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_7798058.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7798058.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7798058.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.32, per 1000 atoms: 0.39 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: 0.57 Conformation dependent library (CDL) restraints added in 187.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.92: 590 0.92 - 1.21: 1105 1.21 - 1.49: 885 1.49 - 1.78: 562 1.78 - 2.06: 11 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 186 " pdb=" N LEU A 187 " ideal model delta sigma weight residual 1.330 1.069 0.262 1.38e-02 5.25e+03 3.59e+02 bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.235 1.417 -0.182 1.02e-02 9.61e+03 3.20e+02 bond pdb=" CA LYS A 182 " pdb=" C LYS A 182 " ideal model delta sigma weight residual 1.523 1.283 0.240 1.35e-02 5.49e+03 3.16e+02 bond pdb=" C ILE A 9 " pdb=" O ILE A 9 " ideal model delta sigma weight residual 1.236 1.043 0.193 1.09e-02 8.42e+03 3.13e+02 bond pdb=" N SER A 155 " pdb=" CA SER A 155 " ideal model delta sigma weight residual 1.457 1.668 -0.211 1.20e-02 6.94e+03 3.09e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 2906 4.17 - 8.33: 1891 8.33 - 12.49: 756 12.49 - 16.65: 197 16.65 - 20.81: 27 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 136.07 -13.40 1.02e+00 9.61e-01 1.73e+02 angle pdb=" O ALA A 114 " pdb=" C ALA A 114 " pdb=" N HIS A 115 " ideal model delta sigma weight residual 122.12 135.44 -13.32 1.06e+00 8.90e-01 1.58e+02 angle pdb=" CA AGLN A 80 " pdb=" C AGLN A 80 " pdb=" N ASN A 81 " ideal model delta sigma weight residual 117.39 102.01 15.38 1.24e+00 6.50e-01 1.54e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 109.34 12.16 1.00e+00 1.00e+00 1.48e+02 angle pdb=" O ALYS A 99 " pdb=" C ALYS A 99 " pdb=" N GLY A 100 " ideal model delta sigma weight residual 122.59 138.13 -15.54 1.33e+00 5.65e-01 1.37e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 1292 16.49 - 32.99: 135 32.99 - 49.48: 36 49.48 - 65.97: 16 65.97 - 82.46: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C THR A 19 " pdb=" N THR A 19 " pdb=" CA THR A 19 " pdb=" CB THR A 19 " ideal model delta harmonic sigma weight residual -122.00 -141.58 19.58 0 2.50e+00 1.60e-01 6.13e+01 dihedral pdb=" C ALA A 167 " pdb=" N ALA A 167 " pdb=" CA ALA A 167 " pdb=" CB ALA A 167 " ideal model delta harmonic sigma weight residual -122.60 -140.97 18.37 0 2.50e+00 1.60e-01 5.40e+01 dihedral pdb=" C ALA A 61 " pdb=" N ALA A 61 " pdb=" CA ALA A 61 " pdb=" CB ALA A 61 " ideal model delta harmonic sigma weight residual -122.60 -140.02 17.42 0 2.50e+00 1.60e-01 4.85e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.194: 104 0.194 - 0.384: 58 0.384 - 0.574: 37 0.574 - 0.764: 37 0.764 - 0.954: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.40 -0.95 2.00e-01 2.50e+01 2.28e+01 chirality pdb=" CG LEU A 72 " pdb=" CB LEU A 72 " pdb=" CD1 LEU A 72 " pdb=" CD2 LEU A 72 " both_signs ideal model delta sigma weight residual False -2.59 -1.68 -0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.39 -0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.037 2.00e-02 2.50e+03 6.63e-02 1.32e+02 pdb=" CG PHE A 162 " 0.111 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.063 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.109 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.075 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.046 2.00e-02 2.50e+03 6.51e-02 1.27e+02 pdb=" CG TYR A 139 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.057 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.090 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.087 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.104 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.075 