Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2686906.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 { 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_2686906.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2686906.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" } 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: 1.16, per 1000 atoms: 0.34 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 201.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 531 0.91 - 1.16: 1106 1.16 - 1.41: 612 1.41 - 1.66: 849 1.66 - 1.91: 55 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.117 0.209 1.10e-02 8.26e+03 3.63e+02 bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.537 1.449 0.088 5.00e-03 4.00e+04 3.07e+02 bond pdb=" C VAL A 146 " pdb=" O VAL A 146 " ideal model delta sigma weight residual 1.236 1.409 -0.173 9.90e-03 1.02e+04 3.06e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.237 1.029 0.208 1.19e-02 7.06e+03 3.04e+02 bond pdb=" N PRO A 43 " pdb=" CD PRO A 43 " ideal model delta sigma weight residual 1.473 1.240 0.233 1.40e-02 5.10e+03 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 3001 4.29 - 8.58: 1829 8.58 - 12.86: 754 12.86 - 17.15: 172 17.15 - 21.44: 21 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.83 108.11 12.72 5.90e-01 2.87e+00 4.65e+02 angle pdb=" O LYS A 148 " pdb=" C LYS A 148 " pdb=" N ASP A 149 " ideal model delta sigma weight residual 123.31 104.50 18.81 1.17e+00 7.31e-01 2.58e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 109.20 10.09 6.50e-01 2.37e+00 2.41e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.52 120.04 -9.52 6.70e-01 2.23e+00 2.02e+02 angle pdb=" O GLY A 137 " pdb=" C GLY A 137 " pdb=" N HIS A 138 " ideal model delta sigma weight residual 122.51 133.94 -11.43 8.10e-01 1.52e+00 1.99e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 1309 17.02 - 34.04: 120 34.04 - 51.06: 36 51.06 - 68.08: 13 68.08 - 85.10: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LEU A 172 " pdb=" N LEU A 172 " pdb=" CA LEU A 172 " pdb=" CB LEU A 172 " ideal model delta harmonic sigma weight residual -122.60 -140.71 18.11 0 2.50e+00 1.60e-01 5.25e+01 dihedral pdb=" N LEU A 172 " pdb=" C LEU A 172 " pdb=" CA LEU A 172 " pdb=" CB LEU A 172 " ideal model delta harmonic sigma weight residual 122.80 139.11 -16.31 0 2.50e+00 1.60e-01 4.26e+01 dihedral pdb=" N AASN A 76 " pdb=" C AASN A 76 " pdb=" CA AASN A 76 " pdb=" CB AASN A 76 " ideal model delta harmonic sigma weight residual 122.80 106.88 15.92 0 2.50e+00 1.60e-01 4.05e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.197: 98 0.197 - 0.393: 74 0.393 - 0.588: 50 0.588 - 0.784: 17 0.784 - 0.979: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 172 " pdb=" N LEU A 172 " pdb=" C LEU A 172 " pdb=" CB LEU A 172 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" CA GLU A 143 " pdb=" N GLU A 143 " pdb=" C GLU A 143 " pdb=" CB GLU A 143 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.31e+01 chirality pdb=" CA ALA A 111 " pdb=" N ALA A 111 " pdb=" C ALA A 111 " pdb=" CB ALA A 111 " both_signs ideal model delta sigma weight residual False 2.48 3.35 -0.86 2.00e-01 2.50e+01 1.86e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.114 2.00e-02 2.50e+03 6.83e-02 1.40e+02 pdb=" CG TYR A 141 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.126 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.073 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.081 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.046 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.028 2.00e-02 2.50e+03 6.07e-02 1.11e+02 pdb=" CG PHE A 164 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.081 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.068 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.076 