Starting phenix.refine on Sat Dec 28 21:06:34 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_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5155044.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5155044.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } 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 } } 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: 2.34, per 1000 atoms: 0.69 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: 0.65 Conformation dependent library (CDL) restraints added in 219.1 milliseconds Time building geometry restraints manager: 0.81 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 2.450 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 2.450 ... (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 } 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 } } 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 = 25.530820 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 0.1208 0.1459 0.0251 0.007 0.9 1.0 0.5 0.0 0 12.765 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 14.59 2.51 3.013 19.050 2008.977 0.017 12.38 15.25 2.87 3.346 19.645 2008.977 0.016 Individual atomic B min max mean iso aniso Overall: 8.80 118.16 21.20 2.92 0 1785 Protein: 8.80 118.16 18.02 2.92 0 1519 Water: 11.29 114.49 39.68 N/A 0 258 Other: 23.34 37.88 29.98 N/A 0 8 Chain A: 8.80 118.16 21.20 N/A 0 1785 Histogram: Values Number of atoms 8.80 - 19.74 1210 19.74 - 30.67 228 30.67 - 41.61 158 41.61 - 52.55 99 52.55 - 63.48 55 63.48 - 74.42 19 74.42 - 85.35 9 85.35 - 96.29 2 96.29 - 107.23 2 107.23 - 118.16 3 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1525 r_work=0.1242 r_free=0.1531 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1242 r_free = 0.1531 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1242 r_free = 0.1537 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 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= 0.1242 r_free= 0.1537 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015326 | | target function (ls_wunit_k1) not normalized (work): 1276.632506 | | target function (ls_wunit_k1) not normalized (free): 114.300845 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1256 0.1242 0.1537 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1704 0.1703 0.1766 n_refl.: 87593 remove outliers: r(all,work,free)=0.1704 0.1703 0.1766 n_refl.: 87593 overall B=0.11 to atoms: r(all,work,free)=0.1722 0.1722 0.1779 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1255 0.1241 0.1528 n_refl.: 87593 remove outliers: r(all,work,free)=0.1255 0.1241 0.1528 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 0.3597 298.430 278.186 0.629 1.002 0.374 11.894-9.307 99.02 97 4 0.1625 478.069 466.398 0.907 1.002 0.370 9.237-7.194 100.00 213 7 0.1812 391.001 386.325 0.950 1.003 0.340 7.162-5.571 100.00 427 22 0.1682 293.425 288.602 0.925 1.003 0.253 5.546-4.326 100.00 867 58 0.0898 402.800 400.436 0.950 1.003 0.204 4.315-3.360 100.00 1859 96 0.0764 383.065 382.198 0.997 1.002 0.190 3.356-2.611 100.00 3867 181 0.1025 251.654 250.958 0.998 1.002 0.090 2.608-2.026 99.99 8198 413 0.0985 166.824 166.155 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1211 81.468 81.634 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1642 36.126 35.590 1.007 0.998 0.000 1.221-1.150 99.97 13689 708 0.2352 22.762 