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.024 2.00e-02 2.50e+03 6.37e-02 1.22e+02 pdb=" CG TYR A 141 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.097 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.080 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.118 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.033 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.103 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.004 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.32: 1068 2.32 - 2.89: 8155 2.89 - 3.46: 10516 3.46 - 4.03: 15147 4.03 - 4.60: 21742 Nonbonded interactions: 56628 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.756 2.100 nonbonded pdb=" HD2 LYS A 32 " pdb=" HZ2 LYS A 32 " model vdw 1.796 2.270 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.818 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.826 2.450 nonbonded pdb=" O ALA A 6 " pdb=" H THR A 34 " model vdw 1.830 2.450 ... (remaining 56623 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_7798058_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= 0.2791 r_free= 0.1812 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.403211 | | target function (ml) not normalized (work): 71521.363765 | | target function (ml) not normalized (free): 3256.291434 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3193 0.2164 7.5384 5.0478| | 2: 3.63 - 2.88 1.00 2711 122 0.2657 0.1757 4.327 4.3295| | 3: 2.88 - 2.52 1.00 2682 148 0.2544 0.1554 4.1794 4.1799| | 4: 2.52 - 2.29 1.00 2661 139 0.2560 0.1555 3.5062 3.5556| | 5: 2.29 - 2.13 1.00 2678 122 0.2670 0.1570 3.4065 3.4771| | 6: 2.13 - 2.00 1.00 2692 117 0.2738 0.1757 3.2981 3.32| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.65 0.77 0.23 1312.00| | 2: 3.63 - 2.88 2711 122 0.83 23.88 1.32 0.23 1312.00| | 3: 2.88 - 2.52 2682 148 0.73 33.03 1.28 0.23 1312.00| | 4: 2.52 - 2.29 2661 139 0.94 10.88 1.30 0.26 129.21| | 5: 2.29 - 2.13 2678 122 0.92 13.21 1.31 0.26 129.21| | 6: 2.13 - 2.00 2692 117 0.90 15.91 1.33 0.26 129.21| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 129.21 max = 1312.00 mean = 727.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.97 mean = 19.10| |phase err.(test): min = 0.00 max = 89.87 mean = 19.45| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.262 1557 Z= 5.405 Angle : 5.160 17.447 2118 Z= 3.572 Chirality : 0.380 0.954 243 Planarity : 0.030 0.097 284 Dihedral : 13.674 82.465 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 24.86 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.47), residues: 224 helix: -2.44 (0.36), residues: 108 sheet: -1.19 (0.71), residues: 38 loop : -0.58 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.101 0.025 ARG A 98 TYR 0.098 0.044 TYR A 141 PHE 0.121 0.043 PHE A 162 HIS 0.060 0.029 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= 0.2791 r_free= 0.1812 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.403211 | | target function (ml) not normalized (work): 71521.363765 | | target function (ml) not normalized (free): 3256.291434 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2694 percent. r_work = 0.2918 r_free = 0.1980 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2864 0.2918 0.1980 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2864 0.2918 0.1980 n_refl.: 17050 remove outliers: r(all,work,free)=0.2155 0.2166 0.1980 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2129 0.2140 0.1962 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1616 0.1614 0.1654 n_refl.: 17045 remove outliers: r(all,work,free)=0.1615 0.1613 0.1654 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 0.4141 394.865 361.307 0.651 1.019 0.399 11.894-9.307 99.02 97 4 0.1915 633.770 616.518 0.929 1.020 0.390 9.237-7.194 100.00 213 7 0.2168 518.360 509.531 0.946 1.019 