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_5155044.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 { 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_5155044.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5155044.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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: 1.38, per 1000 atoms: 0.41 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: 0.31 Conformation dependent library (CDL) restraints added in 124.5 milliseconds Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.91: 552 0.91 - 1.19: 1117 1.19 - 1.46: 769 1.46 - 1.74: 706 1.74 - 2.01: 9 Bond restraints: 3153 Sorted by residual: bond pdb=" C BLYS A 132 " pdb=" O BLYS A 132 " ideal model delta sigma weight residual 1.236 1.026 0.210 1.15e-02 7.56e+03 3.35e+02 bond pdb=" CE1 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 1.321 1.143 0.178 1.00e-02 1.00e+04 3.16e+02 bond pdb=" C ILE A 102 " pdb=" O ILE A 102 " ideal model delta sigma weight residual 1.236 1.060 0.176 9.90e-03 1.02e+04 3.16e+02 bond pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 1.330 1.553 -0.223 1.30e-02 5.92e+03 2.95e+02 bond pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 1.237 1.426 -0.189 1.11e-02 8.12e+03 2.89e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 3108 4.49 - 8.99: 1818 8.99 - 13.48: 707 13.48 - 17.97: 124 17.97 - 22.46: 20 Bond angle restraints: 5777 Sorted by residual: angle pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" C VAL A 20 " ideal model delta sigma weight residual 111.05 132.28 -21.23 1.25e+00 6.40e-01 2.89e+02 angle pdb=" O GLY A 118 " pdb=" C GLY A 118 " pdb=" N PHE A 119 " ideal model delta sigma weight residual 122.41 136.93 -14.52 1.08e+00 8.57e-01 1.81e+02 angle pdb=" CA GLY A 108 " pdb=" C GLY A 108 " pdb=" O GLY A 108 " ideal model delta sigma weight residual 119.69 111.84 7.85 6.30e-01 2.52e+00 1.55e+02 angle pdb=" CA ARG A 156 " pdb=" C ARG A 156 " pdb=" O ARG A 156 " ideal model delta sigma weight residual 119.41 105.48 13.93 1.13e+00 7.83e-01 1.52e+02 angle pdb=" O BASN A 76 " pdb=" C BASN A 76 " pdb=" N LEU A 77 " ideal model delta sigma weight residual 122.09 134.79 -12.70 1.04e+00 9.25e-01 1.49e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.04: 937 17.04 - 34.08: 123 34.08 - 51.12: 32 51.12 - 68.16: 16 68.16 - 85.20: 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 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -158.12 -21.88 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.241: 99 0.241 - 0.481: 85 0.481 - 0.720: 38 0.720 - 0.960: 16 0.960 - 1.200: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 69 " pdb=" CA VAL A 69 " pdb=" CG1 VAL A 69 " pdb=" CG2 VAL A 69 " both_signs ideal model delta sigma weight residual False -2.63 -1.43 -1.20 2.00e-01 2.50e+01 3.60e+01 chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.57 1.14 2.00e-01 2.50e+01 3.27e+01 chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.74e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.125 2.00e-02 2.50e+03 9.34e-02 1.96e+02 pdb=" CG HIS A 126 " -0.095 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.079 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.104 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.103 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.131 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.085 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.052 2.00e-02 2.50e+03 6.73e-02 1.36e+02 pdb=" CG TYR A 139 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.122 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.109 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.067 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.124 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.029 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.048 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.041 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.029 2.00e-02 2.50e+03 5.51e-02 9.11e+01 pdb=" CG ATYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.105 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.061 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.015 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.087 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.024 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.000 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 409 2.20 - 2.80: 7174 2.80 - 3.40: 10810 3.40 - 4.00: 15518 4.00 - 4.60: 22781 Nonbonded interactions: 56692 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.600 2.100 nonbonded pdb=" HB2BGLN A 80 " pdb="HE21BGLN A 80 " model vdw 1.786 2.270 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.805 1.850 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.812 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.829 1.850 ... (remaining 56687 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_5155044_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= 0.2612 r_free= 0.1958 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790788 | | target function (ml) not normalized (work): 232489.416408 | | target function (ml) not normalized (free): 11820.671157 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3044 0.2096 7.0821 4.9444| | 2: 3.57 - 2.84 1.00 2876 122 0.2439 0.1748 4.3467 4.336| | 3: 2.84 - 2.48 1.00 2833 165 0.2345 0.1663 4.1229 4.15| | 4: 2.47 - 2.25 1.00 2825 136 0.2328 0.1598 3.8322 3.8413| | 5: 2.25 - 2.09 1.00 2756 127 0.2539 0.1579 3.8009 