Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2348261.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_2348261.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2348261.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 =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.97, per 1000 atoms: 0.58 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: 0.48 Conformation dependent library (CDL) restraints added in 104.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 609 0.93 - 1.19: 1053 1.19 - 1.45: 737 1.45 - 1.72: 738 1.72 - 1.98: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALYS A 175 " pdb=" CA ALYS A 175 " ideal model delta sigma weight residual 1.459 1.219 0.240 1.23e-02 6.61e+03 3.80e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.462 -0.228 1.19e-02 7.06e+03 3.67e+02 bond pdb=" N ILE A 152 " pdb=" CA ILE A 152 " ideal model delta sigma weight residual 1.459 1.695 -0.236 1.27e-02 6.20e+03 3.46e+02 bond pdb=" C VAL A 181 " pdb=" O VAL A 181 " ideal model delta sigma weight residual 1.237 1.440 -0.203 1.19e-02 7.06e+03 2.91e+02 bond pdb=" CA SER A 121 " pdb=" C SER A 121 " ideal model delta sigma weight residual 1.524 1.305 0.218 1.30e-02 5.92e+03 2.82e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.89: 3308 4.89 - 9.78: 1855 9.78 - 14.67: 527 14.67 - 19.56: 82 19.56 - 24.45: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 114.50 132.51 -18.01 1.16e+00 7.43e-01 2.41e+02 angle pdb=" O AASN A 76 " pdb=" C AASN A 76 " pdb=" N LEU A 77 " ideal model delta sigma weight residual 122.12 105.97 16.15 1.06e+00 8.90e-01 2.32e+02 angle pdb=" O PRO A 54 " pdb=" C PRO A 54 " pdb=" N ASP A 55 " ideal model delta sigma weight residual 123.00 105.52 17.48 1.22e+00 6.72e-01 2.05e+02 angle pdb=" CA ALYS A 93 " pdb=" C ALYS A 93 " pdb=" O ALYS A 93 " ideal model delta sigma weight residual 120.90 135.17 -14.27 1.07e+00 8.73e-01 1.78e+02 angle pdb=" OE1 GLN A 45 " pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 122.60 109.37 13.23 1.00e+00 1.00e+00 1.75e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.24: 1285 16.24 - 32.48: 131 32.48 - 48.72: 43 48.72 - 64.95: 18 64.95 - 81.19: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CA THR A 110 " pdb=" CB THR A 110 " ideal model delta harmonic sigma weight residual 123.40 144.81 -21.41 0 2.50e+00 1.60e-01 7.33e+01 dihedral pdb=" C ILE A 168 " pdb=" N ILE A 168 " pdb=" CA ILE A 168 " pdb=" CB ILE A 168 " ideal model delta harmonic sigma weight residual -122.00 -142.24 20.24 0 2.50e+00 1.60e-01 6.56e+01 dihedral pdb=" N LYS A 62 " pdb=" C LYS A 62 " pdb=" CA LYS A 62 " pdb=" CB LYS A 62 " ideal model delta harmonic sigma weight residual 122.80 142.92 -20.12 0 2.50e+00 1.60e-01 6.47e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.207: 104 0.207 - 0.414: 74 0.414 - 0.620: 38 0.620 - 0.827: 23 0.827 - 1.034: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.49 1.03 2.00e-01 2.50e+01 2.67e+01 chirality pdb=" CA ALA A 104 " pdb=" N ALA A 104 " pdb=" C ALA A 104 " pdb=" CB ALA A 104 " both_signs ideal model delta sigma weight residual False 2.48 3.49 -1.00 2.00e-01 2.50e+01 2.51e+01 chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.41 -0.90 2.00e-01 2.50e+01 2.03e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " 0.058 9.50e-02 1.11e+02 7.06e-02 1.04e+02 pdb=" NE ARG A 28 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.092 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " 0.107 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " 0.052 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " 0.053 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.115 2.00e-02 2.50e+03 5.78e-02 1.00e+02 pdb=" CG PHE A 164 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.064 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.031 