0.355 7.162-5.571 100.00 427 22 0.2327 389.030 377.363 0.913 1.017 0.331 5.546-4.326 100.00 867 58 0.1399 534.075 527.187 0.955 1.014 0.215 4.315-3.360 100.00 1859 96 0.1286 507.911 503.941 1.014 1.008 0.191 3.356-2.611 100.00 3867 181 0.1640 333.668 329.076 1.012 0.999 0.044 2.608-2.000 99.99 8818 434 0.1658 217.495 213.271 1.035 0.982 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4055 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1613 r_free=0.1654 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1613 r_free=0.1654 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.366483 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.920951 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 0.1642 0.0289 0.009 1.0 1.6 0.5 0.0 0 11.183 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.53 16.42 2.89 3.013 18.465 0.921 0.023 12.79 16.67 3.88 3.650 18.695 0.921 0.021 Individual atomic B min max mean iso aniso Overall: 5.84 113.91 19.93 4.13 1785 0 Protein: 5.84 112.88 17.15 4.13 1519 0 Water: 8.83 113.91 36.07 N/A 258 0 Other: 21.73 38.00 26.44 N/A 8 0 Chain A: 5.84 113.91 19.93 N/A 1785 0 Histogram: Values Number of atoms 5.84 - 16.65 1066 16.65 - 27.45 351 27.45 - 38.26 192 38.26 - 49.07 97 49.07 - 59.87 52 59.87 - 70.68 11 70.68 - 81.49 8 81.49 - 92.29 4 92.29 - 103.10 1 103.10 - 113.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1667 r_work=0.1282 r_free=0.1672 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1282 r_free = 0.1672 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 = 0.1277 r_free = 0.1669 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.21 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= 0.1277 r_free= 0.1669 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020108 | | target function (ls_wunit_k1) not normalized (work): 326.497445 | | target function (ls_wunit_k1) not normalized (free): 27.323848 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1277 0.1669 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1910 0.1909 0.1990 n_refl.: 17044 remove outliers: r(all,work,free)=0.1910 0.1909 0.1990 n_refl.: 17044 overall B=-0.37 to atoms: r(all,work,free)=0.1884 0.1882 0.1976 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1294 0.1275 0.1658 n_refl.: 17044 remove outliers: r(all,work,free)=0.1292 0.1274 0.1658 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3580 303.499 278.575 0.626 1.003 0.370 11.894-9.307 99.02 97 4 0.1685 488.130 478.605 0.922 1.004 0.367 9.237-7.194 100.00 213 7 0.1818 399.241 396.774 0.960 1.004 0.325 7.162-5.571 100.00 427 22 0.1824 299.631 294.312 0.932 1.004 0.311 5.546-4.326 100.00 867 58 0.1046 411.345 409.288 0.960 1.003 0.205 4.315-3.360 100.00 1859 96 0.0924 391.193 390.251 1.016 1.003 0.191 3.356-2.611 100.00 3867 181 0.1294 256.992 255.557 1.010 1.001 0.081 2.608-2.000 99.99 8818 434 0.1354 167.515 166.225 1.012 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3119 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1658 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1658 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1658 | n_water=258 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1282 r_free=0.1651 | n_water=252 | time (s): 21.420 (total time: 22.150) Filter (q & B) r_work=0.1282 r_free=0.1650 | n_water=250 | time (s): 1.830 (total time: 23.980) Compute maps r_work=0.1282 r_free=0.1650 | n_water=250 | time (s): 0.720 (total time: 24.700) Filter (map) r_work=0.1317 r_free=0.1643 | n_water=211 | time (s): 2.180 (total time: 26.880) Find peaks r_work=0.1317 r_free=0.1643 | n_water=211 | time (s): 0.470 (total time: 27.350) Add new water r_work=0.1547 r_free=0.1879 | n_water=375 | time (s): 2.070 (total time: 29.420) Refine new water occ: r_work=0.1333 r_free=0.1585 adp: r_work=0.1273 r_free=0.1582 occ: r_work=0.1277 r_free=0.1554 adp: r_work=0.1246 r_free=0.1559 occ: r_work=0.1247 r_free=0.1551 adp: r_work=0.1235 r_free=0.1551 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1551 r_work=0.1235 r_free=0.1551 | n_water=375 | time (s): 25.360 (total time: 54.780) Filter (q & B) r_work=0.1235 r_free=0.1550 | n_water=370 | time (s): 1.810 (total time: 56.590) Filter (dist only) r_work=0.1236 r_free=0.1551 | n_water=369 | time (s): 29.640 (total time: 86.