Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9451893.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 Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9451893.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9451893.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 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 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.17, per 1000 atoms: 0.35 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: 0.56 Conformation dependent library (CDL) restraints added in 210.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.77 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: 494 0.91 - 1.17: 1146 1.17 - 1.43: 671 1.43 - 1.69: 816 1.69 - 1.95: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" C SER A 85 " pdb=" O SER A 85 " ideal model delta sigma weight residual 1.236 1.511 -0.275 1.24e-02 6.50e+03 4.91e+02 bond pdb=" C ARG A 5 " pdb=" O ARG A 5 " ideal model delta sigma weight residual 1.235 1.495 -0.260 1.28e-02 6.10e+03 4.13e+02 bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.241 1.054 0.188 9.80e-03 1.04e+04 3.67e+02 bond pdb=" CA ATYR A 67 " pdb=" C ATYR A 67 " ideal model delta sigma weight residual 1.523 1.289 0.234 1.24e-02 6.50e+03 3.56e+02 bond pdb=" C VAL A 70 " pdb=" O VAL A 70 " ideal model delta sigma weight residual 1.237 1.430 -0.193 1.07e-02 8.73e+03 3.26e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.80: 3262 4.80 - 9.61: 1836 9.61 - 14.41: 578 14.41 - 19.21: 94 19.21 - 24.02: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA VAL A 177 " pdb=" C VAL A 177 " pdb=" O VAL A 177 " ideal model delta sigma weight residual 120.85 105.49 15.36 1.06e+00 8.90e-01 2.10e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N BCYS A 53 " ideal model delta sigma weight residual 123.26 138.41 -15.15 1.08e+00 8.57e-01 1.97e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.91 135.44 -13.53 9.80e-01 1.04e+00 1.91e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.26 137.20 -13.94 1.08e+00 8.57e-01 1.67e+02 angle pdb=" CA ILE A 52 " pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 120.39 107.10 13.29 1.05e+00 9.07e-01 1.60e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 1283 15.68 - 31.35: 129 31.35 - 47.03: 45 47.03 - 62.71: 20 62.71 - 78.38: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual 122.80 146.67 -23.87 0 2.50e+00 1.60e-01 9.11e+01 dihedral pdb=" C ASP A 49 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual -122.60 -145.18 22.58 0 2.50e+00 1.60e-01 8.16e+01 dihedral pdb=" N ALYS A 99 " pdb=" C ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual 122.80 143.40 -20.60 0 2.50e+00 1.60e-01 6.79e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 110 0.234 - 0.469: 74 0.469 - 0.703: 40 0.703 - 0.937: 16 0.937 - 1.171: 3 Chirality restraints: 243 Sorted by residual: 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 1.34 1.17 2.00e-01 2.50e+01 3.43e+01 chirality pdb=" CA ALYS A 99 " pdb=" N ALYS A 99 " pdb=" C ALYS A 99 " pdb=" CB ALYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 chirality pdb=" CA ARG A 5 " pdb=" N ARG A 5 " pdb=" C ARG A 5 " pdb=" CB ARG A 5 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.26e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.030 2.00e-02 2.50e+03 7.08e-02 1.13e+02 pdb=" CG HIS A 138 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.022 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.128 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.080 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.097 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.015 2.00e-02 2.50e+03 5.79e-02 1.01e+02 pdb=" CG BTYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.105 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.010 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.084 