Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6197065.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_6197065.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6197065.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 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.29, per 1000 atoms: 0.38 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: 0.35 Conformation dependent library (CDL) restraints added in 106.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.92: 546 0.92 - 1.18: 1113 1.18 - 1.45: 756 1.45 - 1.72: 725 1.72 - 1.99: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 52 " pdb=" C ILE A 52 " ideal model delta sigma weight residual 1.522 1.303 0.219 1.19e-02 7.06e+03 3.38e+02 bond pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 1.237 1.439 -0.202 1.11e-02 8.12e+03 3.30e+02 bond pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 1.331 1.567 -0.236 1.38e-02 5.25e+03 2.93e+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 2.92e+02 bond pdb=" C PRO A 184 " pdb=" O PRO A 184 " ideal model delta sigma weight residual 1.238 0.996 0.242 1.42e-02 4.96e+03 2.91e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 2838 4.18 - 8.35: 1931 8.35 - 12.52: 780 12.52 - 16.70: 196 16.70 - 20.87: 32 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1 GLN A 45 " pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 122.60 107.47 15.13 1.00e+00 1.00e+00 2.29e+02 angle pdb=" CA GLY A 120 " pdb=" C GLY A 120 " pdb=" O GLY A 120 " ideal model delta sigma weight residual 119.27 133.52 -14.25 1.01e+00 9.80e-01 1.99e+02 angle pdb=" O VAL A 51 " pdb=" C VAL A 51 " pdb=" N ILE A 52 " ideal model delta sigma weight residual 123.10 106.77 16.33 1.17e+00 7.31e-01 1.95e+02 angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.12 136.84 -14.72 1.06e+00 8.90e-01 1.93e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.91 108.45 13.46 9.80e-01 1.04e+00 1.89e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.81: 1316 17.81 - 35.60: 113 35.60 - 53.39: 40 53.39 - 71.18: 10 71.18 - 88.97: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 20 " pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" CB VAL A 20 " ideal model delta harmonic sigma weight residual -122.00 -145.98 23.98 0 2.50e+00 1.60e-01 9.20e+01 dihedral pdb=" N VAL A 20 " pdb=" C VAL A 20 " pdb=" CA VAL A 20 " pdb=" CB VAL A 20 " ideal model delta harmonic sigma weight residual 123.40 143.84 -20.44 0 2.50e+00 1.60e-01 6.68e+01 dihedral pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual 122.80 140.54 -17.74 0 2.50e+00 1.60e-01 5.04e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.209: 97 0.209 - 0.415: 87 0.415 - 0.620: 36 0.620 - 0.826: 18 0.826 - 1.031: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 20 " pdb=" N VAL A 20 " pdb=" C VAL A 20 " pdb=" CB VAL A 20 " both_signs ideal model delta sigma weight residual False 2.44 1.41 1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" CA AASN A 76 " pdb=" N AASN A 76 " pdb=" C AASN A 76 " pdb=" CB AASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 3.48 -0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CG LEU A 101 " pdb=" CB LEU A 101 " pdb=" CD1 LEU A 101 " pdb=" CD2 LEU A 101 " both_signs ideal model delta sigma weight residual False -2.59 -1.66 -0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.050 2.00e-02 2.50e+03 7.04e-02 1.49e+02 pdb=" CG PHE A 162 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.101 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.119 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.081 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.034 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.049 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.076 2.00e-02 2.50e+03 6.09e-02 1.11e+02 pdb=" CG PHE A 119 