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_4023827.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_4023827.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4023827.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 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.04, per 1000 atoms: 0.60 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: 0.44 Conformation dependent library (CDL) restraints added in 157.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.60 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: 502 0.91 - 1.16: 1128 1.16 - 1.41: 621 1.41 - 1.66: 847 1.66 - 1.91: 55 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 117 " pdb=" O ILE A 117 " ideal model delta sigma weight residual 1.237 1.452 -0.215 1.10e-02 8.26e+03 3.83e+02 bond pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 1.329 1.531 -0.201 1.13e-02 7.83e+03 3.18e+02 bond pdb=" C ALA A 179 " pdb=" O ALA A 179 " ideal model delta sigma weight residual 1.237 1.443 -0.207 1.16e-02 7.43e+03 3.17e+02 bond pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta sigma weight residual 1.446 1.598 -0.151 8.70e-03 1.32e+04 3.02e+02 bond pdb=" N ILE A 168 " pdb=" CA ILE A 168 " ideal model delta sigma weight residual 1.461 1.662 -0.201 1.17e-02 7.31e+03 2.94e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 3028 4.41 - 8.81: 1860 8.81 - 13.22: 705 13.22 - 17.62: 166 17.62 - 22.03: 18 Bond angle restraints: 5777 Sorted by residual: angle pdb=" N ARG A 156 " pdb=" CA ARG A 156 " pdb=" C ARG A 156 " ideal model delta sigma weight residual 113.50 132.47 -18.97 1.23e+00 6.61e-01 2.38e+02 angle pdb=" O BGLU A 90 " pdb=" C BGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 122.12 136.84 -14.72 1.06e+00 8.90e-01 1.93e+02 angle pdb=" CA MET A 134 " pdb=" C MET A 134 " pdb=" O MET A 134 " ideal model delta sigma weight residual 119.28 134.81 -15.53 1.21e+00 6.83e-01 1.65e+02 angle pdb=" CA GLY A 108 " pdb=" C GLY A 108 " pdb=" O GLY A 108 " ideal model delta sigma weight residual 119.69 111.84 7.85 6.30e-01 2.52e+00 1.55e+02 angle pdb=" O ARG A 27 " pdb=" C ARG A 27 " pdb=" N ARG A 28 " ideal model delta sigma weight residual 122.15 136.24 -14.09 1.14e+00 7.69e-01 1.53e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 1305 17.43 - 34.85: 127 34.85 - 52.28: 30 52.28 - 69.71: 15 69.71 - 87.14: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 25 " pdb=" N VAL A 25 " pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta harmonic sigma weight residual -122.00 -145.89 23.89 0 2.50e+00 1.60e-01 9.13e+01 dihedral pdb=" C THR A 160 " pdb=" N THR A 160 " pdb=" CA THR A 160 " pdb=" CB THR A 160 " ideal model delta harmonic sigma weight residual -122.00 -141.21 19.21 0 2.50e+00 1.60e-01 5.91e+01 dihedral pdb=" N BLYS A 41 " pdb=" C BLYS A 41 " pdb=" CA BLYS A 41 " pdb=" CB BLYS A 41 " ideal model delta harmonic sigma weight residual 122.80 141.35 -18.55 0 2.50e+00 1.60e-01 5.50e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.235: 122 0.235 - 0.465: 71 0.465 - 0.695: 36 0.695 - 0.925: 12 0.925 - 1.155: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.67 -1.15 2.00e-01 2.50e+01 3.33e+01 chirality pdb=" CA BLEU A 153 " pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CB BLEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.45 -0.94 2.00e-01 2.50e+01 2.23e+01 chirality pdb=" CA THR A 160 " pdb=" N THR A 160 " pdb=" C THR A 160 " pdb=" CB THR A 160 " both_signs ideal model delta sigma weight residual False 2.53 1.62 0.91 2.00e-01 2.50e+01 2.06e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.012 2.00e-02 2.50e+03 6.78e-02 1.38e+02 pdb=" CG BTYR A 67 " -0.037 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.117 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.034 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.094 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.108 