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.021 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.007 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.090 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.095 2.00e-02 2.50e+03 5.26e-02 8.29e+01 pdb=" CG PHE A 164 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.051 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.073 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.104 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 897 2.29 - 2.87: 7938 2.87 - 3.45: 10599 3.45 - 4.02: 15296 4.02 - 4.60: 21855 Nonbonded interactions: 56585 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.718 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.798 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.798 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.815 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.843 2.450 ... (remaining 56580 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 2 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 } ordered_solvent { low_resolution = 4 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_9451893_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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2790 r_free= 0.1870 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.382426 | | target function (ml) not normalized (work): 71183.738737 | | target function (ml) not normalized (free): 3267.445821 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3200 0.2216 7.4181 5.0512| | 2: 3.63 - 2.88 1.00 2711 122 0.2638 0.1767 4.3395 4.3473| | 3: 2.88 - 2.52 1.00 2682 148 0.2588 0.1766 4.1958 4.2053| | 4: 2.52 - 2.29 1.00 2661 139 0.2524 0.1579 3.4883 3.5782| | 5: 2.29 - 2.13 1.00 2678 122 0.2656 0.1449 3.3839 3.4274| | 6: 2.13 - 2.00 1.00 2692 117 0.2747 0.1948 3.3098 3.3849| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2819 159 0.88 18.04 0.77 0.23 1350.93| | 2: 3.63 - 2.88 2711 122 0.82 24.24 1.31 0.23 1350.93| | 3: 2.88 - 2.52 2682 148 0.72 33.51 1.29 0.23 1350.93| | 4: 2.52 - 2.29 2661 139 0.94 10.95 1.29 0.26 128.94| | 5: 2.29 - 2.13 2678 122 0.92 12.97 1.32 0.26 128.94| | 6: 2.13 - 2.00 2692 117 0.90 15.86 1.34 0.26 128.94| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 128.94 max = 1350.93 mean = 746.74| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.95 mean = 19.27| |phase err.(test): min = 0.00 max = 89.60 mean = 19.51| |-----------------------------------------------------------------------------| ----------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 0.275 1557 Z= 5.352 Angle : 5.186 17.364 2118 Z= 3.623 Chirality : 0.393 1.171 243 Planarity : 0.028 0.076 284 Dihedral : 13.704 78.382 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.62 % Allowed : 2.48 % Favored : 96.89 % 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: -2.64 (0.46), residues: 224 helix: -2.29 (0.38), residues: 108 sheet: -1.39 (0.93), residues: 30 loop : -0.79 (0.56), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.097 0.018 ARG A 28 TYR 0.097 0.044 TYR A 139 PHE 0.113 0.031 PHE A 162 HIS 0.065 0.027 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2790 r_free= 0.1870 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.382426 | | target function (ml) not normalized (work): 71183.738737 | | target function (ml) not normalized (free): 3267.445821 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2706 percent. r_work = 0.2917 r_free = 0.2010 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2865 0.2917 0.2010 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2865 0.2917 0.2010 n_refl.: 17050 remove outliers: r(all,work,free)=0.2156 0.2166 0.2010 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2129 0.2139 0.1991 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1608 0.1604 0.1679 n_refl.: 17045 remove outliers: r(all,work,free)=0.1607 0.1603 0.1679 n_refl.: 17043 ======================== 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 32.574-12.150 100.00 89 5 0.4023 394.916 361.821 0.650 1.010 0.397 11.894-9.307 99.02 97 4 0.1813 633.852 614.943 0.923 1.011 0.380 9.237-7.194 100.00 213 7 0.2161 518.427 508.303 0.963 1.011 0.350 7.162-5.571 100.00 427 22 0.2301 389.080 376.639 0.927 1.010 0.294 5.546-4.326 100.00 867 58 0.1391 534.145 528.378 0.961 1.008 0.225 4.315-3.360 100.00 1859 96 0.1293 507.977 503.814 1.015 1.005 0.201 3.356-2.611 100.00 3867 181 0.1641 333.712 329.428 1.014 1.001 0.034 2.608-2.000 99.98 8817 434 0.1637 217.466 213.889 1.026 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4537 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1603 r_free=0.1679 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1607 r_free=0.1696 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.287149 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.861235 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1351 0.1639 0.0289 0.008 1.0 1.3 0.5 0.0 0 11.144 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.39 2.89 3.013 18.452 0.861 0.023 12.76 16.59 3.83 3.631 18.736 0.861 0.020 Individual atomic B min max mean iso aniso Overall: 6.36 113.89 20.02 4.06 1785 0 Protein: 6.36 112.55 17.27 4.06 1519 0 Water: 8.97 113.89 36.02 N/A 258 0 Other: 21.64 37.26 26.54 N/A 8 0 Chain A: 6.36 113.89 20.02 N/A 1785 0 Histogram: Values Number of atoms 6.36 - 17.12 1090 17.12 - 27.87 336 27.87 - 38.62 186 38.62 - 49.38 99 49.38 - 60.13 47 60.13 - 70.88 13 70.88 - 81.63 6 81.63 - 92.39 4 92.39 - 103.14 1 103.14 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1659 r_work=0.1279 r_free=0.1668 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1279 r_free = 0.1668 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1274 r_free = 0.1659 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1274 r_free= 0.1659 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019994 | | target function (ls_wunit_k1) not normalized (work): 324.618930 | | target function (ls_wunit_k1) not normalized (free): 27.266147 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1292 0.1274 0.1659 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1915 0.1914 0.1993 n_refl.: 17043 remove outliers: r(all,work,free)=0.1915 0.1914 0.1993 n_refl.: 17043 overall B=-0.40 to atoms: r(all,work,free)=0.1885 0.1883 0.1976 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1292 0.1275 0.1651 n_refl.: 17043 remove outliers: r(all,work,free)=0.1291 0.1273 0.1651 n_refl.: 17041 ======================== 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 0.3552 302.892 278.080 0.611 1.009 0.360 11.894-9.307 99.02 97 4 0.1723 487.154 476.705 0.912 1.010 0.355 9.237-7.194 100.00 213 7 0.1811 398.443 395.720 0.960 1.010 0.341 7.162-5.571 100.00 427 22 0.1819 299.032 294.417 0.934 1.009 0.301 5.546-4.326 100.00 867 58 0.1045 410.522 408.201 0.959 1.007 0.205 4.315-3.360 100.00 1859 96 0.0928 390.411 389.948 1.018 1.005 0.191 3.356-2.611 100.00 3867 181 0.1298 256.478 255.222 1.018 1.000 0.091 2.608-2.000 99.98 8817 434 0.1347 167.136 165.647 1.025 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.4403 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1651 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1275 r_free=0.1651 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1651 | n_water=258 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1283 r_free=0.1644 | n_water=252 | time (s): 20.070 (total time: 20.700) Filter (q & B) r_work=0.1283 r_free=0.1644 | n_water=250 | time (s): 1.810 (total time: 22.510) Compute maps r_work=0.1283 r_free=0.1644 | n_water=250 | time (s): 0.790 (total time: 23.300) Filter (map) r_work=0.1317 r_free=0.1640 | n_water=212 | time (s): 2.300 (total time: 25.600) Find peaks r_work=0.1317 