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_6470396.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6470396.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6470396.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" 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 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.39, per 1000 atoms: 0.41 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 155.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 498 0.91 - 1.15: 1124 1.15 - 1.40: 600 1.40 - 1.65: 853 1.65 - 1.90: 78 Bond restraints: 3153 Sorted by residual: bond pdb=" C BGLU A 94 " pdb=" O BGLU A 94 " ideal model delta sigma weight residual 1.237 1.448 -0.211 1.19e-02 7.06e+03 3.15e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.150 0.171 1.00e-02 1.00e+04 2.93e+02 bond pdb=" CA ALA A 114 " pdb=" C ALA A 114 " ideal model delta sigma weight residual 1.523 1.739 -0.216 1.30e-02 5.92e+03 2.76e+02 bond pdb=" C LYS A 63 " pdb=" O LYS A 63 " ideal model delta sigma weight residual 1.236 1.444 -0.209 1.29e-02 6.01e+03 2.61e+02 bond pdb=" CA ALA A 14 " pdb=" C ALA A 14 " ideal model delta sigma weight residual 1.525 1.731 -0.207 1.28e-02 6.10e+03 2.61e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.01: 3319 5.01 - 10.01: 1843 10.01 - 15.02: 551 15.02 - 20.03: 59 20.03 - 25.03: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O AGLU A 96 " pdb=" C AGLU A 96 " pdb=" N AASN A 97 " ideal model delta sigma weight residual 122.07 106.39 15.68 1.03e+00 9.43e-01 2.32e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.19 135.28 -14.09 9.40e-01 1.13e+00 2.25e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH1 ARG A 28 " ideal model delta sigma weight residual 121.50 106.70 14.80 1.00e+00 1.00e+00 2.19e+02 angle pdb=" O ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 122.12 136.28 -14.16 1.06e+00 8.90e-01 1.78e+02 angle pdb=" N ILE A 9 " pdb=" CA ILE A 9 " pdb=" CB ILE A 9 " ideal model delta sigma weight residual 111.21 126.44 -15.23 1.17e+00 7.31e-01 1.69e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 16.51: 1284 16.51 - 33.00: 135 33.00 - 49.49: 43 49.49 - 65.98: 16 65.98 - 82.47: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LYS A 182 " pdb=" N LYS A 182 " pdb=" CA LYS A 182 " pdb=" CB LYS A 182 " ideal model delta harmonic sigma weight residual -122.60 -104.13 -18.47 0 2.50e+00 1.60e-01 5.46e+01 dihedral pdb=" C BGLU A 96 " pdb=" N BGLU A 96 " pdb=" CA BGLU A 96 " pdb=" CB BGLU A 96 " ideal model delta harmonic sigma weight residual -122.60 -140.42 17.82 0 2.50e+00 1.60e-01 5.08e+01 dihedral pdb=" C VAL A 123 " pdb=" N VAL A 123 " pdb=" CA VAL A 123 " pdb=" CB VAL A 123 " ideal model delta harmonic sigma weight residual -122.00 -104.99 -17.01 0 2.50e+00 1.60e-01 4.63e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.290: 124 0.290 - 0.576: 87 0.576 - 0.862: 28 0.862 - 1.148: 3 1.148 - 1.434: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.16 -1.43 2.00e-01 2.50e+01 5.14e+01 chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -3.64 1.01 2.00e-01 2.50e+01 2.54e+01 chirality pdb=" CA BGLU A 96 " pdb=" N BGLU A 96 " pdb=" C BGLU A 96 " pdb=" CB BGLU A 96 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.11e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.074 2.00e-02 2.50e+03 5.88e-02 1.04e+02 pdb=" CG ATYR A 67 " -0.079 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.115 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.074 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.067 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.053 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.020 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.035 2.00e-02 2.50e+03 6.75e-02 1.03e+02 pdb=" CG HIS A 115 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.115 