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.029 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.066 2.00e-02 2.50e+03 6.94e-02 1.09e+02 pdb=" CG HIS A 126 " -0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.098 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.097 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.020 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.109 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.044 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.022 2.00e-02 2.50e+03 5.55e-02 9.25e+01 pdb=" CG PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.139 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.038 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.040 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1259 2.35 - 2.91: 8260 2.91 - 3.48: 10522 3.48 - 4.04: 15154 4.04 - 4.60: 21363 Nonbonded interactions: 56558 Sorted by model distance: nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.791 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.812 2.270 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.820 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.825 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.845 2.450 ... (remaining 56553 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_4023827_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= 0.2784 r_free= 0.1794 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.403526 | | target function (ml) not normalized (work): 71526.479086 | | target function (ml) not normalized (free): 3248.422153 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2128 7.6004 5.0359| | 2: 3.63 - 2.88 1.00 2711 122 0.2641 0.1686 4.3234 4.3321| | 3: 2.88 - 2.52 1.00 2682 148 0.2544 0.1736 4.1798 4.1774| | 4: 2.52 - 2.29 1.00 2661 139 0.2541 0.1484 3.4956 3.5504| | 5: 2.29 - 2.13 1.00 2678 122 0.2620 0.1469 3.3641 3.4031| | 6: 2.13 - 2.00 1.00 2692 117 0.2766 0.1746 3.2909 3.3526| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.44 0.77 0.23 1295.06| | 2: 3.63 - 2.88 2711 122 0.83 23.61 1.32 0.23 1295.06| | 3: 2.88 - 2.52 2682 148 0.73 32.64 1.28 0.23 1295.06| | 4: 2.52 - 2.29 2661 139 0.94 10.78 1.30 0.26 124.33| | 5: 2.29 - 2.13 2678 122 0.92 12.87 1.31 0.26 124.33| | 6: 2.13 - 2.00 2692 117 0.90 15.74 1.34 0.26 124.33| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 124.33 max = 1295.06 mean = 716.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.95 mean = 18.85| |phase err.(test): min = 0.00 max = 88.45 mean = 19.04| |-----------------------------------------------------------------------------| ----------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 0.240 1557 Z= 5.502 Angle : 5.255 18.971 2118 Z= 3.703 Chirality : 0.369 1.155 243 Planarity : 0.033 0.120 284 Dihedral : 14.232 87.135 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 29.73 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.47), residues: 224 helix: -2.43 (0.40), residues: 108 sheet: -0.87 (0.81), residues: 38 loop : -0.73 (0.56), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.107 0.020 ARG A 28 TYR 0.121 0.038 TYR A 139 PHE 0.103 0.040 PHE A 162 HIS 0.071 0.039 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= 0.2784 r_free= 0.1794 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.403526 | | target function (ml) not normalized (work): 71526.479086 | | target function (ml) not normalized (free): 3248.422153 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3114 percent. r_work = 0.2915 r_free = 0.1948 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2862 0.2915 0.1948 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2862 0.2915 0.1948 n_refl.: 17050 remove outliers: r(all,work,free)=0.2151 0.2163 0.1948 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2124 0.2136 0.1927 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1619 