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_9291273.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9291273.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9291273.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" 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: 1.25, per 1000 atoms: 0.37 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: 0.40 Conformation dependent library (CDL) restraints added in 114.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 454 0.90 - 1.17: 1203 1.17 - 1.44: 682 1.44 - 1.70: 798 1.70 - 1.97: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLY A 136 " pdb=" N GLY A 137 " ideal model delta sigma weight residual 1.329 1.121 0.208 1.00e-02 1.00e+04 4.32e+02 bond pdb=" N PRO A 127 " pdb=" CD PRO A 127 " ideal model delta sigma weight residual 1.473 1.198 0.275 1.40e-02 5.10e+03 3.85e+02 bond pdb=" C SER A 142 " pdb=" O SER A 142 " ideal model delta sigma weight residual 1.234 1.017 0.216 1.22e-02 6.72e+03 3.15e+02 bond pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " ideal model delta sigma weight residual 1.378 1.189 0.189 1.10e-02 8.26e+03 2.95e+02 bond pdb=" C BTYR A 67 " pdb=" N ASP A 68 " ideal model delta sigma weight residual 1.333 1.584 -0.251 1.49e-02 4.50e+03 2.83e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 2960 4.24 - 8.48: 1845 8.48 - 12.72: 762 12.72 - 16.96: 180 16.96 - 21.20: 30 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.07 108.45 11.62 7.10e-01 1.98e+00 2.68e+02 angle pdb=" OD1 ASN A 81 " pdb=" CG ASN A 81 " pdb=" ND2 ASN A 81 " ideal model delta sigma weight residual 122.60 137.39 -14.79 1.00e+00 1.00e+00 2.19e+02 angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 106.48 12.72 9.00e-01 1.23e+00 2.00e+02 angle pdb=" O ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " ideal model delta sigma weight residual 122.93 108.17 14.76 1.06e+00 8.90e-01 1.94e+02 angle pdb=" O LEU A 72 " pdb=" C LEU A 72 " pdb=" N PRO A 73 " ideal model delta sigma weight residual 120.85 134.61 -13.76 1.01e+00 9.80e-01 1.86e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 1269 15.66 - 31.32: 145 31.32 - 46.97: 46 46.97 - 62.63: 19 62.63 - 78.28: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C GLU A 116 " pdb=" N GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual -122.60 -142.73 20.13 0 2.50e+00 1.60e-01 6.48e+01 dihedral pdb=" C VAL A 186 " pdb=" N VAL A 186 " pdb=" CA VAL A 186 " pdb=" CB VAL A 186 " ideal model delta harmonic sigma weight residual -122.00 -141.43 19.43 0 2.50e+00 1.60e-01 6.04e+01 dihedral pdb=" C ARG A 27 " pdb=" N ARG A 27 " pdb=" CA ARG A 27 " pdb=" CB ARG A 27 " ideal model delta harmonic sigma weight residual -122.60 -141.59 18.99 0 2.50e+00 1.60e-01 5.77e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.244: 104 0.244 - 0.485: 83 0.485 - 0.725: 39 0.725 - 0.966: 15 0.966 - 1.206: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.38 -1.21 2.00e-01 2.50e+01 3.64e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.57 0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" CA ALA A 6 " pdb=" N ALA A 6 " pdb=" C ALA A 6 " pdb=" CB ALA A 6 " both_signs ideal model delta sigma weight residual False 2.48 3.44 -0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.049 2.00e-02 2.50e+03 7.54e-02 1.71e+02 pdb=" CG PHE A 119 " -0.127 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.071 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.064 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.007 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.122 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.053 2.00e-02 2.50e+03 6.15e-02 1.14e+02 pdb=" CG ATYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.132 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.085 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.068 