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_3675081.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" 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3675081.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3675081.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.82, per 1000 atoms: 0.54 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 208.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.91: 511 0.91 - 1.15: 1100 1.15 - 1.38: 528 1.38 - 1.61: 887 1.61 - 1.85: 127 Bond restraints: 3153 Sorted by residual: bond pdb=" N LEU A 7 " pdb=" CA LEU A 7 " ideal model delta sigma weight residual 1.458 1.241 0.217 1.22e-02 6.72e+03 3.16e+02 bond pdb=" CE1 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.321 1.495 -0.174 1.00e-02 1.00e+04 3.04e+02 bond pdb=" C THR A 140 " pdb=" N TYR A 141 " ideal model delta sigma weight residual 1.330 1.091 0.239 1.38e-02 5.25e+03 3.00e+02 bond pdb=" C SER A 142 " pdb=" O SER A 142 " ideal model delta sigma weight residual 1.235 1.430 -0.195 1.22e-02 6.72e+03 2.57e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.236 1.440 -0.204 1.29e-02 6.01e+03 2.51e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 3249 4.84 - 9.68: 1840 9.68 - 14.51: 603 14.51 - 19.35: 78 19.35 - 24.18: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 91 " pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 120.95 135.23 -14.28 1.04e+00 9.25e-01 1.89e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.91 134.83 -12.92 9.80e-01 1.04e+00 1.74e+02 angle pdb=" O BGLU A 94 " pdb=" C BGLU A 94 " pdb=" N GLN A 95 " ideal model delta sigma weight residual 122.15 136.82 -14.67 1.14e+00 7.69e-01 1.66e+02 angle pdb=" O ILE A 91 " pdb=" C ILE A 91 " pdb=" N LEU A 92 " ideal model delta sigma weight residual 121.87 109.39 12.48 9.70e-01 1.06e+00 1.66e+02 angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.61 136.53 -13.92 1.09e+00 8.42e-01 1.63e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 1319 17.80 - 35.59: 109 35.59 - 53.38: 41 53.38 - 71.18: 8 71.18 - 88.97: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ASP A 49 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual -122.60 -140.07 17.47 0 2.50e+00 1.60e-01 4.88e+01 dihedral pdb=" C GLN A 180 " pdb=" N GLN A 180 " pdb=" CA GLN A 180 " pdb=" CB GLN A 180 " ideal model delta harmonic sigma weight residual -122.60 -105.52 -17.08 0 2.50e+00 1.60e-01 4.67e+01 dihedral pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CA BTYR A 67 " pdb=" CB BTYR A 67 " ideal model delta harmonic sigma weight residual 122.80 105.88 16.92 0 2.50e+00 1.60e-01 4.58e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.189: 94 0.189 - 0.375: 57 0.375 - 0.561: 52 0.561 - 0.746: 31 0.746 - 0.932: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.44 -0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" CB THR A 160 " pdb=" CA THR A 160 " pdb=" OG1 THR A 160 " pdb=" CG2 THR A 160 " both_signs ideal model delta sigma weight residual False 2.55 1.66 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.86 0.86 2.00e-01 2.50e+01 1.85e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.120 2.00e-02 2.50e+03 6.91e-02 1.43e+02 pdb=" CG ATYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.078 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.034 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.063 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.098 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.021 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.041 2.00e-02 2.50e+03 6.81e-02 1.39e+02 pdb=" CG PHE A 162 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.094 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.025 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.106 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.162 