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.027 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.014 2.00e-02 2.50e+03 5.76e-02 9.94e+01 pdb=" CG TYR A 141 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.113 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.091 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.044 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.031 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.046 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.061 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.007 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 664 2.26 - 2.84: 7701 2.84 - 3.43: 10651 3.43 - 4.01: 15373 4.01 - 4.60: 22153 Nonbonded interactions: 56542 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.670 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.756 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.809 2.450 nonbonded pdb="HD22BASN A 76 " pdb=" HB2 PHE A 119 " model vdw sym.op. 1.845 2.270 -y,x-y-1,z+1/3 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.847 2.450 ... (remaining 56537 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_2348261_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2791 r_free= 0.1793 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.415165 | | target function (ml) not normalized (work): 71715.519704 | | target function (ml) not normalized (free): 3269.474090 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2089 7.6158 5.0301| | 2: 3.63 - 2.88 1.00 2711 122 0.2627 0.1674 4.3238 4.3207| | 3: 2.88 - 2.52 1.00 2682 148 0.2586 0.1644 4.1725 4.1797| | 4: 2.52 - 2.29 1.00 2661 139 0.2575 0.1610 3.5062 3.5723| | 5: 2.29 - 2.13 1.00 2678 122 0.2623 0.1449 3.3881 3.4691| | 6: 2.13 - 2.00 1.00 2692 117 0.2742 0.1919 3.3176 3.4548| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.44 0.77 0.23 1269.52| | 2: 3.63 - 2.88 2711 122 0.83 23.39 1.31 0.23 1269.52| | 3: 2.88 - 2.52 2682 148 0.73 32.71 1.29 0.23 1269.52| | 4: 2.52 - 2.29 2661 139 0.93 11.52 1.30 0.26 140.05| | 5: 2.29 - 2.13 2678 122 0.92 13.73 1.31 0.26 140.05| | 6: 2.13 - 2.00 2692 117 0.90 16.57 1.33 0.26 140.05| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 140.05 max = 1269.52 mean = 711.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.98 mean = 19.23| |phase err.(test): min = 0.00 max = 89.30 mean = 19.32| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.258 1557 Z= 5.390 Angle : 5.224 18.008 2118 Z= 3.706 Chirality : 0.371 1.034 243 Planarity : 0.032 0.089 284 Dihedral : 13.767 81.187 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 3.11 % Allowed : 1.86 % Favored : 95.03 % Cbeta Deviations : 29.19 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.25 (0.49), residues: 224 helix: -2.33 (0.41), residues: 102 sheet: -1.05 (0.91), residues: 28 loop : -0.30 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.111 0.028 ARG A 27 TYR 0.107 0.036 TYR A 141 PHE 0.121 0.037 PHE A 164 HIS 0.065 0.033 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= 0.2791 r_free= 0.1793 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.415165 | | target function (ml) not normalized (work): 71715.519704 | | target function (ml) not normalized (free): 3269.474090 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3278 percent. r_work = 0.2923 r_free = 0.1944 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2868 0.2923 0.1944 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2868 0.2923 0.1944 n_refl.: 17050 remove outliers: r(all,work,free)=0.2152 0.2165 0.1944 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2125 0.2137 0.1927 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1616 0.1615 0.1637 n_refl.: 17045 remove outliers: r(all,work,free)=0.1615 0.1614 0.1637 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 0.4136 394.517 359.209 0.650 