Starting phenix.refine on Mon May 20 17:15:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4yei.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4yei/4yei.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4yei/4yei.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4yei/4yei.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4yei.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4yei.pdb" } 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 } main { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 9333 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Chain: "B" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Chain: "C" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Time building chain proxies: 1.64, per 1000 atoms: 0.18 Number of scatterers: 9333 At special positions: 0 Unit cell: (110.36, 115.96, 164.12, 90, 90, 90) Space group: I 2 2 2 (No. 23) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 966 8.00 N 909 7.00 C 2865 6.00 H 4584 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 - 3.50 Amino acid : False - 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: 2.31 Conformation dependent library (CDL) restraints added in 307.1 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 9 helices and 0 sheets defined 12.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.638A pdb=" N ARG A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'B' and resid 23 through 31 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.570A pdb=" N ARG B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 229 Processing helix chain 'C' and resid 23 through 31 Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.592A pdb=" N ARG C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 229 39 hydrogen bonds defined for protein. 117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 4581 1.15 - 1.32: 1124 1.32 - 1.49: 1726 1.49 - 1.66: 1935 1.66 - 1.84: 15 Bond restraints: 9381 Sorted by residual: bond pdb=" N GLU A 44 " pdb=" H GLU A 44 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ARG A 186 " pdb=" H ARG A 186 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ALA A 210 " pdb=" H ALA A 210 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU B 177 " pdb=" H LEU B 177 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ALA A 228 " pdb=" H ALA A 228 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 9376 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.44: 223 105.44 - 112.60: 10348 112.60 - 119.75: 2632 119.75 - 126.90: 3592 126.90 - 134.06: 50 Bond angle restraints: 16845 Sorted by residual: angle pdb=" N LEU A 233 " pdb=" CA LEU A 233 " pdb=" C LEU A 233 " ideal model delta sigma weight residual 110.80 119.87 -9.07 2.13e+00 2.20e-01 1.81e+01 angle pdb=" N THR B 209 " pdb=" CA THR B 209 " pdb=" C THR B 209 " ideal model delta sigma weight residual 113.88 119.07 -5.19 1.23e+00 6.61e-01 1.78e+01 angle pdb=" N SER A 211 " pdb=" CA SER A 211 " pdb=" CB SER A 211 " ideal model delta sigma weight residual 110.06 116.02 -5.96 1.51e+00 4.39e-01 1.56e+01 angle pdb=" CG ARG A 191 " pdb=" CD ARG A 191 " pdb=" NE ARG A 191 " ideal model delta sigma weight residual 112.00 103.57 8.43 2.20e+00 2.07e-01 1.47e+01 angle pdb=" CA ALA C 210 " pdb=" C ALA C 210 " pdb=" O ALA C 210 " ideal model delta sigma weight residual 121.47 117.12 4.35 1.15e+00 7.56e-01 1.43e+01 ... (remaining 16840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 3987 15.79 - 31.57: 244 31.57 - 47.36: 121 47.36 - 63.15: 23 63.15 - 78.93: 8 Dihedral angle restraints: 4383 sinusoidal: 2373 harmonic: 2010 Sorted by residual: dihedral pdb=" C ASP A 218 " pdb=" N ASP A 218 " pdb=" CA ASP A 218 " pdb=" CB ASP A 218 " ideal model delta harmonic sigma weight residual -122.60 -113.38 -9.22 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" CA LEU A 233 " pdb=" C LEU A 233 " pdb=" N ALA A 234 " pdb=" CA ALA A 234 " ideal model delta harmonic sigma weight residual -180.00 -162.17 -17.83 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" C VAL C 205 " pdb=" N VAL C 205 " pdb=" CA VAL C 205 " pdb=" CB VAL C 205 " ideal model delta harmonic sigma weight residual -122.00 -130.88 8.88 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 4380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 559 0.093 - 0.186: 157 0.186 - 0.278: 32 0.278 - 0.371: 16 0.371 - 0.464: 1 Chirality restraints: 765 Sorted by residual: chirality pdb=" CA ARG A 208 " pdb=" N ARG A 208 " pdb=" C ARG A 208 " pdb=" CB ARG A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA MET B 171 " pdb=" N MET B 171 " pdb=" C MET B 171 " pdb=" CB MET B 171 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA GLU A 109 " pdb=" N GLU A 109 " pdb=" C GLU A 109 " pdb=" CB GLU A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 