.563 22.180 6718.987 0.014 11.82 14.81 2.99 3.576 22.184 7465.541 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: 186.639 Accepted refinement result: 12.04 14.04 2.00 3.777 21.745 186.639 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 22.12 3.31 189 1746 Protein: 9.11 115.04 17.04 3.32 0 1519 Water: 11.51 76.70 41.02 N/A 189 219 Other: 19.77 26.64 22.10 N/A 0 8 Chain A: 9.11 115.04 19.41 N/A 0 1746 Chain S: 15.38 60.00 47.13 N/A 189 0 Histogram: Values Number of atoms 9.11 - 19.70 1258 19.70 - 30.30 243 30.30 - 40.89 163 40.89 - 51.48 124 51.48 - 62.07 124 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=0.1204 r_free=0.1404 r_work=0.1204 r_free=0.1404 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1404 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 = 0.1204 r_free = 0.1408 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1204 r_free= 0.1408 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015328 | | target function (ls_wunit_k1) not normalized (work): 1276.762070 | | target function (ls_wunit_k1) not normalized (free): 97.516862 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1204 0.1408 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1607 0.1606 0.1656 n_refl.: 87593 remove outliers: r(all,work,free)=0.1607 0.1606 0.1656 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1609 0.1608 0.1658 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1202 0.1402 n_refl.: 87593 remove outliers: r(all,work,free)=0.1210 0.1200 0.1402 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3255 296.811 276.183 0.599 1.002 0.350 11.894-9.307 99.02 97 4 0.1683 482.025 473.195 0.922 1.003 0.333 9.237-7.194 100.00 213 7 0.1759 394.237 393.340 0.980 1.003 0.290 7.162-5.571 100.00 427 22 0.1599 295.853 290.996 0.941 1.003 0.256 5.546-4.326 100.00 867 58 0.0900 406.133 403.384 0.961 1.003 0.210 4.315-3.360 100.00 1859 96 0.0809 386.235 384.994 1.005 1.003 0.210 3.356-2.611 100.00 3867 181 0.1100 253.737 252.816 1.011 1.002 0.100 2.608-2.026 99.99 8198 413 0.1013 168.204 167.571 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1119 82.142 82.311 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1464 36.425 35.943 1.024 0.996 0.000 1.221-1.150 99.97 13689 708 0.2265 22.950 21.463 0.989 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0137 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1402 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1402 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1402 | n_water=408 | time (s): 1.980 (total time: 1.980) Filter (dist) r_work=0.1201 r_free=0.1401 | n_water=404 | time (s): 37.650 (total time: 39.630) Filter (q & B) r_work=0.1201 r_free=0.1401 | n_water=404 | time (s): 1.070 (total time: 40.700) Compute maps r_work=0.1201 r_free=0.1401 | n_water=404 | time (s): 1.640 (total time: 42.340) Filter (map) r_work=0.1242 r_free=0.1404 | n_water=289 | time (s): 2.620 (total time: 44.960) Find peaks r_work=0.1242 r_free=0.1404 | n_water=289 | time (s): 0.460 (total time: 45.420) Add new water r_work=0.1363 r_free=0.1502 | n_water=466 | time (s): 2.800 (total time: 48.220) Refine new