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.050 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.017 2.00e-02 2.50e+03 5.68e-02 9.68e+01 pdb=" CG TYR A 139 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.119 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.097 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.059 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.052 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.24: 611 2.24 - 2.83: 7538 2.83 - 3.42: 10729 3.42 - 4.01: 15393 4.01 - 4.60: 22343 Nonbonded interactions: 56614 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.656 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.752 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.768 2.100 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.790 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.816 2.450 ... (remaining 56609 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_3675081_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= 0.1837 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.402872 | | target function (ml) not normalized (work): 71515.851704 | | target function (ml) not normalized (free): 3266.272346 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3166 0.2171 7.5217 5.0261| | 2: 3.63 - 2.88 1.00 2711 122 0.2643 0.1805 4.3306 4.346| | 3: 2.88 - 2.52 1.00 2682 148 0.2570 0.1659 4.1816 4.1824| | 4: 2.52 - 2.29 1.00 2661 139 0.2572 0.1532 3.5054 3.5957| | 5: 2.29 - 2.13 1.00 2678 122 0.2669 0.1412 3.4 3.3784| | 6: 2.13 - 2.00 1.00 2692 117 0.2741 0.1975 3.315 3.4697| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.59 0.77 0.23 1294.86| | 2: 3.63 - 2.88 2711 122 0.83 23.85 1.32 0.23 1294.86| | 3: 2.88 - 2.52 2682 148 0.73 32.97 1.28 0.23 1294.86| | 4: 2.52 - 2.29 2661 139 0.93 11.30 1.30 0.26 134.19| | 5: 2.29 - 2.13 2678 122 0.92 13.65 1.32 0.26 134.19| | 6: 2.13 - 2.00 2692 117 0.90 16.22 1.33 0.26 134.19| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 134.19 max = 1294.86 mean = 720.99| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 19.27| |phase err.(test): min = 0.00 max = 89.40 mean = 19.33| |-----------------------------------------------------------------------------| ----------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= 5.357 Angle : 5.301 18.512 2118 Z= 3.705 Chirality : 0.382 0.932 243 Planarity : 0.033 0.090 284 Dihedral : 14.152 88.970 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.08 % Favored : 98.38 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 34.05 % 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: -1.90 (0.51), residues: 224 helix: -2.49 (0.38), residues: 103 sheet: -1.14 (0.76), residues: 28 loop : 0.60 (0.67), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.018 ARG A 28 TYR 0.124 0.036 TYR A 139 PHE 0.096 0.028 PHE A 164 HIS 0.086 0.041 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= 0.1837 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.402872 | | target function (ml) not normalized (work): 71515.851704 | | target function (ml) not normalized (free): 3266.272346 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2951 percent. r_work = 0.2916 r_free = 0.1975 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2862 0.2916 0.1975 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2862 0.2916 0.1975 n_refl.: 17050 remove outliers: r(all,work,free)=0.2157 0.2168 0.1975 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2129 0.2140 0.1956 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1617 0.1615 0.1655 n_refl.: 17045 remove outliers: r(all,work,free)=0.1616 0.1614 0.1655 n_refl.: 17044 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.3990 394.686 365.360 0.644 1.025 0.397 11.894-9.307 99.02 97 4 0.1904 633.483 611.770 0.917 1.025 0.380 9.237-7.194 