r_free=0.1640 | n_water=212 | time (s): 0.680 (total time: 26.280) Add new water r_work=0.1527 r_free=0.1846 | n_water=365 | time (s): 1.820 (total time: 28.100) Refine new water occ: r_work=0.1330 r_free=0.1565 adp: r_work=0.1273 r_free=0.1558 occ: r_work=0.1278 r_free=0.1542 adp: r_work=0.1247 r_free=0.1542 occ: r_work=0.1248 r_free=0.1545 adp: r_work=0.1236 r_free=0.1540 ADP+occupancy (water only), MIN, final r_work=0.1236 r_free=0.1540 r_work=0.1236 r_free=0.1540 | n_water=365 | time (s): 20.880 (total time: 48.980) Filter (q & B) r_work=0.1238 r_free=0.1539 | n_water=359 | time (s): 1.600 (total time: 50.580) Filter (dist only) r_work=0.1238 r_free=0.1539 | n_water=358 | time (s): 28.340 (total time: 78.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.750109 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.955604 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1605 0.0398 0.008 0.9 2.6 0.5 0.0 0 12.375 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 16.05 3.98 4.166 21.084 0.956 0.018 11.94 16.32 4.39 4.176 21.399 0.956 0.018 Individual atomic B min max mean iso aniso Overall: 6.46 107.14 21.43 4.27 1885 0 Protein: 6.46 107.14 17.86 4.26 1519 0 Water: 8.57 67.03 36.24 N/A 358 0 Other: 25.26 44.78 35.55 N/A 8 0 Chain A: 6.46 107.14 19.59 N/A 1739 0 Chain S: 17.42 67.03 43.27 N/A 146 0 Histogram: Values Number of atoms 6.46 - 16.53 1002 16.53 - 26.60 394 26.60 - 36.66 220 36.66 - 46.73 162 46.73 - 56.80 69 56.80 - 66.87 25 66.87 - 76.94 6 76.94 - 87.01 3 87.01 - 97.07 2 97.07 - 107.14 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1632 r_work=0.1196 r_free=0.1634 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1634 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1637 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1194 r_free= 0.1637 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017096 | | target function (ls_wunit_k1) not normalized (work): 277.529616 | | target function (ls_wunit_k1) not normalized (free): 24.965055 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1194 0.1637 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1770 0.1758 0.2029 n_refl.: 17041 remove outliers: r(all,work,free)=0.1770 0.1758 0.2029 n_refl.: 17041 overall B=-0.40 to atoms: r(all,work,free)=0.1743 0.1731 0.2009 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1188 0.1630 n_refl.: 17041 remove outliers: r(all,work,free)=0.1208 0.1187 0.1630 n_refl.: 17040 ======================== 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 94.79 86 5 0.3197 299.735 287.580 0.593 1.004 0.340 11.894-9.307 99.02 97 4 0.1570 487.154 483.445 0.914 1.005 0.332 9.237-7.194 100.00 213 7 0.1698 398.443 398.628 0.973 1.005 0.310 7.162-5.571 100.00 427 22 0.1578 299.032 295.404 0.932 1.005 0.281 5.546-4.326 100.00 867 58 0.0877 410.522 407.402 0.962 1.004 0.231 4.315-3.360 100.00 1859 96 0.0810 390.411 389.460 1.016 1.003 0.191 3.356-2.611 100.00 3867 181 0.1201 256.478 255.590 1.015 1.001 0.132 2.608-2.000 99.98 8817 434 0.1326 167.136 166.057 1.021 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4219 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1630 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1630 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1630 | n_water=358 | time (s): 0.930 (total time: 0.930) Filter (dist) r_work=0.1187 r_free=0.1630 | n_water=358 | time (s): 27.380 (total time: 28.310) Filter (q & B) r_work=0.1187 r_free=0.1630 | n_water=358 | time (s): 1.280 (total time: 29.590) Compute maps r_work=0.1187 r_free=0.1630 | n_water=358 | time (s): 0.660 (total time: 30.250) Filter (map) r_work=0.1251 r_free=0.1625 | n_water=268 | time (s): 2.090 (total time: 32.340) Find peaks r_work=0.1251 r_free=0.1625 | n_water=268 | time (s): 0.680 (total time: 33.020) Add new water r_work=0.1431 r_free=0.1779 | n_water=404 | time (s): 1.700 (total time: 34.720) Refine new water occ: r_work=0.1240 r_free=0.1594 adp: r_work=0.1233 r_free=0.1596 occ: r_work=0.1214 r_free=0.1572 adp: r_work=0.1203 r_free=0.1571 occ: r_work=0.1195 r_free=0.1561 adp: r_work=0.1185 r_free=0.1559 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1559 r_work=0.1185 r_free=0.1559 | n_water=404 | time (s): 29.960 (total time: 64.680) Filter (q & B) r_work=0.1188 r_free=0.1562 | n_water=396 | time (s): 2.030 (total time: 66.710) Filter (dist only) r_work=0.1188 r_free=0.1562 | n_water=396 | time (s): 28.890 (total time: 95.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.926577 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.119831 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1168 0.1573 0.0405 0.009 1.0 3.5 0.5 0.0 0 0.963 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.68 15.73 4.05 4.341 21.655 0.120 4.989 11.51 15.88 4.38 4.868 21.509 0.120 4.968 Individual atomic B min max mean iso aniso Overall: 6.32 104.20 20.89 4.51 1923 0 Protein: 6.32 104.20 17.07 4.51 1519 0 Water: 8.42 64.48 35.24 N/A 396 0 Other: 27.55 46.21 35.61 N/A 8 0 Chain A: 6.32 104.20 18.83 N/A 1737 0 Chain S: 15.31 64.48 40.10 N/A 186 0 Histogram: Values Number of atoms 6.32 - 16.11 1044 16.11 - 25.89 366 25.89 - 35.68 223 35.68 - 45.47 175 45.47 - 55.26 74 55.26 - 65.05 29 65.05 - 74.83 5 74.83 - 84.62 3 84.62 - 94.41 2 94.41 - 104.20 2 =========================== Idealize ADP of riding H ========================== r_work=0.1151 r_free=0.1588 r_work=0.1151 r_free=0.1589 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1151 r_free = 0.1589 target_work(ml) = 4.969 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1587 target_work(ml) = 4.965 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1140 r_free= 0.1587 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.964817 | | target function (ml) not normalized (work): 80593.881285 | | target function (ml) not normalized (free): 4189.605166 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1140 0.1587 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1696 0.1689 0.1883 n_refl.: 17040 remove outliers: r(all,work,free)=0.1696 0.1689 0.1883 n_refl.: 17040 overall B=-0.40 to atoms: r(all,work,free)=0.1667 0.1660 0.1871 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1159 0.1137 0.1586 n_refl.: 17040 remove outliers: r(all,work,free)=0.1159 0.1137 0.1586 n_refl.: 17040 ======================== 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 94.79 86 5 0.3410 299.735 279.608 0.577 1.006 0.340 11.894-9.307 99.02 97 4 0.1680 487.154 481.191 0.916 1.006 0.327 9.237-7.194 100.00 213 7 0.1789 398.443 398.556 0.982 1.006 0.290 7.162-5.571 100.00 427 22 0.1607 299.032 293.545 0.937 1.006 0.251 5.546-4.326 100.00 867 58 0.0931 410.522 406.867 0.965 1.005 0.221 4.315-3.360 100.00 1859 96 0.0881 390.411 388.280 1.012 1.004 0.212 3.356-2.611 100.00 3867 181 0.1281 256.478 254.288 1.013 1.001 0.152 2.608-2.000 99.98 8817 434 0.1080 167.136 165.701 1.022 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.4252 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1137 r_free=0.1586 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1137 r_free=0.1586 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1586 | n_water=396 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1141 r_free=0.1585 | n_water=395 | time (s): 28.510 (total time: 29.170) Filter (q & B) r_work=0.1141 r_free=0.1585 | n_water=395 | time (s): 0.800 (total time: 29.970) Compute maps r_work=0.1141 r_free=0.1585 | n_water=395 | time (s): 0.700 (total time: 30.670) Filter (map) r_work=0.1198 r_free=0.1581 | n_water=314 | time (s): 1.530 (total time: 32.200) Find peaks r_work=0.1198 r_free=0.1581 | n_water=314 | time (s): 0.420 (total time: 32.620) Add new water r_work=0.1343 r_free=0.1716 | n_water=447 | time (s): 1.470 (total time: 34.090) Refine new water occ: r_work=0.1181 r_free=0.1526 adp: r_work=0.1173 r_free=0.1537 occ: r_work=0.1158 r_free=0.1500 adp: r_work=0.1148 r_free=0.1511 occ: r_work=0.1142 r_free=0.1486 adp: r_work=0.1133 r_free=0.1495 ADP+occupancy (water only), MIN, final r_work=0.1133 r_free=0.1495 r_work=0.1133 r_free=0.1495 | n_water=447 | time (s): 35.900 (total time: 69.990) Filter (q & B) r_work=0.1135 r_free=0.1509 | n_water=437 | time (s): 1.740 (total time: 71.730) Filter (dist only) r_work=0.1135 r_free=0.1509 | n_water=437 | time (s): 33.520 (total time: 105.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.904384 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.204443 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1124 0.1554 0.0431 0.010 1.0 3.8 0.5 0.0 0 0.952 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.24 15.54 4.31 4.396 21.099 0.204 4.960 11.11 15.54 4.44 4.627 21.166 0.204 4.953 Individual atomic B min max mean iso aniso Overall: 5.90 102.33 21.06 4.97 1964 0 Protein: 5.90 102.33 16.64 4.96 1519 0 Water: 8.28 61.10 36.14 N/A 437 0 Other: 27.59 48.93 36.54 N/A 8 0 Chain A: 5.90 102.33 18.33 N/A 1733 0 Chain S: 16.08 61.10 41.53 N/A 231 0 Histogram: Values Number of atoms 5.90 - 15.54 1043 15.54 - 25.19 367 25.19 - 34.83 209 34.83 - 44.47 186 44.47 - 54.11 108 54.11 - 63.76 36 63.76 - 73.40 6 73.40 - 83.04 4 83.04 - 92.68 3 92.68 - 102.33 2 =========================== Idealize ADP of riding H ========================== r_work=0.1111 r_free=0.1554 r_work=0.1111 r_free=0.1554 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1111 r_free = 0.1554 target_work(ml) = 4.953 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1551 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1103 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.948590 | | target function (ml) not normalized (work): 80330.459610 | | target function (ml) not normalized (free): 4187.857194 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1103 0.1551 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1617 0.1605 0.1871 n_refl.: 17040 remove outliers: r(all,work,free)=0.1617 0.1605 0.1871 n_refl.: 17040 overall B=-0.31 to atoms: r(all,work,free)=0.1596 0.1584 0.1861 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1100 0.1552 n_refl.: 17040 remove outliers: r(all,work,free)=0.1121 0.1099 0.1552 n_refl.: 17039 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3567 296.176 280.669 0.569 1.003 0.340 11.894-9.307 99.02 97 4 0.1675 487.154 480.696 0.924 1.004 0.330 9.237-7.194 100.00 213 7 0.1688 398.443 400.337 0.989 1.004 0.240 7.162-5.571 100.00 427 22 0.1523 299.032 293.870 0.943 1.004 0.230 5.546-4.326 100.00 867 58 0.0924 410.522 406.998 0.964 1.004 0.206 4.315-3.360 100.00 1859 96 0.0842 390.411 388.362 1.007 1.003 0.201 3.356-2.611 100.00 3867 181 0.1253 256.478 254.275 1.005 1.001 0.172 2.608-2.000 99.98 8817 434 0.1032 167.136 165.936 1.007 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.0863 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1099 r_free=0.1552 After: r_work=0.1101 r_free=0.1552 ================================== NQH flips ================================== r_work=0.1101 r_free=0.1552 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1101 r_free=0.1552 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1101 r_free=0.1552 | n_water=437 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1101 r_free=0.1552 | n_water=437 | time (s): 35.250 (total time: 35.900) Filter (q & B) r_work=0.1101 r_free=0.1552 | n_water=437 | time (s): 1.010 (total time: 36.910) Compute maps r_work=0.1101 r_free=0.1552 | n_water=437 | time (s): 0.570 (total time: 37.480) Filter (map) r_work=0.1172 r_free=0.1592 | n_water=333 | time (s): 1.760 (total time: 39.240) Find peaks r_work=0.1172 r_free=0.1592 | n_water=333 | time (s): 0.610 (total