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.056 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.031 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.072 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.055 2.00e-02 2.50e+03 5.97e-02 1.07e+02 pdb=" CG TYR A 141 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.086 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.036 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.093 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.068 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.014 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 911 2.30 - 2.87: 7913 2.87 - 3.45: 10588 3.45 - 4.02: 15323 4.02 - 4.60: 21834 Nonbonded interactions: 56569 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.719 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.823 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.830 2.450 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.844 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.849 2.100 ... (remaining 56564 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_9291273_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= 0.2801 r_free= 0.1835 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.426187 | | target function (ml) not normalized (work): 71894.555573 | | target function (ml) not normalized (free): 3277.528986 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3203 0.2136 7.6421 5.0395| | 2: 3.63 - 2.88 1.00 2711 122 0.2638 0.1600 4.3162 4.3005| | 3: 2.88 - 2.52 1.00 2682 148 0.2571 0.1837 4.1766 4.1855| | 4: 2.52 - 2.29 1.00 2661 139 0.2571 0.1598 3.4971 3.5979| | 5: 2.29 - 2.13 1.00 2678 122 0.2708 0.1557 3.4205 3.4927| | 6: 2.13 - 2.00 1.00 2692 117 0.2755 0.1903 3.3368 3.4694| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.30 0.77 0.23 1270.08| | 2: 3.63 - 2.88 2711 122 0.83 23.50 1.31 0.23 1270.08| | 3: 2.88 - 2.52 2682 148 0.74 32.42 1.28 0.23 1270.08| | 4: 2.52 - 2.29 2661 139 0.93 12.13 1.30 0.26 147.75| | 5: 2.29 - 2.13 2678 122 0.91 14.29 1.33 0.26 147.75| | 6: 2.13 - 2.00 2692 117 0.89 17.09 1.33 0.26 147.75| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 147.75 max = 1270.08 mean = 715.16| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.82 mean = 19.45| |phase err.(test): min = 0.00 max = 87.64 mean = 19.40| |-----------------------------------------------------------------------------| ----------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 0.275 1557 Z= 5.463 Angle : 5.274 19.994 2118 Z= 3.722 Chirality : 0.402 1.206 243 Planarity : 0.031 0.090 284 Dihedral : 13.567 78.285 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 2.48 % Allowed : 3.11 % Favored : 94.41 % Cbeta Deviations : 31.89 % 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: -3.03 (0.45), residues: 224 helix: -2.85 (0.34), residues: 108 sheet: -2.04 (0.68), residues: 30 loop : -0.39 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.094 0.019 ARG A 5 TYR 0.076 0.045 TYR A 141 PHE 0.119 0.031 PHE A 119 HIS 0.069 0.020 HIS A 138 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= 0.2801 r_free= 0.1835 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.426187 | | target function (ml) not normalized (work): 71894.555573 | | target function (ml) not normalized (free): 3277.528986 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2625 percent. r_work = 0.2928 r_free = 0.2001 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2874 0.2928 0.2001 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2874 0.2928 0.2001 n_refl.: 17050 remove outliers: r(all,work,free)=0.2165 0.2176 0.2001 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2137 0.2147 0.1986 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1624 0.1621 0.1695 n_refl.: 17045 remove outliers: r(all,work,free)=0.1623 0.1620 0.1695 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 0.4036 