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.080 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.096 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.070 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.046 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.096 2.00e-02 2.50e+03 5.59e-02 9.37e+01 pdb=" CG PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.083 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.011 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.100 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.053 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.023 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 588 2.24 - 2.83: 7474 2.83 - 3.42: 10735 3.42 - 4.01: 15411 4.01 - 4.60: 22349 Nonbonded interactions: 56557 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.647 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.732 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.800 2.100 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.851 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.864 2.450 ... (remaining 56552 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_6197065_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= 0.2786 r_free= 0.1842 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.412487 | | target function (ml) not normalized (work): 71672.032634 | | target function (ml) not normalized (free): 3269.794876 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3182 0.2144 7.5376 5.036| | 2: 3.63 - 2.88 1.00 2711 122 0.2635 0.1719 4.3271 4.3258| | 3: 2.88 - 2.52 1.00 2682 148 0.2558 0.1804 4.1829 4.1783| | 4: 2.52 - 2.29 1.00 2661 139 0.2564 0.1480 3.511 3.563| | 5: 2.29 - 2.13 1.00 2678 122 0.2675 0.1521 3.417 3.4526| | 6: 2.13 - 2.00 1.00 2692 117 0.2732 0.1994 3.3361 3.474| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.54 0.77 0.23 1303.07| | 2: 3.63 - 2.88 2711 122 0.83 23.81 1.31 0.23 1303.07| | 3: 2.88 - 2.52 2682 148 0.73 32.76 1.29 0.23 1303.07| | 4: 2.52 - 2.29 2661 139 0.93 11.96 1.30 0.26 144.22| | 5: 2.29 - 2.13 2678 122 0.92 14.16 1.32 0.26 144.22| | 6: 2.13 - 2.00 2692 117 0.89 16.89 1.34 0.26 144.22| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 144.22 max = 1303.07 mean = 730.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.96 mean = 19.52| |phase err.(test): min = 0.00 max = 89.57 mean = 19.92| |-----------------------------------------------------------------------------| ----------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 0.248 1557 Z= 5.480 Angle : 5.477 18.164 2118 Z= 3.848 Chirality : 0.364 1.031 243 Planarity : 0.029 0.081 284 Dihedral : 13.920 88.967 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 1.62 % Allowed : 1.62 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Cbeta Deviations : 26.49 % 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: -2.94 (0.46), residues: 224 helix: -2.72 (0.35), residues: 109 sheet: -1.48 (0.69), residues: 38 loop : -0.50 (0.67), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.076 0.019 ARG A 5 TYR 0.067 0.032 TYR A 139 PHE 0.122 0.051 PHE A 162 HIS 0.014 0.008 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= 0.2786 r_free= 0.1842 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.412487 | | target function (ml) not normalized (work): 71672.032634 | | target function (ml) not normalized (free): 3269.794876 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2978 percent. r_work = 0.2915 r_free = 0.1987 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2863 0.2915 0.1987 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2863 0.2915 0.1987 n_refl.: 17050 remove outliers: r(all,work,free)=0.2151 0.2162 0.1987 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2124 0.2134 0.1970 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1608 0.1605 0.1665 n_refl.: 