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.114 2.00e-02 2.50e+03 6.03e-02 1.09e+02 pdb=" CG PHE A 119 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.068 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.098 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.063 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.016 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.007 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 828 2.29 - 2.87: 7894 2.87 - 3.44: 10636 3.44 - 4.02: 15268 4.02 - 4.60: 21897 Nonbonded interactions: 56523 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.711 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.751 2.450 nonbonded pdb=" H LEU A 72 " pdb=" O ALA A 103 " model vdw 1.823 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.851 2.450 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.852 2.450 ... (remaining 56518 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_2686906_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2792 r_free= 0.1864 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.396919 | | target function (ml) not normalized (work): 71419.147311 | | target function (ml) not normalized (free): 3265.969965 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3197 0.2165 7.4714 5.0261| | 2: 3.63 - 2.88 1.00 2711 122 0.2655 0.1748 4.3409 4.3362| | 3: 2.88 - 2.52 1.00 2682 148 0.2544 0.1876 4.1874 4.1979| | 4: 2.52 - 2.29 1.00 2661 139 0.2565 0.1536 3.5235 3.5691| | 5: 2.29 - 2.13 1.00 2678 122 0.2656 0.1460 3.3851 3.4206| | 6: 2.13 - 2.00 1.00 2692 117 0.2747 0.1969 3.3125 3.4453| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.70 0.77 0.23 1323.15| | 2: 3.63 - 2.88 2711 122 0.82 24.11 1.32 0.23 1323.15| | 3: 2.88 - 2.52 2682 148 0.73 33.15 1.28 0.23 1323.15| | 4: 2.52 - 2.29 2661 139 0.93 11.17 1.30 0.26 132.34| | 5: 2.29 - 2.13 2678 122 0.92 13.31 1.32 0.26 132.34| | 6: 2.13 - 2.00 2692 117 0.90 15.89 1.33 0.26 132.34| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 132.34 max = 1323.15 mean = 734.38| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.99 mean = 19.23| |phase err.(test): min = 0.00 max = 89.15 mean = 19.62| |-----------------------------------------------------------------------------| ----------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= 5.529 Angle : 5.240 18.808 2118 Z= 3.762 Chirality : 0.353 0.979 243 Planarity : 0.034 0.118 284 Dihedral : 13.585 85.097 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 27.03 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.48), residues: 224 helix: -2.85 (0.38), residues: 109 sheet: -1.23 (0.83), residues: 28 loop : -0.84 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.017 ARG A 98 TYR 0.136 0.046 TYR A 141 PHE 0.093 0.046 PHE A 119 HIS 0.062 0.030 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2792 r_free= 0.1864 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.396919 | | target function (ml) not normalized (work): 71419.147311 | | target function (ml) not normalized (free): 3265.969965 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3018 percent. r_work = 0.2922 r_free = 0.2018 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2870 0.2922 0.2018 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2870 0.2922 0.2018 n_refl.: 17050 remove outliers: r(all,work,free)=0.2167 0.2177 0.2018 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2140 0.2150 0.2000 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1627 0.1625 0.1673 n_refl.: 17045 remove outliers: r(all,work,free)=0.1625 0.1623 0.1673 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 0.3780 398.991 362.983 0.650 1.016 0.397 11.894-9.307 99.02 97 4 0.1899 633.692 612.291 0.927 1.016 0.380 9.237-7.194 100.00 213 7 0.2239 518.296 509.616 0.952 1.016 0.361 7.162-5.571 100.00 427 22 0.2331 388.982 376.036 0.922 