21.271 0.971 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0429 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1241 r_free=0.1528 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1242 r_free=0.1530 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1242 r_free=0.1530 | n_water=258 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1251 r_free=0.1528 | n_water=252 | time (s): 25.890 (total time: 28.380) Filter (q & B) r_work=0.1254 r_free=0.1527 | n_water=249 | time (s): 3.770 (total time: 32.150) Compute maps r_work=0.1254 r_free=0.1527 | n_water=249 | time (s): 1.920 (total time: 34.070) Filter (map) r_work=0.1282 r_free=0.1543 | n_water=232 | time (s): 3.930 (total time: 38.000) Find peaks r_work=0.1282 r_free=0.1543 | n_water=232 | time (s): 0.710 (total time: 38.710) Add new water r_work=0.1435 r_free=0.1707 | n_water=447 | time (s): 3.860 (total time: 42.570) Refine new water occ: r_work=0.1330 r_free=0.1544 adp: r_work=0.1252 r_free=0.1496 occ: r_work=0.1265 r_free=0.1484 adp: r_work=0.1231 r_free=0.1468 occ: r_work=0.1234 r_free=0.1459 adp: r_work=0.1226 r_free=0.1455 ADP+occupancy (water only), MIN, final r_work=0.1226 r_free=0.1455 r_work=0.1226 r_free=0.1455 | n_water=447 | time (s): 148.960 (total time: 191.530) Filter (q & B) r_work=0.1230 r_free=0.1462 | n_water=429 | time (s): 3.780 (total time: 195.310) Filter (dist only) r_work=0.1230 r_free=0.1462 | n_water=429 | time (s): 40.640 (total time: 235.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.826406 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1550.307608 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 0.1228 0.1494 0.0266 0.007 0.9 1.6 0.5 0.0 0 12.413 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.94 2.66 3.829 23.264 1550.308 0.015 12.10 14.88 2.78 4.194 23.080 1550.308 0.015 Individual atomic B min max mean iso aniso Overall: 8.69 113.27 23.24 2.61 197 1759 Protein: 8.69 113.27 17.78 2.61 0 1519 Water: 10.90 73.05 42.47 N/A 197 232 Other: 23.89 34.96 28.60 N/A 0 8 Chain A: 8.69 113.27 20.50 N/A 0 1759 Chain S: 15.97 70.83 47.68 N/A 197 0 Histogram: Values Number of atoms 8.69 - 19.15 1200 19.15 - 29.61 250 29.61 - 40.06 187 40.06 - 50.52 139 50.52 - 60.98 106 60.98 - 71.44 61 71.44 - 81.90 7 81.90 - 92.36 2 92.36 - 102.82 2 102.82 - 113.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1488 r_work=0.1210 r_free=0.1488 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1488 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1212 r_free = 0.1480 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 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= 0.1212 r_free= 0.1480 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014083 | | target function (ls_wunit_k1) not normalized (work): 1173.086079 | | target function (ls_wunit_k1) not normalized (free): 99.045440 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1225 0.1212 0.1480 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1620 0.1616 0.1733 n_refl.: 87592 remove outliers: r(all,work,free)=0.1620 0.1616 0.1733 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1626 0.1622 0.1737 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1222 0.1209 0.1476 n_refl.: 87592 remove outliers: r(all,work,free)=0.1220 0.1207 0.1476 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3335 291.140 