3.8237| | 6: 2.09 - 1.97 1.00 2846 113 0.2520 0.1826 3.4604 3.5218| | 7: 1.97 - 1.87 1.00 2787 165 0.2510 0.1992 3.1217 3.2322| | 8: 1.87 - 1.79 1.00 2789 144 0.2445 0.1796 3.0629 3.0916| | 9: 1.79 - 1.72 1.00 2745 138 0.2406 0.2164 2.9092 3.0641| | 10: 1.72 - 1.66 1.00 2789 158 0.2402 0.1872 2.8179 2.8877| | 11: 1.66 - 1.61 1.00 2740 147 0.2521 0.1744 2.7519 2.7752| | 12: 1.61 - 1.56 1.00 2787 146 0.2599 0.2019 2.6341 2.656| | 13: 1.56 - 1.52 1.00 2745 130 0.2629 0.1902 2.5792 2.6073| | 14: 1.52 - 1.48 1.00 2803 134 0.2604 0.2104 2.4911 2.5867| | 15: 1.48 - 1.45 1.00 2738 128 0.2592 0.2010 2.4393 2.4365| | 16: 1.45 - 1.42 1.00 2756 161 0.2636 0.2101 2.3687 2.4195| | 17: 1.42 - 1.39 1.00 2785 139 0.2702 0.1947 2.3507 2.3571| | 18: 1.39 - 1.36 1.00 2741 179 0.2687 0.2085 2.2645 2.2976| | 19: 1.36 - 1.34 1.00 2807 134 0.2632 0.2501 2.2401 2.3579| | 20: 1.34 - 1.32 1.00 2696 147 0.2690 0.2374 2.2027 2.2469| | 21: 1.32 - 1.30 1.00 2785 112 0.2697 0.2164 2.1617 2.1385| | 22: 1.29 - 1.27 1.00 2704 152 0.2722 0.2489 2.1345 2.2058| | 23: 1.27 - 1.26 1.00 2802 156 0.2776 0.2264 2.099 2.0936| | 24: 1.26 - 1.24 1.00 2744 132 0.2776 0.2653 2.0739 2.2161| | 25: 1.24 - 1.22 1.00 2734 148 0.2836 0.2671 2.0316 2.1012| | 26: 1.22 - 1.21 1.00 2727 135 0.2832 0.2227 1.9945 2.0264| | 27: 1.21 - 1.19 1.00 2814 148 0.2953 0.2842 2.01 2.0405| | 28: 1.19 - 1.18 1.00 2671 147 0.3003 0.2612 1.9958 1.9789| | 29: 1.18 - 1.16 1.00 2800 134 0.3025 0.2738 1.9657 2.0287| | 30: 1.16 - 1.15 1.00 2740 148 0.3027 0.2934 1.9208 1.9375| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.77 0.76 0.23 1468.00| | 2: 3.57 - 2.84 2876 122 0.81 25.96 1.27 0.23 1468.00| | 3: 2.84 - 2.48 2833 165 0.74 31.83 1.24 0.24 1218.03| | 4: 2.47 - 2.25 2825 136 0.81 25.42 1.26 0.25 569.30| | 5: 2.25 - 2.09 2756 127 0.77 29.35 1.29 0.25 569.30| | 6: 2.09 - 1.97 2846 113 0.83 22.82 1.29 0.25 312.57| | 7: 1.97 - 1.87 2787 165 0.90 16.87 1.28 0.25 93.62| | 8: 1.87 - 1.79 2789 144 0.85 21.42 1.25 0.25 93.62| | 9: 1.79 - 1.72 2745 138 0.88 18.95 1.23 0.25 57.18| | 10: 1.72 - 1.66 2789 158 0.86 20.54 1.22 0.25 49.88| | 11: 1.66 - 1.61 2740 147 0.85 21.77 1.25 0.25 48.01| | 12: 1.61 - 1.56 2787 146 0.88 18.53 1.25 0.25 28.98| | 13: 1.56 - 1.52 2745 130 0.87 20.38 1.25 0.25 28.98| | 14: 1.52 - 1.48 2803 134 0.86 20.74 1.25 0.25 25.92| | 15: 1.48 - 1.45 2738 128 0.87 19.91 1.23 0.25 20.32| | 16: 1.45 - 1.42 2756 161 0.86 21.53 1.23 0.25 20.32| | 17: 1.42 - 1.39 2785 139 0.87 20.63 1.23 0.25 17.17| | 18: 1.39 - 1.36 2741 179 0.87 20.74 1.23 0.25 15.35| | 19: 1.36 - 1.34 2807 134 0.86 21.71 1.21 0.25 15.35| | 20: 1.34 - 1.32 2696 147 0.87 20.62 1.21 0.25 12.92| | 21: 1.32 - 1.30 2785 112 0.86 21.60 1.20 0.25 12.75| | 22: 1.29 - 1.27 2704 152 0.86 22.24 1.21 0.24 12.47| | 23: 1.27 - 1.26 2802 156 0.86 22.02 1.21 0.24 11.01| | 24: 1.26 - 1.24 2744 132 0.85 22.82 1.21 0.24 11.01| | 25: 1.24 - 1.22 2734 148 0.84 23.65 1.21 0.24 10.49| | 26: 1.22 - 1.21 2727 135 0.84 24.33 1.20 0.23 9.93| | 27: 1.21 - 1.19 2814 148 0.83 24.60 1.20 0.23 9.93| | 28: 1.19 - 1.18 2671 147 0.83 25.45 1.17 0.23 9.29| | 29: 1.18 - 1.16 2800 134 0.82 26.06 1.17 0.23 9.06| | 30: 1.16 - 1.15 2740 148 0.81 27.10 1.16 0.23 9.06| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 9.06 max = 1468.00 mean = 213.77| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.61| |phase err.(test): min = 0.00 max = 89.98 mean = 22.41| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.243 1557 Z= 5.592 Angle : 5.321 21.233 2118 Z= 3.749 Chirality : 0.416 1.200 243 Planarity : 0.032 0.094 284 Dihedral : 14.211 85.196 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 2.48 % Allowed : 3.73 % Favored : 93.79 % Cbeta Deviations : 32.97 % 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: -2.56 (0.46), residues: 224 helix: -2.56 (0.37), residues: 102 sheet: -0.71 (0.75), residues: 38 loop : -0.64 (0.57), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.140 0.030 ARG A 156 TYR 0.135 0.040 TYR A 139 PHE 0.117 0.033 PHE A 164 HIS 0.035 0.019 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2612 r_free= 0.1958 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790788 | | target function (ml) not normalized (work): 232489.416408 | | target function (ml) not normalized (free): 11820.671157 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2570 0.2613 0.1959 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2570 0.2613 0.1959 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1987 0.1959 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2006 0.2011 0.1970 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1642 0.1634 0.1792 n_refl.: 87594 remove outliers: r(all,work,free)=0.1642 0.1634 0.1792 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 0.3855 386.417 356.814 0.731 0.930 0.412 11.894-9.307 99.02 97 4 0.1780 613.805 594.300 1.003 0.931 0.400 9.237-7.194 100.00 213 7 0.2099 502.017 491.976 1.030 0.931 0.370 7.162-5.571 100.00 427 22 0.2195 376.736 364.980 1.002 0.931 0.288 5.546-4.326 100.00 867 58 0.1266 517.165 510.536 1.040 0.931 0.224 4.315-3.360 100.00 1859 96 0.1122 491.827 488.237 1.085 0.931 0.199 3.356-2.611 100.00 3867 181 0.1441 323.105 319.898 1.071 0.931 0.048 2.608-2.026 99.99 8198 413 0.1373 214.189 211.776 1.084 0.930 0.000 2.025-1.573 100.00 17313 902 0.1636 104.599 103.881 1.085 0.929 0.000 1.573-1.221 100.00 36679 1900 0.2061 46.383 45.141 1.079 0.928 0.000 1.221-1.150 99.97 13689 708 0.2583 29.225 26.969 1.047 0.927 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0439 