1.014 0.289 5.546-4.326 100.00 867 58 0.1427 534.010 528.464 0.961 1.012 0.261 4.315-3.360 100.00 1859 96 0.1307 507.848 504.109 1.016 1.007 0.171 3.356-2.611 100.00 3867 181 0.1673 333.627 328.696 1.011 0.999 0.111 2.608-2.000 99.99 8818 434 0.1647 217.468 213.526 1.034 0.986 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4440 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1623 r_free=0.1673 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=0.1625 r_free=0.1678 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.375712 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.993132 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 0.1349 0.1633 0.0285 0.009 1.0 1.0 0.5 0.0 0 12.188 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.49 16.33 2.85 3.013 18.454 0.993 0.023 12.73 16.56 3.83 3.655 18.717 0.993 0.020 Individual atomic B min max mean iso aniso Overall: 6.23 113.89 19.98 4.11 1785 0 Protein: 6.23 113.19 17.21 4.12 1519 0 Water: 8.59 113.89 36.08 N/A 258 0 Other: 21.82 37.28 26.83 N/A 8 0 Chain A: 6.23 113.89 19.98 N/A 1785 0 Histogram: Values Number of atoms 6.23 - 17.00 1089 17.00 - 27.76 335 27.76 - 38.53 186 38.53 - 49.30 98 49.30 - 60.06 49 60.06 - 70.83 14 70.83 - 81.60 6 81.60 - 92.36 4 92.36 - 103.13 1 103.13 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1273 r_free=0.1656 r_work=0.1276 r_free=0.1665 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1276 r_free = 0.1665 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 = 0.1271 r_free = 0.1653 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= 0.1271 r_free= 0.1653 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.019861 | | target function (ls_wunit_k1) not normalized (work): 322.467137 | | target function (ls_wunit_k1) not normalized (free): 27.069832 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1289 0.1271 0.1653 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1900 0.1898 0.1994 n_refl.: 17043 remove outliers: r(all,work,free)=0.1900 0.1898 0.1994 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1872 0.1870 0.1978 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1289 0.1271 0.1649 n_refl.: 17043 remove outliers: r(all,work,free)=0.1289 0.1271 0.1649 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 0.3563 307.296 284.509 0.652 1.010 0.389 11.894-9.307 99.02 97 4 0.1694 488.058 477.619 0.916 1.011 0.366 9.237-7.194 100.00 213 7 0.1825 399.182 396.130 0.955 1.010 0.351 7.162-5.571 100.00 427 22 0.1838 299.587 294.894 0.931 1.009 0.301 5.546-4.326 100.00 867 58 0.1046 411.285 408.954 0.958 1.008 0.241 4.315-3.360 100.00 1859 96 0.0928 391.136 390.755 1.016 1.005 0.181 3.356-2.611 100.00 3867 181 0.1294 256.954 255.708 1.012 1.000 0.111 2.608-2.000 99.99 8818 434 0.1342 167.490 166.003 1.021 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3556 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1271 r_free=0.1649 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=0.1273 r_free=0.1647 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1647 | n_water=258 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1279 r_free=0.1636 | n_water=253 | time (s): 19.960 (total time: 20.730) Filter (q & B) r_work=0.1280 r_free=0.1636 | n_water=251 | time (s): 2.070 (total time: 22.800) Compute maps r_work=0.1280 r_free=0.1636 | n_water=251 | time (s): 0.770 (total time: 23.570) Filter (map) r_work=0.1315 r_free=0.1632 | n_water=209 | time (s): 1.700 (total time: 25.270) Find peaks r_work=0.1315 r_free=0.1632 | n_water=209 | time (s): 0.610 (total time: 25.880) Add new water r_work=0.1546 r_free=0.1866 | n_water=362 | time (s): 2.060 (total time: 27.940) Refine new water occ: r_work=0.1344 r_free=0.1598 adp: r_work=0.1285 r_free=0.1583 occ: r_work=0.1290 r_free=0.1565 adp: r_work=0.1256 r_free=0.1560 occ: r_work=0.1255 r_free=0.1563 adp: r_work=0.1244 r_free=0.1558 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1558 r_work=0.1244 r_free=0.1558 | n_water=362 | time (s): 15.570 (total time: 43.510) Filter (q & B) r_work=0.1247 r_free=0.1568 | n_water=352 | time (s): 1.830 (total time: 45.340) Filter (dist only) r_work=0.1248 r_free=0.1571 | n_water=351 | time (s): 26.590 (total time: 71.