time: 39.850) Add new water r_work=0.1303 r_free=0.1699 | n_water=459 | time (s): 2.150 (total time: 42.000) Refine new water occ: r_work=0.1148 r_free=0.1539 adp: r_work=0.1142 r_free=0.1547 occ: r_work=0.1127 r_free=0.1514 adp: r_work=0.1120 r_free=0.1523 occ: r_work=0.1112 r_free=0.1503 adp: r_work=0.1106 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1106 r_free=0.1512 r_work=0.1106 r_free=0.1512 | n_water=459 | time (s): 36.490 (total time: 78.490) Filter (q & B) r_work=0.1108 r_free=0.1525 | n_water=452 | time (s): 1.750 (total time: 80.240) Filter (dist only) r_work=0.1108 r_free=0.1525 | n_water=450 | time (s): 37.410 (total time: 117.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.911388 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.187893 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1122 0.1539 0.0416 0.011 1.0 4.2 0.5 0.0 0 0.956 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.22 15.39 4.16 4.625 20.854 0.188 4.951 11.12 15.24 4.12 4.626 20.943 0.188 4.940 Individual atomic B min max mean iso aniso Overall: 5.69 101.17 20.94 5.02 1977 0 Protein: 5.69 101.17 16.40 5.00 1519 0 Water: 8.20 63.71 36.00 N/A 450 0 Other: 27.57 46.10 35.51 N/A 8 0 Chain A: 5.69 101.17 18.05 N/A 1732 0 Chain S: 17.37 63.71 41.37 N/A 245 0 Histogram: Values Number of atoms 5.69 - 15.24 1030 15.24 - 24.78 371 24.78 - 34.33 206 34.33 - 43.88 201 43.88 - 53.43 116 53.43 - 62.98 35 62.98 - 72.52 8 72.52 - 82.07 4 82.07 - 91.62 2 91.62 - 101.17 4 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1524 r_work=0.1112 r_free=0.1523 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1112 r_free = 0.1523 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1104 r_free = 0.1526 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1104 r_free= 0.1526 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.935623 | | target function (ml) not normalized (work): 80115.035979 | | target function (ml) not normalized (free): 4170.125426 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1119 0.1482 5.4601 5.7102| | 2: 3.63 - 2.88 1.00 2711 122 0.1086 0.1465 5.2234 5.3526| | 3: 2.88 - 2.52 1.00 2681 148 0.1360 0.1623 5.14 5.193| | 4: 2.52 - 2.29 1.00 2661 139 0.0934 0.1460 4.6217 4.9034| | 5: 2.29 - 2.13 1.00 2678 122 0.0957 0.1546 4.5728 4.9186| | 6: 2.13 - 2.00 1.00 2691 117 0.1103 0.1733 4.566 4.7777| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2810 159 0.95 9.17 1.00 0.96 6587.84| | 2: 3.63 - 2.88 2711 122 0.92 13.05 1.01 0.96 6587.84| | 3: 2.88 - 2.52 2681 148 0.87 19.34 0.99 0.96 6587.84| | 4: 2.52 - 2.29 2661 139 0.93 12.05 1.01 0.98 2100.75| | 5: 2.29 - 2.13 2678 122 0.91 14.11 1.00 0.98 2100.75| | 6: 2.13 - 2.00 2691 117 0.89 16.83 0.99 0.98 2100.75| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2100.75 max = 6587.84 mean = 4368.07| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.98 mean = 14.05| |phase err.(test): min = 0.00 max = 89.29 mean = 13.78| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1124 0.1104 0.1526 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1583 0.1575 0.1777 n_refl.: 17039 remove outliers: r(all,work,free)=0.1583 0.1575 0.1777 n_refl.: 17039 overall B=-0.27 to atoms: r(all,work,free)=0.1566 0.1558 0.1770 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1105 0.1530 n_refl.: 17039 remove outliers: r(all,work,free)=0.1126 0.1105 0.1530 n_refl.: 17039 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3638 296.176 275.861 0.537 1.003 0.313 11.894-9.307 99.02 97 4 0.1834 487.154 481.602 0.913 1.004 0.300 9.237-7.194 100.00 213 7 0.1824 398.443 398.672 0.983 1.004 0.241 7.162-5.571 100.00 427 22 0.1581 299.032 293.310 0.938 1.004 0.217 5.546-4.326 100.00 867 58 0.0932 410.522 406.810 0.966 1.004 0.201 4.315-3.360 100.00 1859 96 0.0846 390.411 388.696 1.006 1.003 0.191 3.356-2.611 100.00 3867 181 0.1243 256.478 