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.029 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.113 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " 0.073 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.036 2.00e-02 2.50e+03 5.67e-02 9.65e+01 pdb=" CG TYR A 141 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.022 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.078 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.067 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.086 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.093 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 1194 2.34 - 2.91: 8234 2.91 - 3.47: 10532 3.47 - 4.04: 15142 4.04 - 4.60: 21506 Nonbonded interactions: 56608 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.780 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.791 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.801 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.825 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.834 2.450 ... (remaining 56603 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_6470396_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= 0.2792 r_free= 0.1783 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.419812 | | target function (ml) not normalized (work): 71791.010661 | | target function (ml) not normalized (free): 3243.862357 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3204 0.2111 7.6453 5.037| | 2: 3.63 - 2.88 1.00 2711 122 0.2629 0.1689 4.3207 4.3076| | 3: 2.88 - 2.52 1.00 2682 148 0.2543 0.1667 4.1716 4.1649| | 4: 2.52 - 2.29 1.00 2661 139 0.2543 0.1424 3.5072 3.5067| | 5: 2.29 - 2.13 1.00 2678 122 0.2684 0.1566 3.3941 3.4499| | 6: 2.13 - 2.00 1.00 2692 117 0.2786 0.1769 3.3118 3.3566| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.32 0.77 0.23 1272.15| | 2: 3.63 - 2.88 2711 122 0.83 23.37 1.31 0.23 1272.15| | 3: 2.88 - 2.52 2682 148 0.74 32.41 1.28 0.23 1272.15| | 4: 2.52 - 2.29 2661 139 0.94 10.92 1.29 0.26 125.72| | 5: 2.29 - 2.13 2678 122 0.92 13.05 1.32 0.26 125.72| | 6: 2.13 - 2.00 2692 117 0.90 15.81 1.34 0.26 125.72| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 125.72 max = 1272.15 mean = 705.32| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.99 mean = 18.82| |phase err.(test): min = 0.00 max = 88.67 mean = 19.12| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.236 1557 Z= 5.511 Angle : 5.297 17.365 2118 Z= 3.728 Chirality : 0.379 1.434 243 Planarity : 0.033 0.094 284 Dihedral : 14.260 82.471 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 27.03 % 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: -3.02 (0.45), residues: 224 helix: -2.90 (0.39), residues: 103 sheet: -0.84 (0.85), residues: 28 loop : -1.00 (0.52), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.021 ARG A 156 TYR 0.078 0.030 TYR A 139 PHE 0.110 0.041 PHE A 162 HIS 0.075 0.030 HIS A 126 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= 0.2792 r_free= 0.1783 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.419812 | | target function (ml) not normalized (work): 71791.010661 | | target function (ml) not normalized (free): 3243.862357 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3113 percent. r_work = 0.2923 r_free = 0.1950 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2869 0.2923 0.1950 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2869 0.2923 0.1950 n_refl.: 17050 remove outliers: r(all,work,free)=0.2159 0.2172 0.1950 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2132 0.2144 0.1931 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1617 0.1618 0.1607 n_refl.: 17045 remove outliers: r(all,work,free)=0.1616 0.1617 0.1607 n_refl.: 17044 ======================== 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 0.4102 394.835 358.855 0.646 1.017 