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_6847832.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6847832.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6847832.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_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): 0.02s 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: 2.37, per 1000 atoms: 0.70 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: 0.88 Conformation dependent library (CDL) restraints added in 296.1 milliseconds Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.61 - 0.89: 371 0.89 - 1.16: 1258 1.16 - 1.44: 696 1.44 - 1.71: 812 1.71 - 1.99: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.236 1.009 0.227 1.15e-02 7.56e+03 3.90e+02 bond pdb=" C ILE A 105 " pdb=" O ILE A 105 " ideal model delta sigma weight residual 1.236 1.430 -0.194 9.90e-03 1.02e+04 3.86e+02 bond pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " ideal model delta sigma weight residual 1.326 1.535 -0.209 1.10e-02 8.26e+03 3.61e+02 bond pdb=" C ALA A 104 " pdb=" O ALA A 104 " ideal model delta sigma weight residual 1.234 1.014 0.220 1.18e-02 7.18e+03 3.47e+02 bond pdb=" C BLYS A 93 " pdb=" O BLYS A 93 " ideal model delta sigma weight residual 1.237 1.457 -0.221 1.19e-02 7.06e+03 3.43e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.45: 3029 4.45 - 8.90: 1892 8.90 - 13.35: 700 13.35 - 17.80: 132 17.80 - 22.26: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 118 " pdb=" C GLY A 118 " pdb=" N PHE A 119 " ideal model delta sigma weight residual 122.54 107.69 14.85 1.02e+00 9.61e-01 2.12e+02 angle pdb=" O ALA A 79 " pdb=" C ALA A 79 " pdb=" N AGLN A 80 " ideal model delta sigma weight residual 122.07 136.61 -14.54 1.03e+00 9.43e-01 1.99e+02 angle pdb=" O BTYR A 67 " pdb=" C BTYR A 67 " pdb=" N ASP A 68 " ideal model delta sigma weight residual 123.24 107.34 15.90 1.23e+00 6.61e-01 1.67e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.80 107.28 14.52 1.13e+00 7.83e-01 1.65e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.60 -10.37 8.10e-01 1.52e+00 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 941 17.65 - 35.29: 113 35.29 - 52.93: 45 52.93 - 70.58: 9 70.58 - 88.22: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -158.29 -21.71 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual -180.00 -159.79 -20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA CYS A 106 " pdb=" C CYS A 106 " pdb=" N ALA A 107 " pdb=" CA ALA A 107 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.227: 116 0.227 - 0.453: 75 0.453 - 0.678: 34 0.678 - 0.904: 14 0.904 - 1.129: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 3.56 -1.13 2.00e-01 2.50e+01 3.19e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.53 1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CA GLN A 95 " pdb=" N GLN A 95 " pdb=" C GLN A 95 " pdb=" CB GLN A 95 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.48e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.135 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.112 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.070 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.064 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.026 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG TYR A 139 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.095 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.098 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.061 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.098 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.104 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.021 2.00e-02 2.50e+03 6.54e-02 1.28e+02 pdb=" CG TYR A 141 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.122 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.077 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.108 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.048 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.082 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 619 2.25 - 2.84: 7586 2.84 - 3.42: 10750 3.42 - 4.01: 15382 4.01 - 4.60: 22268 Nonbonded interactions: 56605 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.662 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.798 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.821 2.450 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.838 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.865 2.450 ... (remaining 56600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } 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_6847832_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2603 