271.702 0.616 0.939 0.350 11.894-9.307 99.02 97 4 0.1606 478.069 473.127 0.976 0.940 0.333 9.237-7.194 100.00 213 7 0.1674 391.001 391.814 1.045 0.940 0.280 7.162-5.571 100.00 427 22 0.1494 293.425 289.242 0.999 0.940 0.229 5.546-4.326 100.00 867 58 0.0811 402.800 400.579 1.020 0.941 0.210 4.315-3.360 100.00 1859 96 0.0719 383.065 381.933 1.067 0.941 0.200 3.356-2.611 100.00 3867 181 0.0961 251.654 251.101 1.072 0.942 0.062 2.608-2.026 99.99 8198 413 0.0962 166.824 166.415 1.082 0.943 0.000 2.025-1.573 100.00 17313 902 0.1195 81.468 81.652 1.087 0.945 0.000 1.573-1.221 100.00 36679 1900 0.1640 36.126 35.618 1.070 0.947 0.000 1.221-1.150 99.97 13689 708 0.2363 22.762 21.316 1.026 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0601 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1207 r_free=0.1476 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1207 r_free=0.1476 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1207 r_free=0.1476 | n_water=429 | time (s): 2.280 (total time: 2.280) Filter (dist) r_work=0.1208 r_free=0.1475 | n_water=426 | time (s): 42.530 (total time: 44.810) Filter (q & B) r_work=0.1208 r_free=0.1475 | n_water=426 | time (s): 1.180 (total time: 45.990) Compute maps r_work=0.1208 r_free=0.1475 | n_water=426 | time (s): 1.680 (total time: 47.670) Filter (map) r_work=0.1248 r_free=0.1500 | n_water=300 | time (s): 3.220 (total time: 50.890) Find peaks r_work=0.1248 r_free=0.1500 | n_water=300 | time (s): 0.710 (total time: 51.600) Add new water r_work=0.1368 r_free=0.1592 | n_water=493 | time (s): 3.470 (total time: 55.070) Refine new water occ: r_work=0.1267 r_free=0.1501 adp: r_work=0.1268 r_free=0.1502 occ: r_work=0.1245 r_free=0.1483 adp: r_work=0.1243 r_free=0.1482 occ: r_work=0.1230 r_free=0.1478 adp: r_work=0.1223 r_free=0.1471 ADP+occupancy (water only), MIN, final r_work=0.1223 r_free=0.1471 r_work=0.1223 r_free=0.1471 | n_water=493 | time (s): 178.730 (total time: 233.800) Filter (q & B) r_work=0.1228 r_free=0.1472 | n_water=451 | time (s): 3.130 (total time: 236.930) Filter (dist only) r_work=0.1228 r_free=0.1472 | n_water=451 | time (s): 34.490 (total time: 271.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.135711 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 53.309339 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 0.1234 0.1445 0.0211 0.006 0.9 3.2 0.5 0.0 0 1.068 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.34 14.45 2.11 3.648 22.323 53.309 3.733 12.08 13.88 1.79 4.184 22.126 53.309 3.649 Individual atomic B min max mean iso aniso Overall: 9.22 108.69 21.92 2.38 222 1756 Protein: 9.22 108.69 17.32 2.38 0 1519 Water: 11.52 72.03 37.31 N/A 222 229 Other: 19.62 31.08 25.76 N/A 0 8 Chain A: 9.22 108.69 20.00 N/A 0 1756 Chain S: 15.96 66.58 37.08 N/A 222 0 Histogram: Values Number of atoms 9.22 - 19.17 1227 19.17 - 29.11 267 29.11 - 39.06 215 39.06 - 49.01 149 49.01 - 58.95 82 58.95 - 68.90 25 68.90 - 78.85 7 78.85 - 88.79 2 88.79 - 98.74 2 98.74 - 108.69 2 =========================== Idealize ADP of riding H ========================== r_work=0.1208 r_free=0.1388 r_work=0.1209 r_free=0.1388 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1388 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1385 target_work(ml) = 3.646 | | 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.