water occ: r_work=0.1269 r_free=0.1433 adp: r_work=0.1270 r_free=0.1432 occ: r_work=0.1248 r_free=0.1420 adp: r_work=0.1245 r_free=0.1415 occ: r_work=0.1232 r_free=0.1407 adp: r_work=0.1226 r_free=0.1400 ADP+occupancy (water only), MIN, final r_work=0.1226 r_free=0.1400 r_work=0.1226 r_free=0.1400 | n_water=466 | time (s): 226.210 (total time: 274.430) Filter (q & B) r_work=0.1230 r_free=0.1405 | n_water=440 | time (s): 3.410 (total time: 277.840) Filter (dist only) r_work=0.1230 r_free=0.1404 | n_water=439 | time (s): 37.610 (total time: 315.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.707680 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.253428 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1242 0.1363 0.0120 0.002 0.6 5.1 0.5 0.0 0 0.085 0.1195 0.1326 0.0131 0.003 0.7 4.5 0.5 0.0 0 0.256 0.1178 0.1313 0.0135 0.004 0.8 4.2 0.5 0.0 0 0.512 0.1170 0.1314 0.0144 0.005 0.9 3.8 0.5 0.0 0 0.768 0.1165 0.1311 0.0146 0.006 1.0 3.8 0.5 0.0 0 1.025 0.1163 0.1311 0.0148 0.006 1.0 4.2 0.5 0.0 0 1.281 0.1160 0.1311 0.0150 0.007 1.0 4.2 0.5 0.0 0 1.537 0.1158 0.1310 0.0153 0.008 1.1 4.5 0.5 0.0 0 1.793 0.1169 0.1310 0.0141 0.005 0.9 3.5 0.5 0.0 0 0.854 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1169 0.1310 0.0141 0.005 0.9 3.5 0.5 0.0 0 0.854 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.69 13.10 1.41 3.779 21.308 48.253 3.624 11.69 13.10 1.41 3.779 21.308 1.448 3.624 11.70 13.10 1.41 3.769 21.308 6.032 3.624 11.75 13.21 1.46 3.711 21.294 24.127 3.620 11.76 13.30 1.54 3.728 21.265 48.253 3.619 11.66 13.26 1.60 3.757 21.258 72.380 3.613 11.63 13.22 1.59 3.768 21.250 96.507 3.609 11.62 13.26 1.64 3.783 21.235 120.634 3.607 11.60 13.26 1.66 3.798 21.228 144.760 3.606 11.58 13.23 1.65 3.807 21.226 168.887 3.604 11.56 13.21 1.65 3.815 21.226 193.014 3.602 11.55 13.21 1.66 3.824 21.224 217.140 3.601 11.54 13.20 1.67 3.829 21.225 241.267 3.601 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.448 Accepted refinement result: 11.69 13.10 1.41 3.779 21.308 1.448 3.624 Individual atomic B min max mean iso aniso Overall: 9.12 115.05 21.31 3.31 221 1745 Protein: 9.12 115.05 17.05 3.32 0 1519 Water: 11.52 76.71 36.04 N/A 221 218 Other: 19.77 26.65 22.11 N/A 0 8 Chain A: 9.12 115.05 19.39 N/A 0 1745 Chain S: 15.39 60.01 36.40 N/A 221 0 Histogram: Values Number of atoms 9.12 - 19.71 1260 19.71 - 30.31 281 30.31 - 40.90 225 40.90 - 51.49 120 51.49 - 62.08 57 62.08 - 72.68 12 72.68 - 83.27 5 83.27 - 93.86 4 93.86 - 104.45 0 104.45 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1169 r_free=0.1310 r_work=0.1169 r_free=0.1310 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1169 r_free = 0.1310 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1164 r_free = 0.1306 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1164 r_free= 0.1306 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.619624 | | target function (ml) not normalized (work): 301489.368711 | | target function (ml) not normalized (free): 15847.685743 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1171 0.1164 0.1306 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1510 