100.00 213 7 0.2166 518.125 509.059 0.950 1.024 0.360 7.162-5.571 100.00 427 22 0.2327 388.853 376.222 0.915 1.022 0.340 5.546-4.326 100.00 867 58 0.1386 533.833 528.685 0.951 1.018 0.241 4.315-3.360 100.00 1859 96 0.1292 507.681 503.473 1.008 1.011 0.202 3.356-2.611 100.00 3867 181 0.1669 333.517 328.766 1.013 0.999 0.071 2.608-2.000 99.99 8818 434 0.1643 217.396 213.423 1.043 0.978 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4539 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1614 r_free=0.1655 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1617 r_free=0.1654 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.458331 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.803987 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 0.1353 0.1651 0.0298 0.009 1.0 1.0 0.5 0.0 0 11.229 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.53 16.51 2.98 3.013 18.452 0.804 0.023 12.78 16.76 3.98 3.526 18.694 0.804 0.021 Individual atomic B min max mean iso aniso Overall: 6.27 113.89 19.94 4.01 1785 0 Protein: 6.27 112.76 17.18 4.01 1519 0 Water: 8.87 113.89 36.01 N/A 258 0 Other: 21.64 36.93 26.10 N/A 8 0 Chain A: 6.27 113.89 19.94 N/A 1785 0 Histogram: Values Number of atoms 6.27 - 17.03 1096 17.03 - 27.79 337 27.79 - 38.55 180 38.55 - 49.32 98 49.32 - 60.08 47 60.08 - 70.84 13 70.84 - 81.60 6 81.60 - 92.37 4 92.37 - 103.13 1 103.13 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1676 r_work=0.1281 r_free=0.1684 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1684 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1276 r_free = 0.1675 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1276 r_free= 0.1675 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020183 | | target function (ls_wunit_k1) not normalized (work): 327.706990 | | target function (ls_wunit_k1) not normalized (free): 27.476283 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1295 0.1276 0.1675 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1918 0.1917 0.1995 n_refl.: 17044 remove outliers: r(all,work,free)=0.1918 0.1917 0.1995 n_refl.: 17044 overall B=-0.40 to atoms: r(all,work,free)=0.1889 0.1887 0.1977 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1296 0.1277 0.1664 n_refl.: 17044 remove outliers: r(all,work,free)=0.1294 0.1275 0.1664 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3577 303.018 278.555 0.624 1.011 0.370 11.894-9.307 99.02 97 4 0.1713 487.357 476.269 0.917 1.011 0.367 9.237-7.194 100.00 213 7 0.1840 398.609 395.653 0.959 1.011 0.332 7.162-5.571 100.00 427 22 0.1862 299.157 294.126 0.933 1.010 0.315 5.546-4.326 100.00 867 58 0.1053 410.694 408.346 0.958 1.008 0.210 4.315-3.360 100.00 1859 96 0.0928 390.574 390.106 1.016 1.005 0.191 3.356-2.611 100.00 3867 181 0.1297 256.585 255.363 1.016 1.000 0.091 2.608-2.000 99.99 8818 434 0.1347 167.249 165.741 1.025 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4215 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1664 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1278 r_free=0.1667 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1278 r_free=0.1667 | n_water=258 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1287 r_free=0.1655 | n_water=252 | time (s): 19.730 (total time: 20.390) Filter (q & B) r_work=0.1287 r_free=0.1656 | n_water=250 | time (s): 1.570 (total time: 21.960) Compute maps r_work=0.1287 r_free=0.1656 | n_water=250 | time (s): 0.520 (total time: 22.480) Filter (map) r_work=0.1319 r_free=0.1642 | n_water=210 | time (s): 1.590 (total time: 24.070) Find peaks r_work=0.1319 r_free=0.1642 | n_water=210 | time (s): 0.470 (total time: 24.540) Add new water r_work=0.1543 r_free=0.1880 | n_water=371 | time (s): 2.100 (total time: 26.640) Refine new water occ: r_work=0.1336 r_free=0.1595 adp: r_work=0.1276 r_free=0.1593 occ: r_work=0.1281 r_free=0.1563 adp: r_work=0.1247 r_free=0.1570 occ: r_work=0.1248 r_free=0.1557 adp: r_work=0.1235 r_free=0.1558 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1558 r_work=0.1235 r_free=0.1558 | n_water=371 | time (s): 14.730 (total time: 41.370) Filter (q & B) r_work=0.1237 r_free=0.1561 | n_water=363 | time (s): 1.470 (total time: 42.840) Filter (dist only) r_work=0.1237 r_free=0.1560 | n_water=362 | time (s): 28.220 (total time: 71.