17045 remove outliers: r(all,work,free)=0.1606 0.1603 0.1665 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 0.3815 399.066 363.494 0.657 1.011 0.406 11.894-9.307 99.02 97 4 0.1851 633.811 614.950 0.925 1.013 0.390 9.237-7.194 100.00 213 7 0.2185 518.394 509.043 0.959 1.012 0.345 7.162-5.571 100.00 427 22 0.2349 389.055 377.261 0.925 1.011 0.321 5.546-4.326 100.00 867 58 0.1391 534.110 528.928 0.961 1.009 0.235 4.315-3.360 100.00 1859 96 0.1275 507.944 503.815 1.018 1.006 0.212 3.356-2.611 100.00 3867 181 0.1637 333.690 329.409 1.013 1.000 0.034 2.608-2.000 99.99 8818 434 0.1646 217.509 213.603 1.032 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4864 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1603 r_free=0.1665 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.1605 r_free=0.1668 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.368204 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.897470 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1351 0.1633 0.0283 0.009 1.0 1.6 0.5 0.0 0 11.684 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.33 2.83 3.013 18.442 0.897 0.023 12.76 16.53 3.77 3.644 18.730 0.897 0.020 Individual atomic B min max mean iso aniso Overall: 6.20 113.88 20.02 4.07 1785 0 Protein: 6.20 112.70 17.26 4.07 1519 0 Water: 8.82 113.88 36.02 N/A 258 0 Other: 22.06 36.90 26.51 N/A 8 0 Chain A: 6.20 113.88 20.02 N/A 1785 0 Histogram: Values Number of atoms 6.20 - 16.97 1084 16.97 - 27.74 339 27.74 - 38.51 187 38.51 - 49.28 101 49.28 - 60.04 47 60.04 - 70.81 13 70.81 - 81.58 6 81.58 - 92.35 5 92.35 - 103.11 0 103.11 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1653 r_work=0.1279 r_free=0.1661 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1279 r_free = 0.1661 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 = 0.1655 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.24 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= 0.1655 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019956 | | target function (ls_wunit_k1) not normalized (work): 324.005395 | | target function (ls_wunit_k1) not normalized (free): 27.196891 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1655 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1910 0.1909 0.1993 n_refl.: 17043 remove outliers: r(all,work,free)=0.1910 0.1909 0.1993 n_refl.: 17043 overall B=-0.40 to atoms: r(all,work,free)=0.1881 0.1879 0.1977 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1648 n_refl.: 17043 remove outliers: r(all,work,free)=0.1293 0.1275 0.1648 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 0.3552 306.967 292.491 0.670 1.004 0.393 11.894-9.307 99.02 97 4 0.1699 487.537 476.676 0.922 1.005 0.380 9.237-7.194 100.00 213 7 0.1815 398.756 396.068 0.962 1.005 0.341 7.162-5.571 100.00 427 22 0.1854 299.267 293.739 0.934 1.005 0.311 5.546-4.326 100.00 867 58 0.1046 410.845 408.737 0.962 1.004 0.215 4.315-3.360 100.00 1859 96 0.0932 390.718 389.926 1.019 1.003 0.201 3.356-2.611 100.00 3867 181 0.1295 256.679 255.320 1.015 1.001 0.091 2.608-2.000 99.99 8818 434 0.1348 167.311 165.908 1.020 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.4462 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1648 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1277 r_free=0.1648 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1648 | n_water=258 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1287 r_free=0.1642 | n_water=251 | time (s): 20.350 (total time: 21.080) Filter (q & B) r_work=0.1287 r_free=0.1643 | n_water=249 | time (s): 2.020 (total time: 23.100) Compute maps r_work=0.1287 r_free=0.1643 | n_water=249 | time (s): 0.700 (total time: 23.800) Filter (map) r_work=0.1318 r_free=0.1632 | n_water=209 | time (s): 1.520 (total time: 25.320) Find peaks r_work=0.1318 r_free=0.1632 | n_water=209 | time (s): 0.470 (total time: 25.790) Add new water r_work=0.1552 r_free=0.1885 | n_water=368 | time (s): 1.770 (total time: 27.560) Refine new water occ: r_work=0.1342 r_free=0.1621 adp: r_work=0.1281 r_free=0.1601 occ: r_work=0.1286 r_free=0.1574 adp: r_work=0.1250 r_free=0.1568 occ: r_work=0.1252 r_free=0.1558 adp: r_work=0.1240 r_free=0.1560 ADP+occupancy (water only), MIN, final r_work=0.1240 r_free=0.1560 r_work=0.1240 r_free=0.1560 | n_water=368 | time (s): 16.060 (total time: 43.620) Filter (q & B) r_work=0.1243 r_free=0.1565 | n_water=358 | time (s): 2.400 (total time: 46.020) Filter (dist only) r_work=0.1244 r_free=0.1567 | n_water=357 | time (s): 28.960 (total time: 74.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.573962 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.003656 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 0.1212 0.1602 0.0390 0.008 0.9 1.9 0.5 0.0 0 12.287 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 16.02 3.90 4.174 21.125 1.004 0.018 11.97 16.23 4.26 4.232 21.354 1.004 0.018 Individual atomic B min max mean iso aniso Overall: 6.80 107.30 21.33 4.23 1884 0 Protein: 6.80 107.30 17.71 4.21 1519 0 Water: 8.39 74.64 36.43 N/A 357 0 Other: 25.44 50.79 36.24 N/A 8 0 Chain A: 6.80 107.30 19.40 N/A 1736 0 Chain S: 18.20 65.45 44.04 N/A 148 0 Histogram: Values Number of atoms 6.80 - 16.85 1045 16.85 - 26.90 358 26.90 - 36.95 214 36.95 - 47.00 154 47.00 - 57.05 77 57.05 - 67.10 25 67.10 - 77.15 4 77.15 - 87.20 5 87.20 - 97.25 0 97.25 - 107.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1623 r_work=0.1199 r_free=0.1625 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1625 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 = 0.1198 r_free = 0.1618 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= 0.1198 r_free= 0.1618 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017125 | | target function (ls_wunit_k1) not normalized (work): 278.045135 | | target function (ls_wunit_k1) not normalized (free): 25.407597 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1198 0.1618 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1828 0.1824 0.1977 n_refl.: 17043 remove outliers: r(all,work,free)=0.1828 0.1824 0.1977 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1801 0.1796 0.1958 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1192 0.1614 n_refl.: 17043 remove outliers: r(all,work,free)=0.1212 0.1192 0.1614 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 0.3459 306.967 288.741 0.635 1.004 0.377 11.894-9.307 99.02 97 4 0.1518 487.537 481.580 0.916 1.005 0.360 9.237-7.194 100.00 213 7 0.1653 398.756 399.536 0.975 1.005 0.299 7.162-5.571 100.00 427 22 0.1568 299.267 295.878 0.934 1.005 0.261 5.546-4.326 100.00 867 58 0.0874 410.845 408.295 0.957 1.004 0.211 4.315-3.360 100.00 1859 96 0.0830 390.718 389.770 1.014 1.003 0.201 3.356-2.611 100.00 3867 181 0.1205 256.679 255.811 1.011 1.001 0.121 2.608-2.000 99.99 8818 434 0.1327 167.311 166.341 1.016 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3569 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1614 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1614 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1614 | n_water=357 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1191 r_free=0.1615 | n_water=354 | time (s): 28.850 (total time: 29.560) Filter (q & B) r_work=0.1191 r_free=0.1615 | n_water=354 | time (s): 0.750 (total time: 30.310) Compute maps r_work=0.1191 r_free=0.1615 | n_water=354 | time (s): 0.560 (total time: 30.870) Filter (map) r_work=0.1264 r_free=0.1619 | n_water=254 | time (s): 1.740 (total time: 32.610) Find peaks r_work=0.1264 r_free=0.1619 | n_water=254 | time (s): 0.490 (total time: 33.100) Add new water r_work=0.1465 r_free=0.1863 | n_water=412 | time (s): 1.550 (total time: 34.650) Refine new water occ: r_work=0.1256 r_free=0.1619 adp: r_work=0.1250 r_free=0.1621 occ: r_work=0.1228 r_free=0.1589 adp: r_work=0.1218 r_free=0.1587 occ: r_work=0.1207 r_free=0.1561 adp: r_work=0.1198 r_free=0.1557 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1557 r_work=0.1198 r_free=0.1557 | n_water=412 | time (s): 32.730 (total time: 67.380) Filter (q & B) r_work=0.1199 r_free=0.1567 | n_water=400 | time (s): 2.070 (total time: 69.450) Filter (dist only) r_work=0.1199 r_free=0.1564 | n_water=398 | time (s): 32.270 (total time: 101.