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1634 r_free=0.1792 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1634 r_free=0.1792 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.664099 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2008.976732 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 0.1730 0.1840 0.0110 0.002 0.4 4.5 0.0 0.0 0 0.125 0.1561 0.1694 0.0133 0.002 0.4 4.2 0.0 0.0 0 0.250 0.1450 0.1609 0.0159 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1374 0.1552 0.0178 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1359 0.1552 0.0193 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1358 0.1552 0.0194 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1299 0.1512 0.0213 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1273 0.1498 0.0226 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1256 0.1487 0.0231 0.004 0.7 3.2 0.5 0.0 0 4.000 0.1241 0.1472 0.0230 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1244 0.1479 0.0235 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1234 0.1468 0.0234 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1231 0.1469 0.0237 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1231 0.1474 0.0243 0.006 0.8 3.2 0.5 0.0 0 9.000 0.1228 0.1467 0.0239 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1225 0.1466 0.0241 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1223 0.1468 0.0245 0.007 0.9 3.2 0.5 0.0 0 12.000 0.1224 0.1475 0.0251 0.008 1.0 3.5 0.5 0.6 0 13.332 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1225 0.1466 0.0241 0.007 0.9 3.5 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 14.66 2.41 3.013 19.050 2008.977 0.017 12.25 14.65 2.40 2.989 19.050 60.269 0.017 12.32 14.62 2.30 2.667 19.049 251.122 0.017 12.67 15.22 2.55 2.740 19.211 1004.488 0.016 12.43 15.30 2.87 2.993 19.414 2008.977 0.016 12.41 15.38 2.97 3.265 19.595 3013.465 0.015 12.30 15.35 3.05 3.325 19.619 4017.953 0.015 12.29 15.42 3.13 3.409 19.656 5022.442 0.015 12.24 15.39 3.16 3.351 19.616 6026.930 0.015 12.18 15.36 3.18 3.282 19.572 7031.419 0.015 12.12 15.33 3.21 3.410 19.638 8035.907 0.015 12.07 15.28 3.21 3.426 19.635 9040.395 0.015 12.17 15.49 3.32 3.554 19.682 10044.884 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: 251.122 Accepted refinement result: 12.32 14.62 2.30 2.667 19.049 251.122 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.44 20.08 3.31 0 1785 Protein: 9.06 114.98 16.98 3.31 0 1519 Water: 11.46 119.44 38.22 N/A 0 258 Other: 19.71 26.58 22.05 N/A 0 8 Chain A: 9.06 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1272 20.10 - 31.14 227 31.14 - 42.18 125 42.18 - 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 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1462 r_work=0.1233 r_free=0.1466 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1466 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 = 0.1227 r_free = 0.1460 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= 0.1227 r_free= 0.1460 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016856 | | target function (ls_wunit_k1) not normalized (work): 1404.024521 | | target function (ls_wunit_k1) not normalized (free): 111.685485 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1238 0.1227 0.1460 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1671 0.1673 0.1689 n_refl.: 87593 remove outliers: r(all,work,free)=0.1671 0.1673 0.1689 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1678 0.1679 0.1693 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1227 0.1453 n_refl.: 87593 remove outliers: r(all,work,free)=0.1237 0.1226 0.1453 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3512 301.707 281.916 0.648 1.002 0.375 11.894-9.307 99.02 97 4 0.1631 483.319 471.273 0.923 1.003 0.372 9.237-7.194 100.00 213 7 0.1893 395.295 388.853 0.964 1.003 0.350 7.162-5.571 100.00 427 22 0.1844 296.647 290.615 0.938 1.003 0.259 5.546-4.326 100.00 867 58 0.0997 407.223 404.440 0.964 1.003 0.204 4.315-3.360 100.00 1859 96 0.0871 387.272 386.199 1.009 1.002 0.180 3.356-2.611 100.00 3867 181 0.1173 254.418 253.287 1.009 1.002 0.048 2.608-2.026 99.99 8198 413 0.1025 168.656 167.930 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1111 82.363 82.552 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1449 36.523 36.030 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2248 23.012 21.496 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0531 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1453 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=0.1228 r_free=0.1453 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1228 r_free=0.1453 | n_water=258 | time (s): 1.640 (total time: 1.640) Filter (dist) r_work=0.1235 r_free=0.1452 | n_water=252 | time (s): 22.220 (total time: 23.860) Filter (q & B) r_work=0.1238 r_free=0.1452 | n_water=249 | time (s): 3.510 (total time: 27.370) Compute maps r_work=0.1238 r_free=0.1452 | n_water=249 | time (s): 1.420 (total time: 28.790) Filter (map) r_work=0.1257 r_free=0.1454 | n_water=223 | time (s): 2.720 (total time: 31.510) Find peaks r_work=0.1257 r_free=0.1454 | n_water=223 | time (s): 0.520 (total time: 32.030) Add new water r_work=0.1406 r_free=0.1638 | n_water=433 | time (s): 2.680 (total time: 34.710) Refine new water occ: r_work=0.1309 r_free=0.1489 adp: r_work=0.1227 r_free=0.1436 occ: r_work=0.1241 r_free=0.1424 adp: r_work=0.1206 r_free=0.1408 occ: r_work=0.1208 r_free=0.1399 adp: r_work=0.1199 r_free=0.1397 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1397 r_work=0.1199 r_free=0.1397 | n_water=433 | time (s): 60.990 (total time: 95.700) Filter (q & B) r_work=0.1201 r_free=0.1399 | n_water=422 | time (s): 3.330 (total time: 99.030) Filter (dist only) r_work=0.1202 r_free=0.1397 | n_water=421 | time (s): 36.490 (total time: 135.