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.012752 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.999512 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 0.1607 0.0398 0.008 0.9 3.5 0.5 0.0 0 12.006 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 16.07 3.98 4.196 21.073 1.000 0.018 11.93 16.31 4.38 4.216 21.388 1.000 0.018 Individual atomic B min max mean iso aniso Overall: 6.60 107.51 21.50 4.35 1896 0 Protein: 6.60 107.51 17.81 4.33 1519 0 Water: 8.80 66.26 36.37 N/A 369 0 Other: 25.06 45.37 34.65 N/A 8 0 Chain A: 6.60 107.51 19.54 N/A 1738 0 Chain S: 17.80 66.26 42.99 N/A 158 0 Histogram: Values Number of atoms 6.60 - 16.69 1019 16.69 - 26.78 378 26.78 - 36.87 226 36.87 - 46.96 165 46.96 - 57.05 67 57.05 - 67.14 30 67.14 - 77.24 4 77.24 - 87.33 3 87.33 - 97.42 2 97.42 - 107.51 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1631 r_work=0.1195 r_free=0.1633 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1633 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1636 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 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= 0.1190 r_free= 0.1636 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.016912 | | target function (ls_wunit_k1) not normalized (work): 274.568374 | | target function (ls_wunit_k1) not normalized (free): 25.423928 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1190 0.1636 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1754 0.1744 0.1992 n_refl.: 17042 remove outliers: r(all,work,free)=0.1754 0.1744 0.1992 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1731 0.1719 0.1974 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1186 0.1629 n_refl.: 17042 remove outliers: r(all,work,free)=0.1207 0.1186 0.1629 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 0.3417 303.499 284.144 0.592 1.005 0.350 11.894-9.307 99.02 97 4 0.1489 488.130 487.405 0.912 1.006 0.340 9.237-7.194 100.00 213 7 0.1659 399.241 401.673 0.970 1.006 0.286 7.162-5.571 100.00 427 22 0.1554 299.631 296.243 0.936 1.006 0.273 5.546-4.326 100.00 867 58 0.0857 411.345 408.694 0.959 1.005 0.210 4.315-3.360 100.00 1859 96 0.0827 391.193 390.516 1.015 1.003 0.201 3.356-2.611 100.00 3867 181 0.1193 256.992 256.075 1.011 1.000 0.101 2.608-2.000 99.99 8818 434 0.1329 167.515 166.347 1.017 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3180 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1629 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1188 r_free=0.1627 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1627 | n_water=369 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1188 r_free=0.1627 | n_water=368 | time (s): 29.070 (total time: 29.710) Filter (q & B) r_work=0.1188 r_free=0.1629 | n_water=367 | time (s): 1.810 (total time: 31.520) Compute maps r_work=0.1188 r_free=0.1629 | n_water=367 | time (s): 0.630 (total time: 32.150) Filter (map) r_work=0.1254 r_free=0.1640 | n_water=266 | time (s): 1.720 (total time: 33.870) Find peaks r_work=0.1254 r_free=0.1640 | n_water=266 | time (s): 0.520 (total time: 34.390) Add new water r_work=0.1438 r_free=0.1819 | n_water=412 | time (s): 2.180 (total time: 36.570) Refine new water occ: r_work=0.1253 r_free=0.1623 adp: r_work=0.1245 r_free=0.1621 occ: r_work=0.1227 r_free=0.1598 adp: r_work=0.1215 r_free=0.1595 occ: r_work=0.1207 r_free=0.1579 adp: r_work=0.1197 r_free=0.1580 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1580 r_work=0.1197 r_free=0.1580 | n_water=412 | time (s): 39.280 (total time: 75.850) Filter (q & B) r_work=0.1200 r_free=0.1587 | n_water=404 | time (s): 1.780 (total time: 77.630) Filter (dist only) r_work=0.1200 r_free=0.1587 | n_water=403 | time (s): 31.200 (total time: 108.