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.638445 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.970928 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 0.1209 0.1591 0.0382 0.008 0.9 2.2 0.5 0.0 0 12.319 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 15.91 3.82 4.129 21.012 0.971 0.018 11.94 16.25 4.30 4.162 21.286 0.971 0.018 Individual atomic B min max mean iso aniso Overall: 6.50 107.37 21.34 4.20 1889 0 Protein: 6.50 107.37 17.73 4.19 1519 0 Water: 8.79 65.78 36.20 N/A 362 0 Other: 24.40 43.45 33.78 N/A 8 0 Chain A: 6.50 107.37 19.42 N/A 1737 0 Chain S: 17.51 65.14 43.23 N/A 152 0 Histogram: Values Number of atoms 6.50 - 16.59 1018 16.59 - 26.68 383 26.68 - 36.76 216 36.76 - 46.85 162 46.85 - 56.94 71 56.94 - 67.02 29 67.02 - 77.11 3 77.11 - 87.19 3 87.19 - 97.28 2 97.28 - 107.37 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1625 r_work=0.1196 r_free=0.1626 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1626 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1634 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1196 r_free= 0.1634 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017034 | | target function (ls_wunit_k1) not normalized (work): 276.547818 | | target function (ls_wunit_k1) not normalized (free): 25.276826 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1196 0.1634 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1759 0.1747 0.2012 n_refl.: 17042 remove outliers: r(all,work,free)=0.1759 0.1747 0.2012 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1734 0.1722 0.1994 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1190 0.1635 n_refl.: 17042 remove outliers: r(all,work,free)=0.1210 0.1189 0.1635 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 0.3279 299.860 283.592 0.600 1.002 0.350 11.894-9.307 99.02 97 4 0.1446 487.357 483.726 0.917 1.003 0.350 9.237-7.194 100.00 213 7 0.1674 398.609 398.528 0.976 1.003 0.290 7.162-5.571 100.00 427 22 0.1610 299.157 295.269 0.938 1.003 0.250 5.546-4.326 100.00 867 58 0.0871 410.694 408.478 0.964 1.003 0.231 4.315-3.360 100.00 1859 96 0.0833 390.574 389.501 1.016 1.002 0.201 3.356-2.611 100.00 3867 181 0.1196 256.585 255.762 1.012 1.001 0.131 2.608-2.000 99.99 8818 434 0.1327 167.249 166.203 1.015 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3679 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1635 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.1189 r_free=0.1635 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1635 | n_water=362 | time (s): 0.790 (total time: 0.790) Filter (dist) r_work=0.1189 r_free=0.1635 | n_water=362 | time (s): 28.040 (total time: 28.830) Filter (q & B) r_work=0.1189 r_free=0.1635 | n_water=362 | time (s): 0.850 (total time: 29.680) Compute maps r_work=0.1189 r_free=0.1635 | n_water=362 | time (s): 0.640 (total time: 30.320) Filter (map) r_work=0.1248 r_free=0.1657 | n_water=271 | time (s): 1.560 (total time: 31.880) Find peaks r_work=0.1248 r_free=0.1657 | n_water=271 | time (s): 0.430 (total time: 32.310) Add new water r_work=0.1431 r_free=0.1842 | n_water=421 | time (s): 1.650 (total time: 33.960) Refine new water occ: r_work=0.1242 r_free=0.1590 adp: r_work=0.1233 r_free=0.1603 occ: r_work=0.1217 r_free=0.1562 adp: r_work=0.1205 r_free=0.1573 occ: r_work=0.1198 r_free=0.1545 adp: r_work=0.1188 r_free=0.1552 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1552 r_work=0.1188 r_free=0.1552 | n_water=421 | time (s): 22.090 (total time: 56.050) Filter (q & B) r_work=0.1190 r_free=0.1562 | n_water=409 | time (s): 1.990 (total time: 58.040) Filter (dist only) r_work=0.1190 r_free=0.1562 | n_water=409 | time (s): 32.080 (total time: 90.