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.971376 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1484.212664 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 0.1714 0.1821 0.0107 0.001 0.4 8.3 0.0 0.0 0 0.125 0.1554 0.1681 0.0127 0.001 0.4 7.4 0.0 0.0 0 0.250 0.1426 0.1576 0.0150 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1344 0.1510 0.0166 0.002 0.5 5.4 0.0 0.0 0 0.750 0.1328 0.1504 0.0176 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1324 0.1501 0.0177 0.002 0.5 4.2 0.0 0.0 0 1.000 0.1256 0.1445 0.0189 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1227 0.1438 0.0211 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1214 0.1430 0.0216 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1210 0.1426 0.0217 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1206 0.1426 0.0219 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1203 0.1427 0.0224 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1198 0.1419 0.0221 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1194 0.1418 0.0223 0.006 0.8 3.5 0.5 0.0 0 9.000 0.1192 0.1418 0.0225 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1190 0.1419 0.0229 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1189 0.1421 0.0232 0.007 0.9 4.8 0.5 0.6 0 12.000 0.1186 0.1421 0.0235 0.008 0.9 4.8 0.5 0.6 0 13.986 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1418 0.0223 0.006 0.8 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 11.94 14.18 2.23 3.774 21.771 1484.213 0.016 11.94 14.18 2.23 3.774 21.771 44.526 0.016 11.95 14.18 2.23 3.773 21.771 185.527 0.016 12.21 14.79 2.58 3.565 21.820 742.106 0.016 12.15 14.99 2.84 3.454 22.113 1484.213 0.015 11.97 14.92 2.95 3.482 22.149 2226.319 0.015 11.87 14.89 3.02 3.459 22.131 2968.425 0.014 11.87 15.01 3.14 3.507 22.217 3710.532 0.014 11.81 14.94 3.13 3.504 22.151 4452.638 0.014 11.76 14.94 3.18 3.524 22.187 5194.744 0.014 11.77 15.04 3.27 3.549 22.161 5936.851 0.014 11.73 15.00 3.27 3.572 22.217 6678.957 0.014 11.71 15.00 3.29 3.579 22.191 7421.063 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: 185.527 Accepted refinement result: 11.95 14.18 2.23 3.773 21.771 185.527 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.00 22.18 3.31 198 1750 Protein: 9.10 115.00 17.02 3.31 0 1519 Water: 11.49 76.68 40.81 N/A 198 223 Other: 19.74 26.62 22.08 N/A 0 8 Chain A: 9.10 115.00 19.40 N/A 0 1750 Chain S: 12.70 60.00 46.77 N/A 198 0 Histogram: Values Number of atoms 9.10 - 19.69 1262 19.69 - 30.28 244 30.28 - 40.87 166 40.87 - 51.46 129 51.46 - 62.05 125 62.05 - 72.64 11 72.64 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1418 r_work=0.1195 r_free=0.1418 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1418 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 = 0.1196 r_free = 0.1415 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 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= 0.1196 r_free= 0.1415 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015215 | | target function (ls_wunit_k1) not normalized (work): 1267.368852 | | target function (ls_wunit_k1) not normalized (free): 102.931227 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1196 0.1415 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1585 0.1585 0.1623 n_refl.: 87592 remove outliers: r(all,work,free)=0.1585 0.1585 0.1623 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1587 0.1587 0.1625 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1193 0.1410 n_refl.: 87592 remove outliers: r(all,work,free)=0.1203 0.1192 0.1410 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3304 300.254 275.471 0.593 1.003 0.350 11.894-9.307 99.02 97 4 0.1635 483.319 477.095 0.922 1.003 0.333 9.237-7.194 100.00 213 7 0.1718 395.295 394.524 0.986 1.003 0.290 7.162-5.571 100.00 427 22 0.1609 296.647 292.421 0.937 1.003 0.230 5.546-4.326 100.00 867 58 0.0892 407.223 404.018 0.959 1.003 0.199 4.315-3.360 100.00 1859 96 0.0801 387.272 386.288 1.005 1.003 0.180 3.356-2.611 100.00 3867 181 0.1090 254.418 253.439 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1019 168.656 168.096 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1108 82.363 82.577 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1446 36.523 36.059 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 23.012 21.519 0.987 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0174 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1410 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=0.1192 r_free=0.1410 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1410 | n_water=421 | time (s): 1.890 (total time: 1.890) Filter (dist) r_work=0.1193 r_free=0.1410 | n_water=419 | time (s): 34.180 (total time: 36.070) Filter (q & B) r_work=0.1193 r_free=0.1410 | n_water=419 | time (s): 0.810 (total time: 36.880) Compute maps r_work=0.1193 r_free=0.1410 | n_water=419 | time (s): 1.280 (total time: 38.160) Filter (map) r_work=0.1232 r_free=0.1400 | n_water=289 | time (s): 3.450 (total time: 41.610) Find peaks r_work=0.1232 r_free=0.1400 | n_water=289 | time (s): 0.540 (total time: 42.150) Add new water r_work=0.1348 r_free=0.1517 | n_water=474 | time (s): 2.500 (total time: 44.650) Refine new water occ: r_work=0.1253 r_free=0.1439 adp: r_work=0.1255 r_free=0.1442 occ: r_work=0.1229 r_free=0.1417 adp: r_work=0.1228 r_free=0.1418 occ: r_work=0.1212 r_free=0.1406 adp: r_work=0.1206 r_free=0.1404 ADP+occupancy (water only), MIN, final r_work=0.1206 r_free=0.1404 r_work=0.1206 r_free=0.1404 | n_water=474 | time (s): 202.080 (total time: 246.730) Filter (q & B) r_work=0.1211 r_free=0.1410 | n_water=444 | time (s): 2.580 (total time: 249.310) Filter (dist only) r_work=0.1211 r_free=0.1410 | n_water=442 | time (s): 38.920 (total time: 288.