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789943 | | target function (ml) not normalized (work): 232418.969773 | | target function (ml) not normalized (free): 11838.504851 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3034 0.2077 7.0875 4.9372| | 2: 3.57 - 2.84 1.00 2876 122 0.2446 0.1672 4.3449 4.3155| | 3: 2.84 - 2.48 1.00 2833 165 0.2342 0.1819 4.1244 4.1679| | 4: 2.47 - 2.25 1.00 2825 136 0.2317 0.1417 3.8257 3.8175| | 5: 2.25 - 2.09 1.00 2756 127 0.2461 0.1550 3.7874 3.8036| | 6: 2.09 - 1.97 1.00 2846 113 0.2514 0.1716 3.4542 3.5266| | 7: 1.97 - 1.87 1.00 2787 165 0.2547 0.1659 3.1239 3.1095| | 8: 1.87 - 1.79 1.00 2789 144 0.2475 0.1863 3.0478 3.1129| | 9: 1.79 - 1.72 1.00 2745 138 0.2402 0.1940 2.8787 3.0135| | 10: 1.72 - 1.66 1.00 2789 158 0.2436 0.2045 2.8149 2.9135| | 11: 1.66 - 1.61 1.00 2740 147 0.2511 0.1831 2.752 2.7503| | 12: 1.61 - 1.56 1.00 2787 146 0.2525 0.1993 2.6358 2.6764| | 13: 1.56 - 1.52 1.00 2745 130 0.2544 0.1923 2.56 2.6722| | 14: 1.52 - 1.48 1.00 2803 134 0.2504 0.2041 2.4985 2.5724| | 15: 1.48 - 1.45 1.00 2738 128 0.2630 0.2073 2.419 2.4842| | 16: 1.45 - 1.42 1.00 2756 161 0.2617 0.2102 2.3884 2.4317| | 17: 1.42 - 1.39 1.00 2785 139 0.2665 0.2469 2.3258 2.4371| | 18: 1.39 - 1.36 1.00 2741 179 0.2643 0.2363 2.2905 2.4019| | 19: 1.36 - 1.34 1.00 2807 134 0.2608 0.2342 2.2504 2.3712| | 20: 1.34 - 1.32 1.00 2696 147 0.2711 0.2341 2.2031 2.2296| | 21: 1.32 - 1.30 1.00 2785 112 0.2695 0.2103 2.1552 2.1362| | 22: 1.29 - 1.27 1.00 2704 152 0.2694 0.2452 2.1285 2.1698| | 23: 1.27 - 1.26 1.00 2802 156 0.2743 0.2342 2.0969 2.1437| | 24: 1.26 - 1.24 1.00 2744 132 0.2770 0.2628 2.0649 2.1743| | 25: 1.24 - 1.22 1.00 2734 148 0.2868 0.2492 2.0429 2.041| | 26: 1.22 - 1.21 1.00 2727 135 0.2886 0.2471 2.0234 2.1134| | 27: 1.21 - 1.19 1.00 2814 148 0.3008 0.2605 2.0219 2.0054| | 28: 1.19 - 1.18 1.00 2671 147 0.3051 0.2843 1.9988 2.0419| | 29: 1.18 - 1.16 1.00 2800 134 0.3006 0.2767 1.9659 2.0496| | 30: 1.16 - 1.15 1.00 2740 148 0.3045 0.2692 1.9301 1.9021| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.69 0.76 0.23 1457.91| | 2: 3.57 - 2.84 2876 122 0.80 25.99 1.27 0.23 1457.91| | 3: 2.84 - 2.48 2833 165 0.74 31.68 1.24 0.24 1208.53| | 4: 2.47 - 2.25 2825 136 0.81 25.36 1.25 0.25 561.36| | 5: 2.25 - 2.09 2756 127 0.77 29.05 1.28 0.25 561.36| | 6: 2.09 - 1.97 2846 113 0.84 22.31 1.29 0.25 306.72| | 7: 1.97 - 1.87 2787 165 0.90 16.40 1.29 0.26 89.55| | 8: 1.87 - 1.79 2789 144 0.86 20.75 1.26 0.26 89.55| | 9: 1.79 - 1.72 2745 138 0.88 18.61 1.23 0.26 55.98| | 10: 1.72 - 1.66 2789 158 0.86 20.33 1.23 0.25 49.26| | 11: 1.66 - 1.61 2740 147 0.85 21.68 1.24 0.25 47.57| | 12: 1.61 - 1.56 2787 146 0.88 18.69 1.23 0.25 30.49| | 13: 1.56 - 1.52 2745 130 0.86 20.86 1.24 0.25 30.49| | 14: 1.52 - 1.48 2803 134 0.86 20.96 1.22 0.25 27.42| | 15: 1.48 - 1.45 2738 128 0.86 21.08 1.24 0.25 21.81| | 16: 1.45 - 1.42 2756 161 0.85 22.04 1.23 0.25 21.81| | 17: 1.42 - 1.39 2785 139 0.86 21.62 1.23 0.25 18.68| | 18: 1.39 - 1.36 2741 179 0.86 21.74 1.22 0.25 16.87| | 19: 1.36 - 1.34 2807 134 0.85 22.65 1.21 0.25 16.87| | 20: 1.34 - 1.32 2696 147 0.86 21.68 1.21 0.25 13.81| | 21: 1.32 - 1.30 2785 112 0.85 22.67 1.21 0.25 13.60| | 22: 1.29 - 1.27 2704 152 0.85 22.85 1.21 0.24 13.24| | 23: 1.27 - 1.26 2802 156 0.85 22.60 1.21 0.24 11.40| | 24: 1.26 - 1.24 2744 132 0.84 23.50 1.21 0.24 11.40| | 25: 1.24 - 1.22 2734 148 0.84 24.26 1.20 0.24 10.76| | 26: 1.22 - 1.21 2727 135 0.84 24.22 1.20 0.23 10.04| | 27: 1.21 - 1.19 2814 148 0.83 24.99 1.21 0.23 10.04| | 28: 1.19 - 1.18 2671 147 0.82 25.56 1.19 0.23 9.33| | 29: 1.18 - 1.16 2800 134 0.82 25.90 1.16 0.22 9.06| | 30: 1.16 - 1.15 2740 148 0.81 27.15 1.14 0.22 9.06| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.06 max = 1457.91 mean = 212.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.86| |phase err.(test): min = 0.00 max = 89.91 mean = 22.91| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.227 1557 Z= 5.392 Angle : 5.351 17.239 2118 Z= 3.755 Chirality : 0.369 1.129 243 Planarity : 0.030 0.111 284 Dihedral : 14.223 88.220 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.32 % Favored : 95.14 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 29.73 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.47), residues: 224 helix: -3.19 (0.35), residues: 102 sheet: -0.39 (0.96), residues: 28 loop : -0.30 (0.55), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.084 0.015 ARG A 98 TYR 0.099 0.044 TYR A 141 PHE 0.104 0.043 PHE A 119 HIS 0.067 0.025 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2603 