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.157423 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.974294 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 0.1214 0.1587 0.0373 0.008 0.9 2.2 0.5 0.0 0 12.579 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 15.87 3.73 4.196 21.039 0.974 0.018 12.02 16.09 4.06 4.189 21.276 0.974 0.018 Individual atomic B min max mean iso aniso Overall: 6.44 107.81 21.21 4.22 1878 0 Protein: 6.44 107.81 17.72 4.21 1519 0 Water: 8.40 68.18 36.02 N/A 351 0 Other: 24.85 45.03 34.71 N/A 8 0 Chain A: 6.44 107.81 19.39 N/A 1736 0 Chain S: 19.69 61.75 43.55 N/A 142 0 Histogram: Values Number of atoms 6.44 - 16.57 1014 16.57 - 26.71 381 26.71 - 36.85 224 36.85 - 46.99 149 46.99 - 57.12 77 57.12 - 67.26 22 67.26 - 77.40 4 77.40 - 87.54 4 87.54 - 97.68 1 97.68 - 107.81 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1609 r_work=0.1204 r_free=0.1610 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1610 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 = 0.1201 r_free = 0.1603 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 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= 0.1201 r_free= 0.1603 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017161 | | target function (ls_wunit_k1) not normalized (work): 278.623455 | | target function (ls_wunit_k1) not normalized (free): 25.068854 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1201 0.1603 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1822 0.1818 0.1965 n_refl.: 17043 remove outliers: r(all,work,free)=0.1822 0.1818 0.1965 n_refl.: 17043 overall B=-0.37 to atoms: r(all,work,free)=0.1796 0.1792 0.1946 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1194 0.1593 n_refl.: 17043 remove outliers: r(all,work,free)=0.1211 0.1192 0.1593 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 0.3302 306.733 278.388 0.604 1.007 0.350 11.894-9.307 99.02 97 4 0.1524 488.058 482.353 0.917 1.007 0.346 9.237-7.194 100.00 213 7 0.1661 399.182 398.750 0.966 1.006 0.299 7.162-5.571 100.00 427 22 0.1555 299.587 296.157 0.938 1.006 0.271 5.546-4.326 100.00 867 58 0.0876 411.285 408.681 0.958 1.005 0.221 4.315-3.360 100.00 1859 96 0.0824 391.136 390.546 1.014 1.004 0.211 3.356-2.611 100.00 3867 181 0.1207 256.954 256.263 1.010 1.001 0.058 2.608-2.000 99.99 8818 434 0.1333 167.490 166.439 1.015 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.3187 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1593 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1593 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1593 | n_water=351 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1193 r_free=0.1598 | n_water=348 | time (s): 27.030 (total time: 27.740) Filter (q & B) r_work=0.1193 r_free=0.1598 | n_water=348 | time (s): 1.090 (total time: 28.830) Compute maps r_work=0.1193 r_free=0.1598 | n_water=348 | time (s): 0.780 (total time: 29.610) Filter (map) r_work=0.1261 r_free=0.1610 | n_water=256 | time (s): 1.500 (total time: 31.110) Find peaks r_work=0.1261 r_free=0.1610 | n_water=256 | time (s): 0.430 (total time: 31.540) Add new water r_work=0.1449 r_free=0.1793 | n_water=395 | time (s): 1.340 (total time: 32.880) Refine new water occ: r_work=0.1259 r_free=0.1560 adp: r_work=0.1254 r_free=0.1563 occ: r_work=0.1233 r_free=0.1534 adp: r_work=0.1225 r_free=0.1534 occ: r_work=0.1214 r_free=0.1521 adp: r_work=0.1206 r_free=0.1519 ADP+occupancy (water only), MIN, final r_work=0.1206 r_free=0.1519 r_work=0.1206 r_free=0.1519 | n_water=395 | time (s): 35.600 (total time: 68.480) Filter (q & B) r_work=0.1207 r_free=0.1520 | n_water=387 | time (s): 1.590 (total time: 70.070) Filter (dist only) r_work=0.1207 r_free=0.1520 | n_water=387 | time (s): 28.050 (total time: 98.