0.393 11.894-9.307 99.02 97 4 0.1851 633.722 614.456 0.917 1.017 0.375 9.237-7.194 100.00 213 7 0.2213 518.321 508.592 0.954 1.016 0.371 7.162-5.571 100.00 427 22 0.2309 389.000 376.300 0.923 1.015 0.298 5.546-4.326 100.00 867 58 0.1366 534.035 528.546 0.958 1.012 0.215 4.315-3.360 100.00 1859 96 0.1295 507.872 504.537 1.018 1.007 0.181 3.356-2.611 100.00 3867 181 0.1654 333.643 329.461 1.011 1.000 0.091 2.608-2.000 99.99 8818 434 0.1663 217.478 213.347 1.034 0.987 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4658 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1617 r_free=0.1607 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1618 r_free=0.1609 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.744769 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.921325 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 0.1352 0.1645 0.0293 0.009 1.0 1.3 0.5 0.0 0 11.872 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.45 2.93 3.013 18.448 0.921 0.023 12.78 16.64 3.86 3.622 18.697 0.921 0.020 Individual atomic B min max mean iso aniso Overall: 6.25 113.89 19.95 4.10 1785 0 Protein: 6.25 113.05 17.17 4.10 1519 0 Water: 8.70 113.89 36.08 N/A 258 0 Other: 21.72 37.36 26.23 N/A 8 0 Chain A: 6.25 113.89 19.95 N/A 1785 0 Histogram: Values Number of atoms 6.25 - 17.01 1092 17.01 - 27.78 337 27.78 - 38.54 181 38.54 - 49.30 100 49.30 - 60.07 48 60.07 - 70.83 13 70.83 - 81.60 6 81.60 - 92.36 4 92.36 - 103.12 1 103.12 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1664 r_work=0.1281 r_free=0.1670 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1670 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 = 0.1276 r_free = 0.1662 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1276 r_free= 0.1662 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ls_wunit_k1) (work): 0.020018 | | target function (ls_wunit_k1) not normalized (work): 325.039648 | | target function (ls_wunit_k1) not normalized (free): 27.210275 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1276 0.1662 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1910 0.1909 0.1991 n_refl.: 17044 remove outliers: r(all,work,free)=0.1910 0.1909 0.1991 n_refl.: 17044 overall B=-0.52 to atoms: r(all,work,free)=0.1873 0.1871 0.1970 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1658 n_refl.: 17044 remove outliers: r(all,work,free)=0.1292 0.1273 0.1658 n_refl.: 17042 ======================== 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 0.3528 303.803 279.753 0.629 1.007 0.370 11.894-9.307 99.02 97 4 0.1721 488.620 477.368 0.917 1.007 0.367 9.237-7.194 100.00 213 7 0.1817 399.642 396.753 0.960 1.007 0.351 7.162-5.571 100.00 427 22 0.1838 299.932 294.471 0.932 1.006 0.301 5.546-4.326 100.00 867 58 0.1046 411.758 409.178 0.958 1.005 0.200 4.315-3.360 100.00 1859 96 0.0924 391.586 391.020 1.016 1.004 0.182 3.356-2.611 100.00 3867 181 0.1296 257.250 255.949 1.010 1.001 0.091 2.608-2.000 99.99 8818 434 0.1350 167.683 166.340 1.012 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1665 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1658 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1274 r_free=0.1656 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1656 | n_water=258 | time (s): 0.740 (total time: 0.740) Filter (dist) r_work=0.1279 r_free=0.1646 | n_water=253 | time (s): 22.390 (total time: 23.130) Filter (q & B) r_work=0.1279 r_free=0.1646 | n_water=251 | time (s): 1.540 (total time: 24.670) Compute maps r_work=0.1279 r_free=0.1646 | n_water=251 | time (s): 0.690 (total time: 25.360) Filter (map) r_work=0.1315 r_free=0.1645 | n_water=212 | time (s): 2.210 (total time: 27.570) Find peaks r_work=0.1315 r_free=0.1645 | n_water=212 | time (s): 0.650 (total time: 28.220) Add new water r_work=0.1527 r_free=0.1890 | n_water=370 | time (s): 1.680 (total time: 29.900) Refine new water occ: r_work=0.1322 r_free=0.1596 adp: r_work=0.1266 r_free=0.1593 occ: r_work=0.1273 r_free=0.1562 adp: r_work=0.1241 r_free=0.1569 occ: r_work=0.1244 r_free=0.1560 adp: r_work=0.1233 r_free=0.1555 ADP+occupancy (water only), MIN, final r_work=0.1233 r_free=0.1555 r_work=0.1233 r_free=0.1555 | n_water=370 | time (s): 10.500 (total time: 40.400) Filter (q & B) r_work=0.1235 r_free=0.1562 | n_water=361 | time (s): 1.670 (total time: 42.070) Filter (dist only) r_work=0.1235 r_free=0.1563 | n_water=360 | time (s): 28.470 (total time: 70.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.033103 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.999661 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 0.1211 0.1602 0.0391 0.008 0.9 2.6 0.5 0.0 0 12.017 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 16.02 3.91 4.181 20.890 1.000 0.018 11.96 16.24 4.28 4.262 21.162 1.000 0.018 Individual atomic B min max mean iso aniso Overall: 6.57 107.54 21.17 4.36 1887 0 Protein: 6.57 107.54 17.58 4.34 1519 0 Water: 8.58 67.07 36.00 N/A 360 0 Other: 24.50 46.88 36.27 N/A 8 0 Chain A: 6.57 107.54 19.34 N/A 1739 0 Chain S: 19.53 67.07 42.74 N/A 148 0 Histogram: Values Number of atoms 6.57 - 16.66 1036 16.66 - 26.76 367 26.76 - 36.86 217 36.86 - 46.96 165 46.96 - 57.05 62 57.05 - 67.15 29 67.15 - 77.25 4 77.25 - 87.34 3 87.34 - 97.44 2 97.44 - 107.54 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1624 r_work=0.1197 r_free=0.1624 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1624 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1618 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1192 r_free= 0.1618 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016972 | | target function (ls_wunit_k1) not normalized (work): 275.544550 | | target function (ls_wunit_k1) not normalized (free): 24.353427 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1192 0.1618 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1741 0.1731 0.1956 n_refl.: 17042 remove outliers: r(all,work,free)=0.1741 0.1731 0.1956 n_refl.: 17042 overall B=-0.42 to atoms: r(all,work,free)=0.1715 0.1705 0.1940 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1188 0.1615 n_refl.: 17042 remove outliers: r(all,work,free)=0.1208 0.1187 0.1615 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 94.79 86 5 0.3222 300.637 288.174 0.596 1.006 0.340 11.894-9.307 99.02 97 4 0.1542 488.620 484.871 0.914 1.007 0.334 9.237-7.194 100.00 213 7 0.1651 399.642 401.469 0.973 1.007 0.290 7.162-5.571 100.00 427 22 0.1531 299.932 296.176 0.939 1.006 0.271 5.546-4.326 100.00 867 58 0.0886 411.758 409.148 0.960 1.005 0.211 4.315-3.360 100.00 1859 96 0.0819 391.586 390.779 1.015 1.003 0.191 3.356-2.611 100.00 3867 181 0.1199 257.250 256.396 1.010 1.000 0.101 2.608-2.000 99.99 8818 434 0.1329 167.683 166.581 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1537 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1615 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1615 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1615 | n_water=360 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1188 r_free=0.1614 | n_water=359 | time (s): 30.440 (total time: 31.070) Filter (q & B) r_work=0.1188 r_free=0.1614 | n_water=359 | time (s): 0.770 (total time: 31.840) Compute maps r_work=0.1188 r_free=0.1614 | n_water=359 | time (s): 0.680 (total time: 32.520) Filter (map) r_work=0.1259 r_free=0.1637 | n_water=262 | time (s): 1.800 (total time: 34.320) Find peaks r_work=0.1259 r_free=0.1637 | n_water=262 | time (s): 0.650 (total time: 34.970) Add new water r_work=0.1436 r_free=0.1791 | n_water=409 | time (s): 2.090 (total time: 37.060) Refine new water occ: r_work=0.1240 r_free=0.1590 adp: r_work=0.1230 r_free=0.1589 occ: r_work=0.1214 r_free=0.1577 adp: r_work=0.1202 r_free=0.1572 occ: r_work=0.1196 r_free=0.1567 adp: r_work=0.1186 r_free=0.1564 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1564 r_work=0.1186 r_free=0.1564 | n_water=409 | time (s): 47.460 (total time: 84.520) Filter (q & B) r_work=0.1188 r_free=0.1569 | n_water=399 | time (s): 1.890 (total time: 86.410) Filter (dist only) r_work=0.1188 r_free=0.1569 | n_water=399 | time (s): 32.340 (total time: 118.