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1203 r_free= 0.1385 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.645723 | | target function (ml) not normalized (work): 303659.580994 | | target function (ml) not normalized (free): 16041.859993 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1203 0.1385 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1537 0.1536 0.1592 n_refl.: 87588 remove outliers: r(all,work,free)=0.1537 0.1536 0.1592 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1536 0.1535 0.1591 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1196 0.1374 n_refl.: 87588 remove outliers: r(all,work,free)=0.1202 0.1193 0.1374 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3930 287.783 256.436 0.479 0.999 0.320 11.894-9.307 97.06 95 4 0.2283 471.468 454.708 0.860 1.001 0.272 9.237-7.194 98.18 209 7 0.2241 382.560 386.997 0.961 1.001 0.210 7.162-5.571 100.00 427 22 0.1962 293.425 284.980 0.926 1.001 0.185 5.546-4.326 100.00 867 58 0.1065 402.800 398.576 0.961 1.002 0.175 4.315-3.360 100.00 1859 96 0.0920 383.065 380.507 1.002 1.002 0.173 3.356-2.611 100.00 3867 181 0.1151 251.654 249.963 1.007 1.002 0.081 2.608-2.026 99.99 8198 413 0.1048 166.824 165.871 1.020 1.002 0.000 2.025-1.573 100.00 17313 902 0.1020 81.468 81.604 1.035 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1295 36.126 35.670 1.026 1.002 0.000 1.221-1.150 99.97 13689 708 0.2130 22.762 21.285 0.980 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0193 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1374 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1374 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1374 | n_water=451 | time (s): 1.930 (total time: 1.930) Filter (dist) r_work=0.1193 r_free=0.1372 | n_water=449 | time (s): 40.590 (total time: 42.520) Filter (q & B) r_work=0.1193 r_free=0.1372 | n_water=449 | time (s): 0.870 (total time: 43.390) Compute maps r_work=0.1193 r_free=0.1372 | n_water=449 | time (s): 1.520 (total time: 44.910) Filter (map) r_work=0.1215 r_free=0.1369 | n_water=314 | time (s): 3.580 (total time: 48.490) Find peaks r_work=0.1215 r_free=0.1369 | n_water=314 | time (s): 0.570 (total time: 49.060) Add new water r_work=0.1281 r_free=0.1437 | n_water=479 | time (s): 2.950 (total time: 52.010) Refine new water occ: r_work=0.1209 r_free=0.1361 adp: r_work=0.1208 r_free=0.1361 occ: r_work=0.1194 r_free=0.1350 adp: r_work=0.1192 r_free=0.1348 occ: r_work=0.1184 r_free=0.1346 adp: r_work=0.1180 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1342 r_work=0.1180 r_free=0.1342 | n_water=479 | time (s): 210.320 (total time: 262.330) Filter (q & B) r_work=0.1188 r_free=0.1347 | n_water=435 | time (s): 2.420 (total time: 264.750) Filter (dist only) r_work=0.1188 r_free=0.1346 | n_water=434 | time (s): 37.170 (total time: 301.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.988028 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.634264 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 0.1194 0.1360 0.0166 0.006 1.0 2.9 0.5 0.0 0 0.994 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.60 1.66 3.465 21.606 50.634 3.635 11.82 13.55 1.74 3.751 21.518 50.634 3.623 Individual atomic B min max mean iso aniso Overall: 9.30 104.69 21.38 2.23 206 1755 Protein: 9.30 104.69 17.12 2.23 0 1519 Water: 11.65 71.12 36.24 N/A 206 228 Other: 