1.014 0.398 11.894-9.307 99.02 97 4 0.1965 633.211 611.372 0.928 1.014 0.390 9.237-7.194 100.00 213 7 0.2147 517.903 508.490 0.955 1.013 0.360 7.162-5.571 100.00 427 22 0.2341 388.686 376.278 0.924 1.012 0.321 5.546-4.326 100.00 867 58 0.1414 533.604 527.917 0.960 1.010 0.238 4.315-3.360 100.00 1859 96 0.1303 507.463 502.653 1.017 1.006 0.214 3.356-2.611 100.00 3867 181 0.1646 333.374 329.167 1.013 1.000 0.029 2.608-2.000 99.99 8818 434 0.1642 217.303 213.320 1.030 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4599 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1614 r_free=0.1637 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1617 r_free=0.1640 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.628558 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.807323 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 0.1355 0.1631 0.0276 0.009 1.0 0.6 0.5 0.0 0 11.314 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.55 16.31 2.76 3.013 18.450 0.807 0.023 12.80 16.58 3.78 3.622 18.727 0.807 0.021 Individual atomic B min max mean iso aniso Overall: 6.40 113.89 20.00 4.06 1785 0 Protein: 6.40 112.25 17.26 4.06 1519 0 Water: 8.86 113.89 35.93 N/A 258 0 Other: 22.01 37.17 26.48 N/A 8 0 Chain A: 6.40 113.89 20.00 N/A 1785 0 Histogram: Values Number of atoms 6.40 - 17.15 1095 17.15 - 27.90 332 27.90 - 38.65 187 38.65 - 49.40 98 49.40 - 60.15 47 60.15 - 70.89 13 70.89 - 81.64 5 81.64 - 92.39 4 92.39 - 103.14 1 103.14 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1280 r_free=0.1658 r_work=0.1284 r_free=0.1666 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1284 r_free = 0.1666 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 = 0.1658 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.27 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= 0.1658 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020159 | | target function (ls_wunit_k1) not normalized (work): 327.322521 | | target function (ls_wunit_k1) not normalized (free): 27.103418 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1298 0.1280 0.1658 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1919 0.1919 0.1985 n_refl.: 17044 remove outliers: r(all,work,free)=0.1919 0.1919 0.1985 n_refl.: 17044 overall B=-0.40 to atoms: r(all,work,free)=0.1890 0.1889 0.1968 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1297 0.1279 0.1649 n_refl.: 17044 remove outliers: r(all,work,free)=0.1295 0.1278 0.1649 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 0.3527 302.856 279.100 0.625 1.010 0.370 11.894-9.307 99.02 97 4 0.1684 487.095 477.115 0.918 1.010 0.367 9.237-7.194 100.00 213 7 0.1806 398.395 396.140 0.960 1.010 0.330 7.162-5.571 100.00 427 22 0.1829 298.996 294.187 0.932 1.009 0.311 5.546-4.326 100.00 867 58 0.1046 410.473 408.116 0.959 1.007 0.211 4.315-3.360 100.00 1859 96 0.0933 390.364 389.917 1.018 1.005 0.201 3.356-2.611 100.00 3867 181 0.1302 256.447 255.163 1.016 1.000 0.081 2.608-2.000 99.99 8818 434 0.1355 167.159 165.699 1.025 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4228 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1278 r_free=0.1649 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1280 r_free=0.1650 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1280 r_free=0.1650 | n_water=258 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1286 r_free=0.1638 | n_water=253 | time (s): 20.360 (total time: 21.050) Filter (q & B) r_work=0.1286 r_free=0.1637 | n_water=251 | time (s): 1.530 (total time: 22.580) Compute maps r_work=0.1286 r_free=0.1637 | n_water=251 | time (s): 0.760 (total time: 23.340) Filter (map) r_work=0.1317 r_free=0.1634 | n_water=215 | time (s): 1.760 (total time: 25.100) Find peaks r_work=0.1317 r_free=0.1634 | n_water=215 | time (s): 0.440 (total time: 25.540) Add new water r_work=0.1537 r_free=0.1868 | n_water=371 | time (s): 1.500 (total time: 27.040) Refine new water occ: r_work=0.1338 r_free=0.1566 adp: r_work=0.1280 r_free=0.1579 occ: r_work=0.1284 r_free=0.1528 adp: r_work=0.1253 r_free=0.1547 occ: r_work=0.1253 r_free=0.1530 adp: r_work=0.1242 r_free=0.1540 ADP+occupancy (water only), MIN, final r_work=0.1242 r_free=0.1540 r_work=0.1242 r_free=0.1540 | n_water=371 | time (s): 13.170 (total time: 40.210) Filter (q & B) r_work=0.1244 r_free=0.1542 | n_water=365 | time (s): 1.610 (total time: 41.820) Filter (dist only) r_work=0.1244 r_free=0.1545 | n_water=364 | time (s): 28.600 (total time: 70.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.360786 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.004688 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 0.1217 0.1593 0.0376 0.008 0.9 2.6 0.5 0.0 0 12.180 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.17 15.93 3.76 4.162 21.111 1.005 0.018 11.97 16.19 4.22 4.226 21.369 1.005 0.018 Individual atomic B min max mean iso aniso Overall: 6.41 106.85 21.39 4.29 1891 0 Protein: 6.41 106.85 17.73 4.27 1519 0 Water: 8.68 68.15 36.33 N/A 364 0 Other: 25.98 48.29 37.01 N/A 8 0 Chain A: 6.41 106.85 19.55 N/A 1742 0 Chain S: 17.11 65.54 42.96 N/A 149 0 Histogram: Values Number of atoms 6.41 - 16.45 1007 16.45 - 26.50 386 26.50 - 36.54 220 36.54 - 46.59 167 46.59 - 56.63 73 56.63 - 66.68 26 66.68 - 76.72 4 76.72 - 86.76 4 86.76 - 96.81 2 96.81 - 106.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1619 r_work=0.1199 r_free=0.1621 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1621 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1616 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1196 r_free= 0.1616 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016986 | | target function (ls_wunit_k1) not normalized (work): 275.767593 | | target function (ls_wunit_k1) not normalized (free): 25.281196 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1196 0.1616 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1760 0.1753 0.1942 n_refl.: 17042 remove outliers: r(all,work,free)=0.1760 0.1753 0.1942 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1736 0.1729 0.1926 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1191 0.1612 n_refl.: 17042 remove outliers: r(all,work,free)=0.1211 0.1191 0.1612 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 0.3369 302.856 282.812 0.611 1.003 0.360 11.894-9.307 99.02 97 4 0.1469 487.095 484.716 0.918 1.004 0.360 9.237-7.194 100.00 213 7 0.1660 398.395 401.130 0.980 1.004 0.285 7.162-5.571 100.00 427 22 0.1566 298.996 294.892 0.936 1.003 0.271 5.546-4.326 100.00 867 58 0.0854 410.473 408.170 0.960 1.003 0.211 4.315-3.360 100.00 1859 96 0.0831 390.364 389.627 1.015 1.002 0.211 3.356-2.611 100.00 3867 181 0.1204 256.447 255.416 1.010 1.001 0.101 2.608-2.000 99.99 8818 434 0.1332 167.159 166.097 1.013 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3269 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1612 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1612 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1612 | n_water=364 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1190 r_free=0.1615 | n_water=363 | time (s): 28.810 (total time: 29.540) Filter (q & B) r_work=0.1190 r_free=0.1615 | n_water=363 | time (s): 0.740 (total time: 30.280) Compute maps r_work=0.1190 r_free=0.1615 | n_water=363 | time (s): 0.700 (total time: 30.980) Filter (map) r_work=0.1258 r_free=0.1613 | n_water=262 | time (s): 1.980 (total time: 32.960) Find peaks r_work=0.1258 r_free=0.1613 | n_water=262 | time (s): 0.660 (total time: 33.620) Add new water r_work=0.1447 r_free=0.1775 | n_water=412 | time (s): 1.860 (total time: 35.480) Refine new water occ: r_work=0.1245 r_free=0.1544 adp: r_work=0.1237 r_free=0.1553 occ: r_work=0.1219 r_free=0.1514 adp: r_work=0.1207 r_free=0.1519 occ: r_work=0.1199 r_free=0.1508 adp: r_work=0.1190 r_free=0.1507 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1507 r_work=0.1190 r_free=0.1507 | n_water=412 | time (s): 25.460 (total time: 60.940) Filter (q & B) r_work=0.1191 r_free=0.1510 | n_water=404 | time (s): 1.590 (total time: 62.530) Filter (dist only) r_work=0.1191 r_free=0.1510 | n_water=404 | time (s): 33.340 (total time: 95.