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.888998 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.150421 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 0.1171 0.1550 0.0380 0.009 1.0 3.8 0.5 0.0 0 0.944 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.71 15.50 3.80 4.378 21.304 0.150 4.999 11.49 15.55 4.05 4.947 21.214 0.150 4.974 Individual atomic B min max mean iso aniso Overall: 5.80 104.35 20.62 4.72 1926 0 Protein: 5.80 104.35 16.78 4.71 1519 0 Water: 8.39 66.55 34.95 N/A 399 0 Other: 25.59 46.40 33.73 N/A 8 0 Chain A: 5.80 104.35 18.56 N/A 1737 0 Chain S: 18.80 66.55 39.53 N/A 189 0 Histogram: Values Number of atoms 5.80 - 15.66 1042 15.66 - 25.51 364 25.51 - 35.37 226 35.37 - 45.22 177 45.22 - 55.08 73 55.08 - 64.93 30 64.93 - 74.79 4 74.79 - 84.64 5 84.64 - 94.50 3 94.50 - 104.35 2 =========================== Idealize ADP of riding H ========================== r_work=0.1149 r_free=0.1555 r_work=0.1149 r_free=0.1554 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1149 r_free = 0.1554 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1563 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1150 r_free= 0.1563 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.971665 | | target function (ml) not normalized (work): 80710.013819 | | target function (ml) not normalized (free): 4189.217965 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1170 0.1150 0.1563 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1666 0.1660 0.1824 n_refl.: 17041 remove outliers: r(all,work,free)=0.1666 0.1660 0.1824 n_refl.: 17041 overall B=-0.33 to atoms: r(all,work,free)=0.1645 0.1638 0.1814 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1169 0.1149 0.1567 n_refl.: 17041 remove outliers: r(all,work,free)=0.1168 0.1148 0.1567 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 93.75 85 5 0.3546 297.068 281.813 0.561 1.006 0.340 11.894-9.307 99.02 97 4 0.1724 488.620 481.902 0.907 1.008 0.327 9.237-7.194 100.00 213 7 0.1761 399.642 400.997 0.984 1.008 0.278 7.162-5.571 100.00 427 22 0.1658 299.932 294.709 0.938 1.007 0.257 5.546-4.326 100.00 867 58 0.0961 411.758 407.768 0.962 1.006 0.231 4.315-3.360 100.00 1859 96 0.0876 391.586 389.520 1.012 1.004 0.201 3.356-2.611 100.00 3867 181 0.1276 257.250 254.975 1.011 1.001 0.068 2.608-2.000 99.99 8818 434 0.1102 167.683 166.221 1.011 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1340 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1148 r_free=0.1567 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1148 r_free=0.1567 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1148 r_free=0.1567 | n_water=399 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1148 r_free=0.1567 | n_water=399 | time (s): 31.330 (total time: 31.960) Filter (q & B) r_work=0.1148 r_free=0.1567 | n_water=399 | time (s): 1.030 (total time: 32.990) Compute maps r_work=0.1148 r_free=0.1567 | n_water=399 | time (s): 0.700 (total time: 33.690) Filter (map) r_work=0.1199 r_free=0.1596 | n_water=316 | time (s): 1.710 (total time: 35.400) Find peaks r_work=0.1199 r_free=0.1596 | n_water=316 | time (s): 0.410 (total time: 35.810) Add new water r_work=0.1345 r_free=0.1694 | n_water=455 | time (s): 1.470 (total time: 37.280) Refine new water occ: r_work=0.1184 r_free=0.1535 adp: r_work=0.1176 r_free=0.1534 occ: r_work=0.1159 r_free=0.1522 adp: r_work=0.1150 r_free=0.1519 occ: r_work=0.1142 r_free=0.1512 adp: r_work=0.1135 r_free=0.1510 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1510 r_work=0.1135 r_free=0.1510 | n_water=455 | time (s): 32.250 (total time: 69.530) Filter (q & B) r_work=0.1138 r_free=0.1527 | n_water=446 | time (s): 1.740 (total time: 71.270) Filter (dist only) r_work=0.1138 r_free=0.1527 | n_water=446 | time (s): 34.590 (total time: 105.