19.38 28.30 24.26 N/A 0 8 Chain A: 9.30 104.69 19.74 N/A 0 1755 Chain S: 16.14 58.32 35.38 N/A 206 0 Histogram: Values Number of atoms 9.30 - 18.84 1223 18.84 - 28.38 275 28.38 - 37.92 207 37.92 - 47.45 135 47.45 - 56.99 77 56.99 - 66.53 29 66.53 - 76.07 10 76.07 - 85.61 2 85.61 - 95.15 1 95.15 - 104.69 2 =========================== Idealize ADP of riding H ========================== r_work=0.1182 r_free=0.1355 r_work=0.1182 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1182 r_free = 0.1356 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1178 r_free = 0.1354 target_work(ml) = 3.622 | | 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.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1178 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621930 | | target function (ml) not normalized (work): 301648.812355 | | target function (ml) not normalized (free): 15941.434140 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1187 0.1178 0.1354 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1511 0.1510 0.1551 n_refl.: 87580 remove outliers: r(all,work,free)=0.1511 0.1510 0.1551 n_refl.: 87580 overall B=-0.02 to atoms: r(all,work,free)=0.1507 0.1507 0.1549 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1185 0.1176 0.1351 n_refl.: 87580 remove outliers: r(all,work,free)=0.1183 0.1174 0.1351 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3958 283.083 260.312 0.457 1.000 0.293 11.894-9.307 93.14 91 4 0.2307 472.231 447.522 0.834 1.001 0.275 9.237-7.194 98.18 209 7 0.2450 382.560 376.321 0.917 1.002 0.174 7.162-5.571 100.00 427 22 0.2113 293.425 283.293 0.910 1.002 0.150 5.546-4.326 100.00 867 58 0.1102 402.800 398.917 0.952 1.002 0.139 4.315-3.360 100.00 1859 96 0.0929 383.065 380.906 0.994 1.002 0.133 3.356-2.611 100.00 3867 181 0.1137 251.654 250.123 1.001 1.002 0.053 2.608-2.026 99.99 8198 413 0.1019 166.824 165.995 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0979 81.468 81.731 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.126 35.755 1.023 0.998 0.000 1.221-1.150 99.97 13689 708 0.2122 22.762 21.401 0.981 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0492 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1174 r_free=0.1351 After: r_work=0.1175 r_free=0.1351 ================================== NQH flips ================================== r_work=0.1175 r_free=0.1351 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=0.1175 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1175 r_free=0.1351 | n_water=434 | time (s): 1.940 (total time: 1.940) Filter (dist) r_work=0.1175 r_free=0.1351 | n_water=434 | time (s): 38.080 (total time: 40.020) Filter (q & B) r_work=0.1175 r_free=0.1351 | n_water=432 | time (s): 2.990 (total time: 43.010) Compute maps r_work=0.1175 r_free=0.1351 | n_water=432 | time (s): 1.470 (total time: 44.480) Filter (map) r_work=0.1198 r_free=0.1361 | n_water=336 | time (s): 2.880 (total time: 47.360) Find peaks r_work=0.1198 r_free=0.1361 | n_water=336 | time (s): 0.480 (total time: 47.840) Add new water r_work=0.1251 r_free=0.1407 | n_water=498 | time (s): 3.080 (total time: 50.920) Refine new water occ: r_work=0.1185 r_free=0.1337 adp: r_work=0.1185 r_free=0.1339 occ: r_work=0.1174 r_free=0.1329 adp: r_work=0.1172 r_free=0.1330 occ: r_work=0.1165 r_free=0.1324 adp: r_work=0.1162 r_free=0.1323 ADP+occupancy (water only), MIN, final r_work=0.1162 r_free=0.1323 r_work=0.1162 r_free=0.1323 | n_water=498 | time (s): 156.510 (total time: 207.430) Filter (q & B) r_work=0.1170 r_free=0.1335 | n_water=456 | time (s): 2.840 (total time: 210.270) Filter (dist only) r_work=0.1170 r_free=0.1332 | n_water=454 | time (s): 39.750 (total time: 250.