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_6824987.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_6824987.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6824987.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 1.75, per 1000 atoms: 0.52 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: 0.29 Conformation dependent library (CDL) restraints added in 190.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 585 0.92 - 1.18: 1063 1.18 - 1.44: 702 1.44 - 1.70: 781 1.70 - 1.96: 22 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 9 " pdb=" C ILE A 9 " ideal model delta sigma weight residual 1.526 1.308 0.217 1.13e-02 7.83e+03 3.70e+02 bond pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 1.329 1.527 -0.198 1.13e-02 7.83e+03 3.06e+02 bond pdb=" CA PHE A 164 " pdb=" C PHE A 164 " ideal model delta sigma weight residual 1.524 1.748 -0.224 1.29e-02 6.01e+03 3.02e+02 bond pdb=" N ARG A 27 " pdb=" CA ARG A 27 " ideal model delta sigma weight residual 1.459 1.671 -0.213 1.28e-02 6.10e+03 2.76e+02 bond pdb=" C ALA A 29 " pdb=" N GLY A 30 " ideal model delta sigma weight residual 1.330 1.131 0.199 1.23e-02 6.61e+03 2.63e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 2984 4.29 - 8.57: 1820 8.57 - 12.86: 780 12.86 - 17.14: 180 17.14 - 21.42: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA LEU A 187 " pdb=" C LEU A 187 " pdb=" O LEU A 187 " ideal model delta sigma weight residual 121.47 106.45 15.02 1.15e+00 7.56e-01 1.71e+02 angle pdb=" CA BLYS A 132 " pdb=" C BLYS A 132 " pdb=" O BLYS A 132 " ideal model delta sigma weight residual 120.42 106.68 13.74 1.06e+00 8.90e-01 1.68e+02 angle pdb=" O GLY A 100 " pdb=" C GLY A 100 " pdb=" N LEU A 101 " ideal model delta sigma weight residual 123.21 107.82 15.39 1.20e+00 6.94e-01 1.65e+02 angle pdb=" CA BASN A 76 " pdb=" C BASN A 76 " pdb=" O BASN A 76 " ideal model delta sigma weight residual 120.90 134.44 -13.54 1.07e+00 8.73e-01 1.60e+02 angle pdb=" C ILE A 9 " pdb=" CA ILE A 9 " pdb=" CB ILE A 9 " ideal model delta sigma weight residual 111.23 124.79 -13.56 1.08e+00 8.57e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.85: 1312 17.85 - 35.69: 122 35.69 - 53.53: 35 53.53 - 71.37: 10 71.37 - 89.21: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N PRO A 184 " pdb=" C PRO A 184 " pdb=" CA PRO A 184 " pdb=" CB PRO A 184 " ideal model delta harmonic sigma weight residual 115.10 146.83 -31.73 0 2.50e+00 1.60e-01 1.61e+02 dihedral pdb=" C PRO A 184 " pdb=" N PRO A 184 " pdb=" CA PRO A 184 " pdb=" CB PRO A 184 " ideal model delta harmonic sigma weight residual -120.70 -146.85 26.15 0 2.50e+00 1.60e-01 1.09e+02 dihedral pdb=" C ILE A 9 " pdb=" N ILE A 9 " pdb=" CA ILE A 9 " pdb=" CB ILE A 9 " ideal model delta harmonic sigma weight residual -122.00 -139.48 17.48 0 2.50e+00 1.60e-01 4.89e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.286: 132 0.286 - 0.571: 69 0.571 - 0.856: 36 0.856 - 1.141: 5 1.141 - 1.426: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PRO A 184 " pdb=" N PRO A 184 " pdb=" C PRO A 184 " pdb=" CB PRO A 184 " both_signs ideal model delta sigma weight residual False 2.72 1.29 1.43 2.00e-01 2.50e+01 5.08e+01 chirality pdb=" CA SER A 3 " pdb=" N SER A 3 " pdb=" C SER A 3 " pdb=" CB SER A 3 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA GLU A 163 " pdb=" N GLU A 163 " pdb=" C GLU A 163 " pdb=" CB GLU A 163 " both_signs ideal model delta sigma weight residual False 2.51 3.44 -0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.012 2.00e-02 2.50e+03 6.63e-02 1.32e+02 pdb=" CG BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.086 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.120 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.088 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.001 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.032 