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.926820 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.172244 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 0.1178 0.1531 0.0353 0.009 1.0 5.4 0.5 0.0 0 0.963 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.78 15.31 3.53 4.349 21.576 0.172 4.995 11.59 15.37 3.79 4.884 21.508 0.172 4.971 Individual atomic B min max mean iso aniso Overall: 6.25 104.85 20.97 4.66 1931 0 Protein: 6.25 104.85 17.01 4.65 1519 0 Water: 8.79 65.23 35.56 N/A 404 0 Other: 27.46 49.49 35.54 N/A 8 0 Chain A: 6.25 104.85 18.78 N/A 1736 0 Chain S: 17.22 65.23 40.49 N/A 195 0 Histogram: Values Number of atoms 6.25 - 16.11 1059 16.11 - 25.97 351 25.97 - 35.83 225 35.83 - 45.69 172 45.69 - 55.55 78 55.55 - 65.41 34 65.41 - 75.27 4 75.27 - 85.13 3 85.13 - 94.99 3 94.99 - 104.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1159 r_free=0.1537 r_work=0.1159 r_free=0.1538 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1159 r_free = 0.1538 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1149 r_free = 0.1536 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.12 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= 0.1149 r_free= 0.1536 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.966528 | | target function (ml) not normalized (work): 80631.585949 | | target function (ml) not normalized (free): 4182.083036 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1167 0.1149 0.1536 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1676 0.1670 0.1832 n_refl.: 17042 remove outliers: r(all,work,free)=0.1676 0.1670 0.1832 n_refl.: 17042 overall B=-0.39 to atoms: r(all,work,free)=0.1649 0.1642 0.1817 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1164 0.1145 0.1528 n_refl.: 17042 remove outliers: r(all,work,free)=0.1162 0.1143 0.1528 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 0.3447 296.141 281.741 0.563 1.006 0.328 11.894-9.307 99.02 97 4 0.1790 487.095 478.643 0.907 1.007 0.320 9.237-7.194 100.00 213 7 0.1818 398.395 400.576 0.984 1.006 0.255 7.162-5.571 100.00 427 22 0.1672 298.996 293.380 0.938 1.006 0.241 5.546-4.326 100.00 867 58 0.0933 410.473 406.797 0.965 1.005 0.200 4.315-3.360 100.00 1859 96 0.0896 390.364 388.285 1.012 1.004 0.191 3.356-2.611 100.00 3867 181 0.1281 256.447 254.230 1.013 1.001 0.142 2.608-2.000 99.99 8818 434 0.1079 167.159 165.846 1.020 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.3813 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 r_free=0.1528 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1144 r_free=0.1530 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1144 r_free=0.1530 | n_water=404 | time (s): 0.840 (total time: 0.840) Filter (dist) r_work=0.1144 r_free=0.1530 | n_water=404 | time (s): 33.180 (total time: 34.020) Filter (q & B) r_work=0.1144 r_free=0.1532 | n_water=402 | time (s): 1.940 (total time: 35.960) Compute maps r_work=0.1144 r_free=0.1532 | n_water=402 | time (s): 0.600 (total time: 36.560) Filter (map) r_work=0.1194 r_free=0.1557 | n_water=309 | time (s): 1.440 (total time: 38.000) Find peaks r_work=0.1194 r_free=0.1557 | n_water=309 | time (s): 0.480 (total time: 38.480) Add new water r_work=0.1346 r_free=0.1709 | n_water=453 | time (s): 1.630 (total time: 40.110) Refine new water occ: r_work=0.1182 r_free=0.1520 adp: r_work=0.1174 r_free=0.1523 occ: r_work=0.1158 r_free=0.1503 adp: r_work=0.1148 r_free=0.1502 occ: r_work=0.1140 r_free=0.1492 adp: r_work=0.1131 r_free=0.1492 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1492 r_work=0.1131 r_free=0.1492 | n_water=453 | time (s): 31.330 (total time: 71.440) Filter (q & B) r_work=0.1134 r_free=0.1505 | n_water=446 | time (s): 1.800 (total time: 73.240) Filter (dist only) r_work=0.1134 r_free=0.1505 | n_water=446 | time (s): 33.860 (total time: 107.