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.870141 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.524364 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 0.1196 0.1355 0.0159 0.007 1.0 4.2 0.5 0.0 0 0.935 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.55 1.59 3.354 21.416 45.524 3.629 12.01 13.60 1.60 3.611 21.345 45.524 3.623 Individual atomic B min max mean iso aniso Overall: 9.28 100.87 21.33 2.09 229 1752 Protein: 9.28 100.87 16.90 2.09 0 1519 Water: 11.45 70.20 36.09 N/A 229 225 Other: 19.41 27.40 23.54 N/A 0 8 Chain A: 9.28 100.87 19.45 N/A 0 1752 Chain S: 15.38 58.42 35.66 N/A 229 0 Histogram: Values Number of atoms 9.28 - 18.44 1214 18.44 - 27.60 278 27.60 - 36.76 207 36.76 - 45.92 163 45.92 - 55.07 71 55.07 - 64.23 28 64.23 - 73.39 15 73.39 - 82.55 1 82.55 - 91.71 2 91.71 - 100.87 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1360 r_work=0.1201 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1360 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1363 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1200 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623462 | | target function (ml) not normalized (work): 301758.327336 | | target function (ml) not normalized (free): 15940.592833 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1404 0.1361 5.6771 5.594| | 2: 3.57 - 2.84 1.00 2888 124 0.1110 0.1470 5.1817 5.2523| | 3: 2.83 - 2.48 1.00 2820 163 0.1223 0.1291 4.9884 5.0159| | 4: 2.47 - 2.25 1.00 2825 136 0.1030 0.1075 4.6919 4.7086| | 5: 2.25 - 2.09 1.00 2756 127 0.1002 0.1152 4.6334 4.71| | 6: 2.09 - 1.97 1.00 2846 113 0.0982 0.1213 4.3467 4.4984| | 7: 1.97 - 1.87 1.00 2787 165 0.1015 0.1215 4.0821 4.1866| | 8: 1.87 - 1.79 1.00 2789 144 0.1046 0.1300 3.9995 4.0895| | 9: 1.79 - 1.72 1.00 2745 138 0.0966 0.1327 3.7237 3.9036| | 10: 1.72 - 1.66 1.00 2831 160 0.1017 0.1241 3.6445 3.7639| | 11: 1.66 - 1.61 1.00 2712 147 0.0969 0.1116 3.576 3.6345| | 12: 1.61 - 1.56 1.00 2773 144 0.0927 0.1160 3.3595 3.4946| | 13: 1.56 - 1.52 1.00 2745 130 0.1005 0.1075 3.3541 3.4438| | 14: 1.52 - 1.48 1.00 2803 134 0.1008 0.1124 3.2722 3.342| | 15: 1.48 - 1.45 1.00 2738 128 0.1033 0.1363 3.1825 3.3371| | 16: 1.45 - 1.42 1.00 2756 161 0.1092 0.1253 3.1642 3.2525| | 17: 1.42 - 1.39 1.00 2785 139 0.1134 0.1295 3.1227 3.2456| | 18: 1.39 - 1.36 1.00 2741 179 0.1167 0.1385 3.0935 3.2789| | 19: 1.36 - 1.34 1.00 2807 134 0.1230 0.1616 3.1001 3.2719| | 20: 1.34 - 1.32 1.00 2696 147 0.1322 0.1460 3.0917 3.1351| | 21: 1.32 - 1.30 1.00 2785 112 0.1419 0.1640 3.0895 3.1625| | 22: 1.29 - 1.27 1.00 2704 152 0.1484 0.1904 3.0906 3.2852| | 23: 1.27 - 1.26 1.00 2802 156 0.1574 0.1862 3.1027 3.212| | 24: 1.26 - 1.24 1.00 2744 132 0.1625 0.1769 3.0936 3.1986| | 25: 1.24 - 1.22 1.00 2733 148 0.1791 0.2322 3.1091 3.2945| | 26: 1.22 - 1.21 1.00 2727 135 0.1862 0.1795 3.122 3.1992| | 27: 1.21 - 1.19 1.00 2814 148 0.2011 0.2086 3.1391 3.146| | 28: 1.19 - 1.18 1.00 2671 147 0.2146 0.2312 3.1383 3.1612| | 29: 1.18 - 1.16 1.00 