0.1510 0.1550 n_refl.: 87589 remove outliers: r(all,work,free)=0.1510 0.1510 0.1550 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1509 0.1508 0.1549 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1166 0.1160 0.1298 n_refl.: 87589 remove outliers: r(all,work,free)=0.1164 0.1157 0.1298 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3769 288.009 267.722 0.493 0.999 0.308 11.894-9.307 98.04 96 4 0.2304 482.122 464.811 0.866 1.001 0.293 9.237-7.194 98.64 210 7 0.2330 386.731 386.757 0.940 1.002 0.226 7.162-5.571 100.00 427 22 0.2155 295.853 283.700 0.909 1.002 0.201 5.546-4.326 100.00 867 58 0.1117 406.133 402.233 0.954 1.002 0.175 4.315-3.360 100.00 1859 96 0.0941 386.235 384.216 0.996 1.002 0.170 3.356-2.611 100.00 3867 181 0.1141 253.737 251.869 0.999 1.002 0.053 2.608-2.026 99.99 8198 413 0.0949 168.204 167.337 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0920 82.142 82.419 1.025 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1273 36.425 36.003 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2175 22.950 21.485 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0205 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1157 r_free=0.1298 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=0.1157 r_free=0.1298 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1157 r_free=0.1298 | n_water=439 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1157 r_free=0.1297 | n_water=437 | time (s): 45.260 (total time: 47.750) Filter (q & B) r_work=0.1158 r_free=0.1298 | n_water=434 | time (s): 3.910 (total time: 51.660) Compute maps r_work=0.1158 r_free=0.1298 | n_water=434 | time (s): 1.860 (total time: 53.520) Filter (map) r_work=0.1186 r_free=0.1301 | n_water=321 | time (s): 3.950 (total time: 57.470) Find peaks r_work=0.1186 r_free=0.1301 | n_water=321 | time (s): 0.700 (total time: 58.170) Add new water r_work=0.1260 r_free=0.1387 | n_water=478 | time (s): 3.700 (total time: 61.870) Refine new water occ: r_work=0.1180 r_free=0.1310 adp: r_work=0.1181 r_free=0.1312 occ: r_work=0.1165 r_free=0.1294 adp: r_work=0.1164 r_free=0.1294 occ: r_work=0.1152 r_free=0.1284 adp: r_work=0.1148 r_free=0.1281 ADP+occupancy (water only), MIN, final r_work=0.1148 r_free=0.1281 r_work=0.1148 r_free=0.1281 | n_water=478 | time (s): 313.250 (total time: 375.120) Filter (q & B) r_work=0.1153 r_free=0.1287 | n_water=446 | time (s): 4.080 (total time: 379.200) Filter (dist only) r_work=0.1160 r_free=0.1285 | n_water=444 | time (s): 48.510 (total time: 427.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.695661 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.668646 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 0.1217 0.1324 0.0107 0.002 0.6 5.1 0.5 0.0 0 0.085 0.1178 0.1298 0.0120 0.003 0.7 4.2 0.5 0.0 0 0.254 0.1163 0.1289 0.0126 0.004 0.9 3.8 0.5 0.0 0 0.509 0.1156 0.1289 0.0133 0.005 0.9 4.2 0.5 0.0 0 0.763 0.1153 0.1285 0.0132 0.006 1.0 5.1 0.5 0.0 0 1.017 0.1150 0.1289 0.0139 0.007 1.0 4.2 0.5 0.0 0 1.272 0.1148 0.1290 0.0142 0.008 1.1 4.2 0.5 0.0 0 1.526 0.1146 0.1291 0.0145 0.008 1.1 4.2 0.5 0.0 0 1.780 0.1155 0.1290 0.0135 