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.850999 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.178630 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 0.1185 0.1556 0.0371 0.009 0.9 3.8 0.5 0.0 0 0.925 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.85 15.56 3.71 4.308 21.477 0.179 5.001 11.64 15.60 3.96 4.930 21.423 0.179 4.978 Individual atomic B min max mean iso aniso Overall: 6.34 104.94 20.89 4.81 1925 0 Protein: 6.34 104.94 17.03 4.80 1519 0 Water: 8.67 60.38 35.35 N/A 398 0 Other: 22.80 45.41 32.48 N/A 8 0 Chain A: 6.34 104.94 18.77 N/A 1734 0 Chain S: 17.38 60.26 40.13 N/A 191 0 Histogram: Values Number of atoms 6.34 - 16.20 1060 16.20 - 26.06 358 26.06 - 35.92 208 35.92 - 45.78 179 45.78 - 55.64 84 55.64 - 65.50 24 65.50 - 75.36 4 75.36 - 85.22 4 85.22 - 95.08 2 95.08 - 104.94 2 =========================== Idealize ADP of riding H ========================== r_work=0.1164 r_free=0.1560 r_work=0.1164 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1164 r_free = 0.1563 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1155 r_free = 0.1541 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1155 r_free= 0.1541 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.967721 | | target function (ml) not normalized (work): 80655.917555 | | target function (ml) not normalized (free): 4189.635325 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1174 0.1155 0.1541 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1734 0.1732 0.1829 n_refl.: 17043 remove outliers: r(all,work,free)=0.1734 0.1732 0.1829 n_refl.: 17043 overall B=-0.37 to atoms: r(all,work,free)=0.1707 0.1704 0.1815 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1171 0.1152 0.1537 n_refl.: 17043 remove outliers: r(all,work,free)=0.1169 0.1150 0.1537 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 0.3600 302.916 282.000 0.577 1.006 0.353 11.894-9.307 99.02 97 4 0.1761 487.537 477.953 0.911 1.007 0.340 9.237-7.194 100.00 213 7 0.1815 398.756 399.294 0.980 1.007 0.255 7.162-5.571 100.00 427 22 0.1687 299.267 293.103 0.936 1.007 0.251 5.546-4.326 100.00 867 58 0.0944 410.845 407.698 0.961 1.006 0.201 4.315-3.360 100.00 1859 96 0.0904 390.718 388.848 1.011 1.004 0.201 3.356-2.611 100.00 3867 181 0.1298 256.679 254.586 1.012 1.001 0.131 2.608-2.000 99.99 8818 434 0.1073 167.311 165.970 1.017 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9554 b_overall=-1.3298 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1150 r_free=0.1537 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=0.1151 r_free=0.1535 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1151 r_free=0.1535 | n_water=398 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1154 r_free=0.1531 | n_water=397 | time (s): 33.320 (total time: 34.050) Filter (q & B) r_work=0.1154 r_free=0.1531 | n_water=396 | time (s): 1.650 (total time: 35.700) Compute maps r_work=0.1154 r_free=0.1531 | n_water=396 | time (s): 0.700 (total time: 36.400) Filter (map) r_work=0.1214 r_free=0.1571 | n_water=310 | time (s): 2.040 (total time: 38.440) Find peaks r_work=0.1214 r_free=0.1571 | n_water=310 | time (s): 0.460 (total time: 38.900) Add new water r_work=0.1357 r_free=0.1698 | n_water=454 | time (s): 1.530 (total time: 40.430) Refine new water occ: r_work=0.1190 r_free=0.1529 adp: r_work=0.1184 r_free=0.1534 occ: r_work=0.1166 r_free=0.1500 adp: r_work=0.1158 r_free=0.1505 occ: r_work=0.1149 r_free=0.1481 adp: r_work=0.1141 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1141 r_free=0.1485 r_work=0.1141 r_free=0.1485 | n_water=454 | time (s): 23.220 (total time: 63.650) Filter (q & B) r_work=0.1144 r_free=0.1488 | n_water=445 | time (s): 1.650 (total time: 65.300) Filter (dist only) r_work=0.1144 r_free=0.1488 | n_water=444 | time (s): 36.620 (total time: 101.