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.062 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.060 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.037 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.130 2.00e-02 2.50e+03 6.55e-02 1.29e+02 pdb=" CG PHE A 164 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.069 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.036 2.00e-02 2.50e+03 6.23e-02 1.17e+02 pdb=" CG PHE A 119 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.132 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.044 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.059 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.060 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.048 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.085 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.050 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 903 2.30 - 2.88: 8054 2.88 - 3.45: 10531 3.45 - 4.03: 15257 4.03 - 4.60: 21875 Nonbonded interactions: 56620 Sorted by model distance: nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.728 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.750 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.776 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.819 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.821 2.100 ... (remaining 56615 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_6824987_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2786 r_free= 0.1813 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.393525 | | target function (ml) not normalized (work): 71364.026825 | | target function (ml) not normalized (free): 3243.947951 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3186 0.2138 7.5172 5.021| | 2: 3.63 - 2.88 1.00 2711 122 0.2647 0.1813 4.3313 4.3503| | 3: 2.88 - 2.52 1.00 2682 148 0.2566 0.1651 4.1864 4.1862| | 4: 2.52 - 2.29 1.00 2661 139 0.2557 0.1503 3.4974 3.5014| | 5: 2.29 - 2.13 1.00 2678 122 0.2637 0.1554 3.372 3.4373| | 6: 2.13 - 2.00 1.00 2692 117 0.2739 0.1672 3.2935 3.3271| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.64 0.77 0.23 1310.23| | 2: 3.63 - 2.88 2711 122 0.83 23.93 1.32 0.23 1310.23| | 3: 2.88 - 2.52 2682 148 0.73 32.90 1.29 0.23 1310.23| | 4: 2.52 - 2.29 2661 139 0.94 10.71 1.30 0.26 123.15| | 5: 2.29 - 2.13 2678 122 0.93 12.59 1.32 0.26 123.15| | 6: 2.13 - 2.00 2692 117 0.91 15.40 1.33 0.26 123.15| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 123.15 max = 1310.23 mean = 723.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.98 mean = 18.87| |phase err.(test): min = 0.00 max = 89.50 mean = 19.09| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.241 1557 Z= 5.406 Angle : 5.285 16.769 2118 Z= 3.659 Chirality : 0.394 1.426 243 Planarity : 0.033 0.126 284 Dihedral : 14.106 89.210 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 30.81 % 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: -2.33 (0.45), residues: 224 helix: -2.54 (0.38), residues: 101 sheet: -0.64 (0.92), residues: 28 loop : -0.37 (0.50), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.015 ARG A 98 TYR 0.072 0.026 TYR A 139 PHE 0.125 0.045 PHE A 164 HIS 0.042 0.025 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= 0.2786 r_free= 0.1813 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.393525 | | target function (ml) not normalized (work): 71364.026825 | | target function (ml) not normalized (free): 3243.947951 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3461 percent. r_work = 0.2921 r_free = 0.1980 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2868 0.2921 0.1980 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2868 0.2921 0.1980 n_refl.: 17050 remove outliers: r(all,work,free)=0.2157 0.2169 0.1980 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2129 0.2140 0.1958 