0.006 1.0 3.8 0.5 0.0 0 0.848 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1153 0.1285 0.0132 0.006 1.0 5.1 0.5 0.0 0 1.017 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.53 12.85 1.32 3.780 21.231 43.669 3.610 11.53 12.85 1.32 3.780 21.231 1.310 3.610 11.54 12.85 1.32 3.777 21.231 5.459 3.610 11.56 12.91 1.36 3.712 21.224 21.834 3.605 11.62 13.09 1.47 3.729 21.195 43.669 3.609 11.54 13.06 1.52 3.748 21.184 65.503 3.603 11.48 13.01 1.53 3.766 21.181 87.337 3.598 11.45 12.98 1.53 3.773 21.181 109.172 3.595 11.44 13.01 1.57 3.787 21.170 131.006 3.594 11.44 13.03 1.60 3.802 21.162 152.840 3.594 11.43 13.03 1.60 3.810 21.159 174.675 3.593 11.40 13.01 1.61 3.818 21.159 196.509 3.592 11.40 13.00 1.61 3.824 21.158 218.343 3.590 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.310 Accepted refinement result: 11.53 12.85 1.32 3.780 21.231 1.310 3.610 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.17 3.31 229 1742 Protein: 9.11 115.04 17.04 3.32 0 1519 Water: 11.51 76.70 35.30 N/A 229 215 Other: 19.77 26.64 22.10 N/A 0 8 Chain A: 9.11 115.04 19.38 N/A 0 1742 Chain S: 15.38 60.00 34.82 N/A 229 0 Histogram: Values Number of atoms 9.11 - 19.70 1265 19.70 - 30.30 291 30.30 - 40.89 219 40.89 - 51.48 123 51.48 - 62.08 50 62.08 - 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=0.1153 r_free=0.1285 r_work=0.1153 r_free=0.1285 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1285 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1147 r_free = 0.1279 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1147 r_free= 0.1279 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607360 | | target function (ml) not normalized (work): 300446.169305 | | target function (ml) not normalized (free): 15798.498538 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1154 0.1147 0.1279 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1490 0.1488 0.1547 n_refl.: 87583 remove outliers: r(all,work,free)=0.1490 0.1488 0.1547 n_refl.: 87583 overall B=-0.01 to atoms: r(all,work,free)=0.1489 0.1487 0.1546 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1153 0.1146 0.1279 n_refl.: 87583 remove outliers: r(all,work,free)=0.1150 0.1143 0.1279 n_refl.: 87574 ======================== 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 0.3755 285.426 252.612 0.456 1.000 0.294 11.894-9.307 93.14 91 4 0.2243 476.749 461.509 0.869 1.002 0.275 9.237-7.194 97.73 208 7 0.2331 386.807 380.785 0.931 1.002 0.170 7.162-5.571 100.00 427 22 0.2098 295.853 284.615 0.914 1.002 0.170 5.546-4.326 100.00 867 58 0.1141 406.133 401.660 0.965 1.002 0.150 4.315-3.360 100.00 1859 96 0.0928 386.235 384.062 1.004 1.002 0.150 3.356-2.611 100.00 3867 181 0.1125 253.737 252.074 1.011 1.002 0.070 2.608-2.026 99.99 8198 413 0.0931 168.204 167.492 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0904 82.142 82.479 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1261 36.425 36.027 1.029 0.996 0.000 1.221-1.150 99.97 13689 708 0.2173 22.950 21.493 0.992 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 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=0.1279 After: r_work=0.1144 