254.170 1.004 1.001 0.101 2.608-2.000 99.98 8817 434 0.1033 167.136 165.809 0.999 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9438 ================= 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 : 0.2790 0.1870 0.081 5.186 8.8 119.3 19.9 258 0.000 1_bss: 0.1603 0.1679 0.081 5.186 8.4 118.9 19.5 258 0.000 1_settarget: 0.1603 0.1679 0.081 5.186 8.4 118.9 19.5 258 0.000 1_nqh: 0.1607 0.1696 0.081 5.186 8.4 118.9 19.5 258 0.007 1_weight: 0.1607 0.1696 0.081 5.186 8.4 118.9 19.5 258 0.007 1_xyzrec: 0.1351 0.1639 0.008 0.958 8.4 118.9 19.5 258 0.157 1_adp: 0.1276 0.1659 0.008 0.958 6.4 113.9 20.0 258 0.157 1_regHadp: 0.1279 0.1668 0.008 0.958 6.4 113.9 20.0 258 0.157 1_occ: 0.1274 0.1659 0.008 0.958 6.4 113.9 20.0 258 0.157 2_bss: 0.1273 0.1651 0.008 0.958 6.0 113.5 19.6 258 0.157 2_settarget: 0.1273 0.1651 0.008 0.958 6.0 113.5 19.6 258 0.157 2_updatecdl: 0.1273 0.1651 0.008 0.978 6.0 113.5 19.6 258 0.157 2_nqh: 0.1275 0.1651 0.008 0.978 6.0 113.5 19.6 258 0.151 2_sol: 0.1238 0.1539 0.008 0.978 6.0 112.1 20.8 358 n/a 2_weight: 0.1238 0.1539 0.008 0.978 6.0 112.1 20.8 358 n/a 2_xyzrec: 0.1207 0.1605 0.008 0.933 6.0 112.1 20.8 358 n/a 2_adp: 0.1194 0.1632 0.008 0.933 6.5 107.1 21.4 358 n/a 2_regHadp: 0.1196 0.1634 0.008 0.933 6.5 107.1 21.4 358 n/a 2_occ: 0.1194 0.1637 0.008 0.933 6.5 107.1 21.4 358 n/a 3_bss: 0.1187 0.1630 0.008 0.933 6.1 106.7 21.0 358 n/a 3_settarget: 0.1187 0.1630 0.008 0.933 6.1 106.7 21.0 358 n/a 3_updatecdl: 0.1187 0.1630 0.008 0.929 6.1 106.7 21.0 358 n/a 3_nqh: 0.1187 0.1630 0.008 0.929 6.1 106.7 21.0 358 n/a 3_sol: 0.1188 0.1562 0.008 0.929 6.1 106.7 21.2 396 n/a 3_weight: 0.1188 0.1562 0.008 0.929 6.1 106.7 21.2 396 n/a 3_xyzrec: 0.1168 0.1573 0.009 0.970 6.1 106.7 21.2 396 n/a 3_adp: 0.1151 0.1588 0.009 0.970 6.3 104.2 20.9 396 n/a 3_regHadp: 0.1151 0.1589 0.009 0.970 6.3 104.2 20.9 396 n/a 3_occ: 0.1140 0.1587 0.009 0.970 6.3 104.2 20.9 396 n/a 4_bss: 0.1137 0.1586 0.009 0.970 5.9 103.8 20.5 396 n/a 4_settarget: 0.1137 0.1586 0.009 0.970 5.9 103.8 20.5 396 n/a 4_updatecdl: 0.1137 0.1586 0.009 0.971 5.9 103.8 20.5 396 n/a 4_nqh: 0.1137 0.1586 0.009 0.971 5.9 103.8 20.5 396 n/a 4_sol: 0.1135 0.1509 0.009 0.971 5.9 103.8 20.9 437 n/a 4_weight: 0.1135 0.1509 0.009 0.971 5.9 103.8 20.9 437 n/a 4_xyzrec: 0.1124 0.1554 0.010 0.981 5.9 103.8 20.9 437 n/a 4_adp: 0.1111 0.1554 0.010 0.981 5.9 102.3 21.1 437 n/a 4_regHadp: 0.1111 0.1554 0.010 0.981 5.9 102.3 21.1 437 n/a 4_occ: 0.1103 0.1551 0.010 0.981 5.9 102.3 21.1 437 n/a 5_bss: 0.1099 0.1552 0.010 0.981 5.6 102.0 20.7 437 n/a 5_settarget: 0.1099 0.1552 0.010 0.981 5.6 102.0 20.7 437 n/a 5_updatecdl: 0.1099 0.1552 0.010 0.981 5.6 102.0 20.7 437 n/a 5_setrh: 0.1101 0.1552 0.010 0.981 5.6 102.0 20.7 437 n/a 5_nqh: 0.1101 0.1552 0.010 0.981 5.6 102.0 20.7 437 n/a 5_sol: 0.1108 0.1525 0.010 0.981 5.6 102.0 20.8 450 n/a 5_weight: 0.1108 0.1525 0.010 0.981 5.6 102.0 20.8 450 n/a 5_xyzrec: 0.1122 0.1539 0.011 1.022 5.6 102.0 20.8 450 n/a 5_adp: 0.1112 0.1524 0.011 1.022 5.7 101.2 20.9 450 n/a 5_regHadp: 0.1112 0.1523 0.011 1.022 5.7 101.2 20.9 450 n/a 5_occ: 0.1104 0.1526 0.011 1.022 5.7 101.2 20.9 450 n/a end: 0.1105 0.1530 0.011 1.022 5.4 100.9 20.7 450 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_9451893_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_9451893_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9200 Refinement macro-cycles (run) : 929.7100 Write final files (write_after_run_outputs) : 20.0600 Total : 952.6900 Total CPU time: 16.26 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:18 PST -0800 (1735494078.07 s) Start R-work = 0.1603, R-free = 0.1679 Final R-work = 0.1105, R-free = 0.1530 =============================================================================== Job complete usr+sys time: 999.81 seconds wall clock time: 17 minutes 4.04 seconds (1024.04 seconds total)