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.934295 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.143558 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 0.1177 0.1564 0.0387 0.009 1.0 4.5 0.5 0.0 0 0.967 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.77 15.64 3.87 4.391 21.676 0.144 5.002 11.58 15.75 4.17 4.929 21.595 0.144 4.978 Individual atomic B min max mean iso aniso Overall: 6.52 103.96 21.05 4.65 1930 0 Protein: 6.52 103.96 17.12 4.64 1519 0 Water: 8.79 62.44 35.63 N/A 403 0 Other: 23.71 43.67 31.58 N/A 8 0 Chain A: 6.52 103.96 18.88 N/A 1736 0 Chain S: 17.72 62.44 40.46 N/A 194 0 Histogram: Values Number of atoms 6.52 - 16.27 1061 16.27 - 26.01 351 26.01 - 35.75 209 35.75 - 45.50 179 45.50 - 55.24 83 55.24 - 64.98 34 64.98 - 74.73 4 74.73 - 84.47 4 84.47 - 94.22 3 94.22 - 103.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.1158 r_free=0.1575 r_work=0.1158 r_free=0.1575 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1158 r_free = 0.1575 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1153 r_free = 0.1573 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1153 r_free= 0.1573 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.972415 | | target function (ml) not normalized (work): 80727.150577 | | target function (ml) not normalized (free): 4195.793376 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1174 0.1153 0.1573 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1690 0.1682 0.1900 n_refl.: 17042 remove outliers: r(all,work,free)=0.1690 0.1682 0.1900 n_refl.: 17042 overall B=-0.39 to atoms: r(all,work,free)=0.1662 0.1653 0.1886 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1170 0.1149 0.1576 n_refl.: 17042 remove outliers: r(all,work,free)=0.1170 0.1149 0.1576 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 0.3541 303.499 281.621 0.567 1.005 0.340 11.894-9.307 99.02 97 4 0.1800 488.130 481.101 0.908 1.006 0.327 9.237-7.194 100.00 213 7 0.1778 399.241 400.139 0.978 1.007 0.269 7.162-5.571 100.00 427 22 0.1656 299.631 293.764 0.941 1.006 0.241 5.546-4.326 100.00 867 58 0.0947 411.345 407.146 0.964 1.006 0.229 4.315-3.360 100.00 1859 96 0.0897 391.193 389.084 1.013 1.004 0.222 3.356-2.611 100.00 3867 181 0.1284 256.992 254.658 1.013 1.001 0.142 2.608-2.000 99.99 8818 434 0.1087 167.515 166.082 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=-1.4062 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1149 r_free=0.1576 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1149 r_free=0.1572 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1149 r_free=0.1572 | n_water=403 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1153 r_free=0.1572 | n_water=402 | time (s): 31.160 (total time: 31.960) Filter (q & B) r_work=0.1153 r_free=0.1571 | n_water=401 | time (s): 1.720 (total time: 33.680) Compute maps r_work=0.1153 r_free=0.1571 | n_water=401 | time (s): 0.620 (total time: 34.300) Filter (map) r_work=0.1203 r_free=0.1603 | n_water=315 | time (s): 2.120 (total time: 36.420) Find peaks r_work=0.1203 r_free=0.1603 | n_water=315 | time (s): 0.650 (total time: 37.070) Add new water r_work=0.1338 r_free=0.1770 | n_water=449 | time (s): 1.980 (total time: 39.050) Refine new water occ: r_work=0.1185 r_free=0.1575 adp: r_work=0.1179 r_free=0.1581 occ: r_work=0.1161 r_free=0.1548 adp: r_work=0.1155 r_free=0.1551 occ: r_work=0.1145 r_free=0.1526 adp: r_work=0.1139 r_free=0.1526 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1526 r_work=0.1139 r_free=0.1526 | n_water=449 | time (s): 25.930 (total time: 64.980) Filter (q & B) r_work=0.1142 r_free=0.1531 | n_water=441 | time (s): 1.640 (total time: 66.620) Filter (dist only) r_work=0.1142 r_free=0.1531 | n_water=441 | time (s): 35.450 (total time: 102.