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.108441 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.139015 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 0.1163 0.1573 0.0410 0.010 1.0 3.5 0.5 0.0 0 1.054 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 15.73 4.10 4.301 21.550 0.139 4.987 11.42 15.75 4.33 4.827 21.518 0.139 4.965 Individual atomic B min max mean iso aniso Overall: 6.37 104.64 21.04 4.56 1936 0 Protein: 6.37 104.64 17.05 4.56 1519 0 Water: 8.51 64.73 35.62 N/A 409 0 Other: 24.59 43.19 32.25 N/A 8 0 Chain A: 6.37 104.64 18.76 N/A 1733 0 Chain S: 16.46 64.73 40.48 N/A 203 0 Histogram: Values Number of atoms 6.37 - 16.20 1059 16.20 - 26.02 353 26.02 - 35.85 229 35.85 - 45.68 163 45.68 - 55.50 89 55.50 - 65.33 31 65.33 - 75.16 3 75.16 - 84.99 4 84.99 - 94.81 3 94.81 - 104.64 2 =========================== Idealize ADP of riding H ========================== r_work=0.1142 r_free=0.1575 r_work=0.1142 r_free=0.1575 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1142 r_free = 0.1575 target_work(ml) = 4.965 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1134 r_free = 0.1567 target_work(ml) = 4.958 | | 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= 0.1134 r_free= 0.1567 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.957785 | | target function (ml) not normalized (work): 80484.680617 | | target function (ml) not normalized (free): 4188.976685 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1155 0.1134 0.1567 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1672 0.1663 0.1871 n_refl.: 17041 remove outliers: r(all,work,free)=0.1672 0.1663 0.1871 n_refl.: 17041 overall B=-0.39 to atoms: r(all,work,free)=0.1644 0.1635 0.1856 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1152 0.1132 0.1563 n_refl.: 17041 remove outliers: r(all,work,free)=0.1152 0.1132 0.1563 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 0.3510 299.860 277.306 0.569 1.006 0.340 11.894-9.307 99.02 97 4 0.1750 487.357 480.842 0.907 1.006 0.340 9.237-7.194 100.00 213 7 0.1740 398.609 398.171 0.981 1.006 0.265 7.162-5.571 100.00 427 22 0.1590 299.157 294.193 0.944 1.006 0.251 5.546-4.326 100.00 867 58 0.0934 410.694 407.121 0.964 1.005 0.216 4.315-3.360 100.00 1859 96 0.0879 390.574 388.206 1.012 1.004 0.211 3.356-2.611 100.00 3867 181 0.1274 256.585 254.361 1.012 1.001 0.132 2.608-2.000 99.99 8818 434 0.1071 167.249 165.903 1.021 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3894 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1132 r_free=0.1563 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1132 r_free=0.1563 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1132 r_free=0.1563 | n_water=409 | time (s): 0.880 (total time: 0.880) Filter (dist) r_work=0.1136 r_free=0.1564 | n_water=408 | time (s): 33.890 (total time: 34.770) Filter (q & B) r_work=0.1136 r_free=0.1565 | n_water=407 | time (s): 1.620 (total time: 36.390) Compute maps r_work=0.1136 r_free=0.1565 | n_water=407 | time (s): 0.570 (total time: 36.960) Filter (map) r_work=0.1193 r_free=0.1588 | n_water=322 | time (s): 1.680 (total time: 38.640) Find peaks r_work=0.1193 r_free=0.1588 | n_water=322 | time (s): 0.560 (total time: 39.200) Add new water r_work=0.1328 r_free=0.1718 | n_water=466 | time (s): 1.950 (total time: 41.150) Refine new water occ: r_work=0.1168 r_free=0.1531 adp: r_work=0.1160 r_free=0.1539 occ: r_work=0.1145 r_free=0.1511 adp: r_work=0.1135 r_free=0.1517 occ: r_work=0.1128 r_free=0.1496 adp: r_work=0.1120 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1120 r_free=0.1499 r_work=0.1120 r_free=0.1499 | n_water=466 | time (s): 32.840 (total time: 73.990) Filter (q & B) r_work=0.1123 r_free=0.1504 | n_water=452 | time (s): 2.050 (total time: 76.040) Filter (dist only) r_work=0.1123 r_free=0.1504 | n_water=452 | time (s): 34.520 (total time: 110.