0.1619 0.1608 n_refl.: 17045 remove outliers: r(all,work,free)=0.1617 0.1617 0.1608 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 98.94 88 5 0.3882 398.937 359.684 0.649 1.011 0.397 11.894-9.307 99.02 97 4 0.1870 633.606 614.089 0.927 1.012 0.380 9.237-7.194 100.00 213 7 0.2202 518.226 510.081 0.957 1.011 0.371 7.162-5.571 100.00 427 22 0.2364 388.929 374.543 0.922 1.010 0.295 5.546-4.326 100.00 867 58 0.1392 533.937 529.336 0.962 1.009 0.225 4.315-3.360 100.00 1859 96 0.1304 507.779 503.684 1.019 1.005 0.191 3.356-2.611 100.00 3867 181 0.1661 333.582 329.279 1.012 1.000 0.061 2.608-2.000 99.99 8818 434 0.1648 217.438 213.313 1.027 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4286 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1617 r_free=0.1608 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1622 r_free=0.1620 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.146057 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.948202 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 0.1355 0.1633 0.0279 0.009 1.0 1.9 0.5 0.0 0 11.573 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.55 16.33 2.79 3.012 18.458 0.948 0.023 12.76 16.64 3.88 3.675 18.732 0.948 0.020 Individual atomic B min max mean iso aniso Overall: 6.17 113.90 20.00 4.12 1785 0 Protein: 6.17 112.87 17.23 4.12 1519 0 Water: 9.00 113.90 36.13 N/A 258 0 Other: 21.73 37.69 26.82 N/A 8 0 Chain A: 6.17 113.90 20.00 N/A 1785 0 Histogram: Values Number of atoms 6.17 - 16.94 1084 16.94 - 27.71 341 27.71 - 38.49 184 38.49 - 49.26 101 49.26 - 60.03 48 60.03 - 70.81 12 70.81 - 81.58 7 81.58 - 92.35 4 92.35 - 103.13 1 103.13 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1664 r_work=0.1280 r_free=0.1673 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1673 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 = 0.1275 r_free = 0.1660 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.19 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= 0.1275 r_free= 0.1660 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019874 | | target function (ls_wunit_k1) not normalized (work): 322.670970 | | target function (ls_wunit_k1) not normalized (free): 27.201991 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1275 0.1660 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1904 0.1902 0.1993 n_refl.: 17043 remove outliers: r(all,work,free)=0.1904 0.1902 0.1993 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1876 0.1874 0.1977 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1655 n_refl.: 17043 remove outliers: r(all,work,free)=0.1293 0.1275 0.1655 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 96.88 88 5 0.3591 306.958 284.374 0.650 1.009 0.389 11.894-9.307 99.02 97 4 0.1702 487.522 476.846 0.916 1.010 0.380 9.237-7.194 100.00 213 7 0.1829 398.744 395.804 0.957 1.009 0.351 7.162-5.571 100.00 427 22 0.1838 299.258 294.427 0.931 1.008 0.301 5.546-4.326 100.00 867 58 0.1039 410.833 408.363 0.957 1.007 0.210 4.315-3.360 100.00 1859 96 0.0918 390.706 390.377 1.017 1.004 0.191 3.356-2.611 100.00 3867 181 0.1296 256.672 255.450 1.014 1.000 0.081 2.608-2.000 99.99 8818 434 0.1355 167.306 165.792 1.021 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3652 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1655 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1277 r_free=0.1656 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1656 | n_water=258 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1286 r_free=0.1648 | n_water=252 | time (s): 21.170 (total time: 21.770) Filter (q & B) r_work=0.1285 r_free=0.1648 | n_water=250 | time (s): 1.880 (total time: 23.650) Compute maps r_work=0.1285 r_free=0.1648 | n_water=250 | time (s): 0.790 (total time: 24.440) Filter (map) r_work=0.1321 r_free=0.1637 | n_water=209 | time (s): 2.140 (total time: 26.580) Find peaks