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.930494 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.172317 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 0.1126 0.1551 0.0425 0.009 1.0 5.1 0.5 0.0 0 0.965 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.51 4.25 4.503 20.929 0.172 4.960 11.13 15.48 4.35 4.702 20.946 0.172 4.952 Individual atomic B min max mean iso aniso Overall: 5.18 102.79 20.84 4.87 1973 0 Protein: 5.18 102.79 16.38 4.86 1519 0 Water: 6.57 62.64 35.89 N/A 446 0 Other: 22.53 42.32 30.40 N/A 8 0 Chain A: 5.18 102.79 18.07 N/A 1735 0 Chain S: 16.11 62.64 41.10 N/A 238 0 Histogram: Values Number of atoms 5.18 - 14.94 1016 14.94 - 24.70 385 24.70 - 34.46 221 34.46 - 44.22 193 44.22 - 53.98 105 53.98 - 63.74 39 63.74 - 73.51 5 73.51 - 83.27 4 83.27 - 93.03 3 93.03 - 102.79 2 =========================== Idealize ADP of riding H ========================== r_work=0.1113 r_free=0.1548 r_work=0.1113 r_free=0.1549 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1113 r_free = 0.1549 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1104 r_free = 0.1550 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1104 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.947010 | | target function (ml) not normalized (work): 80304.808508 | | target function (ml) not normalized (free): 4177.544855 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1104 0.1550 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1586 0.1575 0.1838 n_refl.: 17040 remove outliers: r(all,work,free)=0.1586 0.1575 0.1838 n_refl.: 17040 overall B=-0.24 to atoms: r(all,work,free)=0.1572 0.1560 0.1830 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1101 0.1543 n_refl.: 17040 remove outliers: r(all,work,free)=0.1123 0.1101 0.1543 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 93.75 85 5 0.3556 297.068 280.608 0.564 1.004 0.340 11.894-9.307 99.02 97 4 0.1686 488.620 485.098 0.918 1.004 0.330 9.237-7.194 100.00 213 7 0.1672 399.642 400.160 0.990 1.004 0.250 7.162-5.571 100.00 427 22 0.1515 299.932 294.121 0.936 1.004 0.250 5.546-4.326 100.00 867 58 0.0896 411.758 408.680 0.962 1.004 0.205 4.315-3.360 100.00 1859 96 0.0833 391.586 389.338 1.004 1.003 0.201 3.356-2.611 100.00 3867 181 0.1252 257.250 255.041 1.000 1.001 0.131 2.608-2.000 99.99 8818 434 0.1051 167.683 166.439 0.994 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8417 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1101 r_free=0.1543 After: r_work=0.1103 r_free=0.1542 ================================== NQH flips ================================== r_work=0.1103 r_free=0.1542 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1103 r_free=0.1542 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1103 r_free=0.1542 | n_water=446 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1108 r_free=0.1547 | n_water=444 | time (s): 37.640 (total time: 38.260) Filter (q & B) r_work=0.1108 r_free=0.1548 | n_water=443 | time (s): 2.080 (total time: 40.340) Compute maps r_work=0.1108 r_free=0.1548 | n_water=443 | time (s): 0.780 (total time: 41.120) Filter (map) r_work=0.1183 r_free=0.1574 | n_water=336 | time (s): 1.820 (total time: 42.940) Find peaks r_work=0.1183 r_free=0.1574 | n_water=336 | time (s): 0.650 (total time: 43.590) Add new water r_work=0.1321 r_free=0.1677 | n_water=473 | time (s): 2.070 (total time: 45.660) Refine new water occ: r_work=0.1152 r_free=0.1520 adp: r_work=0.1146 r_free=0.1525 occ: r_work=0.1128 r_free=0.1507 adp: r_work=0.1121 r_free=0.1511 occ: r_work=0.1113 r_free=0.1501 adp: r_work=0.1106 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1106 r_free=0.1503 r_work=0.1106 r_free=0.1503 | n_water=473 | time (s): 33.700 (total time: 79.360) Filter (q & B) r_work=0.1110 r_free=0.1516 | n_water=460 | time (s): 2.020 (total time: 81.380) Filter (dist only) r_work=0.1110 r_free=0.1516 | n_water=460 | time (s): 35.730 (total time: 117.