394.873 360.551 0.646 1.018 0.397 11.894-9.307 99.02 97 4 0.1880 633.784 611.905 0.921 1.019 0.380 9.237-7.194 100.00 213 7 0.2231 518.371 508.917 0.956 1.018 0.381 7.162-5.571 100.00 427 22 0.2294 389.038 378.119 0.916 1.016 0.321 5.546-4.326 100.00 867 58 0.1365 534.087 529.309 0.957 1.013 0.236 4.315-3.360 100.00 1859 96 0.1303 507.922 504.027 1.015 1.008 0.218 3.356-2.611 100.00 3867 181 0.1680 333.676 328.958 1.013 0.999 0.071 2.608-2.000 99.99 8818 434 0.1650 217.499 213.492 1.039 0.982 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4718 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1620 r_free=0.1695 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=0.1621 r_free=0.1708 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.227871 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.944351 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 0.1354 0.1643 0.0290 0.009 1.0 1.6 0.5 0.0 0 11.614 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.54 16.43 2.90 3.013 18.447 0.944 0.023 12.81 16.68 3.87 3.680 18.699 0.944 0.021 Individual atomic B min max mean iso aniso Overall: 5.80 113.89 19.95 4.16 1785 0 Protein: 5.80 113.39 17.19 4.16 1519 0 Water: 8.52 113.89 35.99 N/A 258 0 Other: 22.12 37.42 26.74 N/A 8 0 Chain A: 5.80 113.89 19.95 N/A 1785 0 Histogram: Values Number of atoms 5.80 - 16.61 1054 16.61 - 27.42 365 27.42 - 38.23 192 38.23 - 49.04 95 49.04 - 59.84 52 59.84 - 70.65 11 70.65 - 81.46 8 81.46 - 92.27 4 92.27 - 103.08 1 103.08 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1281 r_free=0.1668 r_work=0.1284 r_free=0.1674 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1284 r_free = 0.1674 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 = 0.1280 r_free = 0.1666 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 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= 0.1280 r_free= 0.1666 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020252 | | target function (ls_wunit_k1) not normalized (work): 328.828057 | | target function (ls_wunit_k1) not normalized (free): 27.134990 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1298 0.1280 0.1666 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1918 0.1917 0.1994 n_refl.: 17044 remove outliers: r(all,work,free)=0.1918 0.1917 0.1994 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1890 0.1888 0.1978 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1298 0.1280 0.1654 n_refl.: 17044 remove outliers: r(all,work,free)=0.1296 0.1278 0.1654 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 0.3507 303.559 278.228 0.613 1.010 0.360 11.894-9.307 99.02 97 4 0.1707 488.227 479.434 0.916 1.010 0.357 9.237-7.194 100.00 213 7 0.1874 399.320 395.318 0.960 1.010 0.351 7.162-5.571 100.00 427 22 0.1843 299.690 294.357 0.930 1.009 0.311 5.546-4.326 100.00 867 58 0.1051 411.427 408.931 0.959 1.007 0.215 4.315-3.360 100.00 1859 96 0.0929 391.271 390.948 1.019 1.005 0.201 3.356-2.611 100.00 3867 181 0.1299 257.043 255.788 1.016 1.000 0.081 2.608-2.000 99.99 8818 434 0.1354 167.548 166.039 1.024 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.4034 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1278 r_free=0.1654 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=0.1279 r_free=0.1653 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1279 r_free=0.1653 | n_water=258 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1287 r_free=0.1642 | n_water=252 | time (s): 19.460 (total time: 20.070) Filter (q & B) r_work=0.1287 r_free=0.1643 | n_water=250 | time (s): 1.660 (total time: 21.730) Compute maps r_work=0.1287 r_free=0.1643 | n_water=250 | time (s): 0.570 (total time: 22.300) Filter (map) r_work=0.1318 r_free=0.1630 | n_water=211 | time (s): 1.910 (total time: 24.210) Find peaks r_work=0.1318 r_free=0.1630 | n_water=211 | time (s): 0.660 (total time: 24.870) Add new water