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.976555 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.164586 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 0.1112 0.1531 0.0419 0.010 1.0 4.8 0.5 0.0 0 0.988 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.12 15.31 4.19 4.425 21.219 0.165 4.955 10.98 15.23 4.25 4.640 21.255 0.165 4.945 Individual atomic B min max mean iso aniso Overall: 5.73 102.91 21.22 4.84 1979 0 Protein: 5.73 102.91 16.63 4.84 1519 0 Water: 8.40 67.79 36.53 N/A 452 0 Other: 20.59 38.08 27.34 N/A 8 0 Chain A: 5.73 102.91 18.26 N/A 1731 0 Chain S: 17.95 67.79 41.86 N/A 248 0 Histogram: Values Number of atoms 5.73 - 15.45 1023 15.45 - 25.17 388 25.17 - 34.88 211 34.88 - 44.60 189 44.60 - 54.32 114 54.32 - 64.04 40 64.04 - 73.76 6 73.76 - 83.48 2 83.48 - 93.19 4 93.19 - 102.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1098 r_free=0.1523 r_work=0.1098 r_free=0.1522 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1098 r_free = 0.1522 target_work(ml) = 4.945 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1089 r_free = 0.1513 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1089 r_free= 0.1513 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.940317 | | target function (ml) not normalized (work): 80201.104075 | | target function (ml) not normalized (free): 4174.640849 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1110 0.1089 0.1513 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1585 0.1572 0.1852 n_refl.: 17041 remove outliers: r(all,work,free)=0.1585 0.1572 0.1852 n_refl.: 17041 overall B=-0.31 to atoms: r(all,work,free)=0.1565 0.1552 0.1841 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1107 0.1086 0.1502 n_refl.: 17041 remove outliers: r(all,work,free)=0.1106 0.1086 0.1502 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 0.3542 296.300 276.899 0.556 1.002 0.340 11.894-9.307 99.02 97 4 0.1799 487.357 481.244 0.911 1.003 0.320 9.237-7.194 100.00 213 7 0.1712 398.609 398.745 0.988 1.004 0.260 7.162-5.571 100.00 427 22 0.1478 299.157 293.025 0.943 1.003 0.210 5.546-4.326 100.00 867 58 0.0897 410.694 406.971 0.966 1.003 0.191 4.315-3.360 100.00 1859 96 0.0834 390.574 388.149 1.008 1.002 0.191 3.356-2.611 100.00 3867 181 0.1207 256.585 254.489 1.006 1.001 0.131 2.608-2.000 99.99 8818 434 0.1038 167.249 166.041 1.005 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.0569 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1086 r_free=0.1502 After: r_work=0.1088 r_free=0.1502 ================================== NQH flips ================================== r_work=0.1088 r_free=0.1502 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1088 r_free=0.1502 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1088 r_free=0.1502 | n_water=452 | time (s): 0.790 (total time: 0.790) Filter (dist) r_work=0.1088 r_free=0.1502 | n_water=452 | time (s): 34.870 (total time: 35.660) Filter (q & B) r_work=0.1088 r_free=0.1502 | n_water=452 | time (s): 0.970 (total time: 36.630) Compute maps r_work=0.1088 r_free=0.1502 | n_water=452 | time (s): 0.680 (total time: 37.310) Filter (map) r_work=0.1169 r_free=0.1548 | n_water=342 | time (s): 1.710 (total time: 39.020) Find peaks r_work=0.1169 r_free=0.1548 | n_water=342 | time (s): 0.470 (total time: 39.490) Add new water r_work=0.1289 r_free=0.1643 | n_water=481 | time (s): 1.690 (total time: 41.180) Refine new water occ: r_work=0.1131 r_free=0.1493 adp: r_work=0.1124 r_free=0.1500 occ: r_work=0.1110 r_free=0.1471 adp: r_work=0.1102 r_free=0.1481 occ: r_work=0.1094 r_free=0.1456 adp: r_work=0.1089 r_free=0.1466 ADP+occupancy (water only), MIN, final r_work=0.1089 r_free=0.1466 r_work=0.1089 r_free=0.1466 | n_water=481 | time (s): 31.830 (total time: 73.010) Filter (q & B) r_work=0.1093 r_free=0.1475 | n_water=466 | time (s): 2.050 (total time: 75.060) Filter (dist only) r_work=0.1093 r_free=0.1475 | n_water=466 | time (s): 35.790 (total time: 110.