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.977434 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.152979 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1130 0.1583 0.0453 0.010 1.0 6.1 0.5 0.0 0 0.989 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 15.83 4.53 4.489 21.187 0.153 4.975 11.20 15.85 4.66 4.643 21.206 0.153 4.969 Individual atomic B min max mean iso aniso Overall: 5.82 101.83 21.05 4.73 1968 0 Protein: 5.82 101.83 16.68 4.73 1519 0 Water: 8.24 60.96 35.93 N/A 441 0 Other: 23.01 41.25 30.01 N/A 8 0 Chain A: 5.82 101.83 18.34 N/A 1734 0 Chain S: 16.68 60.96 41.11 N/A 234 0 Histogram: Values Number of atoms 5.82 - 15.42 1020 15.42 - 25.02 382 25.02 - 34.62 222 34.62 - 44.23 183 44.23 - 53.83 108 53.83 - 63.43 38 63.43 - 73.03 5 73.03 - 82.63 5 82.63 - 92.23 2 92.23 - 101.83 3 =========================== Idealize ADP of riding H ========================== r_work=0.1120 r_free=0.1585 r_work=0.1120 r_free=0.1585 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1120 r_free = 0.1585 target_work(ml) = 4.969 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1111 r_free = 0.1585 target_work(ml) = 4.965 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1111 r_free= 0.1585 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.964545 | | target function (ml) not normalized (work): 80599.394311 | | target function (ml) not normalized (free): 4198.248459 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1134 0.1111 0.1585 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1619 0.1607 0.1878 n_refl.: 17042 remove outliers: r(all,work,free)=0.1619 0.1607 0.1878 n_refl.: 17042 overall B=-0.33 to atoms: r(all,work,free)=0.1598 0.1585 0.1866 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1130 0.1108 0.1575 n_refl.: 17042 remove outliers: r(all,work,free)=0.1129 0.1107 0.1575 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 0.3785 300.007 277.669 0.552 1.001 0.340 11.894-9.307 99.02 97 4 0.1743 488.130 481.193 0.909 1.003 0.340 9.237-7.194 100.00 213 7 0.1817 399.241 400.522 0.984 1.004 0.225 7.162-5.571 100.00 427 22 0.1526 299.631 293.940 0.942 1.003 0.210 5.546-4.326 100.00 867 58 0.0915 411.345 407.280 0.964 1.003 0.191 4.315-3.360 100.00 1859 96 0.0854 391.193 388.966 1.011 1.003 0.191 3.356-2.611 100.00 3867 181 0.1231 256.992 254.667 1.008 1.001 0.131 2.608-2.000 99.99 8818 434 0.1049 167.515 166.324 1.008 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1299 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1107 r_free=0.1575 After: r_work=0.1109 r_free=0.1573 ================================== NQH flips ================================== r_work=0.1109 r_free=0.1573 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1109 r_free=0.1573 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1109 r_free=0.1573 | n_water=441 | time (s): 0.780 (total time: 0.780) Filter (dist) r_work=0.1109 r_free=0.1573 | n_water=441 | time (s): 35.260 (total time: 36.040) Filter (q & B) r_work=0.1109 r_free=0.1574 | n_water=439 | time (s): 1.680 (total time: 37.720) Compute maps r_work=0.1109 r_free=0.1574 | n_water=439 | time (s): 0.530 (total time: 38.250) Filter (map) r_work=0.1185 r_free=0.1580 | n_water=334 | time (s): 1.540 (total time: 39.790) Find peaks r_work=0.1185 r_free=0.1580 | n_water=334 | time (s): 0.480 (total time: 40.270) Add new water r_work=0.1305 r_free=0.1667 | n_water=466 | time (s): 1.430 (total time: 41.700) Refine new water occ: r_work=0.1154 r_free=0.1518 adp: r_work=0.1146 r_free=0.1516 occ: r_work=0.1132 r_free=0.1501 adp: r_work=0.1124 r_free=0.1496 occ: r_work=0.1117 r_free=0.1494 adp: r_work=0.1111 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1111 r_free=0.1489 r_work=0.1111 r_free=0.1489 | n_water=466 | time (s): 36.730 (total time: 78.430) Filter (q & B) r_work=0.1113 r_free=0.1499 | n_water=458 | time (s): 1.610 (total time: 80.040) Filter (dist only) r_work=0.1113 r_free=0.1500 | n_water=457 | time (s): 35.880 (total time: 115.