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789943 | | target function (ml) not normalized (work): 232418.969773 | | target function (ml) not normalized (free): 11838.504851 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2562 0.2603 0.1940 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2562 0.2603 0.1940 n_refl.: 87602 remove outliers: r(all,work,free)=0.1971 0.1975 0.1940 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.1998 0.2002 0.1955 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1634 0.1627 0.1763 n_refl.: 87594 remove outliers: r(all,work,free)=0.1633 0.1626 0.1763 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3857 386.214 358.750 0.669 1.002 0.407 11.894-9.307 99.02 97 4 0.1820 613.482 590.998 0.925 1.003 0.385 9.237-7.194 100.00 213 7 0.2118 501.753 490.824 0.947 1.004 0.349 7.162-5.571 100.00 427 22 0.2154 376.538 364.866 0.928 1.004 0.288 5.546-4.326 100.00 867 58 0.1289 516.893 512.052 0.962 1.004 0.234 4.315-3.360 100.00 1859 96 0.1144 491.569 487.594 1.006 1.003 0.209 3.356-2.611 100.00 3867 181 0.1436 322.936 319.686 0.995 1.002 0.057 2.608-2.026 99.99 8198 413 0.1339 214.077 211.864 1.005 1.001 0.000 2.025-1.573 100.00 17313 902 0.1627 104.544 104.017 1.015 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2044 46.359 44.992 1.004 0.994 0.000 1.221-1.150 99.97 13689 708 0.2624 29.209 26.902 0.977 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0493 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1626 r_free=0.1763 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1628 r_free=0.1764 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.782727 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1997.902904 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1215 0.1470 0.0255 0.007 0.9 0.6 0.5 0.0 0 11.891 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.15 14.70 2.55 3.013 19.074 1997.903 0.017 12.38 15.39 3.01 3.115 19.509 1997.903 0.016 Individual atomic B min max mean iso aniso Overall: 8.43 118.34 20.92 2.87 0 1785 Protein: 8.43 118.34 17.82 2.87 0 1519 Water: 11.12 114.87 38.93 N/A 0 258 Other: 22.58 35.50 28.58 N/A 0 8 Chain A: 8.43 118.34 20.92 N/A 0 1785 Histogram: Values Number of atoms 8.43 - 19.42 1208 19.42 - 30.41 230 30.41 - 41.40 164 41.40 - 52.39 102 52.39 - 63.38 52 63.38 - 74.38 18 74.38 - 85.37 4 85.37 - 96.36 4 96.36 - 107.35 0 107.35 - 118.34 3 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1540 r_work=0.1243 r_free=0.1543 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1243 r_free = 0.1543 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 = 0.1544 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.29 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= 0.1544 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015414 | | target function (ls_wunit_k1) not normalized (work): 1283.912426 | | target function (ls_wunit_k1) not normalized (free): 114.780597 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1257 0.1242 0.1544 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1699 0.1698 0.1768 n_refl.: 87593 remove outliers: r(all,work,free)=0.1699 0.1698 0.1768 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1720 0.1719 0.1783 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1255 0.1240 0.1539 n_refl.: 87593 remove outliers: r(all,work,free)=0.1254 0.1240 0.1539 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 0.3626 298.620 277.403 0.688 0.923 0.380 11.894-9.307 99.02 97 4 0.1612 478.373 466.435 0.985 0.924 0.380 9.237-7.194 100.00 213 7 0.1826 391.250 385.764 1.029 0.924 0.340 7.162-5.571 100.00 427 22 0.1725 293.611 288.176 0.998 0.925 0.258 5.546-4.326 100.00 867 58 0.0926 403.056 400.337 1.030 0.926 0.214 4.315-3.360 100.00 1859 96 0.0782 383.309 382.341 1.077 0.927 0.200 3.356-2.611 100.00 3867 181 0.1022 251.814 251.094 1.076 0.929 0.110 2.608-2.026 99.99 8198 413 0.0974 166.930 166.357 1.083 0.933 0.000 2.025-1.573 100.00 17313 902 0.1201 81.520 81.713 1.085 0.939 0.000 1.573-1.221 100.00 36679 1900 0.1640 36.149 35.621 1.059 0.948 0.000 1.221-1.150 99.97 13689 708 0.2356 22.777 21.317 1.013 0.956 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0481 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1240 r_free=0.1539 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1243 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1243 r_free=0.1540 | n_water=258 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1252 r_free=0.1538 | n_water=252 | time (s): 28.070 (total time: 30.470) Filter (q & B) r_work=0.1255 r_free=0.1537 | n_water=249 | time (s): 3.720 (total time: 34.190) Compute maps r_work=0.1255 r_free=0.1537 | n_water=249 | time (s): 1.870 (total time: 36.060) Filter (map) r_work=0.1274 r_free=0.1543 | n_water=235 | time (s): 3.830 (total time: 39.890) Find peaks r_work=0.1274 r_free=0.1543 | n_water=235 | time (s): 0.750 (total time: 40.640) Add new water r_work=0.1427 r_free=0.1695 | n_water=451 | time (s): 3.870 (total time: 44.510) Refine new water occ: r_work=0.1328 r_free=0.1560 adp: r_work=0.1252 r_free=0.1518 occ: r_work=0.1263 r_free=0.1506 adp: r_work=0.1230 r_free=0.1499 occ: r_work=0.1232 r_free=0.1488 adp: r_work=0.1222 r_free=0.1490 ADP+occupancy (water only), MIN, final r_work=0.1222 r_free=0.1490 r_work=0.1222 r_free=0.1490 | n_water=451 | time (s): 83.840 (total time: 128.350) Filter (q & B) r_work=0.1226 r_free=0.1491 | n_water=431 | time (s): 4.120 (total time: 132.470) Filter (dist only) r_work=0.1226 r_free=0.1491 | n_water=431 | time (s): 42.030 (total time: 174.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.545164 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1505.014208 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 0.1225 0.1510 0.0286 0.007 0.9 2.2 0.5 0.0 0 13.273 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 15.10 2.86 3.775 23.100 1505.014 0.015 11.99 14.82 2.83 4.092 22.942 1505.014 0.015 Individual atomic B min max mean iso aniso Overall: 8.70 114.52 23.15 2.59 196 1762 Protein: 8.70 114.52 17.66 2.59 0 1519 Water: 10.95 72.74 42.34 N/A 196 235 Other: 26.12 37.00 30.84 N/A 0 8 Chain A: 8.70 114.52 20.35 N/A 0 1762 Chain S: 17.22 71.30 48.33 N/A 196 0 Histogram: Values Number of atoms 8.70 - 19.28 1204 19.28 - 29.86 250 29.86 - 40.44 195 40.44 - 51.03 137 51.03 - 61.61 120 61.61 - 72.19 41 72.19 - 82.78 5 82.78 - 93.36 3 93.36 - 103.94 1 103.94 - 114.52 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1482 r_work=0.1199 r_free=0.1481 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1481 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1479 target_work(ls_wunit_k1) = 0.014 | | 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= 0.1199 r_free= 0.1479 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013855 | | target function (ls_wunit_k1) not normalized (work): 1154.096389 | | target function (ls_wunit_k1) not normalized (free): 102.021838 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1199 0.1479 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1605 0.1600 0.1725 n_refl.: 87592 remove outliers: r(all,work,free)=0.1605 0.1600 0.1725 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1611 0.1607 0.1729 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1196 0.1478 n_refl.: 87592 remove outliers: r(all,work,free)=0.1208 0.1195 0.1478 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3358 294.562 270.493 0.639 0.939 0.368 11.894-9.307 99.02 97 4 0.1450 478.373 476.670 0.983 0.939 0.360 9.237-7.194 100.00 213 7 0.1657 391.250 392.033 1.044 0.939 0.280 7.162-5.571 100.00 427 22 0.1467 293.611 289.974 1.003 0.939 0.232 5.546-4.326 100.00 867 58 0.0845 403.056 400.657 1.023 0.940 0.219 4.315-3.360 100.00 1859 96 0.0710 383.309 382.222 1.068 0.940 0.218 3.356-2.611 100.00 3867 181 0.0949 251.814 251.096 1.074 0.941 0.072 2.608-2.026 99.99 8198 413 0.0963 166.930 166.504 1.080 0.942 0.000 2.025-1.573 100.00 17313 902 0.1180 81.520 81.703 1.088 0.944 0.000 1.573-1.221 100.00 36679 1900 0.1608 36.149 35.657 1.071 0.947 0.000 1.221-1.150 99.97 13689 708 0.2341 22.777 21.312 1.026 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0598 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1478 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1195 r_free=0.1479 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1479 | n_water=431 | time (s): 1.890 (total time: 1.890) Filter (dist) r_work=0.1195 r_free=0.1479 | n_water=430 | time (s): 37.690 (total time: 39.580) Filter (q & B) r_work=0.1195 r_free=0.1479 | n_water=430 | time (s): 1.060 (total time: 40.640) Compute maps r_work=0.1195 r_free=0.1479 | n_water=430 | time (s): 1.430 (total time: 42.070) Filter (map) r_work=0.1238 r_free=0.1480 | n_water=289 | time (s): 3.390 (total time: 45.460) Find peaks r_work=0.1238 r_free=0.1480 | n_water=289 | time (s): 0.500 (total time: 45.960) Add new water r_work=0.1369 r_free=0.1613 | n_water=483 | time (s): 2.440 (total time: 48.400) Refine new water occ: r_work=0.1263 r_free=0.1516 adp: r_work=0.1264 r_free=0.1518 occ: r_work=0.1240 r_free=0.1498 adp: r_work=0.1238 r_free=0.1497 occ: r_work=0.1223 r_free=0.1490 adp: r_work=0.1216 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1216 r_free=0.1485 r_work=0.1216 r_free=0.1485 | n_water=483 | time (s): 