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.931412 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.162898 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 0.1192 0.1564 0.0372 0.010 1.0 3.8 0.5 0.0 0 0.966 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 15.64 3.72 4.308 21.398 0.163 5.000 11.72 15.73 4.01 4.877 21.342 0.163 4.977 Individual atomic B min max mean iso aniso Overall: 6.49 105.24 20.70 4.67 1914 0 Protein: 6.49 105.24 17.00 4.67 1519 0 Water: 8.66 63.23 34.93 N/A 387 0 Other: 25.41 45.05 33.71 N/A 8 0 Chain A: 6.49 105.24 18.72 N/A 1733 0 Chain S: 18.03 63.23 39.65 N/A 181 0 Histogram: Values Number of atoms 6.49 - 16.37 1065 16.37 - 26.24 361 26.24 - 36.12 225 36.12 - 45.99 150 45.99 - 55.86 74 55.86 - 65.74 26 65.74 - 75.61 5 75.61 - 85.49 3 85.49 - 95.36 3 95.36 - 105.24 2 =========================== Idealize ADP of riding H ========================== r_work=0.1172 r_free=0.1573 r_work=0.1172 r_free=0.1574 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1172 r_free = 0.1574 target_work(ml) = 4.977 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1163 r_free = 0.1564 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.20 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= 0.1163 r_free= 0.1564 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.971883 | | target function (ml) not normalized (work): 80713.544445 | | target function (ml) not normalized (free): 4193.333090 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1183 0.1163 0.1564 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1679 0.1672 0.1860 n_refl.: 17041 remove outliers: r(all,work,free)=0.1679 0.1672 0.1860 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1653 0.1645 0.1847 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1179 0.1160 0.1554 n_refl.: 17041 remove outliers: r(all,work,free)=0.1178 0.1159 0.1554 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 0.3665 303.239 279.096 0.560 1.006 0.340 11.894-9.307 99.02 97 4 0.1884 488.058 479.751 0.912 1.007 0.337 9.237-7.194 100.00 213 7 0.1878 399.182 399.192 0.980 1.007 0.250 7.162-5.571 100.00 427 22 0.1705 299.587 294.193 0.939 1.006 0.241 5.546-4.326 100.00 867 58 0.0939 411.285 407.012 0.962 1.005 0.201 4.315-3.360 100.00 1859 96 0.0908 391.136 388.882 1.012 1.004 0.201 3.356-2.611 100.00 3867 181 0.1298 256.954 254.633 1.014 1.001 0.121 2.608-2.000 99.99 8818 434 0.1085 167.490 166.091 1.019 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3707 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1159 r_free=0.1554 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1159 r_free=0.1554 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1159 r_free=0.1554 | n_water=387 | time (s): 0.820 (total time: 0.820) Filter (dist) r_work=0.1159 r_free=0.1554 | n_water=387 | time (s): 30.010 (total time: 30.830) Filter (q & B) r_work=0.1159 r_free=0.1554 | n_water=387 | time (s): 1.000 (total time: 31.830) Compute maps r_work=0.1159 r_free=0.1554 | n_water=387 | time (s): 0.730 (total time: 32.560) Filter (map) r_work=0.1206 r_free=0.1557 | n_water=299 | time (s): 2.190 (total time: 34.750) Find peaks r_work=0.1206 r_free=0.1557 | n_water=299 | time (s): 0.580 (total time: 35.330) Add new water r_work=0.1340 r_free=0.1654 | n_water=436 | time (s): 1.730 (total time: 37.060) Refine new water occ: r_work=0.1181 r_free=0.1492 adp: r_work=0.1174 r_free=0.1492 occ: r_work=0.1159 r_free=0.1481 adp: r_work=0.1150 r_free=0.1479 occ: r_work=0.1143 r_free=0.1474 adp: r_work=0.1135 r_free=0.1472 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1472 r_work=0.1135 r_free=0.1472 | n_water=436 | time (s): 32.900 (total time: 69.960) Filter (q & B) r_work=0.1139 r_free=0.1482 | n_water=426 | time (s): 1.710 (total time: 71.670) Filter (dist only) r_work=0.1138 r_free=0.1484 | n_water=425 | time (s): 32.640 (total time: 104.