r_work=0.1542 r_free=0.1862 | n_water=363 | time (s): 1.850 (total time: 26.720) Refine new water occ: r_work=0.1341 r_free=0.1594 adp: r_work=0.1283 r_free=0.1598 occ: r_work=0.1287 r_free=0.1557 adp: r_work=0.1253 r_free=0.1571 occ: r_work=0.1252 r_free=0.1554 adp: r_work=0.1241 r_free=0.1554 ADP+occupancy (water only), MIN, final r_work=0.1241 r_free=0.1554 r_work=0.1241 r_free=0.1554 | n_water=363 | time (s): 11.090 (total time: 37.810) Filter (q & B) r_work=0.1243 r_free=0.1560 | n_water=357 | time (s): 1.630 (total time: 39.440) Filter (dist only) r_work=0.1243 r_free=0.1559 | n_water=356 | time (s): 28.160 (total time: 67.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.251622 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.983743 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 0.1616 0.0402 0.009 0.9 2.6 0.5 0.0 0 12.626 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 16.16 4.02 4.212 20.984 0.984 0.018 11.99 16.38 4.40 4.243 21.236 0.984 0.018 Individual atomic B min max mean iso aniso Overall: 6.27 107.99 21.20 4.23 1883 0 Protein: 6.27 107.99 17.67 4.22 1519 0 Water: 8.66 65.86 35.93 N/A 356 0 Other: 25.62 47.46 35.81 N/A 8 0 Chain A: 6.27 107.99 19.41 N/A 1738 0 Chain S: 16.82 65.86 42.69 N/A 145 0 Histogram: Values Number of atoms 6.27 - 16.44 1011 16.44 - 26.61 395 26.61 - 36.78 215 36.78 - 46.96 157 46.96 - 57.13 70 57.13 - 67.30 25 67.30 - 77.48 3 77.48 - 87.65 5 87.65 - 97.82 0 97.82 - 107.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1638 r_work=0.1200 r_free=0.1639 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1639 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 = 0.1197 r_free = 0.1645 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 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= 0.1197 r_free= 0.1645 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017092 | | target function (ls_wunit_k1) not normalized (work): 277.496165 | | target function (ls_wunit_k1) not normalized (free): 25.956391 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1197 0.1645 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1755 0.1746 0.1977 n_refl.: 17042 remove outliers: r(all,work,free)=0.1755 0.1746 0.1977 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1731 0.1721 0.1962 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1190 0.1642 n_refl.: 17042 remove outliers: r(all,work,free)=0.1212 0.1190 0.1642 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 0.3413 303.559 282.809 0.605 1.005 0.350 11.894-9.307 99.02 97 4 0.1484 488.227 486.261 0.913 1.006 0.350 9.237-7.194 100.00 213 7 0.1668 399.320 399.455 0.973 1.006 0.320 7.162-5.571 100.00 427 22 0.1565 299.690 295.807 0.931 1.005 0.281 5.546-4.326 100.00 867 58 0.0871 411.427 408.507 0.959 1.005 0.216 4.315-3.360 100.00 1859 96 0.0838 391.271 390.496 1.014 1.003 0.211 3.356-2.611 100.00 3867 181 0.1196 257.043 256.390 1.012 1.001 0.063 2.608-2.000 99.99 8818 434 0.1327 167.548 166.601 1.016 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3344 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1642 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1190 r_free=0.1644 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1644 | n_water=356 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1191 r_free=0.1644 | n_water=355 | time (s): 28.930 (total time: 29.610) Filter (q & B) r_work=0.1191 r_free=0.1644 | n_water=355 | time (s): 0.730 (total time: 30.340) Compute maps r_work=0.1191 r_free=0.1644 | n_water=355 | time (s): 0.630 (total time: 30.970) Filter (map) r_work=0.1255 r_free=0.1637 | n_water=267 | time (s): 1.920 (total time: 32.890) Find peaks r_work=0.1255 r_free=0.1637 | n_water=267 | time (s): 0.650 (total time: 33.540) Add new water r_work=0.1442 r_free=0.1760 | n_water=406 | time (s): 1.960 (total time: 35.500) Refine new water occ: r_work=0.1246 r_free=0.1563 adp: r_work=0.1240 r_free=0.1564 occ: r_work=0.1219 r_free=0.1559 adp: r_work=0.1210 r_free=0.1552 occ: r_work=0.1200 r_free=0.1560 adp: r_work=0.1191 r_free=0.1555 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1555 r_work=0.1191 r_free=0.1555 | n_water=406 | time (s): 34.080 (total time: 69.580) Filter (q & B) r_work=0.1195 r_free=0.1559 | n_water=396 | time (s): 1.540 (total time: 71.120) Filter (dist only) r_work=0.1195 r_free=0.1559 | n_water=396 | time (s): 28.560 (total time: 99.