r_free=0.1279 ================================== NQH flips ================================== r_work=0.1144 r_free=0.1279 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=0.1279 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1144 r_free=0.1279 | n_water=444 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1144 r_free=0.1280 | n_water=443 | time (s): 46.810 (total time: 49.220) Filter (q & B) r_work=0.1144 r_free=0.1280 | n_water=442 | time (s): 4.040 (total time: 53.260) Compute maps r_work=0.1144 r_free=0.1280 | n_water=442 | time (s): 1.890 (total time: 55.150) Filter (map) r_work=0.1162 r_free=0.1284 | n_water=356 | time (s): 4.020 (total time: 59.170) Find peaks r_work=0.1162 r_free=0.1284 | n_water=356 | time (s): 0.760 (total time: 59.930) Add new water r_work=0.1215 r_free=0.1349 | n_water=485 | time (s): 3.880 (total time: 63.810) Refine new water occ: r_work=0.1165 r_free=0.1302 adp: r_work=0.1165 r_free=0.1304 occ: r_work=0.1153 r_free=0.1289 adp: r_work=0.1152 r_free=0.1290 occ: r_work=0.1144 r_free=0.1274 adp: r_work=0.1141 r_free=0.1275 ADP+occupancy (water only), MIN, final r_work=0.1141 r_free=0.1275 r_work=0.1141 r_free=0.1275 | n_water=485 | time (s): 312.500 (total time: 376.310) Filter (q & B) r_work=0.1146 r_free=0.1287 | n_water=451 | time (s): 4.050 (total time: 380.360) Filter (dist only) r_work=0.1146 r_free=0.1287 | n_water=450 | time (s): 48.210 (total time: 428.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.732722 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.725481 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 0.1215 0.1326 0.0110 0.003 0.7 5.4 0.0 0.0 0 0.087 0.1173 0.1299 0.0126 0.004 0.8 5.1 0.5 0.0 0 0.260 0.1153 0.1289 0.0136 0.005 1.0 5.1 0.5 0.0 0 0.520 0.1147 0.1287 0.0139 0.006 1.0 4.8 0.5 0.0 0 0.780 0.1146 0.1287 0.0140 0.006 1.0 4.8 0.5 0.0 0 1.040 0.1146 0.1286 0.0141 0.007 1.0 4.8 0.5 0.0 0 1.300 0.1144 0.1286 0.0142 0.007 1.0 4.8 0.5 0.0 0 1.559 0.1143 0.1285 0.0142 0.008 1.1 4.8 0.5 0.0 0 1.819 0.1147 0.1286 0.0140 0.006 1.0 4.8 0.5 0.0 0 0.866 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1143 0.1285 0.0142 0.008 1.1 4.8 0.5 0.0 0 1.819 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.43 12.85 1.42 3.779 21.261 41.725 3.605 11.43 12.85 1.42 3.779 21.261 1.252 3.605 11.43 12.85 1.42 3.779 21.261 5.216 3.605 11.45 12.91 1.46 3.712 21.256 20.863 3.600 11.54 13.11 1.57 3.723 21.226 41.725 3.605 11.44 13.05 1.61 3.751 21.217 62.588 3.598 11.41 13.04 1.63 3.761 21.212 83.451 3.595 11.36 13.00 1.64 3.772 21.211 104.314 3.591 11.35 13.01 1.66 3.782 21.207 125.176 3.590 11.33 12.99 1.66 3.791 21.206 146.039 3.588 11.34 13.02 1.68 3.806 21.195 166.902 3.589 11.31 13.00 1.68 3.813 21.195 187.765 3.587 11.30 12.98 1.68 3.817 21.196 208.627 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: 1.252 Accepted refinement result: 11.43 12.85 1.42 3.779 21.261 1.252 3.605 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.23 3.31 235 1742 Protein: 9.11 115.03 17.03 3.32 0 1519 Water: 11.51 76.70 35.40 N/A 235 215 Other: 19.76 26.63 22.10 N/A 0 8 Chain A: 9.11 115.03 19.37 N/A 0 1742 