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.921173 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.183036 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 0.1117 0.1555 0.0438 0.010 1.0 5.4 0.5 0.0 0 0.961 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.17 15.55 4.38 4.482 21.165 0.183 4.956 11.05 15.62 4.57 4.646 21.207 0.183 4.950 Individual atomic B min max mean iso aniso Overall: 5.90 102.76 21.14 4.91 1973 0 Protein: 5.90 102.76 16.62 4.90 1519 0 Water: 8.66 63.73 36.30 N/A 446 0 Other: 26.74 47.62 34.50 N/A 8 0 Chain A: 5.90 102.76 18.34 N/A 1735 0 Chain S: 14.10 63.73 41.56 N/A 238 0 Histogram: Values Number of atoms 5.90 - 15.59 1045 15.59 - 25.27 362 25.27 - 34.96 215 34.96 - 44.65 198 44.65 - 54.33 97 54.33 - 64.02 42 64.02 - 73.70 5 73.70 - 83.39 2 83.39 - 93.08 4 93.08 - 102.76 3 =========================== Idealize ADP of riding H ========================== r_work=0.1105 r_free=0.1562 r_work=0.1105 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1105 r_free = 0.1563 target_work(ml) = 4.950 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1096 r_free = 0.1579 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1096 r_free= 0.1579 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.948206 | | target function (ml) not normalized (work): 80324.233496 | | target function (ml) not normalized (free): 4183.875321 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1119 0.1096 0.1579 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1584 0.1571 0.1857 n_refl.: 17040 remove outliers: r(all,work,free)=0.1584 0.1571 0.1857 n_refl.: 17040 overall B=-0.31 to atoms: r(all,work,free)=0.1564 0.1551 0.1847 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1117 0.1094 0.1576 n_refl.: 17040 remove outliers: r(all,work,free)=0.1117 0.1094 0.1576 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 0.3620 296.141 273.176 0.547 1.001 0.330 11.894-9.307 99.02 97 4 0.1777 487.095 480.256 0.920 1.002 0.330 9.237-7.194 100.00 213 7 0.1696 398.395 400.483 0.993 1.002 0.236 7.162-5.571 100.00 427 22 0.1581 298.996 293.260 0.943 1.002 0.214 5.546-4.326 100.00 867 58 0.0888 410.473 407.019 0.968 1.002 0.191 4.315-3.360 100.00 1859 96 0.0822 390.364 388.377 1.009 1.002 0.191 3.356-2.611 100.00 3867 181 0.1228 256.447 254.223 1.005 1.002 0.111 2.608-2.000 99.99 8818 434 0.1045 167.159 166.026 1.004 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0804 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1094 r_free=0.1576 After: r_work=0.1096 r_free=0.1575 ================================== NQH flips ================================== r_work=0.1096 r_free=0.1575 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1096 r_free=0.1575 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1096 r_free=0.1575 | n_water=446 | time (s): 0.930 (total time: 0.930) Filter (dist) r_work=0.1100 r_free=0.1573 | n_water=445 | time (s): 39.270 (total time: 40.200) Filter (q & B) r_work=0.1101 r_free=0.1569 | n_water=443 | time (s): 1.990 (total time: 42.190) Compute maps r_work=0.1101 r_free=0.1569 | n_water=443 | time (s): 0.640 (total time: 42.830) Filter (map) r_work=0.1176 r_free=0.1576 | n_water=342 | time (s): 1.510 (total time: 44.340) Find peaks r_work=0.1176 r_free=0.1576 | n_water=342 | time (s): 0.490 (total time: 44.830) Add new water r_work=0.1286 r_free=0.1673 | n_water=475 | time (s): 1.800 (total time: 46.630) Refine new water occ: r_work=0.1136 r_free=0.1517 adp: r_work=0.1128 r_free=0.1525 occ: r_work=0.1115 r_free=0.1501 adp: r_work=0.1107 r_free=0.1508 occ: r_work=0.1100 r_free=0.1492 adp: r_work=0.1094 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1094 r_free=0.1499 r_work=0.1094 r_free=0.1499 | n_water=475 | time (s): 23.890 (total time: 70.520) Filter (q & B) r_work=0.1098 r_free=0.1508 | n_water=464 | time (s): 2.390 (total time: 72.910) Filter (dist only) r_work=0.1098 r_free=0.1508 | n_water=464 | time (s): 35.160 (total time: 108.