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.830607 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.163643 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 0.1173 0.1569 0.0396 0.009 1.0 3.5 0.5 0.0 0 0.915 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.73 15.69 3.96 4.308 21.468 0.164 4.996 11.52 15.66 4.14 4.836 21.364 0.164 4.973 Individual atomic B min max mean iso aniso Overall: 5.98 106.52 20.82 4.62 1923 0 Protein: 5.98 106.52 16.94 4.61 1519 0 Water: 8.54 60.40 35.37 N/A 396 0 Other: 28.53 46.57 36.35 N/A 8 0 Chain A: 5.98 106.52 18.73 N/A 1736 0 Chain S: 15.50 59.89 40.19 N/A 187 0 Histogram: Values Number of atoms 5.98 - 16.03 1058 16.03 - 26.09 357 26.09 - 36.14 217 36.14 - 46.20 178 46.20 - 56.25 75 56.25 - 66.31 26 66.31 - 76.36 5 76.36 - 86.41 3 86.41 - 96.47 2 96.47 - 106.52 2 =========================== Idealize ADP of riding H ========================== r_work=0.1152 r_free=0.1566 r_work=0.1153 r_free=0.1568 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1568 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1142 r_free = 0.1564 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.24 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= 0.1142 r_free= 0.1564 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.966661 | | target function (ml) not normalized (work): 80633.741796 | | target function (ml) not normalized (free): 4187.859249 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1142 0.1564 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1670 0.1663 0.1862 n_refl.: 17042 remove outliers: r(all,work,free)=0.1670 0.1663 0.1862 n_refl.: 17042 overall B=-0.47 to atoms: r(all,work,free)=0.1638 0.1630 0.1849 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1161 0.1141 0.1563 n_refl.: 17042 remove outliers: r(all,work,free)=0.1161 0.1141 0.1563 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 303.559 279.520 0.582 1.006 0.350 11.894-9.307 99.02 97 4 0.1808 488.227 480.779 0.909 1.007 0.327 9.237-7.194 100.00 213 7 0.1849 399.320 399.055 0.987 1.007 0.255 7.162-5.571 100.00 427 22 0.1612 299.690 294.920 0.938 1.007 0.251 5.546-4.326 100.00 867 58 0.0942 411.427 407.684 0.964 1.006 0.211 4.315-3.360 100.00 1859 96 0.0874 391.271 388.995 1.011 1.004 0.211 3.356-2.611 100.00 3867 181 0.1282 257.043 254.909 1.010 1.001 0.122 2.608-2.000 99.99 8818 434 0.1078 167.548 166.241 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1823 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1141 r_free=0.1563 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1141 r_free=0.1563 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1141 r_free=0.1563 | n_water=396 | time (s): 0.910 (total time: 0.910) Filter (dist) r_work=0.1141 r_free=0.1563 | n_water=396 | time (s): 32.370 (total time: 33.280) Filter (q & B) r_work=0.1141 r_free=0.1563 | n_water=396 | time (s): 1.000 (total time: 34.280) Compute maps r_work=0.1141 r_free=0.1563 | n_water=396 | time (s): 0.670 (total time: 34.950) Filter (map) r_work=0.1201 r_free=0.1559 | n_water=311 | time (s): 2.180 (total time: 37.130) Find peaks r_work=0.1201 r_free=0.1559 | n_water=311 | time (s): 0.470 (total time: 37.600) Add new water r_work=0.1356 r_free=0.1706 | n_water=457 | time (s): 1.730 (total time: 39.330) Refine new water occ: r_work=0.1177 r_free=0.1499 adp: r_work=0.1168 r_free=0.1508 occ: r_work=0.1151 r_free=0.1477 adp: r_work=0.1141 r_free=0.1484 occ: r_work=0.1134 r_free=0.1467 adp: r_work=0.1125 r_free=0.1472 ADP+occupancy (water only), MIN, final r_work=0.1125 r_free=0.1472 r_work=0.1125 r_free=0.1472 | n_water=457 | time (s): 22.630 (total time: 61.960) Filter (q & B) r_work=0.1128 r_free=0.1482 | n_water=451 | time (s): 2.010 (total time: 63.970) Filter (dist only) r_work=0.1128 r_free=0.1482 | n_water=451 | time (s): 34.870 (total time: 98.