262.000 (total time: 310.400) Filter (q & B) r_work=0.1221 r_free=0.1487 | n_water=444 | time (s): 3.620 (total time: 314.020) Filter (dist only) r_work=0.1221 r_free=0.1487 | n_water=444 | time (s): 36.240 (total time: 350.260) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.084197 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 32.022177 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 0.1226 0.1437 0.0211 0.006 0.9 1.9 0.5 0.0 0 1.042 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.37 2.11 3.614 22.099 32.022 3.720 12.27 14.06 1.78 4.097 21.915 32.022 3.663 Individual atomic B min max mean iso aniso Overall: 9.23 109.59 21.64 2.25 212 1759 Protein: 9.23 109.59 17.25 2.25 0 1519 Water: 11.57 71.98 36.54 N/A 212 232 Other: 22.08 32.57 27.80 N/A 0 8 Chain A: 9.23 109.59 19.90 N/A 0 1759 Chain S: 15.49 63.92 36.11 N/A 212 0 Histogram: Values Number of atoms 9.23 - 19.27 1231 19.27 - 29.30 281 29.30 - 39.34 217 39.34 - 49.38 132 49.38 - 59.41 77 59.41 - 69.45 20 69.45 - 79.49 7 79.49 - 89.52 3 89.52 - 99.56 1 99.56 - 109.59 2 =========================== Idealize ADP of riding H ========================== r_work=0.1227 r_free=0.1406 r_work=0.1229 r_free=0.1407 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1229 r_free = 0.1407 target_work(ml) = 3.663 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1225 r_free = 0.1407 target_work(ml) = 3.661 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1225 r_free= 0.1407 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.660997 | | target function (ml) not normalized (work): 304935.463728 | | target function (ml) not normalized (free): 16082.934776 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1225 0.1407 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1550 0.1549 0.1603 n_refl.: 87589 remove outliers: r(all,work,free)=0.1550 0.1549 0.1603 n_refl.: 87589 overall B=-0.02 to atoms: r(all,work,free)=0.1548 0.1546 0.1601 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1225 0.1217 0.1378 n_refl.: 87589 remove outliers: r(all,work,free)=0.1222 0.1214 0.1378 n_refl.: 87582 ======================== 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 0.4013 289.162 263.492 0.486 1.000 0.320 11.894-9.307 97.06 95 4 0.2340 471.768 461.259 0.862 1.002 0.280 9.237-7.194 98.18 209 7 0.2317 382.803 385.952 0.951 1.002 0.170 7.162-5.571 100.00 427 22 0.2011 293.611 283.838 0.912 1.002 0.168 5.546-4.326 100.00 867 58 0.1110 403.056 398.276 0.953 1.002 0.167 4.315-3.360 100.00 1859 96 0.0945 383.309 380.493 0.995 1.002 0.160 3.356-2.611 100.00 3867 181 0.1161 251.814 249.737 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1068 166.930 165.800 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1037 81.520 81.662 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1316 36.149 35.710 1.021 0.999 0.000 1.221-1.150 99.97 13689 708 0.2141 22.777 21.388 0.982 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0423 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1214 r_free=0.1378 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1214 r_free=0.1378 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1214 r_free=0.1378 | n_water=444 | time (s): 1.650 (total time: 1.650) Filter (dist) r_work=0.1214 r_free=0.1377 | n_water=442 | time (s): 42.780 (total time: 44.430) Filter (q & B) r_work=0.1214 r_free=0.1377 | n_water=441 | time (s): 2.680 (total time: 47.110) Compute maps r_work=0.1214 r_free=0.1377 | n_water=441 | time (s): 1.300 (total time: 48.410) Filter (map) r_work=0.1239 r_free=0.1382 | n_water=313 | time (s): 2.540 (total time: 50.950) Find peaks r_work=0.1239 r_free=0.1382 | n_water=313 | time (s): 0.460 (total time: 51.410) Add new water r_work=0.1307 r_free=0.1448 | n_water=478 | time (s): 2.480 (total time: 53.890) Refine new water occ: r_work=0.1232 r_free=0.1392 adp: r_work=0.1233 r_free=0.1393 occ: r_work=0.1216 r_free=0.1385 adp: r_work=0.1214 r_free=0.1384 occ: r_work=0.1204 r_free=0.1381 adp: r_work=0.1200 r_free=0.1378 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1378 r_work=0.1200 r_free=0.1378 | n_water=478 | time (s): 159.220 (total time: 213.110) Filter (q & B) r_work=0.1209 r_free=0.1381 | n_water=439 | time (s): 2.760 (total time: 215.870) Filter (dist only) r_work=0.1209 r_free=0.1380 | n_water=438 | time (s): 37.210 (total time: 253.