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.881153 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.208705 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 0.1130 0.1524 0.0394 0.010 1.0 5.8 0.5 0.0 0 0.941 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 15.24 3.94 4.548 20.734 0.209 4.946 11.16 15.18 4.02 4.652 20.847 0.209 4.937 Individual atomic B min max mean iso aniso Overall: 4.81 103.11 20.98 5.14 1987 0 Protein: 4.81 103.11 16.16 5.14 1519 0 Water: 7.10 65.69 36.77 N/A 460 0 Other: 22.12 38.15 28.88 N/A 8 0 Chain A: 4.81 103.11 17.80 N/A 1734 0 Chain S: 19.84 65.69 42.76 N/A 253 0 Histogram: Values Number of atoms 4.81 - 14.64 1001 14.64 - 24.47 400 24.47 - 34.30 208 34.30 - 44.13 200 44.13 - 53.96 118 53.96 - 63.79 43 63.79 - 73.62 8 73.62 - 83.45 2 83.45 - 93.28 3 93.28 - 103.11 4 =========================== Idealize ADP of riding H ========================== r_work=0.1116 r_free=0.1518 r_work=0.1116 r_free=0.1518 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1116 r_free = 0.1518 target_work(ml) = 4.937 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1109 r_free = 0.1512 target_work(ml) = 4.932 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1109 r_free= 0.1512 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.932152 | | target function (ml) not normalized (work): 80063.628701 | | target function (ml) not normalized (free): 4159.388061 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1125 0.1440 5.4562 5.6717| | 2: 3.63 - 2.88 1.00 2711 122 0.1095 0.1467 5.2302 5.3414| | 3: 2.88 - 2.52 1.00 2681 148 0.1363 0.1670 5.1355 5.2121| | 4: 2.52 - 2.29 1.00 2661 139 0.0924 0.1481 4.6116 4.9231| | 5: 2.29 - 2.13 1.00 2678 122 0.0960 0.1399 4.5691 4.824| | 6: 2.13 - 2.00 1.00 2692 117 0.1121 0.1802 4.5605 4.8009| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.94 9.25 1.00 0.96 6504.91| | 2: 3.63 - 2.88 2711 122 0.92 12.87 1.01 0.96 6504.91| | 3: 2.88 - 2.52 2681 148 0.87 19.17 0.99 0.96 6504.91| | 4: 2.52 - 2.29 2661 139 0.93 11.79 1.01 0.98 2036.38| | 5: 2.29 - 2.13 2678 122 0.92 13.74 1.00 0.98 2036.38| | 6: 2.13 - 2.00 2692 117 0.90 16.53 0.99 0.98 2036.38| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2036.38 max = 6504.91 mean = 4294.18| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.87 mean = 13.86| |phase err.(test): min = 0.00 max = 86.90 mean = 13.55| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1109 0.1512 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1583 0.1573 0.1821 n_refl.: 17040 remove outliers: r(all,work,free)=0.1583 0.1573 0.1821 n_refl.: 17040 overall B=-0.20 to atoms: r(all,work,free)=0.1571 0.1560 0.1814 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1109 0.1512 n_refl.: 17040 remove outliers: r(all,work,free)=0.1129 0.1109 0.1512 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 93.75 85 5 0.3522 297.068 280.181 0.557 1.005 0.330 11.894-9.307 99.02 97 4 0.1727 488.620 485.211 0.919 1.006 0.330 9.237-7.194 100.00 213 7 0.1751 399.642 399.142 0.985 1.006 0.250 7.162-5.571 100.00 427 22 0.1568 299.932 294.136 0.933 1.006 0.240 5.546-4.326 100.00 867 58 0.0936 411.758 408.597 0.960 1.005 0.200 4.315-3.360 100.00 1859 96 0.0879 391.586 389.124 1.001 1.003 0.201 3.356-2.611 100.00 3867 181 0.1249 257.250 255.046 0.999 1.001 0.121 2.608-2.000 99.99 8818 