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.782267 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.991452 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 0.1237 0.1367 0.0130 0.002 0.6 5.1 0.5 0.0 0 0.089 0.1188 0.1335 0.0148 0.003 0.7 4.2 0.5 0.0 0 0.267 0.1170 0.1323 0.0153 0.004 0.8 3.5 0.5 0.0 0 0.535 0.1161 0.1318 0.0157 0.005 0.9 3.5 0.5 0.0 0 0.802 0.1158 0.1317 0.0159 0.006 1.0 3.2 0.5 0.0 0 1.069 0.1155 0.1318 0.0163 0.007 1.0 3.5 0.5 0.0 0 1.337 0.1154 0.1317 0.0163 0.007 1.1 3.5 0.5 0.0 0 1.604 0.1151 0.1316 0.0164 0.008 1.1 3.2 0.5 0.0 0 1.871 0.1161 0.1319 0.0158 0.005 0.9 3.5 0.5 0.0 0 0.891 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1151 0.1316 0.0164 0.008 1.1 3.2 0.5 0.0 0 1.871 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.51 13.16 1.64 3.776 21.325 43.991 3.619 11.51 13.16 1.64 3.776 21.325 1.320 3.619 11.51 13.16 1.65 3.773 21.325 5.499 3.619 11.55 13.20 1.66 3.710 21.317 21.996 3.612 11.61 13.36 1.75 3.721 21.282 43.991 3.615 11.52 13.31 1.79 3.752 21.272 65.987 3.608 11.49 13.30 1.81 3.763 21.265 87.983 3.604 11.44 13.26 1.82 3.776 21.263 109.979 3.601 11.42 13.27 1.85 3.789 21.252 131.974 3.599 11.42 13.31 1.89 3.806 21.241 153.970 3.599 11.40 13.28 1.89 3.815 21.237 175.966 3.597 11.39 13.27 1.89 3.821 21.237 197.962 3.596 11.37 13.25 1.88 3.827 21.236 219.957 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: 1.320 Accepted refinement result: 11.51 13.16 1.64 3.776 21.325 1.320 3.619 Individual atomic B min max mean iso aniso Overall: 9.11 115.02 21.35 3.31 222 1747 Protein: 9.11 115.02 17.03 3.31 0 1519 Water: 11.50 76.69 36.20 N/A 222 220 Other: 19.75 26.63 22.09 N/A 0 8 Chain A: 9.11 115.02 19.36 N/A 0 1747 Chain S: 12.71 60.01 37.04 N/A 222 0 Histogram: Values Number of atoms 9.11 - 19.70 1266 19.70 - 30.29 279 30.29 - 40.88 207 40.88 - 51.47 133 51.47 - 62.06 62 62.06 - 72.65 11 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1151 r_free=0.1316 r_work=0.1151 r_free=0.1316 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1151 r_free = 0.1316 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1142 r_free = 0.1318 target_work(ml) = 3.613 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1142 r_free= 0.1318 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.612646 | | target function (ml) not normalized (work): 300911.771352 | | target function (ml) not normalized (free): 15852.773351 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1151 0.1142 0.1318 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1486 0.1484 0.1553 n_refl.: 87590 remove outliers: r(all,work,free)=0.1486 0.1484 0.1553 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1485 0.1483 0.1553 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1147 0.1138 0.1317 n_refl.: 87590 remove outliers: r(all,work,free)=0.1144 0.1135 0.1317 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 92.71 84 5 0.3832 297.608 274.298 0.513 1.001 0.330 11.894-9.307 96.08 94 4 0.2197 484.154 463.765 0.875 1.002 0.285 9.237-7.194 98.64 210 7 0.2239 388.792 390.593 0.966 1.003 0.190 7.162-5.571 100.00 427 22 0.2006 296.647 286.697 0.926 1.003 0.180 5.546-4.326 100.00 867 58 0.1102 407.223 402.085 0.964 1.003 0.180 4.315-3.360 100.00 1859 96 0.0911 387.272 385.053 1.004 1.002 0.150 3.356-2.611 100.00 3867 181 0.1135 254.418 252.511 1.007 1.002 0.034 2.608-2.026 99.99 8198 413 0.0931 168.656 167.953 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0897 82.363 82.661 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.523 36.114 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2162 23.012 21.558 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0095 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1135 r_free=0.1317 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1135 r_free=0.1317 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1135 r_free=0.1317 | n_water=442 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1135 r_free=0.1318 | n_water=441 | time (s): 49.090 (total time: 51.590) Filter (q & B) r_work=0.1137 r_free=0.1318 | n_water=439 | time (s): 3.890 (total time: 55.480) Compute maps r_work=0.1137 r_free=0.1318 | n_water=439 | time (s): 1.890 (total time: 57.370) Filter (map) r_work=0.1163 r_free=0.1316 | n_water=342 | time (s): 3.830 (total time: 61.200) Find peaks r_work=0.1163 r_free=0.1316 | n_water=342 | time (s): 0.730 (total time: 61.930) Add new water r_work=0.1231 r_free=0.1396 | n_water=495 | time (s): 3.880 (total time: 65.810) Refine new water occ: r_work=0.1163 r_free=0.1335 adp: r_work=0.1164 r_free=0.1336 occ: r_work=0.1149 r_free=0.1321 adp: r_work=0.1148 r_free=0.1322 occ: r_work=0.1137 r_free=0.1312 adp: r_work=0.1134 r_free=0.1311 ADP+occupancy (water only), MIN, final r_work=0.1134 r_free=0.1311 r_work=0.1134 r_free=0.1311 | n_water=495 | time (s): 244.690 (total time: 310.500) Filter (q & B) r_work=0.1140 r_free=0.1319 | n_water=455 | time (s): 3.950 (total time: 314.450) Filter (dist only) r_work=0.1140 r_free=0.1318 | n_water=453 | time (s): 47.540 (total time: 361.