2800 134 0.2224 0.2362 3.1277 3.2227| | 30: 1.16 - 1.15 1.00 2739 148 0.2380 0.2494 3.1152 3.1625| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2917 171 0.95 8.73 1.00 0.97 5865.19| | 2: 3.57 - 2.84 2888 124 0.92 12.83 1.01 0.97 5865.19| | 3: 2.83 - 2.48 2820 163 0.89 16.93 0.99 0.97 4927.73| | 4: 2.47 - 2.25 2825 136 0.91 14.18 1.00 0.98 2510.30| | 5: 2.25 - 2.09 2756 127 0.90 16.38 1.01 0.98 2510.30| | 6: 2.09 - 1.97 2846 113 0.92 13.42 1.02 0.98 1495.22| | 7: 1.97 - 1.87 2787 165 0.94 10.83 1.02 0.98 629.49| | 8: 1.87 - 1.79 2789 144 0.91 14.44 1.00 0.98 629.49| | 9: 1.79 - 1.72 2745 138 0.93 11.56 0.98 0.97 343.24| | 10: 1.72 - 1.66 2831 160 0.93 12.38 0.98 0.97 285.91| | 11: 1.66 - 1.61 2712 147 0.93 13.01 0.98 0.97 272.98| | 12: 1.61 - 1.56 2773 144 0.95 9.69 0.99 0.97 151.02| | 13: 1.56 - 1.52 2745 130 0.94 11.30 1.02 0.97 151.02| | 14: 1.52 - 1.48 2803 134 0.94 11.49 1.02 0.97 134.81| | 15: 1.48 - 1.45 2738 128 0.95 10.60 1.02 0.98 105.13| | 16: 1.45 - 1.42 2756 161 0.94 11.78 1.02 0.98 105.13| | 17: 1.42 - 1.39 2785 139 0.94 11.60 1.01 0.98 94.76| | 18: 1.39 - 1.36 2741 179 0.94 11.91 1.01 0.98 88.76| | 19: 1.36 - 1.34 2807 134 0.94 12.49 1.00 0.98 88.76| | 20: 1.34 - 1.32 2696 147 0.94 12.57 0.99 0.97 83.25| | 21: 1.32 - 1.30 2785 112 0.93 13.46 0.99 0.97 82.87| | 22: 1.29 - 1.27 2704 152 0.93 14.02 0.99 0.96 82.95| | 23: 1.27 - 1.26 2802 156 0.92 14.91 0.98 0.95 83.36| | 24: 1.26 - 1.24 2744 132 0.92 15.06 0.97 0.95 83.36| | 25: 1.24 - 1.22 2733 148 0.91 16.40 0.96 0.94 84.78| | 26: 1.22 - 1.21 2727 135 0.90 18.15 1.03 0.94 86.35| | 27: 1.21 - 1.19 2814 148 0.89 18.81 1.02 0.94 86.35| | 28: 1.19 - 1.18 2671 147 0.88 20.25 1.01 0.93 89.48| | 29: 1.18 - 1.16 2800 134 0.88 20.58 0.99 0.93 90.66| | 30: 1.16 - 1.15 2739 148 0.86 22.01 0.98 0.93 90.66| |alpha: min = 0.93 max = 0.98 mean = 0.97| |beta: min = 82.87 max = 5865.19 mean = 928.80| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 14.04| |phase err.(test): min = 0.00 max = 89.79 mean = 14.14| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1200 0.1363 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1522 0.1521 0.1579 n_refl.: 87575 remove outliers: r(all,work,free)=0.1522 0.1521 0.1579 n_refl.: 87575 overall B=-0.02 to atoms: r(all,work,free)=0.1519 0.1517 0.1576 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1200 0.1368 n_refl.: 87575 remove outliers: r(all,work,free)=0.1208 0.1200 0.1368 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 0.4017 283.083 253.249 0.440 0.999 0.298 11.894-9.307 93.14 91 4 0.2388 472.231 454.631 0.848 1.000 0.212 9.237-7.194 97.73 208 7 0.2511 382.084 376.389 0.907 1.000 0.140 7.162-5.571 100.00 427 22 0.2208 293.425 282.012 0.900 1.001 0.110 5.546-4.326 100.00 867 58 0.1178 402.800 397.821 0.952 1.001 0.110 4.315-3.360 100.00 1859 96 0.0983 383.065 380.681 0.996 1.001 0.110 3.356-2.611 100.00 3867 181 0.1185 251.654 249.671 1.001 1.001 0.053 2.608-2.026 99.99 8198 413 0.1044 166.824 165.778 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0993 81.468 81.700 1.028 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1240 36.126 35.772 1.022 1.000 0.000 1.221-1.150 99.97 13689 708 0.2118 22.762 21.368 0.978 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0558 ================= 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: 0.1208 