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.951526 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.168909 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 0.1114 0.1516 0.0402 0.010 1.0 5.1 0.5 0.0 0 0.976 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.14 15.16 4.02 4.452 21.002 0.169 4.950 11.02 15.11 4.09 4.594 21.048 0.169 4.941 Individual atomic B min max mean iso aniso Overall: 5.72 104.15 21.00 4.82 1978 0 Protein: 5.72 104.15 16.48 4.81 1519 0 Water: 8.35 64.17 36.00 N/A 451 0 Other: 26.76 44.58 34.53 N/A 8 0 Chain A: 5.72 104.15 18.22 N/A 1735 0 Chain S: 18.69 64.17 40.87 N/A 243 0 Histogram: Values Number of atoms 5.72 - 15.56 1060 15.56 - 25.40 355 25.40 - 35.25 221 35.25 - 45.09 199 45.09 - 54.94 100 54.94 - 64.78 30 64.78 - 74.62 6 74.62 - 84.47 2 84.47 - 94.31 3 94.31 - 104.15 2 =========================== Idealize ADP of riding H ========================== r_work=0.1102 r_free=0.1511 r_work=0.1102 r_free=0.1511 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1102 r_free = 0.1511 target_work(ml) = 4.941 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1094 r_free = 0.1509 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1094 r_free= 0.1509 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.934774 | | target function (ml) not normalized (work): 80116.058911 | | target function (ml) not normalized (free): 4160.974417 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1114 0.1094 0.1509 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1570 0.1560 0.1793 n_refl.: 17042 remove outliers: r(all,work,free)=0.1570 0.1560 0.1793 n_refl.: 17042 overall B=-0.27 to atoms: r(all,work,free)=0.1553 0.1543 0.1786 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1112 0.1092 0.1505 n_refl.: 17042 remove outliers: r(all,work,free)=0.1110 0.1090 0.1505 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 0.3616 302.246 272.448 0.553 1.001 0.350 11.894-9.307 99.02 97 4 0.1769 488.227 483.658 0.912 1.002 0.350 9.237-7.194 100.00 213 7 0.1730 399.320 400.206 0.991 1.002 0.230 7.162-5.571 100.00 427 22 0.1527 299.690 294.451 0.942 1.002 0.230 5.546-4.326 100.00 867 58 0.0902 411.427 408.237 0.968 1.002 0.195 4.315-3.360 100.00 1859 96 0.0815 391.271 388.847 1.006 1.002 0.191 3.356-2.611 100.00 3867 181 0.1215 257.043 254.923 1.003 1.001 0.101 2.608-2.000 99.99 8818 434 0.1044 167.548 166.416 0.997 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9584 b_overall=-0.9427 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1090 r_free=0.1505 After: r_work=0.1092 r_free=0.1504 ================================== NQH flips ================================== r_work=0.1092 r_free=0.1504 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1092 r_free=0.1504 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1092 r_free=0.1504 | n_water=451 | time (s): 0.920 (total time: 0.920) Filter (dist) r_work=0.1094 r_free=0.1501 | n_water=449 | time (s): 39.680 (total time: 40.600) Filter (q & B) r_work=0.1094 r_free=0.1501 | n_water=449 | time (s): 0.810 (total time: 41.410) Compute maps r_work=0.1094 r_free=0.1501 | n_water=449 | time (s): 0.690 (total time: 42.100) Filter (map) r_work=0.1166 r_free=0.1528 | n_water=340 | time (s): 1.900 (total time: 44.000) Find peaks r_work=0.1166 r_free=0.1528 | n_water=340 | time (s): 0.410 (total time: 44.410) Add new water r_work=0.1288 r_free=0.1624 | n_water=480 | time (s): 1.510 (total time: 45.920) Refine new water occ: r_work=0.1131 r_free=0.1458 adp: r_work=0.1122 r_free=0.1463 occ: r_work=0.1110 r_free=0.1448 adp: r_work=0.1100 r_free=0.1454 occ: r_work=0.1095 r_free=0.1441 adp: r_work=0.1087 r_free=0.1445 ADP+occupancy (water only), MIN, final r_work=0.1087 r_free=0.1445 r_work=0.1087 r_free=0.1445 | n_water=480 | time (s): 16.890 (total time: 62.810) Filter (q & B) r_work=0.1091 r_free=0.1455 | n_water=468 | time (s): 2.150 (total time: 64.960) Filter (dist only) r_work=0.1092 r_free=0.1454 | n_water=467 | time (s): 38.690 (total time: 103.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.849449 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.189660 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1112 0.1472 0.0359 0.011 1.1 3.8 0.5 0.0 0 0.925 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.12 14.72 3.59 4.529 20.853 0.190 4.934 11.01 14.64 3.63 4.659 20.921 0.190 4.926 Individual atomic B min max mean iso aniso Overall: 5.43 104.29 21.05 5.13 1994 0 Protein: 5.43 104.29 16.22 5.11 1519 0 Water: 8.06 71.36 36.54 N/A 467 0 Other: 26.07 43.94 34.06 N/A 8 0 Chain A: 5.43 104.29 17.92 N/A 1734 0 Chain S: 16.85 71.36 41.92 N/A 260 0 Histogram: Values Number of atoms 5.43 - 15.31 1066 15.31 - 25.20 352 25.20 - 35.09 204 35.09 - 44.97 210 44.97 - 54.86 117 54.86 - 64.74 27 64.74 - 74.63 9 74.63 - 84.51 3 84.51 - 94.40 3 94.40 - 104.29 3 =========================== Idealize ADP of riding H ========================== r_work=0.1101 r_free=0.1464 r_work=0.1101 r_free=0.1463 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1101 r_free = 0.1463 target_work(ml) = 4.926 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1095 r_free = 0.1455 target_work(ml) = 4.920 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1095 r_free= 0.1455 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.920444 | | target function (ml) not normalized (work): 79873.564873 | | target function (ml) not normalized (free): 4144.290442 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1109 0.1392 5.4535 5.6526| | 2: 3.63 - 2.88 1.00 2711 122 0.1065 0.1360 5.1925 5.2945| | 3: 2.88 - 2.52 1.00 2681 148 0.1335 0.1609 5.101 5.1774| | 4: 2.52 - 2.29 1.00 2661 139 0.0930 0.1423 4.616 4.905| | 5: 2.29 - 2.13 1.00 2678 122 0.0964 0.1440 4.5687 4.869| | 6: 2.13 - 2.00 1.00 2692 117 0.1118 0.1696 4.561 4.7652| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.60 1.00 0.96 5884.65| | 2: 3.63 - 2.88 2711 122 0.93 12.23 1.01 0.96 5884.65| | 3: 2.88 - 2.52 2681 148 0.88 18.12 0.99 0.96 5884.65| | 4: 2.52 - 2.29 2661 139 0.93 11.79 1.01 0.97 2035.76| | 5: 2.29 - 2.13 2678 122 0.92 13.79 1.00 0.97 2035.76| | 6: 2.13 - 2.00 2692 117 0.90 16.42 0.99 0.97 2035.76| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2035.76 max = 5884.65 mean = 3980.48| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.92 mean = 13.45| |phase err.(test): min = 0.00 max = 87.38 mean = 12.94| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1112 0.1095 0.1455 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1537 0.1526 0.1769 n_refl.: 17040 remove outliers: r(all,work,free)=0.1537 0.1526 0.1769 n_refl.: 17040 overall B=-0.22 to atoms: r(all,work,free)=0.1525 0.1514 0.1762 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1112 0.1095 0.1453 n_refl.: 17040 remove outliers: r(all,work,free)=0.1111 0.1094 0.1453 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 0.3363 298.996 284.231 0.550 1.002 0.310 11.894-9.307 99.02 97 4 0.1840 488.227 481.960 0.909 1.004 0.295 9.237-7.194 100.00 213 7 0.1757 399.320 399.429 0.989 1.005 0.220 7.162-5.571 100.00 427 22 0.1527 299.690 294.533 0.937 1.005 0.218 5.546-4.326 100.00 867 58 0.0922 411.427 408.144 0.963 1.004 0.185 4.315-3.360 100.00 1859 96 0.0853 391.271 388.757 1.002 1.003 0.181 3.356-2.611 100.00 3867 181 0.1215 257.043 254.964 