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.818704 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.746041 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 0.1202 0.1353 0.0151 0.002 0.6 4.5 0.5 0.0 0 0.091 0.1168 0.1332 0.0163 0.003 0.8 3.5 0.5 0.0 0 0.273 0.1155 0.1327 0.0172 0.005 0.9 3.8 0.5 0.0 0 0.546 0.1148 0.1322 0.0174 0.006 0.9 3.8 0.5 0.0 0 0.818 0.1145 0.1323 0.0179 0.006 1.0 3.5 0.5 0.0 0 1.091 0.1142 0.1321 0.0180 0.007 1.1 3.5 0.5 0.0 0 1.364 0.1140 0.1323 0.0183 0.008 1.1 3.5 0.5 0.0 0 1.637 0.1138 0.1322 0.0184 0.009 1.1 3.8 0.5 0.0 0 1.910 0.1147 0.1322 0.0176 0.006 1.0 3.8 0.5 0.0 0 0.909 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1142 0.1321 0.0180 0.007 1.1 3.5 0.5 0.0 0 1.364 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.42 13.21 1.80 3.777 21.258 48.746 3.614 11.42 13.21 1.80 3.777 21.258 1.462 3.614 11.43 13.22 1.79 3.762 21.259 6.093 3.614 11.49 13.33 1.84 3.711 21.247 24.373 3.611 11.50 13.44 1.94 3.738 21.220 48.746 3.610 11.42 13.40 1.98 3.760 21.214 73.119 3.604 11.38 13.36 1.98 3.771 21.211 97.492 3.600 11.37 13.40 2.02 3.787 21.200 121.865 3.599 11.34 13.36 2.02 3.798 21.200 146.238 3.596 11.32 13.35 2.03 3.808 21.197 170.611 3.595 11.32 13.37 2.05 3.823 21.188 194.984 3.595 11.31 13.36 2.05 3.831 21.187 219.357 3.594 11.29 13.33 2.04 3.835 21.187 243.730 3.592 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.462 Accepted refinement result: 11.42 13.21 1.80 3.777 21.258 1.462 3.614 Individual atomic B min max mean iso aniso Overall: 9.11 115.01 21.23 3.31 235 1745 Protein: 9.11 115.01 17.03 3.31 0 1519 Water: 11.50 76.69 35.33 N/A 235 218 Other: 19.75 26.62 22.09 N/A 0 8 Chain A: 9.11 115.01 19.33 N/A 0 1745 Chain S: 12.71 60.01 35.36 N/A 235 0 Histogram: Values Number of atoms 9.11 - 19.70 1265 19.70 - 30.29 297 30.29 - 40.88 216 40.88 - 51.47 130 51.47 - 62.06 50 62.06 - 72.65 11 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1142 r_free=0.1321 r_work=0.1142 r_free=0.1321 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1142 r_free = 0.1321 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1136 r_free = 0.1318 target_work(ml) = 3.611 | | 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.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1136 r_free= 0.1318 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.611318 | | target function (ml) not normalized (work): 300775.865480 | | target function (ml) not normalized (free): 15855.757962 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1145 0.1136 0.1318 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1467 0.1466 0.1526 n_refl.: 87583 remove outliers: r(all,work,free)=0.1467 0.1466 0.1526 n_refl.: 87583 overall B=-0.00 to atoms: r(all,work,free)=0.1467 0.1465 0.1525 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1143 0.1134 0.1319 n_refl.: 87583 remove outliers: r(all,work,free)=0.1141 0.1132 0.1319 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3885 290.943 254.644 0.454 1.000 0.308 11.894-9.307 95.10 93 4 0.2384 477.223 468.716 0.869 1.002 0.233 9.237-7.194 98.18 209 7 0.2367 386.761 382.653 0.934 1.002 0.165 7.162-5.571 100.00 427 22 0.2138 296.647 286.548 0.920 1.002 0.160 5.546-4.326 100.00 867 58 0.1136 407.223 402.194 0.962 1.002 0.116 4.315-3.360 100.00 1859 96 0.0917 387.272 385.063 1.003 1.002 0.097 3.356-2.611 100.00 3867 181 0.1101 254.418 252.420 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0920 168.656 167.975 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.363 82.663 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.523 36.111 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 23.012 21.543 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=-0.0088 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1132 r_free=0.1319 After: r_work=0.1133 r_free=0.1319 ================================== NQH flips ================================== r_work=0.1133 r_free=0.1319 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=0.1133 r_free=0.1319 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1133 r_free=0.1319 | n_water=453 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1133 r_free=0.1316 | n_water=452 | time (s): 50.370 (total time: 52.900) Filter (q & B) r_work=0.1133 r_free=0.1318 | n_water=451 | time (s): 3.840 (total time: 56.740) Compute maps r_work=0.1133 r_free=0.1318 | n_water=451 | time (s): 1.930 (total time: 58.670) Filter (map) r_work=0.1158 r_free=0.1322 | n_water=355 | time (s): 3.990 (total time: 62.660) Find peaks r_work=0.1158 r_free=0.1322 | n_water=355 | time (s): 0.690 (total time: 63.350) Add new water r_work=0.1198 r_free=0.1369 | n_water=496 | time (s): 3.690 (total time: 67.040) Refine new water occ: r_work=0.1148 r_free=0.1319 adp: r_work=0.1149 r_free=0.1322 occ: r_work=0.1138 r_free=0.1306 adp: r_work=0.1138 r_free=0.1309 occ: r_work=0.1130 r_free=0.1294 adp: r_work=0.1128 r_free=0.1296 ADP+occupancy (water only), MIN, final r_work=0.1128 r_free=0.1296 r_work=0.1128 r_free=0.1296 | n_water=496 | time (s): 208.600 (total time: 275.640) Filter (q & B) r_work=0.1135 r_free=0.1304 | n_water=455 | time (s): 4.000 (total time: 279.640) Filter (dist only) r_work=0.1135 r_free=0.1304 | n_water=453 | time (s): 48.330 (total time: 327.