0.1459 0.007 0.948 9.0 119.5 20.1 258 0.124 1_adp: 0.1239 0.1525 0.007 0.948 8.8 118.2 21.2 258 0.124 1_regHadp: 0.1242 0.1531 0.007 0.948 8.8 118.2 21.2 258 0.124 1_occ: 0.1242 0.1537 0.007 0.948 8.8 118.2 21.2 258 0.124 2_bss: 0.1241 0.1528 0.007 0.948 8.9 118.3 21.3 258 0.124 2_settarget: 0.1241 0.1528 0.007 0.948 8.9 118.3 21.3 258 0.124 2_updatecdl: 0.1241 0.1528 0.007 0.955 8.9 118.3 21.3 258 0.124 2_nqh: 0.1242 0.1530 0.007 0.955 8.9 118.3 21.3 258 0.127 2_sol: 0.1230 0.1462 0.007 0.955 8.9 118.3 23.6 429 n/a 2_weight: 0.1230 0.1462 0.007 0.955 8.9 118.3 23.6 429 n/a 2_xyzrec: 0.1228 0.1494 0.007 0.880 8.9 118.3 23.6 429 n/a 2_adp: 0.1210 0.1488 0.007 0.880 8.7 113.3 23.2 429 n/a 2_regHadp: 0.1210 0.1488 0.007 0.880 8.7 113.3 23.2 429 n/a 2_occ: 0.1212 0.1480 0.007 0.880 8.7 113.3 23.2 429 n/a 3_bss: 0.1207 0.1476 0.007 0.880 8.7 113.3 23.3 429 n/a 3_settarget: 0.1207 0.1476 0.007 0.880 8.7 113.3 23.3 429 n/a 3_updatecdl: 0.1207 0.1476 0.007 0.883 8.7 113.3 23.3 429 n/a 3_nqh: 0.1207 0.1476 0.007 0.883 8.7 113.3 23.3 429 n/a 3_sol: 0.1228 0.1472 0.007 0.883 8.7 113.3 22.3 451 n/a 3_weight: 0.1228 0.1472 0.007 0.883 8.7 113.3 22.3 451 n/a 3_xyzrec: 0.1234 0.1445 0.006 0.923 8.7 113.3 22.3 451 n/a 3_adp: 0.1208 0.1388 0.006 0.923 9.2 108.7 21.9 451 n/a 3_regHadp: 0.1209 0.1388 0.006 0.923 9.2 108.7 21.9 451 n/a 3_occ: 0.1203 0.1385 0.006 0.923 9.2 108.7 21.9 451 n/a 4_bss: 0.1193 0.1374 0.006 0.923 9.2 108.7 21.9 451 n/a 4_settarget: 0.1193 0.1374 0.006 0.923 9.2 108.7 21.9 451 n/a 4_updatecdl: 0.1193 0.1374 0.006 0.923 9.2 108.7 21.9 451 n/a 4_nqh: 0.1193 0.1374 0.006 0.923 9.2 108.7 21.9 451 n/a 4_sol: 0.1188 0.1346 0.006 0.923 9.2 108.7 21.5 434 n/a 4_weight: 0.1188 0.1346 0.006 0.923 9.2 108.7 21.5 434 n/a 4_xyzrec: 0.1194 0.1360 0.006 0.958 9.2 108.7 21.5 434 n/a 4_adp: 0.1182 0.1355 0.006 0.958 9.3 104.7 21.4 434 n/a 4_regHadp: 0.1182 0.1356 0.006 0.958 9.3 104.7 21.4 434 n/a 4_occ: 0.1178 0.1354 0.006 0.958 9.3 104.7 21.4 434 n/a 5_bss: 0.1174 0.1351 0.006 0.958 9.3 104.7 21.4 434 n/a 5_settarget: 0.1174 0.1351 0.006 0.958 9.3 104.7 21.4 434 n/a 5_updatecdl: 0.1174 0.1351 0.006 0.957 9.3 104.7 21.4 434 n/a 5_setrh: 0.1175 0.1351 0.006 0.957 9.3 104.7 21.4 434 n/a 5_nqh: 0.1175 0.1351 0.006 0.957 9.3 104.7 21.4 434 n/a 5_sol: 0.1170 0.1332 0.006 0.957 9.3 104.7 21.5 454 n/a 5_weight: 0.1170 0.1332 0.006 0.957 9.3 104.7 21.5 454 n/a 5_xyzrec: 0.1196 0.1355 0.007 1.022 9.3 104.7 21.5 454 n/a 5_adp: 0.1201 0.1360 0.007 1.022 9.3 100.9 21.3 454 n/a 5_regHadp: 0.1201 0.1360 0.007 1.022 9.3 100.9 21.3 454 n/a 5_occ: 0.1200 0.1363 0.007 1.022 9.3 100.9 21.3 454 n/a end: 0.1200 0.1368 0.007 1.022 9.3 100.9 21.3 454 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5155044_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5155044_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8300 Refinement macro-cycles (run) : 3516.2300 Write final files (write_after_run_outputs) : 65.8600 Total : 3586.9200 Total CPU time: 60.41 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:22 PST -0800 (1735452682.01 s) Start R-work = 0.1634, R-free = 0.1792 Final R-work = 0.1200, R-free = 0.1368 =============================================================================== Job complete usr+sys time: 3726.59 seconds wall clock time: 66 minutes 35.39 seconds (3995.39 seconds total)