0.999 1.000 0.101 2.608-2.000 99.99 8818 434 0.1033 167.548 166.326 0.991 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.7450 ================= 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 : 0.2801 0.1835 0.083 5.274 8.8 119.3 19.9 258 0.000 1_bss: 0.1620 0.1695 0.083 5.274 8.4 118.9 19.5 258 0.000 1_settarget: 0.1620 0.1695 0.083 5.274 8.4 118.9 19.5 258 0.000 1_nqh: 0.1621 0.1708 0.083 5.274 8.4 118.9 19.5 258 0.003 1_weight: 0.1621 0.1708 0.083 5.274 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1354 0.1643 0.009 0.990 8.4 118.9 19.5 258 0.150 1_adp: 0.1281 0.1668 0.009 0.990 5.8 113.9 20.0 258 0.150 1_regHadp: 0.1284 0.1674 0.009 0.990 5.8 113.9 20.0 258 0.150 1_occ: 0.1280 0.1666 0.009 0.990 5.8 113.9 20.0 258 0.150 2_bss: 0.1278 0.1654 0.009 0.990 5.4 113.5 19.6 258 0.150 2_settarget: 0.1278 0.1654 0.009 0.990 5.4 113.5 19.6 258 0.150 2_updatecdl: 0.1278 0.1654 0.009 0.991 5.4 113.5 19.6 258 0.150 2_nqh: 0.1279 0.1653 0.009 0.991 5.4 113.5 19.6 258 0.148 2_sol: 0.1243 0.1559 0.009 0.991 5.4 113.0 20.7 356 n/a 2_weight: 0.1243 0.1559 0.009 0.991 5.4 113.0 20.7 356 n/a 2_xyzrec: 0.1214 0.1616 0.009 0.945 5.4 113.0 20.7 356 n/a 2_adp: 0.1199 0.1638 0.009 0.945 6.3 108.0 21.2 356 n/a 2_regHadp: 0.1200 0.1639 0.009 0.945 6.3 108.0 21.2 356 n/a 2_occ: 0.1197 0.1645 0.009 0.945 6.3 108.0 21.2 356 n/a 3_bss: 0.1190 0.1642 0.009 0.945 5.9 107.6 20.8 356 n/a 3_settarget: 0.1190 0.1642 0.009 0.945 5.9 107.6 20.8 356 n/a 3_updatecdl: 0.1190 0.1642 0.009 0.946 5.9 107.6 20.8 356 n/a 3_nqh: 0.1190 0.1644 0.009 0.946 5.9 107.6 20.8 356 n/a 3_sol: 0.1195 0.1559 0.009 0.946 5.9 107.6 21.0 396 n/a 3_weight: 0.1195 0.1559 0.009 0.946 5.9 107.6 21.0 396 n/a 3_xyzrec: 0.1173 0.1569 0.009 0.954 5.9 107.6 21.0 396 n/a 3_adp: 0.1152 0.1566 0.009 0.954 6.0 106.5 20.8 396 n/a 3_regHadp: 0.1153 0.1568 0.009 0.954 6.0 106.5 20.8 396 n/a 3_occ: 0.1142 0.1564 0.009 0.954 6.0 106.5 20.8 396 n/a 4_bss: 0.1141 0.1563 0.009 0.954 5.5 106.1 20.3 396 n/a 4_settarget: 0.1141 0.1563 0.009 0.954 5.5 106.1 20.3 396 n/a 4_updatecdl: 0.1141 0.1563 0.009 0.952 5.5 106.1 20.3 396 n/a 4_nqh: 0.1141 0.1563 0.009 0.952 5.5 106.1 20.3 396 n/a 4_sol: 0.1128 0.1482 0.009 0.952 5.5 106.1 20.9 451 n/a 4_weight: 0.1128 0.1482 0.009 0.952 5.5 106.1 20.9 451 n/a 4_xyzrec: 0.1114 0.1516 0.010 0.998 5.5 106.1 20.9 451 n/a 4_adp: 0.1102 0.1511 0.010 0.998 5.7 104.2 21.0 451 n/a 4_regHadp: 0.1102 0.1511 0.010 0.998 5.7 104.2 21.0 451 n/a 4_occ: 0.1094 0.1509 0.010 0.998 5.7 104.2 21.0 451 n/a 5_bss: 0.1090 0.1505 0.010 0.998 5.4 103.9 20.7 451 n/a 5_settarget: 0.1090 0.1505 0.010 0.998 5.4 103.9 20.7 451 n/a 5_updatecdl: 0.1090 0.1505 0.010 1.001 5.4 103.9 20.7 451 n/a 5_setrh: 0.1092 0.1504 0.010 1.001 5.4 103.9 20.7 451 n/a 5_nqh: 0.1092 0.1504 0.010 1.001 5.4 103.9 20.7 451 n/a 5_sol: 0.1092 0.1454 0.010 1.001 5.4 103.9 20.9 467 n/a 5_weight: 0.1092 0.1454 0.010 1.001 5.4 103.9 20.9 467 n/a 5_xyzrec: 0.1112 0.1472 0.011 1.082 5.4 103.9 20.9 467 n/a 5_adp: 0.1101 0.1464 0.011 1.082 5.4 104.3 21.1 467 n/a 5_regHadp: 0.1101 0.1463 0.011 1.082 5.4 104.3 21.1 467 n/a 5_occ: 0.1095 0.1455 0.011 1.082 5.4 104.3 21.1 467 n/a end: 0.1094 0.1453 0.011 1.082 5.2 104.1 20.8 467 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_9291273_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_9291273_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8500 Refinement macro-cycles (run) : 898.4400 Write final files (write_after_run_outputs) : 21.1600 Total : 923.4500 Total CPU time: 15.75 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:46 PST -0800 (1735494046.64 s) Start R-work = 0.1620, R-free = 0.1695 Final R-work = 0.1094, R-free = 0.1453 =============================================================================== Job complete usr+sys time: 970.81 seconds wall clock time: 16 minutes 34.04 seconds (994.04 seconds total)