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.069051 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.161526 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 0.1117 0.1531 0.0413 0.010 1.1 7.0 0.5 0.0 0 1.035 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.17 15.31 4.13 4.592 21.007 0.162 4.950 11.04 15.10 4.06 4.667 21.058 0.162 4.938 Individual atomic B min max mean iso aniso Overall: 5.38 100.25 21.15 5.01 1991 0 Protein: 5.38 100.25 16.31 5.01 1519 0 Water: 8.25 70.10 36.79 N/A 464 0 Other: 26.68 45.20 33.57 N/A 8 0 Chain A: 5.38 100.25 17.99 N/A 1734 0 Chain S: 15.80 70.10 42.53 N/A 257 0 Histogram: Values Number of atoms 5.38 - 14.87 1011 14.87 - 24.35 383 24.35 - 33.84 216 33.84 - 43.33 181 43.33 - 52.81 135 52.81 - 62.30 43 62.30 - 71.79 11 71.79 - 81.28 2 81.28 - 90.76 5 90.76 - 100.25 4 =========================== Idealize ADP of riding H ========================== r_work=0.1104 r_free=0.1510 r_work=0.1104 r_free=0.1510 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1104 r_free = 0.1510 target_work(ml) = 4.938 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1099 r_free = 0.1517 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1099 r_free= 0.1517 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.934912 | | target function (ml) not normalized (work): 80108.432450 | | target function (ml) not normalized (free): 4161.727508 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1090 0.1384 5.4328 5.6148| | 2: 3.63 - 2.88 1.00 2711 122 0.1075 0.1441 5.2022 5.3258| | 3: 2.88 - 2.52 1.00 2681 148 0.1358 0.1757 5.1168 5.2215| | 4: 2.52 - 2.29 1.00 2661 139 0.0942 0.1575 4.6426 4.9776| | 5: 2.29 - 2.13 1.00 2678 122 0.0976 0.1453 4.5992 4.872| | 6: 2.13 - 2.00 1.00 2692 117 0.1132 0.1748 4.5878 4.7878| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.66 1.00 0.95 6082.24| | 2: 3.63 - 2.88 2711 122 0.93 12.45 1.01 0.95 6082.24| | 3: 2.88 - 2.52 2681 148 0.88 18.57 0.99 0.95 6082.24| | 4: 2.52 - 2.29 2661 139 0.93 12.40 1.01 0.97 2211.79| | 5: 2.29 - 2.13 2678 122 0.91 14.51 1.00 0.97 2211.79| | 6: 2.13 - 2.00 2692 117 0.89 17.30 0.99 0.97 2211.79| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2211.79 max = 6082.24 mean = 4167.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.90 mean = 13.94| |phase err.(test): min = 0.00 max = 89.81 mean = 13.62| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1119 0.1099 0.1517 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1565 0.1553 0.1821 n_refl.: 17040 remove outliers: r(all,work,free)=0.1565 0.1553 0.1821 n_refl.: 17040 overall B=-0.24 to atoms: r(all,work,free)=0.1550 0.1538 0.1812 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1121 0.1100 0.1521 n_refl.: 17040 remove outliers: r(all,work,free)=0.1121 0.1100 0.1521 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 0.3459 296.141 280.360 0.542 1.005 0.313 11.894-9.307 99.02 97 4 0.1764 487.095 479.647 0.916 1.005 0.300 9.237-7.194 100.00 213 7 0.1654 398.395 400.816 0.995 1.005 0.220 7.162-5.571 100.00 427 22 0.1505 298.996 294.152 0.936 1.005 0.205 5.546-4.326 100.00 867 58 0.0904 410.473 407.343 0.964 1.004 0.201 4.315-3.360 100.00 1859 96 0.0863 390.364 388.177 1.004 1.003 0.201 3.356-2.611 100.00 3867 181 0.1234 256.447 254.265 