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.916600 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.173085 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 0.1127 0.1536 0.0409 0.010 1.0 3.2 0.5 0.0 0 0.958 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.27 15.36 4.09 4.486 20.989 0.173 4.953 11.16 15.37 4.21 4.643 20.992 0.173 4.948 Individual atomic B min max mean iso aniso Overall: 6.14 103.57 20.76 4.86 1952 0 Protein: 6.14 103.57 16.60 4.85 1519 0 Water: 8.73 64.53 35.41 N/A 425 0 Other: 24.56 45.12 32.32 N/A 8 0 Chain A: 6.14 103.57 18.24 N/A 1732 0 Chain S: 16.88 64.53 40.62 N/A 220 0 Histogram: Values Number of atoms 6.14 - 15.88 1064 15.88 - 25.63 353 25.63 - 35.37 226 35.37 - 45.11 176 45.11 - 54.85 87 54.85 - 64.60 31 64.60 - 74.34 7 74.34 - 84.08 3 84.08 - 93.82 3 93.82 - 103.57 2 =========================== Idealize ADP of riding H ========================== r_work=0.1116 r_free=0.1537 r_work=0.1116 r_free=0.1537 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1116 r_free = 0.1537 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1109 r_free = 0.1539 target_work(ml) = 4.945 | | occupancies: max = 1.00 min = 0.17 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= 0.1109 r_free= 0.1539 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.945218 | | target function (ml) not normalized (work): 80275.730798 | | target function (ml) not normalized (free): 4177.723588 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1130 0.1109 0.1539 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1596 0.1583 0.1873 n_refl.: 17040 remove outliers: r(all,work,free)=0.1596 0.1583 0.1873 n_refl.: 17040 overall B=-0.30 to atoms: r(all,work,free)=0.1577 0.1563 0.1861 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1109 0.1532 n_refl.: 17040 remove outliers: r(all,work,free)=0.1129 0.1109 0.1532 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 0.3719 303.239 275.900 0.539 1.001 0.313 11.894-9.307 99.02 97 4 0.1899 488.058 480.514 0.916 1.002 0.302 9.237-7.194 100.00 213 7 0.1785 399.182 400.162 0.987 1.003 0.237 7.162-5.571 100.00 427 22 0.1567 299.587 294.706 0.940 1.003 0.212 5.546-4.326 100.00 867 58 0.0927 411.285 407.520 0.966 1.002 0.189 4.315-3.360 100.00 1859 96 0.0861 391.136 389.031 1.009 1.002 0.174 3.356-2.611 100.00 3867 181 0.1231 256.954 254.808 1.009 1.000 0.131 2.608-2.000 99.99 8818 434 0.1042 167.490 166.334 1.004 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0524 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1109 r_free=0.1532 After: r_work=0.1111 r_free=0.1531 ================================== NQH flips ================================== r_work=0.1111 r_free=0.1531 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1111 r_free=0.1531 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1111 r_free=0.1531 | n_water=425 | time (s): 0.870 (total time: 0.870) Filter (dist) r_work=0.1111 r_free=0.1531 | n_water=425 | time (s): 31.620 (total time: 32.490) Filter (q & B) r_work=0.1111 r_free=0.1531 | n_water=425 | time (s): 0.990 (total time: 33.480) Compute maps r_work=0.1111 r_free=0.1531 | n_water=425 | time (s): 0.680 (total time: 34.160) Filter (map) r_work=0.1180 r_free=0.1554 | n_water=330 | time (s): 1.480 (total time: 35.640) Find peaks r_work=0.1180 r_free=0.1554 | n_water=330 | time (s): 0.410 (total time: 36.050) Add new water r_work=0.1298 r_free=0.1650 | n_water=464 | time (s): 1.620 (total time: 37.670) Refine new water occ: r_work=0.1144 r_free=0.1492 adp: r_work=0.1135 r_free=0.1486 occ: r_work=0.1123 r_free=0.1480 adp: r_work=0.1113 r_free=0.1473 occ: r_work=0.1107 r_free=0.1472 adp: r_work=0.1100 r_free=0.1469 ADP+occupancy (water only), MIN, final r_work=0.1100 r_free=0.1469 r_work=0.1100 r_free=0.1469 | n_water=464 | time (s): 23.600 (total time: 61.270) Filter (q & B) r_work=0.1103 r_free=0.1482 | n_water=454 | time (s): 2.110 (total time: 63.380) Filter (dist only) r_work=0.1103 r_free=0.1484 | n_water=453 | time (s): 37.070 (total time: 100.