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.743999 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.170826 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 0.1218 0.1357 0.0139 0.004 0.7 6.1 0.0 0.0 0 0.087 0.1171 0.1326 0.0155 0.004 0.8 5.8 0.0 0.0 0 0.262 0.1152 0.1314 0.0162 0.005 0.9 5.1 0.5 0.0 0 0.523 0.1143 0.1309 0.0166 0.006 1.0 5.1 0.5 0.0 0 0.785 0.1137 0.1305 0.0168 0.007 1.1 4.5 0.5 0.0 0 1.046 0.1135 0.1304 0.0169 0.007 1.1 4.5 0.5 0.0 0 1.308 0.1135 0.1304 0.0170 0.007 1.1 4.5 0.5 0.0 0 1.570 0.1134 0.1304 0.0170 0.008 1.1 4.5 0.5 0.0 0 1.831 0.1140 0.1306 0.0166 0.006 1.0 4.8 0.5 0.0 0 0.872 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1134 0.1304 0.0170 0.008 1.1 4.5 0.5 0.0 0 1.831 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.34 13.04 1.70 3.777 21.237 38.171 3.608 11.34 13.04 1.70 3.777 21.237 1.145 3.608 11.34 13.04 1.70 3.777 21.237 4.771 3.608 11.37 13.08 1.71 3.709 21.231 19.085 3.604 11.49 13.31 1.81 3.721 21.204 38.171 3.611 11.38 13.25 1.87 3.750 21.193 57.256 3.603 11.33 13.21 1.88 3.765 21.189 76.342 3.598 11.30 13.19 1.89 3.774 21.186 95.427 3.596 11.27 13.17 1.90 3.782 21.186 114.512 3.593 11.26 13.16 1.90 3.792 21.183 133.598 3.592 11.25 13.18 1.93 3.804 21.177 152.683 3.591 11.25 13.20 1.95 3.818 21.169 171.769 3.591 11.24 13.19 1.95 3.825 21.167 190.854 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: 1.145 Accepted refinement result: 11.34 13.04 1.70 3.777 21.237 1.145 3.608 Individual atomic B min max mean iso aniso Overall: 9.10 115.01 21.20 3.31 236 1744 Protein: 9.10 115.01 17.02 3.31 0 1519 Water: 11.49 76.68 35.19 N/A 236 217 Other: 19.75 26.62 22.09 N/A 0 8 Chain A: 9.10 115.01 19.31 N/A 0 1744 Chain S: 12.70 60.00 35.16 N/A 236 0 Histogram: Values Number of atoms 9.10 - 19.69 1264 19.69 - 30.28 303 30.28 - 40.87 210 40.87 - 51.47 132 51.47 - 62.06 49 62.06 - 72.65 11 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1134 r_free=0.1304 r_work=0.1134 r_free=0.1304 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1134 r_free = 0.1304 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1130 r_free = 0.1299 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1130 r_free= 0.1299 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.606374 | | target function (ml) not normalized (work): 300346.040225 | | target function (ml) not normalized (free): 15827.788886 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1330 0.1383 5.6355 5.6346| | 2: 3.57 - 2.84 1.00 2888 124 0.1040 0.1420 5.1661 5.2424| | 3: 2.83 - 2.48 1.00 2820 163 0.1105 0.1189 4.9635 4.9953| | 4: 2.47 - 2.25 1.00 2825 136 0.0904 0.1020 4.6447 4.6789| | 5: 2.25 - 2.09 1.00 2756 127 0.0874 0.0967 4.5932 4.6441| | 6: 2.09 - 1.97 1.00 2846 113 0.0852 0.0991 4.2746 4.3835| | 7: 1.97 - 1.87 1.00 2787 165 0.0883 0.1107 3.9769 4.0811| | 8: 1.87 - 1.79 1.00 2789 144 0.0919 0.1108 3.8893 3.9919| | 9: 1.79 - 1.72 1.00 2745 138 0.0876 0.1168 3.6468 3.8126| | 10: 1.72 - 1.66 1.00 2831 160 0.0919 0.1194 3.5649 3.7138| | 11: 1.66 - 1.61 1.00 2712 147 0.0863 0.1029 3.495 3.5678| | 12: 1.61 - 1.56 1.00 2773 144 0.0903 0.1152 3.3313 3.4677| | 13: 1.56 - 1.52 1.00 2745 130 0.0946 0.1063 3.3091 3.4123| | 14: 1.52 - 1.48 1.00 2803 134 0.0983 0.1059 3.2424 3.3306| | 15: 1.48 - 1.45 1.00 2738 128 0.1000 0.1236 3.156 3.2763| | 16: 1.45 - 1.42 1.00 2756 161 0.1053 0.1225 3.1369 3.2379| | 17: 1.42 - 1.39 1.00 2785 139 0.1138 0.1290 3.1192 3.2258| | 18: 1.39 - 1.36 1.00 2741 179 0.1198 0.1331 3.1062 3.2393| | 19: 1.36 - 1.34 1.00 2807 134 0.1263 0.1553 3.1135 3.2618| | 20: 1.34 - 1.32 1.00 2696 147 0.1370 0.1455 3.1133 3.1523| | 21: 1.32 - 1.30 1.00 2785 112 0.1469 0.1525 3.115 3.1139| | 22: 1.29 - 1.27 1.00 2704 152 0.1562 0.1991 3.1242 3.2998| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1793 3.1334 3.202| | 24: 1.26 - 1.24 1.00 2744 132 0.1710 0.1829 3.1292 3.2261| | 25: 1.24 - 1.22 1.00 2733 148 0.1880 0.2141 3.1434 3.2608| | 26: 1.22 - 1.21 1.00 2727 135 0.1907 0.1763 3.1488 3.2013| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2169 3.1723 3.1635| | 28: 1.19 - 1.18 1.00 2671 147 0.2201 0.2302 3.1673 3.1731| | 29: 1.18 - 1.16 1.00 2800 134 0.2269 0.2389 3.1497 3.2301| | 30: 1.16 - 1.15 1.00 2739 148 0.2448 0.2449 3.1445 3.1687| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2920 171 0.95 8.90 1.00 0.97 6042.24| | 2: 3.57 - 2.84 2888 124 0.92 12.99 1.01 0.97 6042.24| | 3: 2.83 - 2.48 2820 163 0.89 16.87 0.99 0.97 5040.66| | 4: 2.47 - 2.25 2825 136 0.92 13.74 1.00 0.98 2457.90| | 5: 2.25 - 2.09 2756 127 0.90 15.98 1.01 0.98 2457.90| | 6: 2.09 - 1.97 2846 113 0.92 12.50 1.02 0.98 1406.95| | 7: 1.97 - 1.87 2787 165 0.95 9.25 1.02 0.98 510.62| | 8: 1.87 - 1.79 2789 144 0.93 12.63 1.00 0.98 510.62| | 9: 1.79 - 1.72 2745 138 0.94 10.03 0.98 0.97 290.01| | 10: 1.72 - 1.66 2831 160 0.94 11.15 0.98 0.97 245.83| | 11: 1.66 - 1.61 2712 147 0.93 11.73 0.98 0.97 235.56| | 12: 1.61 - 1.56 2773 144 0.95 8.92 0.99 0.97 138.72| | 13: 1.56 - 1.52 2745 130 0.95 10.46 1.03 0.97 138.72| | 14: 1.52 - 1.48 2803 134 0.94 10.79 1.02 0.98 124.55| | 15: 1.48 - 1.45 2738 128 0.95 9.96 1.02 0.98 98.60| | 16: 1.45 - 1.42 2756 161 0.94 11.13 1.02 0.98 98.60| | 17: 1.42 - 1.39 2785 139 0.95 10.95 1.01 0.98 89.54| | 18: 1.39 - 1.36 2741 179 0.94 11.54 1.01 0.98 84.29| | 19: 1.36 - 1.34 2807 134 0.94 11.89 0.99 0.98 84.29| | 20: 1.34 - 1.32 2696 147 0.94 12.15 0.98 0.97 80.26| | 21: 1.32 - 1.30 2785 112 0.94 13.10 0.98 0.97 79.97| | 22: 1.29 - 1.27 2704 152 0.93 13.65 0.98 0.96 80.37| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.97 0.95 82.41| | 24: 1.26 - 1.24 2744 132 0.92 14.86 0.96 0.95 82.41| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.94 84.38| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.02 0.93 86.57| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.57| | 28: 1.19 - 1.18 2671 147 0.88 20.39 1.01 0.93 90.15| | 29: 1.18 - 1.16 2800 134 0.88 20.50 0.99 0.93 91.49| | 30: 1.16 - 1.15 2739 148 0.86 22.01 0.98 0.93 91.49| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 79.97 max = 6042.24 mean = 924.00| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.52| |phase err.