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.881939 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.168563 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 0.1529 0.0399 0.009 1.0 4.8 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 15.29 3.99 4.567 21.176 0.169 4.959 11.19 15.22 4.03 4.706 21.180 0.169 4.952 Individual atomic B min max mean iso aniso Overall: 5.44 103.26 21.05 4.90 1971 0 Protein: 5.44 103.26 16.60 4.90 1519 0 Water: 8.31 63.64 36.09 N/A 444 0 Other: 21.34 40.47 29.78 N/A 8 0 Chain A: 5.44 103.26 18.26 N/A 1733 0 Chain S: 17.79 63.64 41.35 N/A 238 0 Histogram: Values Number of atoms 5.44 - 15.22 1001 15.22 - 25.00 402 25.00 - 34.78 223 34.78 - 44.57 189 44.57 - 54.35 99 54.35 - 64.13 42 64.13 - 73.92 7 73.92 - 83.70 3 83.70 - 93.48 3 93.48 - 103.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.1119 r_free=0.1522 r_work=0.1119 r_free=0.1522 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1119 r_free = 0.1522 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1108 r_free = 0.1539 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1108 r_free= 0.1539 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ml) (work): 4.948763 | | target function (ml) not normalized (work): 80333.275083 | | target function (ml) not normalized (free): 4181.391701 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1108 0.1539 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1590 0.1577 0.1871 n_refl.: 17040 remove outliers: r(all,work,free)=0.1590 0.1577 0.1871 n_refl.: 17040 overall B=-0.28 to atoms: r(all,work,free)=0.1573 0.1559 0.1862 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1105 0.1540 n_refl.: 17040 remove outliers: r(all,work,free)=0.1126 0.1105 0.1540 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 0.3704 302.916 279.020 0.561 1.002 0.350 11.894-9.307 99.02 97 4 0.1866 487.537 480.214 0.911 1.004 0.330 9.237-7.194 100.00 213 7 0.1759 398.756 400.745 0.983 1.004 0.230 7.162-5.571 100.00 427 22 0.1552 299.267 293.177 0.936 1.004 0.200 5.546-4.326 100.00 867 58 0.0910 410.845 407.560 0.964 1.003 0.191 4.315-3.360 100.00 1859 96 0.0837 390.718 388.558 1.007 1.002 0.181 3.356-2.611 100.00 3867 181 0.1245 256.679 254.475 1.005 1.001 0.131 2.608-2.000 99.99 8818 434 0.1044 167.311 166.208 1.001 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9692 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1105 r_free=0.1540 After: r_work=0.1107 r_free=0.1540 ================================== NQH flips ================================== r_work=0.1107 r_free=0.1540 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1107 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1107 r_free=0.1540 | n_water=444 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1107 r_free=0.1540 | n_water=444 | time (s): 34.810 (total time: 35.530) Filter (q & B) r_work=0.1107 r_free=0.1540 | n_water=444 | time (s): 1.470 (total time: 37.000) Compute maps r_work=0.1107 r_free=0.1540 | n_water=444 | time (s): 0.760 (total time: 37.760) Filter (map) r_work=0.1173 r_free=0.1571 | n_water=334 | time (s): 1.860 (total time: 39.620) Find peaks r_work=0.1173 r_free=0.1571 | n_water=334 | time (s): 0.470 (total time: 40.090) Add new water r_work=0.1291 r_free=0.1689 | n_water=464 | time (s): 1.450 (total time: 41.540) Refine new water occ: r_work=0.1142 r_free=0.1529 adp: r_work=0.1136 r_free=0.1527 occ: r_work=0.1123 r_free=0.1511 adp: r_work=0.1116 r_free=0.1509 occ: r_work=0.1111 r_free=0.1495 adp: r_work=0.1105 r_free=0.1496 ADP+occupancy (water only), MIN, final r_work=0.1105 r_free=0.1496 r_work=0.1105 r_free=0.1496 | n_water=464 | time (s): 31.250 (total time: 72.790) Filter (q & B) r_work=0.1108 r_free=0.1499 | n_water=458 | time (s): 2.180 (total time: 74.970) Filter (dist only) r_work=0.1107 r_free=0.1502 | n_water=457 | time (s): 37.910 (total time: 112.