434 0.1032 167.683 166.309 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7097 ================= 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 : 0.2792 0.1783 0.083 5.297 8.8 119.3 19.9 258 0.000 1_bss: 0.1617 0.1607 0.083 5.297 8.4 118.9 19.5 258 0.000 1_settarget: 0.1617 0.1607 0.083 5.297 8.4 118.9 19.5 258 0.000 1_nqh: 0.1618 0.1609 0.083 5.297 8.4 118.9 19.5 258 0.003 1_weight: 0.1618 0.1609 0.083 5.297 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1352 0.1645 0.009 0.983 8.4 118.9 19.5 258 0.152 1_adp: 0.1278 0.1664 0.009 0.983 6.2 113.9 19.9 258 0.152 1_regHadp: 0.1281 0.1670 0.009 0.983 6.2 113.9 19.9 258 0.152 1_occ: 0.1276 0.1662 0.009 0.983 6.2 113.9 19.9 258 0.152 2_bss: 0.1273 0.1658 0.009 0.983 5.7 113.4 19.4 258 0.152 2_settarget: 0.1273 0.1658 0.009 0.983 5.7 113.4 19.4 258 0.152 2_updatecdl: 0.1273 0.1658 0.009 0.991 5.7 113.4 19.4 258 0.152 2_nqh: 0.1274 0.1656 0.009 0.991 5.7 113.4 19.4 258 0.149 2_sol: 0.1235 0.1563 0.009 0.991 5.7 112.5 20.7 360 n/a 2_weight: 0.1235 0.1563 0.009 0.991 5.7 112.5 20.7 360 n/a 2_xyzrec: 0.1211 0.1602 0.008 0.921 5.7 112.5 20.7 360 n/a 2_adp: 0.1196 0.1624 0.008 0.921 6.6 107.5 21.2 360 n/a 2_regHadp: 0.1197 0.1624 0.008 0.921 6.6 107.5 21.2 360 n/a 2_occ: 0.1192 0.1618 0.008 0.921 6.6 107.5 21.2 360 n/a 3_bss: 0.1187 0.1615 0.008 0.921 6.2 107.1 20.8 360 n/a 3_settarget: 0.1187 0.1615 0.008 0.921 6.2 107.1 20.8 360 n/a 3_updatecdl: 0.1187 0.1615 0.008 0.928 6.2 107.1 20.8 360 n/a 3_nqh: 0.1187 0.1615 0.008 0.928 6.2 107.1 20.8 360 n/a 3_sol: 0.1188 0.1569 0.008 0.928 6.2 107.1 20.8 399 n/a 3_weight: 0.1188 0.1569 0.008 0.928 6.2 107.1 20.8 399 n/a 3_xyzrec: 0.1171 0.1550 0.009 0.955 6.2 107.1 20.8 399 n/a 3_adp: 0.1149 0.1555 0.009 0.955 5.8 104.4 20.6 399 n/a 3_regHadp: 0.1149 0.1554 0.009 0.955 5.8 104.4 20.6 399 n/a 3_occ: 0.1150 0.1563 0.009 0.955 5.8 104.4 20.6 399 n/a 4_bss: 0.1148 0.1567 0.009 0.955 5.5 104.0 20.3 399 n/a 4_settarget: 0.1148 0.1567 0.009 0.955 5.5 104.0 20.3 399 n/a 4_updatecdl: 0.1148 0.1567 0.009 0.953 5.5 104.0 20.3 399 n/a 4_nqh: 0.1148 0.1567 0.009 0.953 5.5 104.0 20.3 399 n/a 4_sol: 0.1138 0.1527 0.009 0.953 5.5 104.0 20.8 446 n/a 4_weight: 0.1138 0.1527 0.009 0.953 5.5 104.0 20.8 446 n/a 4_xyzrec: 0.1126 0.1551 0.009 0.965 5.5 104.0 20.8 446 n/a 4_adp: 0.1113 0.1548 0.009 0.965 5.2 102.8 20.8 446 n/a 4_regHadp: 0.1113 0.1549 0.009 0.965 5.2 102.8 20.8 446 n/a 4_occ: 0.1104 0.1550 0.009 0.965 5.2 102.8 20.8 446 n/a 5_bss: 0.1101 0.1543 0.009 0.965 4.9 102.5 20.6 446 n/a 5_settarget: 0.1101 0.1543 0.009 0.965 4.9 102.5 20.6 446 n/a 5_updatecdl: 0.1101 0.1543 0.009 0.967 4.9 102.5 20.6 446 n/a 5_setrh: 0.1103 0.1542 0.009 0.967 4.9 102.5 20.6 446 n/a 5_nqh: 0.1103 0.1542 0.009 0.967 4.9 102.5 20.6 446 n/a 5_sol: 0.1110 0.1516 0.009 0.967 4.9 102.5 20.8 460 n/a 5_weight: 0.1110 0.1516 0.009 0.967 4.9 102.5 20.8 460 n/a 5_xyzrec: 0.1130 0.1524 0.010 1.018 4.9 102.5 20.8 460 n/a 5_adp: 0.1116 0.1518 0.010 1.018 4.8 103.1 21.0 460 n/a 5_regHadp: 0.1116 0.1518 0.010 1.018 4.8 103.1 21.0 460 n/a 5_occ: 0.1109 0.1512 0.010 1.018 4.8 103.1 21.0 460 n/a end: 0.1109 0.1512 0.010 1.018 4.6 102.9 20.8 460 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6470396_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6470396_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1600 Refinement macro-cycles (run) : 936.9800 Write final files (write_after_run_outputs) : 19.8500 Total : 960.9900 Total CPU time: 16.40 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:24 PST -0800 (1735494084.71 s) Start R-work = 0.1617, R-free = 0.1607 Final R-work = 0.1109, R-free = 0.1512 =============================================================================== Job complete usr+sys time: 1004.13 seconds wall clock time: 17 minutes 6.52 seconds (1026.52 seconds total)