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1617 0.1617 0.1628 n_refl.: 17045 remove outliers: r(all,work,free)=0.1614 0.1614 0.1628 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 97.87 87 5 0.3900 393.793 356.069 0.633 1.011 0.369 11.894-9.307 99.02 97 4 0.1899 633.355 616.378 0.929 1.012 0.369 9.237-7.194 100.00 213 7 0.2226 518.020 509.307 0.959 1.012 0.360 7.162-5.571 100.00 427 22 0.2347 388.775 374.413 0.921 1.011 0.289 5.546-4.326 100.00 867 58 0.1393 533.725 529.234 0.961 1.009 0.232 4.315-3.360 100.00 1859 96 0.1292 507.578 503.687 1.020 1.006 0.205 3.356-2.611 100.00 3867 181 0.1666 333.450 329.145 1.014 1.000 0.101 2.608-2.000 99.99 8818 434 0.1640 217.352 213.415 1.029 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9553 b_overall=-1.4723 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1614 r_free=0.1628 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1615 r_free=0.1627 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.817209 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.880745 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1351 0.1643 0.0292 0.008 1.0 1.0 0.5 0.0 0 10.909 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.43 2.92 3.013 18.445 0.881 0.023 12.76 16.60 3.84 3.617 18.703 0.881 0.020 Individual atomic B min max mean iso aniso Overall: 6.10 113.89 19.96 4.09 1785 0 Protein: 6.10 113.24 17.20 4.09 1519 0 Water: 8.87 113.89 36.02 N/A 258 0 Other: 21.81 38.15 26.45 N/A 8 0 Chain A: 6.10 113.89 19.96 N/A 1785 0 Histogram: Values Number of atoms 6.10 - 16.88 1077 16.88 - 27.66 347 27.66 - 38.44 187 38.44 - 49.21 100 49.21 - 59.99 47 59.99 - 70.77 13 70.77 - 81.55 6 81.55 - 92.33 4 92.33 - 103.11 1 103.11 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1660 r_work=0.1279 r_free=0.1666 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1279 r_free = 0.1666 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1274 r_free = 0.1661 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1274 r_free= 0.1661 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.020013 | | target function (ls_wunit_k1) not normalized (work): 324.907298 | | target function (ls_wunit_k1) not normalized (free): 26.958530 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1274 0.1661 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1851 0.1846 0.1993 n_refl.: 17042 remove outliers: r(all,work,free)=0.1851 0.1846 0.1993 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1826 0.1820 0.1977 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1290 0.1272 0.1654 n_refl.: 17042 remove outliers: r(all,work,free)=0.1290 0.1272 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 0.3517 303.819 282.390 0.618 1.005 0.360 11.894-9.307 99.02 97 4 0.1697 488.645 477.215 0.915 1.005 0.360 9.237-7.194 100.00 213 7 0.1825 399.663 395.976 0.958 1.006 0.341 7.162-5.571 100.00 427 22 0.1861 299.947 294.581 0.933 1.005 0.301 5.546-4.326 100.00 867 58 0.1046 411.780 408.956 0.957 1.005 0.210 4.315-3.360 100.00 1859 96 0.0921 391.606 390.811 1.017 1.003 0.191 3.356-2.611 100.00 3867 181 0.1294 257.263 255.981 1.012 1.000 0.101 2.608-2.000 99.99 8818 434 0.1348 167.691 166.388 1.018 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3512 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1654 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1272 r_free=0.1654 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1654 | n_water=258 | time (s): 0.890 (total time: 0.890) Filter (dist) r_work=0.1277 r_free=0.1641 | n_water=254 | time (s): 22.060 (total time: 22.950) Filter (q & B) r_work=0.1277 r_free=0.1639 | n_water=252 | time (s): 1.860 (total time: 24.810) Compute maps r_work=0.1277 r_free=0.1639 | n_water=252 | time (s): 0.760 (total time: 25.570) Filter (map) r_work=0.1310 r_free=0.1645 | n_water=214 | time (s): 1.740 (total time: 