r_work=0.1321 r_free=0.1637 | n_water=209 | time (s): 0.560 (total time: 27.140) Add new water r_work=0.1549 r_free=0.1874 | n_water=366 | time (s): 2.010 (total time: 29.150) Refine new water occ: r_work=0.1341 r_free=0.1617 adp: r_work=0.1282 r_free=0.1611 occ: r_work=0.1287 r_free=0.1585 adp: r_work=0.1252 r_free=0.1585 occ: r_work=0.1254 r_free=0.1577 adp: r_work=0.1241 r_free=0.1583 ADP+occupancy (water only), MIN, final r_work=0.1241 r_free=0.1583 r_work=0.1241 r_free=0.1583 | n_water=366 | time (s): 11.430 (total time: 40.580) Filter (q & B) r_work=0.1244 r_free=0.1591 | n_water=357 | time (s): 1.610 (total time: 42.190) Filter (dist only) r_work=0.1244 r_free=0.1591 | n_water=356 | time (s): 27.450 (total time: 69.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.396577 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.007401 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 0.1218 0.1612 0.0394 0.009 0.9 2.2 0.5 0.0 0 12.698 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.18 16.12 3.94 4.195 21.111 1.007 0.018 12.04 16.29 4.25 4.254 21.297 1.007 0.018 Individual atomic B min max mean iso aniso Overall: 6.83 107.49 21.25 4.24 1883 0 Protein: 6.83 107.49 17.61 4.23 1519 0 Water: 8.49 74.68 36.44 N/A 356 0 Other: 24.78 46.66 35.33 N/A 8 0 Chain A: 6.83 107.49 19.32 N/A 1736 0 Chain S: 17.62 63.36 44.05 N/A 147 0 Histogram: Values Number of atoms 6.83 - 16.90 1046 16.90 - 26.96 357 26.96 - 37.03 221 37.03 - 47.09 151 47.09 - 57.16 72 57.16 - 67.23 24 67.23 - 77.29 5 77.29 - 87.36 5 87.36 - 97.42 0 97.42 - 107.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1629 r_work=0.1205 r_free=0.1631 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1631 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 = 0.1200 r_free = 0.1638 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1200 r_free= 0.1638 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017163 | | target function (ls_wunit_k1) not normalized (work): 278.651116 | | target function (ls_wunit_k1) not normalized (free): 26.689767 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1200 0.1638 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1805 0.1798 0.1987 n_refl.: 17043 remove outliers: r(all,work,free)=0.1805 0.1798 0.1987 n_refl.: 17043 overall B=-0.51 to atoms: r(all,work,free)=0.1770 0.1762 0.1964 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1194 0.1625 n_refl.: 17043 remove outliers: r(all,work,free)=0.1213 0.1192 0.1625 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 0.3328 306.396 280.568 0.606 1.005 0.351 11.894-9.307 99.02 97 4 0.1559 487.522 482.951 0.921 1.006 0.345 9.237-7.194 100.00 213 7 0.1666 398.744 400.043 0.972 1.006 0.288 7.162-5.571 100.00 427 22 0.1573 299.258 295.389 0.939 1.005 0.272 5.546-4.326 100.00 867 58 0.0896 410.833 408.082 0.959 1.005 0.206 4.315-3.360 100.00 1859 96 0.0834 390.706 390.474 1.015 1.003 0.202 3.356-2.611 100.00 3867 181 0.1200 256.672 255.900 1.009 1.001 0.049 2.608-2.000 99.99 8818 434 0.1325 167.306 166.353 1.010 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9584 b_overall=-1.1501 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1625 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1193 r_free=0.1625 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1625 | n_water=356 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1193 r_free=0.1630 | n_water=352 | time (s): 27.260 (total time: 27.860) Filter (q & B) r_work=0.1193 r_free=0.1630 | n_water=352 | time (s): 0.810 (total time: 28.670) Compute maps r_work=0.1193 r_free=0.1630 | n_water=352 | time (s): 0.630 (total time: 29.300) Filter (map) r_work=0.1253 r_free=0.1624 | n_water=260 | time (s): 2.020 (total time: 31.320) Find peaks r_work=0.1253 r_free=0.1624 | n_water=260 | time (s): 0.540 (total time: 31.860) Add new water r_work=0.1439 r_free=0.1824 | n_water=409 | time (s): 2.200 (total time: 34.060) Refine new water occ: r_work=0.1248 r_free=0.1588 adp: r_work=0.1239 r_free=0.1591 occ: r_work=0.1225 r_free=0.1563 adp: r_work=0.1213 r_free=0.1564 occ: r_work=0.1210 r_free=0.1556 adp: r_work=0.1198 r_free=0.1554 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1554 r_work=0.1198 r_free=0.1554 | n_water=409 | time (s): 32.870 (total time: 66.930) Filter (q & B) r_work=0.1202 r_free=0.1558 | n_water=398 | time (s): 1.590 (total time: 68.520) Filter (dist only) r_work=0.1202 r_free=0.1558 | n_water=398 | time (s): 29.790 (total time: 98.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.848042 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.167110 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 0.1179 0.1560 0.0381 0.009 0.9 4.5 0.5 0.0 0 0.924 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.79 15.60 3.81 4.316 21.227 0.167 4.999 11.59 15.80 4.21 4.872 21.158 0.167 4.981 Individual atomic B min max mean iso aniso Overall: 6.15 105.16 20.56 4.67 1925 0 Protein: 6.15 105.16 16.78 4.66 1519 0 Water: 8.40 61.43 34.74 N/A 398 0 Other: 26.23 44.70 34.50 N/A 8 0 Chain A: 6.15 105.16 18.44 N/A 1730 0 Chain S: 12.76 61.43 39.37 N/A 195 0 Histogram: Values Number of atoms 6.15 - 16.05 1074 16.05 - 25.95 341 25.95 - 35.85 230 35.85 - 45.75 173 45.75 - 55.66 67 55.66 - 65.56 28 65.56 - 75.46 4 75.46 - 85.36 3 85.36 - 95.26 3 95.26 - 105.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1159 r_free=0.1580 r_work=0.1159 r_free=0.1579 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1159 r_free = 0.1579 target_work(ml) = 4.981 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1153 r_free = 0.1579 target_work(ml) = 4.976 | | occupancies: max = 1.00 min = 0.13 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= 0.1153 r_free= 0.1579 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.976439 | | target function (ml) not normalized (work): 80787.516242 | | target function (ml) not normalized (free): 4202.514155 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1173 0.1153 0.1579 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1638 0.1626 0.1915 n_refl.: 17041 remove outliers: r(all,work,free)=0.1638 0.1626 0.1915 n_refl.: 17041 overall B=-0.34 to atoms: r(all,work,free)=0.1617 0.1604 0.1902 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1168 0.1147 0.1573 n_refl.: 17041 remove outliers: r(all,work,free)=0.1166 0.1145 0.1573 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 92.71 84 5 0.3467 299.674 279.563 0.573 1.001 0.340 11.894-9.307 99.02 97 4 0.1728 487.522 479.806 0.917 1.002 0.323 9.237-7.194 100.00 213 7 0.1799 398.744 396.518 0.981 1.002 0.269 7.162-5.571 100.00 427 22 0.1676 299.258 292.686 0.943 1.002 0.220 5.546-4.326 100.00 867 58 0.0960 410.833 406.442 0.964 1.002 0.201 4.315-3.360 100.00 1859 96 0.0886 390.706 388.059 1.012 1.002 0.201 3.356-2.611 100.00 3867 181 0.1283 256.672 254.355 1.009 1.002 0.121 2.608-2.000 99.99 8818 434 0.1083 167.306 166.321 1.009 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9584 b_overall=-1.1802 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1573 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1145 r_free=0.1573 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1145 r_free=0.1573 | n_water=398 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1146 r_free=0.1576 | n_water=396 | time (s): 30.440 (total time: 31.040) Filter (q & B) r_work=0.1146 r_free=0.1577 | n_water=395 | time (s): 1.730 (total time: 32.770) Compute maps r_work=0.1146 r_free=0.1577 | n_water=395 | time (s): 0.640 (total time: 33.410) Filter (map) r_work=0.1203 r_free=0.1586 | n_water=316 | time (s): 1.910 (total time: 35.320) Find peaks r_work=0.1203 r_free=0.1586 | n_water=316 | time (s): 0.630 (total time: 35.950) Add new water r_work=0.1337 r_free=0.1708 | n_water=462 | time (s): 2.020 (total time: 37.970) Refine new water occ: r_work=0.1174 r_free=0.1549 adp: r_work=0.1167 r_free=0.1546 occ: r_work=0.1152 r_free=0.1538 adp: r_work=0.1144 r_free=0.1531 occ: r_work=0.1137 r_free=0.1536 adp: r_work=0.1130 r_free=0.1529 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1529 r_work=0.1130 r_free=0.1529 | n_water=462 | time (s): 32.770 (total time: 70.740) Filter (q & B) r_work=0.1133 r_free=0.1538 | n_water=454 | time (s): 1.980 (total time: 72.720) Filter (dist only) r_work=0.1133 r_free=0.1538 | n_water=454 | time (s): 36.210 (total time: 108.