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.923320 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.154546 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 0.1116 0.1510 0.0394 0.010 1.0 6.1 0.5 0.0 0 0.962 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.10 3.94 4.555 20.776 0.155 4.939 11.07 15.10 4.03 4.574 20.845 0.155 4.934 Individual atomic B min max mean iso aniso Overall: 5.56 102.09 20.85 4.94 1980 0 Protein: 5.56 102.09 16.34 4.93 1519 0 Water: 8.39 67.95 35.77 N/A 453 0 Other: 23.69 42.47 30.49 N/A 8 0 Chain A: 5.56 102.09 17.94 N/A 1732 0 Chain S: 18.08 67.95 41.12 N/A 248 0 Histogram: Values Number of atoms 5.56 - 15.22 1049 15.22 - 24.87 366 24.87 - 34.52 215 34.52 - 44.18 197 44.18 - 53.83 99 53.83 - 63.48 35 63.48 - 73.13 10 73.13 - 82.79 3 82.79 - 92.44 2 92.44 - 102.09 4 =========================== Idealize ADP of riding H ========================== r_work=0.1107 r_free=0.1510 r_work=0.1107 r_free=0.1510 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1107 r_free = 0.1510 target_work(ml) = 4.934 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1101 r_free = 0.1507 target_work(ml) = 4.931 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1101 r_free= 0.1507 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.930848 | | target function (ml) not normalized (work): 80042.450986 | | target function (ml) not normalized (free): 4160.592265 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1111 0.1380 5.4565 5.6331| | 2: 3.63 - 2.88 1.00 2711 122 0.1088 0.1532 5.2161 5.3723| | 3: 2.88 - 2.52 1.00 2681 148 0.1340 0.1665 5.1217 5.1936| | 4: 2.52 - 2.29 1.00 2661 139 0.0928 0.1462 4.6191 4.9264| | 5: 2.29 - 2.13 1.00 2678 122 0.0964 0.1506 4.5736 4.9015| | 6: 2.13 - 2.00 1.00 2692 117 0.1119 0.1726 4.5683 4.7701| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.86 1.00 0.96 6298.71| | 2: 3.63 - 2.88 2711 122 0.92 12.74 1.01 0.96 6298.71| | 3: 2.88 - 2.52 2681 148 0.88 18.79 0.99 0.96 6298.71| | 4: 2.52 - 2.29 2661 139 0.93 11.96 1.01 0.98 2088.00| | 5: 2.29 - 2.13 2678 122 0.91 14.04 1.00 0.98 2088.00| | 6: 2.13 - 2.00 2692 117 0.90 16.67 0.99 0.98 2088.00| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2088.00 max = 6298.71 mean = 4215.53| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.99 mean = 13.81| |phase err.(test): min = 0.00 max = 88.73 mean = 13.57| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1120 0.1101 0.1507 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1567 0.1554 0.1843 n_refl.: 17040 remove outliers: r(all,work,free)=0.1567 0.1554 0.1843 n_refl.: 17040 overall B=-0.25 to atoms: r(all,work,free)=0.1552 0.1539 0.1833 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1121 0.1101 0.1511 n_refl.: 17040 remove outliers: r(all,work,free)=0.1119 0.1100 0.1511 n_refl.: 17039 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3469 305.479 277.295 0.542 1.004 0.322 11.894-9.307 99.02 97 4 0.1766 488.058 482.123 0.918 1.005 0.316 9.237-7.194 100.00 213 7 0.1758 399.182 400.167 0.985 1.005 0.230 7.162-5.571 100.00 427 22 0.1528 299.587 294.455 0.935 1.005 0.200 5.546-4.326 100.00 867 58 0.0927 411.285 407.724 0.963 1.004 0.191 4.315-3.360 100.00 1859 96 0.0854 391.136 389.329 1.005 1.003 0.191 3.356-2.611 100.00 3867 181 0.1235 256.954 254.972 1.003 1.000 