27.310) Find peaks r_work=0.1310 r_free=0.1645 | n_water=214 | time (s): 0.570 (total time: 27.880) Add new water r_work=0.1529 r_free=0.1834 | n_water=367 | time (s): 2.070 (total time: 29.950) Refine new water occ: r_work=0.1338 r_free=0.1583 adp: r_work=0.1278 r_free=0.1572 occ: r_work=0.1282 r_free=0.1553 adp: r_work=0.1250 r_free=0.1553 occ: r_work=0.1251 r_free=0.1541 adp: r_work=0.1240 r_free=0.1542 ADP+occupancy (water only), MIN, final r_work=0.1240 r_free=0.1542 r_work=0.1240 r_free=0.1542 | n_water=367 | time (s): 23.480 (total time: 53.430) Filter (q & B) r_work=0.1243 r_free=0.1548 | n_water=356 | time (s): 1.550 (total time: 54.980) Filter (dist only) r_work=0.1243 r_free=0.1552 | n_water=355 | time (s): 28.830 (total time: 83.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.658295 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.982208 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 0.1215 0.1600 0.0385 0.008 0.9 1.6 0.5 0.0 0 11.829 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.15 16.00 3.85 4.175 21.090 0.982 0.018 12.05 16.29 4.24 4.240 21.350 0.982 0.018 Individual atomic B min max mean iso aniso Overall: 6.85 107.86 21.39 4.27 1882 0 Protein: 6.85 107.86 17.74 4.26 1519 0 Water: 8.68 74.80 36.74 N/A 355 0 Other: 22.61 42.18 31.77 N/A 8 0 Chain A: 6.85 107.86 19.52 N/A 1741 0 Chain S: 19.32 64.33 44.42 N/A 141 0 Histogram: Values Number of atoms 6.85 - 16.95 1039 16.95 - 27.06 367 27.06 - 37.16 207 37.16 - 47.26 163 47.26 - 57.36 66 57.36 - 67.46 29 67.46 - 77.56 4 77.56 - 87.66 4 87.66 - 97.76 1 97.76 - 107.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1629 r_work=0.1207 r_free=0.1630 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1630 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1627 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1201 r_free= 0.1627 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.017130 | | target function (ls_wunit_k1) not normalized (work): 278.102797 | | target function (ls_wunit_k1) not normalized (free): 25.020227 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1222 0.1201 0.1627 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1759 0.1749 0.1990 n_refl.: 17042 remove outliers: r(all,work,free)=0.1759 0.1749 0.1990 n_refl.: 17042 overall B=-0.39 to atoms: r(all,work,free)=0.1734 0.1724 0.1972 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1197 0.1616 n_refl.: 17042 remove outliers: r(all,work,free)=0.1218 0.1197 0.1616 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 0.3386 303.819 283.079 0.594 1.005 0.340 11.894-9.307 99.02 97 4 0.1530 488.645 485.289 0.912 1.006 0.330 9.237-7.194 100.00 213 7 0.1651 399.663 400.920 0.968 1.006 0.300 7.162-5.571 100.00 427 22 0.1562 299.947 296.456 0.936 1.006 0.271 5.546-4.326 100.00 867 58 0.0866 411.780 409.445 0.956 1.005 0.205 4.315-3.360 100.00 1859 96 0.0833 391.606 391.025 1.016 1.003 0.191 3.356-2.611 100.00 3867 181 0.1213 257.263 256.483 1.014 1.000 0.121 2.608-2.000 99.99 8818 434 0.1338 167.691 166.589 1.020 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3823 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1616 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1616 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1616 | n_water=355 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1197 r_free=0.1619 | n_water=354 | time (s): 27.860 (total time: 28.630) Filter (q & B) r_work=0.1197 r_free=0.1619 | n_water=354 | time (s): 0.970 (total time: 29.600) Compute maps r_work=0.1197 r_free=0.1619 | n_water=354 | time (s): 0.840 (total time: 30.440) Filter (map) r_work=0.1265 r_free=0.1647 | n_water=255 | time (s): 1.940 (total time: 32.380) Find peaks r_work=0.1265 r_free=0.1647 | n_water=255 | time (s): 0.530 (total time: 32.910) Add new water r_work=0.1455 r_free=0.1804 | n_water=405 | time (s): 1.990 (total time: 34.900) Refine new water occ: r_work=0.1250 r_free=0.1594 adp: r_work=0.1242 r_free=0.1593 occ: r_work=0.1225 r_free=0.1569 adp: r_work=0.1213 r_free=0.1569 occ: r_work=0.1207 r_free=0.1559 adp: r_work=0.1197 r_free=0.1559 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1559 r_work=0.1197 r_free=0.1559 | n_water=405 | time (s): 27.880 (total time: 62.780) Filter (q & B) r_work=0.1199 r_free=0.1575 | n_water=396 | time (s): 1.890 (total time: 64.670) Filter (dist only) r_work=0.1199 r_free=0.1575 | n_water=396 | time (s): 30.880 (total time: 95.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.959361 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.187412 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 0.1181 0.1552 0.0370 0.009 1.0 4.2 0.5 0.0 0 0.980 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.81 15.52 3.70 4.333 21.474 0.187 4.999 11.57 15.49 3.92 4.945 21.408 0.187 4.976 Individual atomic B min max mean iso aniso Overall: 6.23 106.41 20.85 4.86 1923 0 Protein: 6.23 106.41 17.02 4.86 1519 0 Water: 9.12 69.42 35.36 N/A 396 0 Other: 20.80 40.64 28.51 N/A 8 0 Chain A: 6.23 106.41 18.78 N/A 1737 0 Chain S: 16.04 63.34 40.12 N/A 186 0 Histogram: Values Number of atoms 6.23 - 16.24 1074 16.24 - 26.26 349 26.26 - 36.28 218 36.28 - 46.30 164 46.30 - 56.32 80 56.32 - 66.33 25 66.33 - 76.35 5 76.35 - 86.37 3 86.37 - 96.39 3 96.39 - 106.41 2 =========================== Idealize ADP of riding H ========================== r_work=0.1157 r_free=0.1549 r_work=0.1157 r_free=0.1551 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1157 r_free = 0.1551 target_work(ml) = 4.976 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1148 r_free = 0.1545 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.21 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= 0.1148 r_free= 0.1545 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.970600 | | target function (ml) not normalized (work): 80697.691217 | | target function (ml) not normalized (free): 4187.342288 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1167 0.1148 0.1545 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1663 0.1657 0.1831 n_refl.: 17042 remove outliers: r(all,work,free)=0.1663 0.1657 0.1831 n_refl.: 17042 overall B=-0.46 to atoms: r(all,work,free)=0.1633 0.1626 0.1817 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1166 0.1147 0.1541 n_refl.: 17042 remove outliers: r(all,work,free)=0.1165 0.1146 0.1541 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 0.3738 300.324 279.502 0.555 1.005 0.335 11.894-9.307 99.02 97 4 0.1764 488.645 483.570 0.912 1.007 0.331 9.237-7.194 100.00 213 7 0.1781 399.663 399.964 0.980 1.007 0.255 7.162-5.571 100.00 427 22 0.1613 299.947 294.644 0.938 1.006 0.220 5.546-4.326 100.00 867 58 0.0943 411.780 408.209 0.962 1.006 0.196 4.315-3.360 100.00 1859 96 0.0875 391.606 389.281 1.013 1.004 0.192 3.356-2.611 100.00 3867 181 0.1265 257.263 255.215 1.013 1.001 0.142 2.608-2.000 99.99 8818 434 0.1106 167.691 166.255 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1600 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 r_free=0.1541 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1146 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1541 | n_water=396 | time (s): 0.870 (total time: 0.870) Filter (dist) r_work=0.1146 r_free=0.1541 | n_water=396 | time (s): 30.460 (total time: 31.330) Filter (q & B) r_work=0.1146 r_free=0.1541 | n_water=396 | time (s): 0.820 (total time: 32.150) Compute maps r_work=0.1146 r_free=0.1541 | n_water=396 | time (s): 0.720 (total time: 32.870) Filter (map) r_work=0.1199 r_free=0.1603 | n_water=307 | time (s): 1.560 (total time: 34.430) Find peaks r_work=0.1199 r_free=0.1603 | n_water=307 | time (s): 0.600 (total time: 35.030) Add new water r_work=0.1339 r_free=0.1741 | n_water=443 | time (s): 1.690 (total time: 36.720) Refine new water occ: r_work=0.1173 r_free=0.1546 adp: r_work=0.1166 r_free=0.1552 occ: r_work=0.1152 r_free=0.1518 adp: r_work=0.1144 r_free=0.1525 occ: r_work=0.1138 r_free=0.1501 adp: r_work=0.1131 r_free=0.1506 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1506 r_work=0.1131 r_free=0.1506 | n_water=443 | time (s): 27.440 (total time: 64.160) Filter (q & B) r_work=0.1134 r_free=0.1515 | n_water=434 | time (s): 1.910 (total time: 66.070) Filter (dist only) r_work=0.1134 r_free=0.1515 | n_water=434 | time (s): 33.900 (total time: 99.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.998364 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.141686 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1119 0.1569 0.0450 0.010 1.0 3.8 0.5 0.0 0 0.999 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.19 15.69 4.50 4.600 20.942 0.142 4.963 11.12 15.58 4.47 4.725 20.939 0.142 4.954 Individual atomic B min max mean iso aniso Overall: 5.39 104.19 20.72 4.78 1961 0 Protein: 5.39 104.19 16.50 4.78 1519 0 Water: 8.79 66.17 35.41 N/A 434 0 Other: 18.88 35.70 25.45 N/A 8 0 Chain A: 5.39 104.19 18.17 N/A 1736 0 Chain S: 15.77 66.17 40.43 N/A 225 0 Histogram: Values Number of atoms 5.39 - 15.27 1020 15.27 - 25.15 387 25.15 - 35.03 238 35.03 - 44.91 179 44.91 - 54.79 87 54.79 - 64.67 35 64.67 - 74.55 7 74.55 - 84.43 3 84.43 - 94.31 3 94.31 - 104.19 2 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1558 r_work=0.1112 r_free=0.1560 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1112 r_free = 0.1560 target_work(ml) = 4.955 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1104 r_free = 0.1560 target_work(ml) = 4.953 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1104 r_free= 0.1560 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.952521 | | target function (ml) not normalized (work): 80399.218084 | | target function (ml) not normalized (free): 4190.050220 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1104 0.1560 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1587 0.1574 0.1868 n_refl.: 17041 remove outliers: r(all,work,free)=0.1587 0.1574 0.1868 n_refl.: 17041 overall B=-0.28 to atoms: r(all,work,free)=0.1570 0.1557 0.1860 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1125 0.1103 0.1556 n_refl.: 17041 remove outliers: r(all,work,free)=0.1125 0.1103 0.1556 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 0.3777 300.324 276.089 0.535 1.002 0.330 11.894-9.307 99.02 97 4 0.1819 488.645 484.333 0.913 1.003 0.320 9.237-7.194 100.00 213 7 0.1730 399.663 401.464 0.986 1.004 0.225 7.162-5.571 100.00 427 22 0.1527 299.947 294.815 0.939 1.004 0.203 5.546-4.326 100.00 867 58 0.0914 411.780 408.533 0.963 1.003 0.183 4.315-3.360 100.00 1859 96 0.0859 391.606 389.176 1.008 1.002 0.168 3.356-2.611 100.00 3867 181 0.1231 257.263 255.037 1.006 1.001 0.121 2.608-2.000 99.99 8818 434 0.1040 167.691 166.501 1.000 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9682 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1103 r_free=0.1556 After: r_work=0.1105 r_free=0.1555 ================================== NQH flips ================================== r_work=0.1105 r_free=0.1555 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1105 r_free=0.1555 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1105 r_free=0.1555 | n_water=434 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1106 r_free=0.1552 | n_water=433 | time (s): 36.170 (total time: 36.780) Filter (q & B) r_work=0.1106 r_free=0.1552 | n_water=433 | time (s): 1.110 (total time: 37.890) Compute maps r_work=0.1106 r_free=0.1552 | n_water=433 | time (s): 0.640 (total time: 38.530) Filter (map) r_work=0.1182 r_free=0.1556 | n_water=333 | time (s): 1.660 (total time: 40.190) Find peaks r_work=0.1182 r_free=0.1556 | n_water=333 | time (s): 0.420 (total time: 40.610) Add new water r_work=0.1289 r_free=0.1636 | n_water=469 | time (s): 1.720 (total time: 42.330) Refine new water occ: r_work=0.1141 r_free=0.1512 adp: r_work=0.1134 r_free=0.1503 occ: r_work=0.1123 r_free=0.1502 adp: r_work=0.1114 r_free=0.1491 occ: r_work=0.1109 r_free=0.1492 adp: r_work=0.1103 r_free=0.1486 ADP+occupancy (water only), MIN, final r_work=0.1103 r_free=0.1486 r_work=0.1103 r_free=0.1486 | n_water=469 | time (s): 35.750 (total time: 78.080) Filter (q & B) r_work=0.1106 r_free=0.1498 | n_water=457 | time (s): 2.240 (total time: 80.320) Filter (dist only) r_work=0.1106 r_free=0.1499 | n_water=456 | time (s): 35.250 (total time: 115.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.975332 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.164937 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 0.1122 0.1519 0.0397 0.010 1.0 6.7 0.5 0.0 0 0.988 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.22 15.19 3.97 4.507 20.706 0.165 4.957 11.12 15.08 3.96 4.604 20.759 0.165 4.949 Individual atomic B min max mean iso aniso Overall: 5.33 103.23 20.79 4.98 1983 0 Protein: 5.33 103.23 16.21 4.98 1519 0 Water: 8.26 67.94 35.94 N/A 456 0 Other: 19.02 35.13 25.65 N/A 8 0 Chain A: 5.33 103.23 17.85 N/A 1735 0 Chain S: 14.08 67.94 41.35 N/A 248 0 Histogram: Values Number of atoms 5.33 - 15.12 1050 15.12 - 24.91 366 24.91 - 34.70 220 34.70 - 44.49 187 44.49 - 54.28 106 54.28 - 64.07 34 64.07 - 73.86 11 73.86 - 83.65 3 83.65 - 93.44 2 93.44 - 103.23 4 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1508 r_work=0.1112 r_free=0.1507 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1112 r_free = 0.1507 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1107 r_free = 0.1514 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1107 r_free= 0.1514 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.947436 | | target function (ml) not normalized (work): 80316.679775 | | target function (ml) not normalized (free): 4178.402619 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1110 0.1358 5.4591 5.6588| | 2: 3.63 - 2.88 1.00 2711 122 0.1082 0.1472 5.2223 5.3626| | 3: 2.88 - 2.52 1.00 2681 148 0.1359 0.1744 5.1373 5.2274| | 4: 2.52 - 2.29 1.00 2661 139 0.0954 0.1519 4.6471 4.9522| | 5: 2.29 - 2.13 1.00 2678 122 0.0968 0.1514 4.5994 4.9192| | 6: 2.13 - 2.00 1.00 2692 117 0.1128 0.1782 4.5904 4.8056| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.12 1.00 0.96 6524.45| | 2: 3.63 - 2.88 2711 122 0.92 12.96 1.01 0.96 6524.45| | 3: 2.88 - 2.52 2681 148 0.87 19.24 0.99 0.96 6524.45| | 4: 2.52 - 2.29 2661 139 0.92 12.50 1.01 0.97 2225.63| | 5: 2.29 - 2.13 2678 122 0.91 14.54 1.00 0.97 2225.63| | 6: 2.13 - 2.00 2692 117 0.89 17.30 0.99 0.97 2225.63| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2225.63 max = 6524.45 mean = 4397.81| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.94 mean = 14.24| |phase err.(test): min = 0.00 max = 88.96 mean = 13.86| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1107 0.1514 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1563 0.1548 0.1868 n_refl.: 17041 remove outliers: r(all,work,free)=0.1563 0.1548 0.1868 n_refl.: 17041 overall B=-0.22 to atoms: r(all,work,free)=0.1550 0.1535 0.1860 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1127 0.1107 0.1516 n_refl.: 17041 remove outliers: r(all,work,free)=0.1127 0.1107 0.1516 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 0.3807 300.324 277.991 0.534 1.005 0.330 11.894-9.307 99.02 97 4 0.1739 488.645 483.163 0.910 1.006 0.323 9.237-7.194 100.00 213 7 0.1708 399.663 402.169 0.984 1.006 0.207 7.162-5.571 100.00 427 22 0.1565 299.947 294.761 0.931 1.005 0.196 5.546-4.326 100.00 867 58 0.0902 411.780 408.964 0.961 1.005 0.187 4.315-3.360 100.00 1859 96 0.0868 391.606 389.442 1.004 1.003 0.181 3.356-2.611 100.00 3867 181 0.1234 257.263 