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.947036 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.189158 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 0.1560 0.0435 0.009 1.0 5.1 0.5 0.0 0 0.974 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.24 15.60 4.35 4.467 20.948 0.189 4.954 11.11 15.51 4.39 4.679 20.962 0.189 4.946 Individual atomic B min max mean iso aniso Overall: 5.37 102.89 20.90 4.92 1981 0 Protein: 5.37 102.89 16.34 4.91 1519 0 Water: 8.43 68.74 35.94 N/A 454 0 Other: 25.95 44.49 33.57 N/A 8 0 Chain A: 5.37 102.89 17.97 N/A 1730 0 Chain S: 14.29 68.74 41.10 N/A 251 0 Histogram: Values Number of atoms 5.37 - 15.12 1032 15.12 - 24.88 373 24.88 - 34.63 226 34.63 - 44.38 192 44.38 - 54.13 104 54.13 - 63.88 38 63.88 - 73.64 7 73.64 - 83.39 3 83.39 - 93.14 4 93.14 - 102.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1111 r_free=0.1551 r_work=0.1111 r_free=0.1551 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1111 r_free = 0.1551 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1100 r_free = 0.1566 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1100 r_free= 0.1566 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ml) (work): 4.942802 | | target function (ml) not normalized (work): 80231.559581 | | target function (ml) not normalized (free): 4183.992225 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1122 0.1100 0.1566 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1562 0.1546 0.1887 n_refl.: 17039 remove outliers: r(all,work,free)=0.1562 0.1546 0.1887 n_refl.: 17039 overall B=-0.25 to atoms: r(all,work,free)=0.1547 0.1531 0.1878 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1099 0.1565 n_refl.: 17039 remove outliers: r(all,work,free)=0.1122 0.1099 0.1565 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 92.71 84 5 0.3427 299.674 277.851 0.552 1.005 0.330 11.894-9.307 99.02 97 4 0.1731 487.522 483.502 0.914 1.006 0.320 9.237-7.194 100.00 213 7 0.1730 398.744 398.683 0.982 1.006 0.250 7.162-5.571 100.00 427 22 0.1546 299.258 292.832 0.938 1.005 0.195 5.546-4.326 100.00 867 58 0.0914 410.833 407.106 0.961 1.005 0.185 4.315-3.360 100.00 1859 96 0.0854 390.706 388.419 1.004 1.003 0.181 3.356-2.611 100.00 3867 181 0.1236 256.672 254.382 1.002 1.000 0.151 2.608-2.000 99.99 8818 434 0.1038 167.306 165.995 0.997 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8529 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1099 r_free=0.1565 After: r_work=0.1101 r_free=0.1563 ================================== NQH flips ================================== r_work=0.1101 r_free=0.1563 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1101 r_free=0.1563 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1101 r_free=0.1563 | n_water=454 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.1101 r_free=0.1563 | n_water=454 | time (s): 36.020 (total time: 36.720) Filter (q & B) r_work=0.1101 r_free=0.1566 | n_water=452 | time (s): 1.610 (total time: 38.330) Compute maps r_work=0.1101 r_free=0.1566 | n_water=452 | time (s): 0.690 (total time: 39.020) Filter (map) r_work=0.1172 r_free=0.1531 | n_water=348 | time (s): 1.980 (total time: 41.000) Find peaks r_work=0.1172 r_free=0.1531 | n_water=348 | time (s): 0.510 (total time: 41.510) Add new water r_work=0.1283 