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.946486 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.156395 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 0.1110 0.1500 0.0390 0.010 1.1 7.4 0.5 0.0 0 0.973 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.10 15.00 3.90 4.544 20.961 0.156 4.936 11.00 14.86 3.86 4.592 21.036 0.156 4.926 Individual atomic B min max mean iso aniso Overall: 5.80 103.19 21.18 4.99 1993 0 Protein: 5.80 103.19 16.39 4.99 1519 0 Water: 8.32 65.35 36.67 N/A 466 0 Other: 20.22 36.57 26.56 N/A 8 0 Chain A: 5.80 103.19 18.01 N/A 1731 0 Chain S: 17.12 65.35 42.11 N/A 262 0 Histogram: Values Number of atoms 5.80 - 15.54 1061 15.54 - 25.28 354 25.28 - 35.02 207 35.02 - 44.75 205 44.75 - 54.49 115 54.49 - 64.23 34 64.23 - 73.97 8 73.97 - 83.71 3 83.71 - 93.45 3 93.45 - 103.19 3 =========================== Idealize ADP of riding H ========================== r_work=0.1100 r_free=0.1486 r_work=0.1100 r_free=0.1486 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1100 r_free = 0.1486 target_work(ml) = 4.925 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1095 r_free = 0.1481 target_work(ml) = 4.922 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1095 r_free= 0.1481 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.922041 | | target function (ml) not normalized (work): 79899.487713 | | target function (ml) not normalized (free): 4151.506874 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1096 0.1324 5.4359 5.5991| | 2: 3.63 - 2.88 1.00 2711 122 0.1070 0.1495 5.1978 5.3695| | 3: 2.88 - 2.52 1.00 2681 148 0.1337 0.1601 5.1105 5.1782| | 4: 2.52 - 2.29 1.00 2661 139 0.0935 0.1502 4.6195 4.924| | 5: 2.29 - 2.13 1.00 2678 122 0.0972 0.1529 4.5726 4.8894| | 6: 2.13 - 2.00 1.00 2692 117 0.1127 0.1744 4.567 4.7765| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.71 1.00 0.96 6080.12| | 2: 3.63 - 2.88 2711 122 0.93 12.49 1.01 0.96 6080.12| | 3: 2.88 - 2.52 2681 148 0.88 18.51 0.99 0.96 6080.12| | 4: 2.52 - 2.29 2661 139 0.93 11.86 1.01 0.98 2053.81| | 5: 2.29 - 2.13 2678 122 0.92 13.89 1.00 0.98 2053.81| | 6: 2.13 - 2.00 2692 117 0.90 16.58 0.99 0.98 2053.81| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2053.81 max = 6080.12 mean = 4088.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.95 mean = 13.64| |phase err.(test): min = 0.00 max = 89.17 mean = 13.33| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1114 0.1095 0.1481 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1577 0.1567 0.1796 n_refl.: 17040 remove outliers: r(all,work,free)=0.1577 0.1567 0.1796 n_refl.: 17040 overall B=-0.27 to atoms: r(all,work,free)=0.1561 0.1550 0.1785 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1114 0.1096 0.1478 n_refl.: 17040 remove outliers: r(all,work,free)=0.1114 0.1096 0.1478 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 0.3554 296.300 276.108 0.552 1.004 0.340 11.894-9.307 99.02 97 4 0.1746 487.357 482.141 0.910 1.005 0.330 9.237-7.194 100.00 213 7 0.1729 398.609 399.140 0.986 1.005 0.250 7.162-5.571 100.00 427 22 0.1501 299.157 294.026 0.936 1.005 0.203 5.546-4.326 100.00 867 58 0.0919 410.694 407.426 0.964 1.004 0.182 4.315-3.360 100.00 1859 96 0.0858 390.574 388.556 1.004 1.003 0.167 3.356-2.611 100.00 3867 181 0.1214 256.585 254.460 1.005 1.001 0.121 2.608-2.000 99.99 8818 