1.000 1.001 0.121 2.608-2.000 99.99 8818 434 0.1045 167.159 165.899 0.995 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8408 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2791 0.1793 0.081 5.224 8.8 119.3 19.9 258 0.000 1_bss: 0.1614 0.1637 0.081 5.224 8.4 118.9 19.5 258 0.000 1_settarget: 0.1614 0.1637 0.081 5.224 8.4 118.9 19.5 258 0.000 1_nqh: 0.1617 0.1640 0.081 5.224 8.4 118.9 19.5 258 0.006 1_weight: 0.1617 0.1640 0.081 5.224 8.4 118.9 19.5 258 0.006 1_xyzrec: 0.1355 0.1631 0.009 0.969 8.4 118.9 19.5 258 0.154 1_adp: 0.1280 0.1658 0.009 0.969 6.4 113.9 20.0 258 0.154 1_regHadp: 0.1284 0.1666 0.009 0.969 6.4 113.9 20.0 258 0.154 1_occ: 0.1280 0.1658 0.009 0.969 6.4 113.9 20.0 258 0.154 2_bss: 0.1278 0.1649 0.009 0.969 6.0 113.5 19.6 258 0.154 2_settarget: 0.1278 0.1649 0.009 0.969 6.0 113.5 19.6 258 0.154 2_updatecdl: 0.1278 0.1649 0.009 0.986 6.0 113.5 19.6 258 0.154 2_nqh: 0.1280 0.1650 0.009 0.986 6.0 113.5 19.6 258 0.151 2_sol: 0.1244 0.1545 0.009 0.986 6.0 111.9 20.9 364 n/a 2_weight: 0.1244 0.1545 0.009 0.986 6.0 111.9 20.9 364 n/a 2_xyzrec: 0.1217 0.1593 0.008 0.922 6.0 111.9 20.9 364 n/a 2_adp: 0.1197 0.1619 0.008 0.922 6.4 106.9 21.4 364 n/a 2_regHadp: 0.1199 0.1621 0.008 0.922 6.4 106.9 21.4 364 n/a 2_occ: 0.1196 0.1616 0.008 0.922 6.4 106.9 21.4 364 n/a 3_bss: 0.1191 0.1612 0.008 0.922 6.0 106.5 21.0 364 n/a 3_settarget: 0.1191 0.1612 0.008 0.922 6.0 106.5 21.0 364 n/a 3_updatecdl: 0.1191 0.1612 0.008 0.928 6.0 106.5 21.0 364 n/a 3_nqh: 0.1191 0.1612 0.008 0.928 6.0 106.5 21.0 364 n/a 3_sol: 0.1191 0.1510 0.008 0.928 6.0 106.5 21.1 404 n/a 3_weight: 0.1191 0.1510 0.008 0.928 6.0 106.5 21.1 404 n/a 3_xyzrec: 0.1178 0.1531 0.009 0.967 6.0 106.5 21.1 404 n/a 3_adp: 0.1159 0.1537 0.009 0.967 6.3 104.8 21.0 404 n/a 3_regHadp: 0.1159 0.1538 0.009 0.967 6.3 104.8 21.0 404 n/a 3_occ: 0.1149 0.1536 0.009 0.967 6.3 104.8 21.0 404 n/a 4_bss: 0.1143 0.1528 0.009 0.967 5.9 104.5 20.6 404 n/a 4_settarget: 0.1143 0.1528 0.009 0.967 5.9 104.5 20.6 404 n/a 4_updatecdl: 0.1143 0.1528 0.009 0.967 5.9 104.5 20.6 404 n/a 4_nqh: 0.1144 0.1530 0.009 0.967 5.9 104.5 20.6 404 n/a 4_sol: 0.1134 0.1505 0.009 0.967 5.9 104.5 21.1 446 n/a 4_weight: 0.1134 0.1505 0.009 0.967 5.9 104.5 21.1 446 n/a 4_xyzrec: 0.1117 0.1555 0.010 0.984 5.9 104.5 21.1 446 n/a 4_adp: 0.1105 0.1562 0.010 0.984 5.9 102.8 21.1 446 n/a 4_regHadp: 0.1105 0.1563 0.010 0.984 5.9 102.8 21.1 446 n/a 4_occ: 0.1096 0.1579 0.010 0.984 5.9 102.8 21.1 446 n/a 5_bss: 0.1094 0.1576 0.010 0.984 5.6 102.5 20.8 446 n/a 5_settarget: 0.1094 0.1576 0.010 0.984 5.6 102.5 20.8 446 n/a 5_updatecdl: 0.1094 0.1576 0.010 0.984 5.6 102.5 20.8 446 n/a 5_setrh: 0.1096 0.1575 0.010 0.984 5.6 102.5 20.8 446 n/a 5_nqh: 0.1096 0.1575 0.010 0.984 5.6 102.5 20.8 446 n/a 5_sol: 0.1098 0.1508 0.010 0.984 5.6 102.5 21.1 464 n/a 5_weight: 0.1098 0.1508 0.010 0.984 5.6 102.5 21.1 464 n/a 5_xyzrec: 0.1117 0.1531 0.010 1.070 5.6 102.5 21.1 464 n/a 5_adp: 0.1104 0.1510 0.010 1.070 5.4 100.3 21.2 464 n/a 5_regHadp: 0.1104 0.1510 0.010 1.070 5.4 100.3 21.2 464 n/a 5_occ: 0.1099 0.1517 0.010 1.070 5.4 100.3 21.2 464 n/a end: 0.1100 0.1521 0.010 1.070 5.1 100.0 20.9 464 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2348261_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2348261_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.0700 Refinement macro-cycles (run) : 899.5000 Write final files (write_after_run_outputs) : 21.2000 Total : 924.7700 Total CPU time: 15.83 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:52 PST -0800 (1735494052.90 s) Start R-work = 0.1614, R-free = 0.1637 Final R-work = 0.1100, R-free = 0.1521 =============================================================================== Job complete usr+sys time: 975.56 seconds wall clock time: 16 minutes 40.14 seconds (1000.14 seconds total)