r_free=0.1619 | n_water=484 | time (s): 2.040 (total time: 43.550) Refine new water occ: r_work=0.1136 r_free=0.1520 adp: r_work=0.1128 r_free=0.1514 occ: r_work=0.1116 r_free=0.1515 adp: r_work=0.1108 r_free=0.1506 occ: r_work=0.1103 r_free=0.1510 adp: r_work=0.1097 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1097 r_free=0.1503 r_work=0.1097 r_free=0.1503 | n_water=484 | time (s): 33.710 (total time: 77.260) Filter (q & B) r_work=0.1102 r_free=0.1512 | n_water=469 | time (s): 2.240 (total time: 79.500) Filter (dist only) r_work=0.1102 r_free=0.1513 | n_water=468 | time (s): 36.030 (total time: 115.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.899819 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.181174 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 0.1118 0.1508 0.0390 0.010 1.0 7.0 0.5 0.0 0 0.950 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.18 15.08 3.90 4.572 20.708 0.181 4.940 11.06 15.01 3.95 4.707 20.762 0.181 4.929 Individual atomic B min max mean iso aniso Overall: 5.25 102.30 20.88 5.08 1995 0 Protein: 5.25 102.30 16.04 5.07 1519 0 Water: 8.11 64.42 36.36 N/A 468 0 Other: 24.93 43.67 32.47 N/A 8 0 Chain A: 5.25 102.30 17.65 N/A 1730 0 Chain S: 16.58 64.42 41.96 N/A 265 0 Histogram: Values Number of atoms 5.25 - 14.96 1039 14.96 - 24.66 371 24.66 - 34.37 216 34.37 - 44.07 191 44.07 - 53.77 126 53.77 - 63.48 31 63.48 - 73.18 12 73.18 - 82.89 3 82.89 - 92.59 2 92.59 - 102.30 4 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1501 r_work=0.1106 r_free=0.1501 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1501 target_work(ml) = 4.928 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1100 r_free = 0.1509 target_work(ml) = 4.926 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1100 r_free= 0.1509 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.926242 | | target function (ml) not normalized (work): 79962.762174 | | target function (ml) not normalized (free): 4159.250936 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2809 159 0.1108 0.1443 5.4512 5.6783| | 2: 3.63 - 2.88 1.00 2711 122 0.1091 0.1514 5.2307 5.3794| | 3: 2.88 - 2.52 1.00 2681 148 0.1354 0.1662 5.1393 5.2029| | 4: 2.52 - 2.29 1.00 2661 139 0.0918 0.1483 4.6019 4.927| | 5: 2.29 - 2.13 1.00 2678 122 0.0952 0.1421 4.5563 4.8424| | 6: 2.13 - 2.00 1.00 2692 117 0.1113 0.1625 4.5483 4.739| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2809 159 0.94 9.51 1.00 0.95 6636.04| | 2: 3.63 - 2.88 2711 122 0.92 13.26 1.01 0.95 6636.04| | 3: 2.88 - 2.52 2681 148 0.87 19.42 0.99 0.95 6636.04| | 4: 2.52 - 2.29 2661 139 0.93 11.65 1.01 0.97 1982.91| | 5: 2.29 - 2.13 2678 122 0.92 13.62 1.00 0.97 1982.91| | 6: 2.13 - 2.00 2692 117 0.90 16.34 0.99 0.97 1982.91| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 1982.91 max = 6636.04 mean = 4333.84| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.85 mean = 13.93| |phase err.(test): min = 0.00 max = 87.91 mean = 13.56| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1119 0.1100 0.1509 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1539 0.1524 0.1847 n_refl.: 17039 remove outliers: r(all,work,free)=0.1539 0.1524 0.1847 n_refl.: 17039 overall B=-0.19 to atoms: r(all,work,free)=0.1529 0.1513 0.1840 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1120 0.1100 0.1509 n_refl.: 17039 remove outliers: r(all,work,free)=0.1120 0.1100 0.1509 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 92.71 84 5 0.3504 299.674 277.098 0.550 1.004 0.324 11.894-9.307 99.02 97 4 0.1773 487.522 481.341 0.920 1.005 0.320 9.237-7.194 100.00 213 7 0.1743 398.744 399.914 0.991 1.005 0.250 7.162-5.571 100.00 427 22 0.1557 299.258 292.591 0.941 1.005 0.195 5.546-4.326 100.00 867 58 0.0913 410.833 406.957 0.968 1.004 0.180 4.315-3.360 100.00 1859 96 0.0869 390.706 388.499 1.008 1.002 0.171 3.356-2.611 100.00 3867 181 0.1237 