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.085157 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.163696 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 0.1119 0.1535 0.0416 0.010 1.0 7.0 0.5 0.0 0 1.043 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.19 15.35 4.16 4.583 20.866 0.164 4.952 11.10 15.20 4.10 4.700 20.861 0.164 4.941 Individual atomic B min max mean iso aniso Overall: 5.34 102.67 20.82 5.00 1984 0 Protein: 5.34 102.67 16.23 5.00 1519 0 Water: 8.09 63.86 35.96 N/A 457 0 Other: 20.98 37.15 27.36 N/A 8 0 Chain A: 5.34 102.67 17.86 N/A 1733 0 Chain S: 18.34 63.86 41.26 N/A 251 0 Histogram: Values Number of atoms 5.34 - 15.07 1032 15.07 - 24.80 381 24.80 - 34.54 215 34.54 - 44.27 194 44.27 - 54.00 114 54.00 - 63.74 30 63.74 - 73.47 9 73.47 - 83.20 3 83.20 - 92.94 2 92.94 - 102.67 4 =========================== Idealize ADP of riding H ========================== r_work=0.1110 r_free=0.1520 r_work=0.1109 r_free=0.1520 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1109 r_free = 0.1520 target_work(ml) = 4.941 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1106 r_free = 0.1517 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1106 r_free= 0.1517 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.936399 | | target function (ml) not normalized (work): 80132.571183 | | target function (ml) not normalized (free): 4165.519779 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1126 0.1425 5.4667 5.6759| | 2: 3.63 - 2.88 1.00 2711 122 0.1079 0.1429 5.2147 5.3197| | 3: 2.88 - 2.52 1.00 2681 148 0.1350 0.1696 5.125 5.2014| | 4: 2.52 - 2.29 1.00 2661 139 0.0933 0.1528 4.6308 4.938| | 5: 2.29 - 2.13 1.00 2678 122 0.0964 0.1483 4.5802 4.8928| | 6: 2.13 - 2.00 1.00 2692 117 0.1122 0.1759 4.5712 4.7943| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.95 8.93 1.00 0.96 6318.56| | 2: 3.63 - 2.88 2711 122 0.92 12.83 1.01 0.96 6318.56| | 3: 2.88 - 2.52 2681 148 0.88 18.86 0.99 0.96 6318.56| | 4: 2.52 - 2.29 2661 139 0.93 12.16 1.01 0.97 2131.93| | 5: 2.29 - 2.13 2678 122 0.91 14.23 1.00 0.97 2131.93| | 6: 2.13 - 2.00 2692 117 0.89 16.97 0.99 0.97 2131.93| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2131.93 max = 6318.56 mean = 4247.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.95 mean = 13.96| |phase err.(test): min = 0.00 max = 89.18 mean = 13.54| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1106 0.1517 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1570 0.1557 0.1829 n_refl.: 17040 remove outliers: r(all,work,free)=0.1570 0.1557 0.1829 n_refl.: 17040 overall B=-0.22 to atoms: r(all,work,free)=0.1557 0.1544 0.1822 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1127 0.1108 0.1519 n_refl.: 17040 remove outliers: r(all,work,free)=0.1127 0.1108 0.1519 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 0.3693 302.916 280.436 0.543 1.000 0.330 11.894-9.307 99.02 97 4 0.1890 487.537 482.103 0.914 1.002 0.297 9.237-7.194 100.00 213 7 0.1775 398.756 400.716 0.983 1.002 0.220 7.162-5.571 100.00 427 22 0.1579 299.267 293.753 0.934 1.003 0.195 5.546-4.326 100.00 867 58 0.0931 410.845 407.603 0.966 1.003 0.190 4.315-3.360 100.00 1859 96 0.0860 390.718 388.625 1.004 1.002 0.191 3.356-2.611 100.00 3867 181 0.1234 256.679 254.458 1.002 1.001 0.111 