Chain S: 15.37 60.00 35.03 N/A 235 0 Histogram: Values Number of atoms 9.11 - 19.70 1265 19.70 - 30.29 291 30.29 - 40.88 221 40.88 - 51.48 126 51.48 - 62.07 51 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=0.1143 r_free=0.1285 r_work=0.1143 r_free=0.1285 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1285 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1139 r_free = 0.1279 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1139 r_free= 0.1279 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.602996 | | target function (ml) not normalized (work): 300050.262243 | | target function (ml) not normalized (free): 15793.774903 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1319 0.1259 5.6463 5.5355| | 2: 3.57 - 2.84 1.00 2888 124 0.1065 0.1385 5.1357 5.203| | 3: 2.83 - 2.48 1.00 2820 163 0.1130 0.1275 4.925 4.9718| | 4: 2.47 - 2.25 1.00 2825 136 0.0912 0.0961 4.6056 4.6271| | 5: 2.25 - 2.09 1.00 2756 127 0.0875 0.0977 4.5474 4.5996| | 6: 2.09 - 1.97 1.00 2846 113 0.0872 0.0993 4.2585 4.3274| | 7: 1.97 - 1.87 1.00 2787 165 0.0899 0.1137 3.9864 4.1052| | 8: 1.87 - 1.79 1.00 2789 144 0.0928 0.1103 3.8943 4.0008| | 9: 1.79 - 1.72 1.00 2745 138 0.0881 0.1222 3.6515 3.8525| | 10: 1.72 - 1.66 1.00 2831 160 0.0930 0.1142 3.5745 3.6996| | 11: 1.66 - 1.61 1.00 2712 147 0.0879 0.1078 3.5039 3.5881| | 12: 1.61 - 1.56 1.00 2773 144 0.0917 0.1134 3.3394 3.4593| | 13: 1.56 - 1.52 1.00 2745 130 0.0953 0.1059 3.3162 3.4103| | 14: 1.52 - 1.48 1.00 2803 134 0.0991 0.1060 3.2483 3.3203| | 15: 1.48 - 1.45 1.00 2738 128 0.1014 0.1237 3.1614 3.2678| | 16: 1.45 - 1.42 1.00 2756 161 0.1056 0.1254 3.1374 3.2516| | 17: 1.42 - 1.39 1.00 2785 139 0.1143 0.1298 3.123 3.2304| | 18: 1.39 - 1.36 1.00 2741 179 0.1202 0.1325 3.1075 3.2449| | 19: 1.36 - 1.34 1.00 2807 134 0.1261 0.1550 3.1137 3.2649| | 20: 1.34 - 1.32 1.00 2696 147 0.1370 0.1464 3.1139 3.1492| | 21: 1.32 - 1.30 1.00 2785 112 0.1478 0.1515 3.1159 3.1064| | 22: 1.29 - 1.27 1.00 2704 152 0.1572 0.1968 3.1263 3.2911| | 23: 1.27 - 1.26 1.00 2802 156 0.1656 0.1799 3.1356 3.2049| | 24: 1.26 - 1.24 1.00 2744 132 0.1711 0.1840 3.1274 3.2303| | 25: 1.24 - 1.22 1.00 2733 148 0.1883 0.2165 3.1427 3.2636| | 26: 1.22 - 1.21 1.00 2727 135 0.1904 0.1768 3.1456 3.2031| | 27: 1.21 - 1.19 1.00 2814 148 0.2076 0.2178 3.1695 3.1629| | 28: 1.19 - 1.18 1.00 2671 147 0.2207 0.2313 3.1666 3.1738| | 29: 1.18 - 1.16 1.00 2800 134 0.2273 0.2386 3.1483 3.2253| | 30: 1.16 - 1.15 1.00 2739 148 0.2447 0.2471 3.1421 3.1716| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2916 171 0.95 7.75 1.00 0.97 5161.70| | 2: 3.57 - 2.84 2888 124 0.93 11.70 1.01 0.97 5161.70| | 3: 2.83 - 2.48 2820 163 0.90 15.59 0.99 0.97 4323.83| | 4: 2.47 - 2.25 2825 136 0.92 12.86 1.00 0.98 2163.22| | 5: 2.25 - 2.09 2756 127 0.91 14.86 1.01 0.98 2163.22| | 6: 2.09 - 1.97 2846 113 0.93 12.03 1.02 0.98 1271.18| | 7: 1.97 - 1.87 2787 165 0.95 9.26 1.02 0.97 510.38| | 8: 1.87 - 1.79 2789 144 0.93 12.62 1.00 0.97 510.38| | 9: 1.79 - 1.72 2745 138 0.94 10.14 0.98 0.97 292.26| | 10: 1.72 - 1.66 2831 160 0.94 11.21 0.98 0.97 248.58| | 11: 1.66 - 1.61 2712 147 0.93 11.89 0.98 