434 0.1042 167.249 165.960 0.999 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9181 ================= 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 0.1837 0.083 5.301 8.8 119.3 19.9 258 0.000 1_bss: 0.1614 0.1655 0.083 5.301 8.4 118.9 19.5 258 0.000 1_settarget: 0.1614 0.1655 0.083 5.301 8.4 118.9 19.5 258 0.000 1_nqh: 0.1617 0.1654 0.083 5.301 8.4 118.9 19.5 258 0.003 1_weight: 0.1617 0.1654 0.083 5.301 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1353 0.1651 0.009 0.971 8.4 118.9 19.5 258 0.156 1_adp: 0.1278 0.1676 0.009 0.971 6.3 113.9 19.9 258 0.156 1_regHadp: 0.1281 0.1684 0.009 0.971 6.3 113.9 19.9 258 0.156 1_occ: 0.1276 0.1675 0.009 0.971 6.3 113.9 19.9 258 0.156 2_bss: 0.1275 0.1664 0.009 0.971 5.9 113.5 19.5 258 0.156 2_settarget: 0.1275 0.1664 0.009 0.971 5.9 113.5 19.5 258 0.156 2_updatecdl: 0.1275 0.1664 0.009 0.988 5.9 113.5 19.5 258 0.156 2_nqh: 0.1278 0.1667 0.009 0.988 5.9 113.5 19.5 258 0.153 2_sol: 0.1237 0.1560 0.009 0.988 5.9 112.4 20.8 362 n/a 2_weight: 0.1237 0.1560 0.009 0.988 5.9 112.4 20.8 362 n/a 2_xyzrec: 0.1209 0.1591 0.008 0.937 5.9 112.4 20.8 362 n/a 2_adp: 0.1194 0.1625 0.008 0.937 6.5 107.4 21.3 362 n/a 2_regHadp: 0.1196 0.1626 0.008 0.937 6.5 107.4 21.3 362 n/a 2_occ: 0.1196 0.1634 0.008 0.937 6.5 107.4 21.3 362 n/a 3_bss: 0.1189 0.1635 0.008 0.937 6.1 107.0 21.0 362 n/a 3_settarget: 0.1189 0.1635 0.008 0.937 6.1 107.0 21.0 362 n/a 3_updatecdl: 0.1189 0.1635 0.008 0.937 6.1 107.0 21.0 362 n/a 3_nqh: 0.1189 0.1635 0.008 0.937 6.1 107.0 21.0 362 n/a 3_sol: 0.1190 0.1562 0.008 0.937 6.1 107.0 21.1 409 n/a 3_weight: 0.1190 0.1562 0.008 0.937 6.1 107.0 21.1 409 n/a 3_xyzrec: 0.1163 0.1573 0.010 0.993 6.1 107.0 21.1 409 n/a 3_adp: 0.1142 0.1575 0.010 0.993 6.4 104.6 21.0 409 n/a 3_regHadp: 0.1142 0.1575 0.010 0.993 6.4 104.6 21.0 409 n/a 3_occ: 0.1134 0.1567 0.010 0.993 6.4 104.6 21.0 409 n/a 4_bss: 0.1132 0.1563 0.010 0.993 6.0 104.3 20.6 409 n/a 4_settarget: 0.1132 0.1563 0.010 0.993 6.0 104.3 20.6 409 n/a 4_updatecdl: 0.1132 0.1563 0.010 0.991 6.0 104.3 20.6 409 n/a 4_nqh: 0.1132 0.1563 0.010 0.991 6.0 104.3 20.6 409 n/a 4_sol: 0.1123 0.1504 0.010 0.991 6.0 104.3 21.2 452 n/a 4_weight: 0.1123 0.1504 0.010 0.991 6.0 104.3 21.2 452 n/a 4_xyzrec: 0.1112 0.1531 0.010 0.982 6.0 104.3 21.2 452 n/a 4_adp: 0.1098 0.1523 0.010 0.982 5.7 102.9 21.2 452 n/a 4_regHadp: 0.1098 0.1522 0.010 0.982 5.7 102.9 21.2 452 n/a 4_occ: 0.1089 0.1513 0.010 0.982 5.7 102.9 21.2 452 n/a 5_bss: 0.1086 0.1502 0.010 0.982 5.4 102.6 20.9 452 n/a 5_settarget: 0.1086 0.1502 0.010 0.982 5.4 102.6 20.9 452 n/a 5_updatecdl: 0.1086 0.1502 0.010 0.982 5.4 102.6 20.9 452 n/a 5_setrh: 0.1088 0.1502 0.010 0.982 5.4 102.6 20.9 452 n/a 5_nqh: 0.1088 0.1502 0.010 0.982 5.4 102.6 20.9 452 n/a 5_sol: 0.1093 0.1475 0.010 0.982 5.4 102.6 21.0 466 n/a 5_weight: 0.1093 0.1475 0.010 0.982 5.4 102.6 21.0 466 n/a 5_xyzrec: 0.1110 0.1500 0.010 1.053 5.4 102.6 21.0 466 n/a 5_adp: 0.1100 0.1486 0.010 1.053 5.8 103.2 21.2 466 n/a 5_regHadp: 0.1100 0.1486 0.010 1.053 5.8 103.2 21.2 466 n/a 5_occ: 0.1095 0.1481 0.010 1.053 5.8 103.2 21.2 466 n/a end: 0.1096 0.1478 0.010 1.053 5.5 102.9 20.9 466 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3675081_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3675081_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1600 Refinement macro-cycles (run) : 920.0600 Write final files (write_after_run_outputs) : 20.7600 Total : 944.9800 Total CPU time: 16.15 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:09 PST -0800 (1735494069.96 s) Start R-work = 0.1614, R-free = 0.1655 Final R-work = 0.1096, R-free = 0.1478 =============================================================================== Job complete usr+sys time: 991.59 seconds wall clock time: 16 minutes 54.27 seconds (1014.27 seconds total)