2.608-2.000 99.99 8818 434 0.1036 167.311 166.037 0.988 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7776 ================= 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 : 0.2786 0.1842 0.083 5.477 8.8 119.3 19.9 258 0.000 1_bss: 0.1603 0.1665 0.083 5.477 8.4 118.9 19.5 258 0.000 1_settarget: 0.1603 0.1665 0.083 5.477 8.4 118.9 19.5 258 0.000 1_nqh: 0.1605 0.1668 0.083 5.477 8.4 118.9 19.5 258 0.006 1_weight: 0.1605 0.1668 0.083 5.477 8.4 118.9 19.5 258 0.006 1_xyzrec: 0.1351 0.1633 0.009 0.984 8.4 118.9 19.5 258 0.152 1_adp: 0.1276 0.1653 0.009 0.984 6.2 113.9 20.0 258 0.152 1_regHadp: 0.1279 0.1661 0.009 0.984 6.2 113.9 20.0 258 0.152 1_occ: 0.1275 0.1655 0.009 0.984 6.2 113.9 20.0 258 0.152 2_bss: 0.1275 0.1648 0.009 0.984 5.8 113.5 19.6 258 0.152 2_settarget: 0.1275 0.1648 0.009 0.984 5.8 113.5 19.6 258 0.152 2_updatecdl: 0.1275 0.1648 0.009 0.998 5.8 113.5 19.6 258 0.152 2_nqh: 0.1277 0.1648 0.009 0.998 5.8 113.5 19.6 258 0.149 2_sol: 0.1244 0.1567 0.009 0.998 5.8 112.3 20.9 357 n/a 2_weight: 0.1244 0.1567 0.009 0.998 5.8 112.3 20.9 357 n/a 2_xyzrec: 0.1212 0.1602 0.008 0.931 5.8 112.3 20.9 357 n/a 2_adp: 0.1197 0.1623 0.008 0.931 6.8 107.3 21.3 357 n/a 2_regHadp: 0.1199 0.1625 0.008 0.931 6.8 107.3 21.3 357 n/a 2_occ: 0.1198 0.1618 0.008 0.931 6.8 107.3 21.3 357 n/a 3_bss: 0.1192 0.1614 0.008 0.931 6.4 106.9 21.0 357 n/a 3_settarget: 0.1192 0.1614 0.008 0.931 6.4 106.9 21.0 357 n/a 3_updatecdl: 0.1192 0.1614 0.008 0.933 6.4 106.9 21.0 357 n/a 3_nqh: 0.1192 0.1614 0.008 0.933 6.4 106.9 21.0 357 n/a 3_sol: 0.1199 0.1564 0.008 0.933 6.4 106.9 21.0 398 n/a 3_weight: 0.1199 0.1564 0.008 0.933 6.4 106.9 21.0 398 n/a 3_xyzrec: 0.1185 0.1556 0.009 0.935 6.4 106.9 21.0 398 n/a 3_adp: 0.1164 0.1560 0.009 0.935 6.3 104.9 20.9 398 n/a 3_regHadp: 0.1164 0.1563 0.009 0.935 6.3 104.9 20.9 398 n/a 3_occ: 0.1155 0.1541 0.009 0.935 6.3 104.9 20.9 398 n/a 4_bss: 0.1150 0.1537 0.009 0.935 6.0 104.6 20.5 398 n/a 4_settarget: 0.1150 0.1537 0.009 0.935 6.0 104.6 20.5 398 n/a 4_updatecdl: 0.1150 0.1537 0.009 0.934 6.0 104.6 20.5 398 n/a 4_nqh: 0.1151 0.1535 0.009 0.934 6.0 104.6 20.5 398 n/a 4_sol: 0.1144 0.1488 0.009 0.934 6.0 104.6 21.0 444 n/a 4_weight: 0.1144 0.1488 0.009 0.934 6.0 104.6 21.0 444 n/a 4_xyzrec: 0.1130 0.1529 0.009 0.963 6.0 104.6 21.0 444 n/a 4_adp: 0.1119 0.1522 0.009 0.963 5.4 103.3 21.0 444 n/a 4_regHadp: 0.1119 0.1522 0.009 0.963 5.4 103.3 21.0 444 n/a 4_occ: 0.1108 0.1539 0.009 0.963 5.4 103.3 21.0 444 n/a 5_bss: 0.1105 0.1540 0.009 0.963 5.2 103.0 20.8 444 n/a 5_settarget: 0.1105 0.1540 0.009 0.963 5.2 103.0 20.8 444 n/a 5_updatecdl: 0.1105 0.1540 0.009 0.964 5.2 103.0 20.8 444 n/a 5_setrh: 0.1107 0.1540 0.009 0.964 5.2 103.0 20.8 444 n/a 5_nqh: 0.1107 0.1540 0.009 0.964 5.2 103.0 20.8 444 n/a 5_sol: 0.1107 0.1502 0.009 0.964 5.2 103.0 20.8 457 n/a 5_weight: 0.1107 0.1502 0.009 0.964 5.2 103.0 20.8 457 n/a 5_xyzrec: 0.1119 0.1535 0.010 1.045 5.2 103.0 20.8 457 n/a 5_adp: 0.1110 0.1520 0.010 1.045 5.3 102.7 20.8 457 n/a 5_regHadp: 0.1109 0.1520 0.010 1.045 5.3 102.7 20.8 457 n/a 5_occ: 0.1106 0.1517 0.010 1.045 5.3 102.7 20.8 457 n/a end: 0.1108 0.1519 0.010 1.045 5.1 102.4 20.6 457 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6197065_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6197065_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9900 Refinement macro-cycles (run) : 916.1300 Write final files (write_after_run_outputs) : 22.6800 Total : 941.8000 Total CPU time: 16.06 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:05 PST -0800 (1735494065.31 s) Start R-work = 0.1603, R-free = 0.1665 Final R-work = 0.1108, R-free = 0.1519 =============================================================================== Job complete usr+sys time: 987.11 seconds wall clock time: 16 minutes 50.08 seconds (1010.08 seconds total)