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.858003 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.388347 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 0.1213 0.1382 0.0169 0.006 0.9 1.6 0.5 0.0 0 0.929 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 13.82 1.69 3.403 21.513 47.388 3.650 11.93 13.74 1.81 4.064 21.320 47.388 3.623 Individual atomic B min max mean iso aniso Overall: 9.21 104.58 21.11 2.17 209 1756 Protein: 9.21 104.58 16.78 2.17 0 1519 Water: 11.42 69.66 36.05 N/A 209 229 Other: 19.97 29.43 24.42 N/A 0 8 Chain A: 9.21 104.58 19.32 N/A 0 1756 Chain S: 14.47 62.70 36.15 N/A 209 0 Histogram: Values Number of atoms 9.21 - 18.74 1233 18.74 - 28.28 271 28.28 - 37.82 210 37.82 - 47.36 139 47.36 - 56.89 72 56.89 - 66.43 28 66.43 - 75.97 7 75.97 - 85.50 2 85.50 - 95.04 1 95.04 - 104.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1374 r_work=0.1193 r_free=0.1375 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1375 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1372 target_work(ml) = 3.622 | | 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.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1187 r_free= 0.1372 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621524 | | target function (ml) not normalized (work): 301622.274606 | | target function (ml) not normalized (free): 15938.936550 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1187 0.1372 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1521 0.1520 0.1578 n_refl.: 87582 remove outliers: r(all,work,free)=0.1521 0.1520 0.1578 n_refl.: 87582 overall B=-0.02 to atoms: r(all,work,free)=0.1518 0.1516 0.1576 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1186 0.1374 n_refl.: 87582 remove outliers: r(all,work,free)=0.1194 0.1184 0.1374 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.4095 291.720 251.077 0.443 1.001 0.320 11.894-9.307 96.08 94 4 0.2274 473.681 454.649 0.839 1.002 0.320 9.237-7.194 97.73 208 7 0.2425 383.877 377.554 0.914 1.002 0.135 7.162-5.571 100.00 427 22 0.2180 293.611 282.180 0.899 1.002 0.130 5.546-4.326 100.00 867 58 0.1155 403.056 398.784 0.953 1.002 0.130 4.315-3.360 100.00 1859 96 0.0967 383.309 381.047 0.995 1.002 0.130 3.356-2.611 100.00 3867 181 0.1160 251.814 249.880 1.002 1.002 0.043 2.608-2.026 99.99 8198 413 0.1034 166.930 166.073 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0967 81.520 81.799 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1237 36.149 35.789 1.023 0.998 0.000 1.221-1.150 99.97 13689 708 0.2116 22.777 21.417 0.982 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0515 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1185 r_free=0.1374 After: r_work=0.1185 r_free=0.1374 ================================== NQH flips ================================== r_work=0.1185 r_free=0.1374 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1185 r_free=0.1374 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1374 | n_water=438 | time (s): 1.840 (total time: 1.840) Filter (dist) r_work=0.1185 r_free=0.1373 | n_water=437 | time (s): 39.330 (total time: 41.170) Filter (q & B) r_work=0.1185 r_free=0.1373 | n_water=437 | time (s): 0.910 (total time: 42.080) Compute maps r_work=0.1185 r_free=0.1373 | n_water=437 | time (s): 1.260 (total time: 43.340) Filter (map) r_work=0.1213 r_free=0.1391 | n_water=323 | time (s): 2.650 (total time: 45.990) Find peaks r_work=0.1213 r_free=0.1391 | n_water=323 | time (s): 0.520 (total time: 46.510) Add new water r_work=0.1262 r_free=0.1440 | n_water=467 | time (s): 3.030 (total time: 49.540) Refine new water occ: r_work=0.1197 r_free=0.1386 adp: r_work=0.1198 r_free=0.1388 occ: r_work=0.1186 r_free=0.1376 adp: r_work=0.1185 r_free=0.1376 occ: r_work=0.1177 r_free=0.1368 adp: r_work=0.1174 r_free=0.1367 ADP+occupancy (water only), MIN, final r_work=0.1174 r_free=0.1367 r_work=0.1174 r_free=0.1367 | n_water=467 | time (s): 223.100 (total time: 272.640) Filter (q & B) r_work=0.1182 r_free=0.1375 | n_water=432 | time (s): 2.830 (total time: 275.470) Filter (dist only) r_work=0.1189 r_free=0.1374 | n_water=430 | time (s): 38.760 (total time: 314.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.965084 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.202978 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 0.1214 0.1391 0.0177 0.007 1.0 2.2 0.5 0.0 0 0.983 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 13.91 1.77 3.256 20.843 48.203 3.630 12.12 13.89 1.77 3.363 20.810 48.203 3.623 Individual atomic B min max mean iso aniso Overall: 9.29 100.86 20.74 2.01 203 1754 Protein: 9.29 100.86 16.68 2.01 0 1519 Water: 11.32 69.00 35.02 N/A 203 227 Other: 20.39 28.42 24.51 N/A 0 8 Chain A: 9.29 100.86 19.18 N/A 0 1754 Chain S: 14.98 58.82 34.20 N/A 203 0 Histogram: Values Number of atoms 9.29 - 18.45 1220 18.45 - 27.60 282 27.60 - 36.76 215 36.76 - 45.92 129 45.92 - 55.07 71 55.07 - 64.23 24 64.23 - 73.39 11 73.39 - 82.55 2 82.55 - 91.70 1 91.70 - 100.