254.937 1.002 1.000 0.131 2.608-2.000 99.99 8818 434 0.1046 167.691 166.257 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7555 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2786 0.1813 0.082 5.285 8.8 119.3 19.9 258 0.000 1_bss: 0.1614 0.1628 0.082 5.285 8.4 118.9 19.5 258 0.000 1_settarget: 0.1614 0.1628 0.082 5.285 8.4 118.9 19.5 258 0.000 1_nqh: 0.1615 0.1627 0.082 5.285 8.4 118.9 19.5 258 0.003 1_weight: 0.1615 0.1627 0.082 5.285 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1351 0.1643 0.008 0.953 8.4 118.9 19.5 258 0.152 1_adp: 0.1276 0.1660 0.008 0.953 6.1 113.9 20.0 258 0.152 1_regHadp: 0.1279 0.1666 0.008 0.953 6.1 113.9 20.0 258 0.152 1_occ: 0.1274 0.1661 0.008 0.953 6.1 113.9 20.0 258 0.152 2_bss: 0.1272 0.1654 0.008 0.953 5.7 113.5 19.6 258 0.152 2_settarget: 0.1272 0.1654 0.008 0.953 5.7 113.5 19.6 258 0.152 2_updatecdl: 0.1272 0.1654 0.008 0.974 5.7 113.5 19.6 258 0.152 2_nqh: 0.1272 0.1654 0.008 0.974 5.7 113.5 19.6 258 0.149 2_sol: 0.1243 0.1552 0.008 0.974 5.7 112.9 20.9 355 n/a 2_weight: 0.1243 0.1552 0.008 0.974 5.7 112.9 20.9 355 n/a 2_xyzrec: 0.1215 0.1600 0.008 0.912 5.7 112.9 20.9 355 n/a 2_adp: 0.1205 0.1629 0.008 0.912 6.9 107.9 21.4 355 n/a 2_regHadp: 0.1207 0.1630 0.008 0.912 6.9 107.9 21.4 355 n/a 2_occ: 0.1201 0.1627 0.008 0.912 6.9 107.9 21.4 355 n/a 3_bss: 0.1197 0.1616 0.008 0.912 6.5 107.5 21.0 355 n/a 3_settarget: 0.1197 0.1616 0.008 0.912 6.5 107.5 21.0 355 n/a 3_updatecdl: 0.1197 0.1616 0.008 0.910 6.5 107.5 21.0 355 n/a 3_nqh: 0.1197 0.1616 0.008 0.910 6.5 107.5 21.0 355 n/a 3_sol: 0.1199 0.1575 0.008 0.910 6.5 107.5 21.0 396 n/a 3_weight: 0.1199 0.1575 0.008 0.910 6.5 107.5 21.0 396 n/a 3_xyzrec: 0.1181 0.1552 0.009 0.954 6.5 107.5 21.0 396 n/a 3_adp: 0.1157 0.1549 0.009 0.954 6.2 106.4 20.8 396 n/a 3_regHadp: 0.1157 0.1551 0.009 0.954 6.2 106.4 20.8 396 n/a 3_occ: 0.1148 0.1545 0.009 0.954 6.2 106.4 20.8 396 n/a 4_bss: 0.1146 0.1541 0.009 0.954 5.8 105.9 20.4 396 n/a 4_settarget: 0.1146 0.1541 0.009 0.954 5.8 105.9 20.4 396 n/a 4_updatecdl: 0.1146 0.1541 0.009 0.953 5.8 105.9 20.4 396 n/a 4_nqh: 0.1146 0.1541 0.009 0.953 5.8 105.9 20.4 396 n/a 4_sol: 0.1134 0.1515 0.009 0.953 5.8 105.9 20.7 434 n/a 4_weight: 0.1134 0.1515 0.009 0.953 5.8 105.9 20.7 434 n/a 4_xyzrec: 0.1119 0.1569 0.010 0.970 5.8 105.9 20.7 434 n/a 4_adp: 0.1112 0.1558 0.010 0.970 5.4 104.2 20.7 434 n/a 4_regHadp: 0.1112 0.1560 0.010 0.970 5.4 104.2 20.7 434 n/a 4_occ: 0.1104 0.1560 0.010 0.970 5.4 104.2 20.7 434 n/a 5_bss: 0.1103 0.1556 0.010 0.970 5.1 103.9 20.4 434 n/a 5_settarget: 0.1103 0.1556 0.010 0.970 5.1 103.9 20.4 434 n/a 5_updatecdl: 0.1103 0.1556 0.010 0.972 5.1 103.9 20.4 434 n/a 5_setrh: 0.1105 0.1555 0.010 0.972 5.1 103.9 20.4 434 n/a 5_nqh: 0.1105 0.1555 0.010 0.972 5.1 103.9 20.4 434 n/a 5_sol: 0.1106 0.1499 0.010 0.972 5.1 103.9 20.7 456 n/a 5_weight: 0.1106 0.1499 0.010 0.972 5.1 103.9 20.7 456 n/a 5_xyzrec: 0.1122 0.1519 0.010 1.044 5.1 103.9 20.7 456 n/a 5_adp: 0.1112 0.1508 0.010 1.044 5.3 103.2 20.8 456 n/a 5_regHadp: 0.1112 0.1507 0.010 1.044 5.3 103.2 20.8 456 n/a 5_occ: 0.1107 0.1514 0.010 1.044 5.3 103.2 20.8 456 n/a end: 0.1107 0.1516 0.010 1.044 5.1 103.0 20.6 456 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6824987_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6824987_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0500 Refinement macro-cycles (run) : 913.2900 Write final files (write_after_run_outputs) : 20.0500 Total : 936.3900 Total CPU time: 15.99 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:00 PST -0800 (1735494060.16 s) Start R-work = 0.1614, R-free = 0.1628 Final R-work = 0.1107, R-free = 0.1516 =============================================================================== Job complete usr+sys time: 983.50 seconds wall clock time: 16 minutes 45.98 seconds (1005.98 seconds total)