0.97 238.17| | 12: 1.61 - 1.56 2773 144 0.95 9.03 0.99 0.97 140.00| | 13: 1.56 - 1.52 2745 130 0.95 10.53 1.03 0.97 140.00| | 14: 1.52 - 1.48 2803 134 0.94 10.92 1.02 0.97 125.49| | 15: 1.48 - 1.45 2738 128 0.95 10.00 1.02 0.98 98.92| | 16: 1.45 - 1.42 2756 161 0.94 11.18 1.02 0.98 98.92| | 17: 1.42 - 1.39 2785 139 0.95 11.01 1.01 0.98 89.84| | 18: 1.39 - 1.36 2741 179 0.94 11.60 1.01 0.98 84.59| | 19: 1.36 - 1.34 2807 134 0.94 12.00 1.00 0.98 84.59| | 20: 1.34 - 1.32 2696 147 0.94 12.14 0.98 0.96 80.25| | 21: 1.32 - 1.30 2785 112 0.94 13.14 0.98 0.96 79.95| | 22: 1.29 - 1.27 2704 152 0.93 13.70 0.98 0.96 80.36| | 23: 1.27 - 1.26 2802 156 0.92 14.88 0.97 0.94 82.43| | 24: 1.26 - 1.24 2744 132 0.92 14.92 0.96 0.94 82.43| | 25: 1.24 - 1.22 2733 148 0.91 16.43 0.96 0.94 84.43| | 26: 1.22 - 1.21 2727 135 0.90 18.16 1.03 0.93 86.64| | 27: 1.21 - 1.19 2814 148 0.89 18.82 1.02 0.93 86.64| | 28: 1.19 - 1.18 2671 147 0.88 20.50 1.01 0.93 90.45| | 29: 1.18 - 1.16 2800 134 0.88 20.61 0.99 0.92 91.89| | 30: 1.16 - 1.15 2739 148 0.86 22.13 0.98 0.92 91.89| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.95 max = 5161.70 mean = 814.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.85 mean = 13.37| |phase err.(test): min = 0.00 max = 89.92 mean = 13.35| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1145 0.1139 0.1279 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1463 0.1461 0.1514 n_refl.: 87574 remove outliers: r(all,work,free)=0.1463 0.1461 0.1514 n_refl.: 87574 overall B=-0.01 to atoms: r(all,work,free)=0.1462 0.1460 0.1513 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1145 0.1138 0.1280 n_refl.: 87574 remove outliers: r(all,work,free)=0.1144 0.1137 0.1280 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 88.54 80 5 0.3829 285.426 249.876 0.451 1.001 0.302 11.894-9.307 92.16 90 4 0.2341 478.765 458.725 0.864 1.002 0.290 9.237-7.194 97.27 207 7 0.2237 387.910 379.171 0.931 1.002 0.170 7.162-5.571 100.00 427 22 0.2103 295.853 284.381 0.907 1.002 0.160 5.546-4.326 100.00 867 58 0.1121 406.133 401.652 0.965 1.002 0.130 4.315-3.360 100.00 1859 96 0.0920 386.235 384.157 1.004 1.002 0.130 3.356-2.611 100.00 3867 181 0.1120 253.737 252.142 1.011 1.002 0.050 2.608-2.026 99.99 8198 413 0.0926 168.204 167.506 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0901 82.142 82.501 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.425 36.038 1.029 0.996 0.000 1.221-1.150 99.97 13689 708 0.2169 22.950 21.503 0.991 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0161 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2603 0.1940 0.081 5.351 8.8 119.3 19.9 258 0.000 1_bss: 0.1626 0.1763 0.081 5.351 9.1 119.5 20.1 258 0.000 1_settarget: 0.1626 0.1763 0.081 5.351 9.1 119.5 20.1 258 0.000 1_nqh: 0.1628 0.1764 0.081 5.351 9.1 119.5 20.1 258 0.003 1_weight: 0.1628 0.1764 0.081 5.351 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1232 0.1468 0.006 0.852 9.1 119.5 20.1 258 0.135 1_adp: 0.1238 0.1464 0.006 0.852 9.1 119.5 20.1 258 0.135 1_regHadp: 0.1239 0.1468 0.006 0.852 9.1 119.5 20.1 258 0.135 1_occ: 0.1233 0.1459 0.006 0.852 9.1 119.5 20.1 258 