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.020807 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.161278 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1130 0.1532 0.0402 0.010 1.1 5.4 0.5 0.0 0 1.010 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 15.32 4.02 4.492 20.923 0.161 4.955 11.18 15.25 4.07 4.606 20.981 0.161 4.947 Individual atomic B min max mean iso aniso Overall: 5.68 99.72 21.03 4.95 1984 0 Protein: 5.68 99.72 16.36 4.95 1519 0 Water: 8.23 62.57 36.45 N/A 457 0 Other: 21.29 37.36 27.87 N/A 8 0 Chain A: 5.68 99.72 18.01 N/A 1734 0 Chain S: 18.66 62.57 42.02 N/A 250 0 Histogram: Values Number of atoms 5.68 - 15.08 1030 15.08 - 24.49 373 24.49 - 33.89 202 33.89 - 43.30 191 43.30 - 52.70 125 52.70 - 62.10 40 62.10 - 71.51 13 71.51 - 80.91 3 80.91 - 90.32 3 90.32 - 99.72 4 =========================== Idealize ADP of riding H ========================== r_work=0.1118 r_free=0.1525 r_work=0.1118 r_free=0.1524 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1118 r_free = 0.1524 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1112 r_free = 0.1520 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1112 r_free= 0.1520 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.943593 | | target function (ml) not normalized (work): 80254.280757 | | target function (ml) not normalized (free): 4170.918261 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1113 0.1353 5.4543 5.6424| | 2: 3.63 - 2.88 1.00 2711 122 0.1081 0.1494 5.212 5.3669| | 3: 2.88 - 2.52 1.00 2681 148 0.1364 0.1725 5.1282 5.1915| | 4: 2.52 - 2.29 1.00 2661 139 0.0956 0.1562 4.6472 4.9625| | 5: 2.29 - 2.13 1.00 2678 122 0.0975 0.1545 4.5957 4.9218| | 6: 2.13 - 2.00 1.00 2692 117 0.1154 0.1752 4.5952 4.7901| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2811 159 0.95 8.86 1.00 0.96 6285.20| | 2: 3.63 - 2.88 2711 122 0.92 12.69 1.01 0.96 6285.20| | 3: 2.88 - 2.52 2681 148 0.88 18.79 0.99 0.96 6285.20| | 4: 2.52 - 2.29 2661 139 0.93 12.41 1.01 0.97 2201.96| | 5: 2.29 - 2.13 2678 122 0.91 14.48 1.00 0.97 2201.96| | 6: 2.13 - 2.00 2692 117 0.89 17.15 0.99 0.97 2201.96| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2201.96 max = 6285.20 mean = 4265.21| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.96 mean = 14.02| |phase err.(test): min = 0.00 max = 84.66 mean = 13.63| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1132 0.1112 0.1520 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1597 0.1582 0.1883 n_refl.: 17041 remove outliers: r(all,work,free)=0.1597 0.1582 0.1883 n_refl.: 17041 overall B=-0.25 to atoms: r(all,work,free)=0.1581 0.1567 0.1873 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1112 0.1522 n_refl.: 17041 remove outliers: r(all,work,free)=0.1132 0.1112 0.1522 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 0.3685 300.007 280.593 0.542 1.003 0.330 11.894-9.307 99.02 97 4 0.1753 488.130 482.144 0.914 1.005 0.330 9.237-7.194 100.00 213 7 0.1736 399.241 401.469 0.986 1.005 0.219 7.162-5.571 100.00 427 22 0.1543 299.631 294.225 0.940 1.005 0.217 5.546-4.326 100.00 867 58 0.0902 411.345 408.075 0.961 1.004 0.195 4.315-3.360 100.00 1859 96 0.0869 391.193 388.856 1.006 1.003 0.191 3.356-2.611 100.00 3867 181 0.1244 256.992 254.844 1.003 1.000 0.121 2.608-2.000 99.99 8818 434 