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1212 r_free=0.1389 r_work=0.1212 r_free=0.1389 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1212 r_free = 0.1389 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1389 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1210 r_free= 0.1389 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 3.622631 | | target function (ml) not normalized (work): 301703.616687 | | target function (ml) not normalized (free): 15937.255766 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1452 0.1463 5.719 5.6537| | 2: 3.57 - 2.84 1.00 2888 124 0.1146 0.1524 5.2165 5.2795| | 3: 2.83 - 2.48 1.00 2820 163 0.1244 0.1302 5.0192 5.0313| | 4: 2.47 - 2.25 1.00 2825 136 0.1048 0.1160 4.7196 4.7716| | 5: 2.25 - 2.09 1.00 2756 127 0.1016 0.1085 4.6608 4.7225| | 6: 2.09 - 1.97 1.00 2846 113 0.0989 0.1235 4.3647 4.4897| | 7: 1.97 - 1.87 1.00 2787 165 0.1001 0.1260 4.084 4.2034| | 8: 1.87 - 1.79 1.00 2789 144 0.1030 0.1254 3.9995 4.0811| | 9: 1.79 - 1.72 1.00 2745 138 0.0953 0.1295 3.7143 3.8834| | 10: 1.72 - 1.66 1.00 2831 160 0.1007 0.1225 3.6336 3.7529| | 11: 1.66 - 1.61 1.00 2712 147 0.0965 0.1141 3.5679 3.6236| | 12: 1.61 - 1.56 1.00 2773 144 0.0914 0.1163 3.3441 3.4711| | 13: 1.56 - 1.52 1.00 2745 130 0.0971 0.1115 3.3377 3.4594| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1107 3.259 3.3357| | 15: 1.48 - 1.45 1.00 2738 128 0.0999 0.1322 3.1624 3.3097| | 16: 1.45 - 1.42 1.00 2756 161 0.1057 0.1252 3.1466 3.2402| | 17: 1.42 - 1.39 1.00 2785 139 0.1112 0.1295 3.1085 3.2203| | 18: 1.39 - 1.36 1.00 2741 179 0.1145 0.1364 3.0792 3.2573| | 19: 1.36 - 1.34 1.00 2807 134 0.1199 0.1597 3.0834 3.2624| | 20: 1.34 - 1.32 1.00 2696 147 0.1304 0.1445 3.0784 3.1231| | 21: 1.32 - 1.30 1.00 2785 112 0.1410 0.1605 3.0796 3.1556| | 22: 1.29 - 1.27 1.00 2704 152 0.1462 0.1883 3.0773 3.2807| | 23: 1.27 - 1.26 1.00 2802 156 0.1569 0.1848 3.0971 3.2113| | 24: 1.26 - 1.24 1.00 2744 132 0.1616 0.1762 3.0879 3.1856| | 25: 1.24 - 1.22 1.00 2733 148 0.1792 0.2303 3.1052 3.2883| | 26: 1.22 - 1.21 1.00 2727 135 0.1849 0.1768 3.1189 3.1901| | 27: 1.21 - 1.19 1.00 2814 148 0.2006 0.2104 3.1382 3.1484| | 28: 1.19 - 1.18 1.00 2671 147 0.2136 0.2282 3.1368 3.1555| | 29: 1.18 - 1.16 1.00 2800 134 0.2215 0.2384 3.1245 3.2261| | 30: 1.16 - 1.15 1.00 2739 148 0.2375 0.2484 3.1155 3.1594| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2921 171 0.94 9.28 1.00 0.97 6416.45| | 2: 3.57 - 2.84 2888 124 0.92 13.58 1.01 0.97 6416.45| | 3: 2.83 - 2.48 2820 163 0.88 17.74 0.99 0.97 5378.16| | 4: 2.47 - 2.25 2825 136 0.91 14.82 1.00 0.97 2700.75| | 5: 2.25 - 2.09 2756 127 0.89 17.04 1.01 0.97 2700.75| | 6: 2.09 - 1.97 2846 113 0.91 13.82 1.02 0.97 1586.31| | 7: 1.97 - 1.87 2787 165 0.94 10.90 1.02 0.97 635.84| | 8: 1.87 - 1.79 2789 144 0.91 14.49 1.00 0.97 635.84| | 9: 1.79 - 1.72 2745 138 0.93 11.49 0.98 0.97 340.73| | 10: 1.72 - 1.66 2831 160 0.93 12.26 0.98 0.97 281.63| | 11: 1.66 - 1.61 2712 147 0.93 12.90 0.98 0.97 268.91| | 12: 1.61 - 1.56 2773 144 0.95 9.63 0.99 0.97 148.98| | 13: 1.56 - 1.52 2745 130 0.94 11.20 1.02 0.97 148.98| | 14: 1.52 - 1.48 2803 134 0.94 11.32 1.02 0.97 132.52| | 15: 1.48 - 1.45 2738 128 0.95 10.33 1.01 0.98 102.37| | 16: 1.45 - 1.42 2756 161 0.94 11.54 1.01 0.98 102.37| | 17: 1.42 - 1.39 2785 139 0.94 11.36 1.01 0.98 92.07| | 18: 1.39 - 1.36 2741 179 0.94 11.63 1.01 0.98 86.11| | 19: 1.36 - 1.34 2807 134 0.94 12.20 1.00 0.98 86.11| | 20: 1.34 - 1.32 2696 147 0.94 12.25 0.99 0.96 80.84| | 21: 1.32 - 1.30 2785 112 0.94 13.19 0.98 0.96 80.47| | 22: 1.29 - 1.27 2704 152 0.93 13.69 0.98 0.96 80.68| | 23: 1.27 - 1.26 2802 156 0.93 14.72 0.97 0.94 81.75| | 24: 1.26 - 1.24 2744 132 0.93 14.82 0.97 0.94 81.75| | 25: 1.24 - 1.22 2733 148 0.91 16.26 0.96 0.94 83.45| | 26: 1.22 - 1.21 2727 135 0.90 17.98 1.02 0.93 85.33| | 27: 1.21 - 1.19 2814 148 0.89 18.66 1.02 0.93 85.33| | 28: 1.19 - 1.18 2671 147 0.88 20.16 1.01 0.92 88.92| | 29: 1.18 - 1.16 2800 134 0.88 20.53 0.99 0.92 90.27| | 30: 1.16 - 1.15 2739 148 0.86 21.88 0.98 0.92 90.27| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 80.47 max = 6416.45 mean = 997.52| |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 = 88.99 mean = 14.14| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1210 0.1389 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1538 0.1539 0.1558 n_refl.: 87579 remove outliers: r(all,work,free)=0.1538 0.1539 0.1558 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1536 0.1537 0.1557 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1220 0.1211 0.1392 