762 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 208 " 0.046 9.50e-02 1.11e+02 3.78e-02 2.72e+01 pdb=" NE ARG A 208 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 208 " -0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG A 208 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 208 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 208 " 0.058 2.00e-02 2.50e+03 pdb="HH12 ARG A 208 " -0.020 2.00e-02 2.50e+03 pdb="HH21 ARG A 208 " 0.056 2.00e-02 2.50e+03 pdb="HH22 ARG A 208 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 59 " -0.022 2.00e-02 2.50e+03 2.61e-02 2.05e+01 pdb=" CG TYR A 59 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 59 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 59 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 59 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 59 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 59 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 59 " 0.012 2.00e-02 2.50e+03 pdb=" HD1 TYR A 59 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 59 " 0.062 2.00e-02 2.50e+03 pdb=" HE1 TYR A 59 " 0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR A 59 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 59 " -0.005 2.00e-02 2.50e+03 2.61e-02 2.05e+01 pdb=" CG TYR C 59 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 59 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR C 59 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR C 59 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 59 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR C 59 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 59 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 TYR C 59 " -0.023 2.00e-02 2.50e+03 pdb=" HD2 TYR C 59 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 TYR C 59 " 0.030 2.00e-02 2.50e+03 pdb=" HE2 TYR C 59 " -0.049 2.00e-02 2.50e+03 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.94: 308 1.94 - 2.60: 9685 2.60 - 3.27: 30900 3.27 - 3.93: 40764 3.93 - 4.60: 59750 Nonbonded interactions: 141407 Sorted by model distance: nonbonded pdb=" HE1 HIS A 198 " pdb=" HB3 ALA A 234 " model vdw sym.op. 1.270 2.270 x,-y+2,-z+2 nonbonded pdb=" HD3 ARG A 208 " pdb=" O ARG A 208 " model vdw sym.op. 1.352 2.620 -x+2,y,-z+2 nonbonded pdb=" O ARG A 208 " pdb=" HD3 ARG A 208 " model vdw sym.op. 1.352 2.620 -x+2,y,-z+2 nonbonded pdb=" HB3 ALA B 234 " pdb=" HE ARG C 216 " model vdw sym.op. 1.398 2.270 x,-y+2,-z+2 nonbonded pdb=" OXT ALA B 234 " pdb="HH21 ARG C 216 " model vdw sym.op. 1.425 1.850 x,-y+2,-z+2 ... (remaining 141402 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: 5 Type Number sf(0) Gaussians S 9 15.91 1 O 966 7.97 1 N 909 6.97 1 C 2865 5.97 1 H 4584 1.00 1 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 ===================== Setting occupancies to: 1.000: selected atoms: 4584 of 9333 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 9333 n_use_u_iso = 4587 n_use_u_aniso = 4746 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 = 9333 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (9333 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4587 aniso = 4746) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 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 } main { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 23 through 31 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 204 through 209 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 219 through 229 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'B' and resid 23 through 31 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'B' and resid 204 through 209 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'B' and resid 219 through 229 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'C' and resid 23 through 31 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'C' and resid 204 through 209 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'C' and resid 219 through 229 } } enabled = True } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "4yei_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4584 occupancy sum: 4584.00 (% of total atoms 49.12) Rotatable: count: 1419 occupancy sum: 1419.00 (% of total atoms 15.20) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.55 - 37.43 A, n_refl.