256.672 254.328 1.005 1.000 0.067 2.608-2.000 99.99 8818 434 0.1028 167.306 165.999 0.994 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.6682 ================= 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 : 0.2784 0.1794 0.083 5.255 8.8 119.3 19.9 258 0.000 1_bss: 0.1617 0.1608 0.083 5.255 8.4 118.9 19.5 258 0.000 1_settarget: 0.1617 0.1608 0.083 5.255 8.4 118.9 19.5 258 0.000 1_nqh: 0.1622 0.1620 0.083 5.255 8.4 118.9 19.5 258 0.010 1_weight: 0.1622 0.1620 0.083 5.255 8.4 118.9 19.5 258 0.010 1_xyzrec: 0.1355 0.1633 0.009 0.970 8.4 118.9 19.5 258 0.164 1_adp: 0.1276 0.1664 0.009 0.970 6.2 113.9 20.0 258 0.164 1_regHadp: 0.1280 0.1673 0.009 0.970 6.2 113.9 20.0 258 0.164 1_occ: 0.1275 0.1660 0.009 0.970 6.2 113.9 20.0 258 0.164 2_bss: 0.1275 0.1655 0.009 0.970 5.8 113.5 19.6 258 0.164 2_settarget: 0.1275 0.1655 0.009 0.970 5.8 113.5 19.6 258 0.164 2_updatecdl: 0.1275 0.1655 0.009 0.990 5.8 113.5 19.6 258 0.164 2_nqh: 0.1277 0.1656 0.009 0.990 5.8 113.5 19.6 258 0.158 2_sol: 0.1244 0.1591 0.009 0.990 5.8 112.5 20.9 356 n/a 2_weight: 0.1244 0.1591 0.009 0.990 5.8 112.5 20.9 356 n/a 2_xyzrec: 0.1218 0.1612 0.009 0.941 5.8 112.5 20.9 356 n/a 2_adp: 0.1204 0.1629 0.009 0.941 6.8 107.5 21.2 356 n/a 2_regHadp: 0.1205 0.1631 0.009 0.941 6.8 107.5 21.2 356 n/a 2_occ: 0.1200 0.1638 0.009 0.941 6.8 107.5 21.2 356 n/a 3_bss: 0.1192 0.1625 0.009 0.941 6.3 107.0 20.7 356 n/a 3_settarget: 0.1192 0.1625 0.009 0.941 6.3 107.0 20.7 356 n/a 3_updatecdl: 0.1192 0.1625 0.009 0.939 6.3 107.0 20.7 356 n/a 3_nqh: 0.1193 0.1625 0.009 0.939 6.3 107.0 20.7 356 n/a 3_sol: 0.1202 0.1558 0.009 0.939 6.3 107.0 20.7 398 n/a 3_weight: 0.1202 0.1558 0.009 0.939 6.3 107.0 20.7 398 n/a 3_xyzrec: 0.1179 0.1560 0.009 0.945 6.3 107.0 20.7 398 n/a 3_adp: 0.1159 0.1580 0.009 0.945 6.1 105.2 20.6 398 n/a 3_regHadp: 0.1159 0.1579 0.009 0.945 6.1 105.2 20.6 398 n/a 3_occ: 0.1153 0.1579 0.009 0.945 6.1 105.2 20.6 398 n/a 4_bss: 0.1145 0.1573 0.009 0.945 5.8 104.8 20.2 398 n/a 4_settarget: 0.1145 0.1573 0.009 0.945 5.8 104.8 20.2 398 n/a 4_updatecdl: 0.1145 0.1573 0.009 0.944 5.8 104.8 20.2 398 n/a 4_nqh: 0.1145 0.1573 0.009 0.944 5.8 104.8 20.2 398 n/a 4_sol: 0.1133 0.1538 0.009 0.944 5.8 104.8 20.9 454 n/a 4_weight: 0.1133 0.1538 0.009 0.944 5.8 104.8 20.9 454 n/a 4_xyzrec: 0.1124 0.1560 0.009 0.969 5.8 104.8 20.9 454 n/a 4_adp: 0.1111 0.1551 0.009 0.969 5.4 102.9 20.9 454 n/a 4_regHadp: 0.1111 0.1551 0.009 0.969 5.4 102.9 20.9 454 n/a 4_occ: 0.1100 0.1566 0.009 0.969 5.4 102.9 20.9 454 n/a 5_bss: 0.1099 0.1565 0.009 0.969 5.1 102.6 20.7 454 n/a 5_settarget: 0.1099 0.1565 0.009 0.969 5.1 102.6 20.7 454 n/a 5_updatecdl: 0.1099 0.1565 0.009 0.972 5.1 102.6 20.7 454 n/a 5_setrh: 0.1101 0.1563 0.009 0.972 5.1 102.6 20.7 454 n/a 5_nqh: 0.1101 0.1563 0.009 0.972 5.1 102.6 20.7 454 n/a 5_sol: 0.1102 0.1513 0.009 0.972 5.1 102.6 20.8 468 n/a 5_weight: 0.1102 0.1513 0.009 0.972 5.1 102.6 20.8 468 n/a 5_xyzrec: 0.1118 0.1508 0.010 1.046 5.1 102.6 20.8 468 n/a 5_adp: 0.1106 0.1501 0.010 1.046 5.3 102.3 20.9 468 n/a 5_regHadp: 0.1106 0.1501 0.010 1.046 5.3 102.3 20.9 468 n/a 5_occ: 0.1100 0.1509 0.010 1.046 5.3 102.3 20.9 468 n/a end: 0.1100 0.1509 0.010 1.046 5.1 102.1 20.7 468 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4023827_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4023827_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3200 Refinement macro-cycles (run) : 924.3400 Write final files (write_after_run_outputs) : 21.9400 Total : 949.6000 Total CPU time: 16.26 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:16 PST -0800 (1735494076.25 s) Start R-work = 0.1617, R-free = 0.1608 Final R-work = 0.1100, R-free = 0.1509 =============================================================================== Job complete usr+sys time: 998.55 seconds wall clock time: 17 minutes 1.19 seconds (1021.19 seconds total)