0.067 2.608-2.000 99.99 8818 434 0.1032 167.490 166.198 0.997 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.8715 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2792 0.1864 0.083 5.240 8.8 119.3 19.9 258 0.000 1_bss: 0.1623 0.1673 0.083 5.240 8.4 118.9 19.5 258 0.000 1_settarget: 0.1623 0.1673 0.083 5.240 8.4 118.9 19.5 258 0.000 1_nqh: 0.1625 0.1678 0.083 5.240 8.4 118.9 19.5 258 0.003 1_weight: 0.1625 0.1678 0.083 5.240 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1349 0.1633 0.009 0.987 8.4 118.9 19.5 258 0.144 1_adp: 0.1273 0.1656 0.009 0.987 6.2 113.9 20.0 258 0.144 1_regHadp: 0.1276 0.1665 0.009 0.987 6.2 113.9 20.0 258 0.144 1_occ: 0.1271 0.1653 0.009 0.987 6.2 113.9 20.0 258 0.144 2_bss: 0.1271 0.1649 0.009 0.987 5.9 113.5 19.6 258 0.144 2_settarget: 0.1271 0.1649 0.009 0.987 5.9 113.5 19.6 258 0.144 2_updatecdl: 0.1271 0.1649 0.009 1.008 5.9 113.5 19.6 258 0.144 2_nqh: 0.1273 0.1647 0.009 1.008 5.9 113.5 19.6 258 0.141 2_sol: 0.1248 0.1571 0.009 1.008 5.9 112.8 20.8 351 n/a 2_weight: 0.1248 0.1571 0.009 1.008 5.9 112.8 20.8 351 n/a 2_xyzrec: 0.1214 0.1587 0.008 0.939 5.9 112.8 20.8 351 n/a 2_adp: 0.1202 0.1609 0.008 0.939 6.4 107.8 21.2 351 n/a 2_regHadp: 0.1204 0.1610 0.008 0.939 6.4 107.8 21.2 351 n/a 2_occ: 0.1201 0.1603 0.008 0.939 6.4 107.8 21.2 351 n/a 3_bss: 0.1192 0.1593 0.008 0.939 6.1 107.4 20.8 351 n/a 3_settarget: 0.1192 0.1593 0.008 0.939 6.1 107.4 20.8 351 n/a 3_updatecdl: 0.1192 0.1593 0.008 0.936 6.1 107.4 20.8 351 n/a 3_nqh: 0.1192 0.1593 0.008 0.936 6.1 107.4 20.8 351 n/a 3_sol: 0.1207 0.1520 0.008 0.936 6.1 107.4 20.8 387 n/a 3_weight: 0.1207 0.1520 0.008 0.936 6.1 107.4 20.8 387 n/a 3_xyzrec: 0.1192 0.1564 0.010 0.977 6.1 107.4 20.8 387 n/a 3_adp: 0.1172 0.1573 0.010 0.977 6.5 105.2 20.7 387 n/a 3_regHadp: 0.1172 0.1574 0.010 0.977 6.5 105.2 20.7 387 n/a 3_occ: 0.1163 0.1564 0.010 0.977 6.5 105.2 20.7 387 n/a 4_bss: 0.1159 0.1554 0.010 0.977 6.1 104.9 20.3 387 n/a 4_settarget: 0.1159 0.1554 0.010 0.977 6.1 104.9 20.3 387 n/a 4_updatecdl: 0.1159 0.1554 0.010 0.977 6.1 104.9 20.3 387 n/a 4_nqh: 0.1159 0.1554 0.010 0.977 6.1 104.9 20.3 387 n/a 4_sol: 0.1138 0.1484 0.010 0.977 6.1 104.9 20.8 425 n/a 4_weight: 0.1138 0.1484 0.010 0.977 6.1 104.9 20.8 425 n/a 4_xyzrec: 0.1127 0.1536 0.010 0.986 6.1 104.9 20.8 425 n/a 4_adp: 0.1116 0.1537 0.010 0.986 6.1 103.6 20.8 425 n/a 4_regHadp: 0.1116 0.1537 0.010 0.986 6.1 103.6 20.8 425 n/a 4_occ: 0.1109 0.1539 0.010 0.986 6.1 103.6 20.8 425 n/a 5_bss: 0.1109 0.1532 0.010 0.986 5.8 103.3 20.5 425 n/a 5_settarget: 0.1109 0.1532 0.010 0.986 5.8 103.3 20.5 425 n/a 5_updatecdl: 0.1109 0.1532 0.010 0.986 5.8 103.3 20.5 425 n/a 5_setrh: 0.1111 0.1531 0.010 0.986 5.8 103.3 20.5 425 n/a 5_nqh: 0.1111 0.1531 0.010 0.986 5.8 103.3 20.5 425 n/a 5_sol: 0.1103 0.1484 0.010 0.986 5.8 103.3 20.7 453 n/a 5_weight: 0.1103 0.1484 0.010 0.986 5.8 103.3 20.7 453 n/a 5_xyzrec: 0.1116 0.1510 0.010 1.028 5.8 103.3 20.7 453 n/a 5_adp: 0.1107 0.1510 0.010 1.028 5.6 102.1 20.8 453 n/a 5_regHadp: 0.1107 0.1510 0.010 1.028 5.6 102.1 20.8 453 n/a 5_occ: 0.1101 0.1507 0.010 1.028 5.6 102.1 20.8 453 n/a end: 0.1100 0.1511 0.010 1.028 5.3 101.8 20.6 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2686906_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2686906_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7500 Refinement macro-cycles (run) : 896.2600 Write final files (write_after_run_outputs) : 21.6300 Total : 921.6400 Total CPU time: 15.78 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:47 PST -0800 (1735494047.13 s) Start R-work = 0.1623, R-free = 0.1673 Final R-work = 0.1100, R-free = 0.1511 =============================================================================== Job complete usr+sys time: 970.43 seconds wall clock time: 16 minutes 32.64 seconds (992.64 seconds total)