0.135 2_bss: 0.1231 0.1452 0.006 0.852 9.1 119.5 20.1 258 0.135 2_settarget: 0.1231 0.1452 0.006 0.852 9.1 119.5 20.1 258 0.135 2_updatecdl: 0.1231 0.1452 0.006 0.866 9.1 119.5 20.1 258 0.135 2_nqh: 0.1230 0.1451 0.006 0.866 9.1 119.5 20.1 258 0.135 2_sol: 0.1205 0.1393 0.006 0.866 9.1 115.0 22.1 408 n/a 2_weight: 0.1205 0.1393 0.006 0.866 9.1 115.0 22.1 408 n/a 2_xyzrec: 0.1204 0.1404 0.004 0.701 9.1 115.0 22.1 408 n/a 2_adp: 0.1204 0.1404 0.004 0.701 9.1 115.0 22.1 408 n/a 2_regHadp: 0.1204 0.1404 0.004 0.701 9.1 115.0 22.1 408 n/a 2_occ: 0.1204 0.1408 0.004 0.701 9.1 115.0 22.1 408 n/a 3_bss: 0.1200 0.1402 0.004 0.701 9.1 115.0 22.1 408 n/a 3_settarget: 0.1200 0.1402 0.004 0.701 9.1 115.0 22.1 408 n/a 3_updatecdl: 0.1200 0.1402 0.004 0.702 9.1 115.0 22.1 408 n/a 3_nqh: 0.1200 0.1402 0.004 0.702 9.1 115.0 22.1 408 n/a 3_sol: 0.1230 0.1404 0.004 0.702 9.1 115.0 21.3 439 n/a 3_weight: 0.1230 0.1404 0.004 0.702 9.1 115.0 21.3 439 n/a 3_xyzrec: 0.1169 0.1310 0.005 0.920 9.1 115.0 21.3 439 n/a 3_adp: 0.1169 0.1310 0.005 0.920 9.1 115.0 21.3 439 n/a 3_regHadp: 0.1169 0.1310 0.005 0.920 9.1 115.0 21.3 439 n/a 3_occ: 0.1164 0.1306 0.005 0.920 9.1 115.0 21.3 439 n/a 4_bss: 0.1157 0.1298 0.005 0.920 9.1 115.0 21.3 439 n/a 4_settarget: 0.1157 0.1298 0.005 0.920 9.1 115.0 21.3 439 n/a 4_updatecdl: 0.1157 0.1298 0.005 0.921 9.1 115.0 21.3 439 n/a 4_nqh: 0.1157 0.1298 0.005 0.921 9.1 115.0 21.3 439 n/a 4_sol: 0.1160 0.1285 0.005 0.921 9.1 115.0 21.2 444 n/a 4_weight: 0.1160 0.1285 0.005 0.921 9.1 115.0 21.2 444 n/a 4_xyzrec: 0.1153 0.1285 0.006 1.000 9.1 115.0 21.2 444 n/a 4_adp: 0.1153 0.1285 0.006 1.000 9.1 115.0 21.2 444 n/a 4_regHadp: 0.1153 0.1285 0.006 1.000 9.1 115.0 21.2 444 n/a 4_occ: 0.1147 0.1279 0.006 1.000 9.1 115.0 21.2 444 n/a 5_bss: 0.1143 0.1279 0.006 1.000 9.1 115.0 21.2 444 n/a 5_settarget: 0.1143 0.1279 0.006 1.000 9.1 115.0 21.2 444 n/a 5_updatecdl: 0.1143 0.1279 0.006 1.001 9.1 115.0 21.2 444 n/a 5_setrh: 0.1144 0.1279 0.006 1.001 9.1 115.0 21.2 444 n/a 5_nqh: 0.1144 0.1279 0.006 1.001 9.1 115.0 21.2 444 n/a 5_sol: 0.1146 0.1287 0.006 1.001 9.1 115.0 21.2 450 n/a 5_weight: 0.1146 0.1287 0.006 1.001 9.1 115.0 21.2 450 n/a 5_xyzrec: 0.1143 0.1285 0.008 1.075 9.1 115.0 21.2 450 n/a 5_adp: 0.1143 0.1285 0.008 1.075 9.1 115.0 21.2 450 n/a 5_regHadp: 0.1143 0.1285 0.008 1.075 9.1 115.0 21.2 450 n/a 5_occ: 0.1139 0.1279 0.008 1.075 9.1 115.0 21.2 450 n/a end: 0.1137 0.1280 0.008 1.075 9.1 115.0 21.2 450 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6847832_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6847832_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3200 Refinement macro-cycles (run) : 14323.7700 Write final files (write_after_run_outputs) : 72.3600 Total : 14399.4500 Total CPU time: 4.01 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:19:37 PST -0800 (1735366777.86 s) Start R-work = 0.1626, R-free = 0.1763 Final R-work = 0.1137, R-free = 0.1280 =============================================================================== Job complete usr+sys time: 14534.92 seconds wall clock time: 263 minutes 2.03 seconds (15782.03 seconds total)