(test): min = 0.00 max = 89.53 mean = 13.50| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1138 0.1130 0.1299 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1447 0.1446 0.1505 n_refl.: 87578 remove outliers: r(all,work,free)=0.1447 0.1446 0.1505 n_refl.: 87578 overall B=-0.00 to atoms: r(all,work,free)=0.1447 0.1445 0.1504 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1130 0.1300 n_refl.: 87578 remove outliers: r(all,work,free)=0.1137 0.1129 0.1300 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 0.4091 286.192 251.990 0.446 0.999 0.298 11.894-9.307 94.12 92 4 0.2341 478.399 461.166 0.859 1.002 0.228 9.237-7.194 98.18 209 7 0.2345 386.761 380.115 0.929 1.002 0.170 7.162-5.571 100.00 427 22 0.2121 296.647 286.664 0.916 1.002 0.150 5.546-4.326 100.00 867 58 0.1134 407.223 402.501 0.962 1.002 0.120 4.315-3.360 100.00 1859 96 0.0908 387.272 385.119 1.004 1.002 0.110 3.356-2.611 100.00 3867 181 0.1091 254.418 252.587 1.010 1.002 0.050 2.608-2.026 99.99 8198 413 0.0916 168.656 168.032 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0887 82.363 82.707 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.523 36.132 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 23.012 21.563 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0096 ================= 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 : 0.2612 0.1958 0.084 5.321 8.8 119.3 19.9 258 0.000 1_bss: 0.1634 0.1792 0.084 5.321 9.0 119.5 20.1 258 0.000 1_settarget: 0.1634 0.1792 0.084 5.321 9.0 119.5 20.1 258 0.000 1_nqh: 0.1634 0.1792 0.084 5.321 9.0 119.5 20.1 258 0.000 1_weight: 0.1634 0.1792 0.084 5.321 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1225 0.1466 0.007 0.904 9.0 119.5 20.1 258 0.133 1_adp: 0.1232 0.1462 0.007 0.904 9.1 119.4 20.1 258 0.133 1_regHadp: 0.1233 0.1466 0.007 0.904 9.1 119.4 20.1 258 0.133 1_occ: 0.1227 0.1460 0.007 0.904 9.1 119.4 20.1 258 0.133 2_bss: 0.1226 0.1453 0.007 0.904 9.1 119.5 20.1 258 0.133 2_settarget: 0.1226 0.1453 0.007 0.904 9.1 119.5 20.1 258 0.133 2_updatecdl: 0.1226 0.1453 0.007 0.912 9.1 119.5 20.1 258 0.133 2_nqh: 0.1228 0.1453 0.007 0.912 9.1 119.5 20.1 258 0.136 2_sol: 0.1202 0.1397 0.007 0.912 9.1 115.0 22.2 421 n/a 2_weight: 0.1202 0.1397 0.007 0.912 9.1 115.0 22.2 421 n/a 2_xyzrec: 0.1194 0.1418 0.006 0.829 9.1 115.0 22.2 421 n/a 2_adp: 0.1195 0.1418 0.006 0.829 9.1 115.0 22.2 421 n/a 2_regHadp: 0.1195 0.1418 0.006 0.829 9.1 115.0 22.2 421 n/a 2_occ: 0.1196 0.1415 0.006 0.829 9.1 115.0 22.2 421 n/a 3_bss: 0.1192 0.1410 0.006 0.829 9.1 115.0 22.2 421 n/a 3_settarget: 0.1192 0.1410 0.006 0.829 9.1 115.0 22.2 421 n/a 3_updatecdl: 0.1192 0.1410 0.006 0.829 9.1 115.0 22.2 421 n/a 3_nqh: 0.1192 0.1410 0.006 0.829 9.1 115.0 22.2 421 n/a 3_sol: 0.1211 0.1410 0.006 0.829 9.1 115.0 21.4 442 n/a 3_weight: 0.1211 0.1410 0.006 0.829 9.1 115.0 21.4 442 n/a 3_xyzrec: 0.1151 0.1316 0.008 1.089 9.1 115.0 21.4 442 n/a 3_adp: 0.1151 0.1316 0.008 1.089 9.1 115.0 21.4 442 n/a 3_regHadp: 0.1151 0.1316 0.008 1.089 9.1 115.0 21.4 442 n/a 3_occ: 0.1142 0.1318 0.008 1.089 9.1 115.0 21.4 442 n/a 4_bss: 0.1135 0.1317 0.008 1.089 9.1 115.0 21.4 442 n/a 4_settarget: 0.1135 0.1317 0.008 1.089 9.1 115.0 21.4 442 n/a 4_updatecdl: 0.1135 0.1317 0.008 1.093 9.1 115.0 21.4 442 n/a 4_nqh: 0.1135 0.1317 0.008 1.093 9.1 115.0 21.4 442 n/a 4_sol: 0.1140 0.1318 0.008 1.093 9.1 115.0 21.2 453 n/a 4_weight: 0.1140 0.1318 0.008 1.093 9.1 115.0 21.2 453 n/a 4_xyzrec: 0.1142 0.1321 0.007 1.056 9.1 115.0 21.2 453 n/a 4_adp: 0.1142 0.1321 0.007 1.056 9.1 115.0 21.2 453 n/a 4_regHadp: 0.1142 0.1321 0.007 1.056 9.1 115.0 21.2 453 n/a 4_occ: 0.1136 0.1318 0.007 1.056 9.1 115.0 21.2 453 n/a 5_bss: 0.1132 0.1319 0.007 1.056 9.1 115.0 21.2 453 n/a 5_settarget: 0.1132 0.1319 0.007 1.056 9.1 115.0 21.2 453 n/a 5_updatecdl: 0.1132 0.1319 0.007 1.056 9.1 115.0 21.2 453 n/a 5_setrh: 0.1133 0.1319 0.007 1.056 9.1 115.0 21.2 453 n/a 5_nqh: 0.1133 0.1319 0.007 1.056 9.1 115.0 21.2 453 n/a 5_sol: 0.1135 0.1304 0.007 1.056 9.1 115.0 21.2 453 n/a 5_weight: 0.1135 0.1304 0.007 1.056 9.1 115.0 21.2 453 n/a 5_xyzrec: 0.1134 0.1304 0.008 1.088 9.1 115.0 21.2 453 n/a 5_adp: 0.1134 0.1304 0.008 1.088 9.1 115.0 21.2 453 n/a 5_regHadp: 0.1134 0.1304 0.008 1.088 9.1 115.0 21.2 453 n/a 5_occ: 0.1130 0.1299 0.008 1.088 9.1 115.0 21.2 453 n/a end: 0.1129 0.1300 0.008 1.088 9.1 115.0 21.2 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5155044_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5155044_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.5700 Refinement macro-cycles (run) : 14189.0000 Write final files (write_after_run_outputs) : 73.0700 Total : 14265.6400 Total CPU time: 3.97 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:18:10 PST -0800 (1735366690.75 s) Start R-work = 0.1634, R-free = 0.1792 Final R-work = 0.1129, R-free = 0.1300 =============================================================================== Job complete usr+sys time: 14405.51 seconds wall clock time: 261 minutes 40.19 seconds (15700.19 seconds total)