0.1055 167.515 166.108 0.998 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8821 ================= 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 : 0.2791 0.1812 0.081 5.160 8.8 119.3 19.9 258 0.000 1_bss: 0.1613 0.1654 0.081 5.160 8.5 118.9 19.5 258 0.000 1_settarget: 0.1613 0.1654 0.081 5.160 8.5 118.9 19.5 258 0.000 1_nqh: 0.1613 0.1654 0.081 5.160 8.5 118.9 19.5 258 0.000 1_weight: 0.1613 0.1654 0.081 5.160 8.5 118.9 19.5 258 0.000 1_xyzrec: 0.1353 0.1642 0.009 0.967 8.5 118.9 19.5 258 0.153 1_adp: 0.1279 0.1667 0.009 0.967 5.8 113.9 19.9 258 0.153 1_regHadp: 0.1282 0.1672 0.009 0.967 5.8 113.9 19.9 258 0.153 1_occ: 0.1277 0.1669 0.009 0.967 5.8 113.9 19.9 258 0.153 2_bss: 0.1274 0.1658 0.009 0.967 5.5 113.5 19.6 258 0.153 2_settarget: 0.1274 0.1658 0.009 0.967 5.5 113.5 19.6 258 0.153 2_updatecdl: 0.1274 0.1658 0.009 0.977 5.5 113.5 19.6 258 0.153 2_nqh: 0.1274 0.1658 0.009 0.977 5.5 113.5 19.6 258 0.153 2_sol: 0.1236 0.1551 0.009 0.977 5.5 112.5 20.9 369 n/a 2_weight: 0.1236 0.1551 0.009 0.977 5.5 112.5 20.9 369 n/a 2_xyzrec: 0.1209 0.1607 0.008 0.927 5.5 112.5 20.9 369 n/a 2_adp: 0.1193 0.1631 0.008 0.927 6.6 107.5 21.5 369 n/a 2_regHadp: 0.1195 0.1633 0.008 0.927 6.6 107.5 21.5 369 n/a 2_occ: 0.1190 0.1636 0.008 0.927 6.6 107.5 21.5 369 n/a 3_bss: 0.1186 0.1629 0.008 0.927 6.2 107.1 21.1 369 n/a 3_settarget: 0.1186 0.1629 0.008 0.927 6.2 107.1 21.1 369 n/a 3_updatecdl: 0.1186 0.1629 0.008 0.932 6.2 107.1 21.1 369 n/a 3_nqh: 0.1188 0.1627 0.008 0.932 6.2 107.1 21.1 369 n/a 3_sol: 0.1200 0.1587 0.008 0.932 6.2 107.1 21.2 403 n/a 3_weight: 0.1200 0.1587 0.008 0.932 6.2 107.1 21.2 403 n/a 3_xyzrec: 0.1177 0.1564 0.009 0.956 6.2 107.1 21.2 403 n/a 3_adp: 0.1158 0.1575 0.009 0.956 6.5 104.0 21.0 403 n/a 3_regHadp: 0.1158 0.1575 0.009 0.956 6.5 104.0 21.0 403 n/a 3_occ: 0.1153 0.1573 0.009 0.956 6.5 104.0 21.0 403 n/a 4_bss: 0.1149 0.1576 0.009 0.956 6.1 103.6 20.7 403 n/a 4_settarget: 0.1149 0.1576 0.009 0.956 6.1 103.6 20.7 403 n/a 4_updatecdl: 0.1149 0.1576 0.009 0.954 6.1 103.6 20.7 403 n/a 4_nqh: 0.1149 0.1572 0.009 0.954 6.1 103.6 20.7 403 n/a 4_sol: 0.1142 0.1531 0.009 0.954 6.1 103.6 21.0 441 n/a 4_weight: 0.1142 0.1531 0.009 0.954 6.1 103.6 21.0 441 n/a 4_xyzrec: 0.1130 0.1583 0.010 0.977 6.1 103.6 21.0 441 n/a 4_adp: 0.1120 0.1585 0.010 0.977 5.8 101.8 21.0 441 n/a 4_regHadp: 0.1120 0.1585 0.010 0.977 5.8 101.8 21.0 441 n/a 4_occ: 0.1111 0.1585 0.010 0.977 5.8 101.8 21.0 441 n/a 5_bss: 0.1107 0.1575 0.010 0.977 5.5 101.5 20.7 441 n/a 5_settarget: 0.1107 0.1575 0.010 0.977 5.5 101.5 20.7 441 n/a 5_updatecdl: 0.1107 0.1575 0.010 0.980 5.5 101.5 20.7 441 n/a 5_setrh: 0.1109 0.1573 0.010 0.980 5.5 101.5 20.7 441 n/a 5_nqh: 0.1109 0.1573 0.010 0.980 5.5 101.5 20.7 441 n/a 5_sol: 0.1113 0.1500 0.010 0.980 5.5 101.5 20.9 457 n/a 5_weight: 0.1113 0.1500 0.010 0.980 5.5 101.5 20.9 457 n/a 5_xyzrec: 0.1130 0.1532 0.010 1.072 5.5 101.5 20.9 457 n/a 5_adp: 0.1118 0.1525 0.010 1.072 5.7 99.7 21.0 457 n/a 5_regHadp: 0.1118 0.1524 0.010 1.072 5.7 99.7 21.0 457 n/a 5_occ: 0.1112 0.1520 0.010 1.072 5.7 99.7 21.0 457 n/a end: 0.1112 0.1522 0.010 1.072 5.4 99.5 20.8 457 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7798058_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7798058_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3600 Refinement macro-cycles (run) : 928.8800 Write final files (write_after_run_outputs) : 18.5800 Total : 950.8200 Total CPU time: 16.21 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:14 PST -0800 (1735494074.20 s) Start R-work = 0.1613, R-free = 0.1654 Final R-work = 0.1112, R-free = 0.1522 =============================================================================== Job complete usr+sys time: 993.59 seconds wall clock time: 16 minutes 56.76 seconds (1016.76 seconds total)