n_refl.: 87579 remove outliers: r(all,work,free)=0.1219 0.1210 0.1392 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 89.58 81 5 0.4260 287.116 250.066 0.435 1.001 0.304 11.894-9.307 94.12 92 4 0.2240 475.035 461.070 0.847 1.002 0.300 9.237-7.194 97.27 207 7 0.2546 383.403 377.152 0.903 1.002 0.130 7.162-5.571 100.00 427 22 0.2275 293.611 282.693 0.893 1.002 0.130 5.546-4.326 100.00 867 58 0.1239 403.056 398.029 0.953 1.002 0.130 4.315-3.360 100.00 1859 96 0.1022 383.309 380.194 0.994 1.002 0.120 3.356-2.611 100.00 3867 181 0.1204 251.814 249.807 1.002 1.002 0.043 2.608-2.026 99.99 8198 413 0.1062 166.930 165.886 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0985 81.520 81.768 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1220 36.149 35.786 1.018 1.000 0.000 1.221-1.150 99.97 13689 708 0.2112 22.777 21.372 0.974 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0279 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2603 0.1940 0.081 5.351 8.8 119.3 19.9 258 0.000 1_bss: 0.1626 0.1763 0.081 5.351 9.1 119.5 20.1 258 0.000 1_settarget: 0.1626 0.1763 0.081 5.351 9.1 119.5 20.1 258 0.000 1_nqh: 0.1628 0.1764 0.081 5.351 9.1 119.5 20.1 258 0.003 1_weight: 0.1628 0.1764 0.081 5.351 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1215 0.1470 0.007 0.934 9.1 119.5 20.1 258 0.127 1_adp: 0.1239 0.1540 0.007 0.934 8.4 118.3 20.9 258 0.127 1_regHadp: 0.1243 0.1543 0.007 0.934 8.4 118.3 20.9 258 0.127 1_occ: 0.1242 0.1544 0.007 0.934 8.4 118.3 20.9 258 0.127 2_bss: 0.1240 0.1539 0.007 0.934 8.6 118.5 21.0 258 0.127 2_settarget: 0.1240 0.1539 0.007 0.934 8.6 118.5 21.0 258 0.127 2_updatecdl: 0.1240 0.1539 0.007 0.944 8.6 118.5 21.0 258 0.127 2_nqh: 0.1243 0.1540 0.007 0.944 8.6 118.5 21.0 258 0.128 2_sol: 0.1226 0.1491 0.007 0.944 8.6 118.5 23.4 431 n/a 2_weight: 0.1226 0.1491 0.007 0.944 8.6 118.5 23.4 431 n/a 2_xyzrec: 0.1225 0.1510 0.007 0.885 8.6 118.5 23.4 431 n/a 2_adp: 0.1199 0.1482 0.007 0.885 8.7 114.5 23.1 431 n/a 2_regHadp: 0.1199 0.1481 0.007 0.885 8.7 114.5 23.1 431 n/a 2_occ: 0.1199 0.1479 0.007 0.885 8.7 114.5 23.1 431 n/a 3_bss: 0.1195 0.1478 0.007 0.885 8.7 114.6 23.2 431 n/a 3_settarget: 0.1195 0.1478 0.007 0.885 8.7 114.6 23.2 431 n/a 3_updatecdl: 0.1195 0.1478 0.007 0.887 8.7 114.6 23.2 431 n/a 3_nqh: 0.1195 0.1479 0.007 0.887 8.7 114.6 23.2 431 n/a 3_sol: 0.1221 0.1487 0.007 0.887 8.7 114.6 22.0 444 n/a 3_weight: 0.1221 0.1487 0.007 0.887 8.7 114.6 22.0 444 n/a 3_xyzrec: 0.1226 0.1437 0.006 0.926 8.7 114.6 22.0 444 n/a 3_adp: 0.1227 0.1406 0.006 0.926 9.2 109.6 21.6 444 n/a 3_regHadp: 0.1229 0.1407 0.006 0.926 9.2 109.6 21.6 444 n/a 3_occ: 0.1225 0.1407 0.006 0.926 9.2 109.6 21.6 444 n/a 4_bss: 0.1214 0.1378 0.006 0.926 9.2 109.6 21.6 444 n/a 4_settarget: 0.1214 0.1378 0.006 0.926 9.2 109.6 21.6 444 n/a 4_updatecdl: 0.1214 0.1378 0.006 0.923 9.2 109.6 21.6 444 n/a 4_nqh: 0.1214 0.1378 0.006 0.923 9.2 109.6 21.6 444 n/a 4_sol: 0.1209 0.1380 0.006 0.923 9.2 109.6 21.5 438 n/a 4_weight: 0.1209 0.1380 0.006 0.923 9.2 109.6 21.5 438 n/a 4_xyzrec: 0.1213 0.1382 0.006 0.942 9.2 109.6 21.5 438 n/a 4_adp: 0.1193 0.1374 0.006 0.942 9.2 104.6 21.1 438 n/a 4_regHadp: 0.1193 0.1375 0.006 0.942 9.2 104.6 21.1 438 n/a 4_occ: 0.1187 0.1372 0.006 0.942 9.2 104.6 21.1 438 n/a 5_bss: 0.1185 0.1374 0.006 0.942 9.2 104.6 21.1 438 n/a 5_settarget: 0.1185 0.1374 0.006 0.942 9.2 104.6 21.1 438 n/a 5_updatecdl: 0.1185 0.1374 0.006 0.943 9.2 104.6 21.1 438 n/a 5_setrh: 0.1185 0.1374 0.006 0.943 9.2 104.6 21.1 438 n/a 5_nqh: 0.1185 0.1374 0.006 0.943 9.2 104.6 21.1 438 n/a 5_sol: 0.1189 0.1374 0.006 0.943 9.2 104.6 20.8 430 n/a 5_weight: 0.1189 0.1374 0.006 0.943 9.2 104.6 20.8 430 n/a 5_xyzrec: 0.1214 0.1391 0.007 1.033 9.2 104.6 20.8 430 n/a 5_adp: 0.1212 0.1389 0.007 1.033 9.3 100.9 20.7 430 n/a 5_regHadp: 0.1212 0.1389 0.007 1.033 9.3 100.9 20.7 430 n/a 5_occ: 0.1210 0.1389 0.007 1.033 9.3 100.9 20.7 430 n/a end: 0.1210 0.1392 0.007 1.033 9.3 100.9 20.7 430 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6847832_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6847832_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.6400 Refinement macro-cycles (run) : 3563.2600 Write final files (write_after_run_outputs) : 62.1200 Total : 3630.0200 Total CPU time: 61.10 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:23 PST -0800 (1735452743.12 s) Start R-work = 0.1626, R-free = 0.1763 Final R-work = 0.1210, R-free = 0.1392 =============================================================================== Job complete usr+sys time: 3764.33 seconds wall clock time: 67 minutes 32.55 seconds (4052.55 seconds total)