=12716 (all), 4.90 % free)------------| | | | r_work= 0.4648 r_free= 0.3724 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 6.850734 | | target function (ml) not normalized (work): 82845.930745 | | target function (ml) not normalized (free): 4160.088940 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 37.43 - 5.64 0.98 3160 150 0.4377 0.4107 7.9301 7.1801| | 2: 5.64 - 4.48 0.97 3007 139 0.4270 0.3140 6.6996 6.8358| | 3: 4.48 - 3.91 0.98 2977 158 0.4835 0.3449 6.4646 6.5718| | 4: 3.91 - 3.55 0.98 2949 176 0.5523 0.4277 6.238 6.2191| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 37.43 - 5.64 3160 150 0.58 44.13 0.74 0.59 276018.49| | 2: 5.64 - 4.48 3007 139 0.64 40.12 1.64 0.84 146839.46| | 3: 4.48 - 3.91 2977 158 0.77 28.52 1.84 0.98 70891.22| | 4: 3.91 - 3.55 2949 176 0.73 33.00 2.00 1.01 48173.76| |alpha: min = 0.59 max = 1.01 mean = 0.85| |beta: min = 48173.76 max = 276018.49 mean = 137837.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.68| |phase err.(work): min = 0.00 max = 89.82 mean = 36.58| |phase err.(test): min = 0.00 max = 89.91 mean = 35.81| |-----------------------------------------------------------------------------| ----------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 : 0.017 0.091 4797 Z= 1.134 Angle : 1.564 10.417 6522 Z= 0.950 Chirality : 0.097 0.464 765 Planarity : 0.008 0.044 900 Dihedral : 14.850 78.933 1683 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.49 % Allowed : 5.94 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.82 (0.25), residues: 639 helix: -0.76 (0.52), residues: 93 sheet: None (None), residues: 0 loop : -1.42 (0.19), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG A 208 TYR 0.030 0.009 TYR C 30 PHE 0.030 0.007 PHE B 225 TRP 0.026 0.009 TRP C 207 HIS 0.015 0.004 HIS A 198 Individual atomic B min max mean iso aniso Overall: 49.64 289.79 106.35 4.55 4749 0 Protein: 49.64 289.79 106.35 4.55 4749 0 Chain A: 49.64 180.30 105.91 N/A 1583 0 Chain B: 56.85 174.83 98.34 N/A 1583 0 Chain C: 58.38 289.79 114.82 N/A 1583 0 Histogram: Values Number of atoms 49.64 - 73.66 630 73.66 - 97.67 1454 97.67 - 121.69 1256 121.69 - 145.70 892 145.70 - 169.72 426 169.72 - 193.73 50 193.73 - 217.74 22 217.74 - 241.76 11 241.76 - 265.77 5 265.77 - 289.79 3 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.55 - 37.43 A, n_refl.=12716 (all), 4.90 % free)------------| | | | r_work= 0.4648 r_free= 0.3724 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 6.850734 | | target function (ml) not normalized (work): 82845.930745 | | target function (ml) not normalized (free): 4160.088940 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 7.9863 percent. r_work = 0.5447 r_free = 0.4722 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.5420 0.5447 0.4722 n_refl.: 12716 re-set all scales: r(all,work,free)=0.5420 0.5447 0.4722 n_refl.: 12716 remove outliers: r(all,work,free)=0.5326 0.5350 0.4722 n_refl.: 12706 overall B=-19.52 to atoms: r(all,work,free)=0.4761 0.4780 0.4317 n_refl.: 12706 bulk-solvent and scaling: r(all,work,free)=0.2831 0.2821 0.3031 n_refl.: 12706 remove outliers: r(all,work,free)=0.2830 0.2820 0.3031 n_refl.: 12705 ======================== 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 32.244-17.658 90.00 95 4 0.2361 2888.741 2836.860 1.377 1.103 0.425 17.650-14.285 98.02 94 5 0.1437 3045.471 3027.032 1.043 1.100 0.372 14.282-11.568 95.90 180 7 0.1422 3015.142 2972.767 1.162 1.084 0.366 11.530-9.354 97.49 335 14 0.2123 1633.314 1609.041 1.151 1.071 0.367 9.349-7.570 98.64 624 29 0.2492 1223.678 1175.786 0.914 1.049 0.311 7.566-6.123 98.85 1143 56 0.2819 950.581 897.392 0.914 1.017 0.268 6.123-4.955 97.48 2111 97 0.3017 843.953 800.215 1.013 0.964 0.260 4.954-4.009 97.40 3921 193 0.2745 1174.560 1150.097 1.226 0.888 0.193 4.009-3.554 97.79 3579 218 0.3563 708.485 625.652 1.175 0.814 0.156 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0608 b_overall=6.4247 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2820 r_free=0.3031 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2820 r_free=0.3031 ========================= Local real-space refinement ========================= Before: r_work=0.2820 r_free=0.3031 231 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 224 time to evaluate : 0.476 outliers start: 7 outliers final: 4 residues processed: 7 average time/residue: 0.7472 time to fit residues: 6.5267 After: r_work=0.2823 r_free=0.3034 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.363753 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.141123 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2910 0.3137 0.0228 0.001 0.4 0.3 0.0 0.2 0 0.125 0.2844 0.3123 0.0279 0.002 0.5 0.3 0.0 0.2 0 0.250 0.2757 0.3126 0.0368 0.002 0.5 0.4 0.0 0.4 0 0.500 0.2659 0.3131 0.0472 0.003 0.6 1.3 0.0 0.6 0 1.000 0.2553 0.3163 0.0609 0.005 0.7 2.8 0.0 2.1 0 2.000 0.2503 0.3168 0.0665 0.006 0.8 4.1 0.0 3.6 0 3.000 0.2467 0.3168 0.0702 0.008 0.9 6.0 0.0 4.2 0 4.000 0.2424 0.3165 0.0741 0.009 1.0 7.4 0.0 6.4 0 5.000 0.2401 0.3140 0.0739 0.010 1.1 9.5 0.2 7.0 0 6.000 0.2375 0.3130 0.0755 0.011 1.2 11.9 0.0 7.9 0 7.000 0.2360 0.3136 0.0776 0.012 1.3 12.8 0.5 8.3 0 8.000 0.2345 0.3130 0.0784 0.013 1.4 14.9 0.3 9.6 0 9.000 0.2331 0.3127 0.0797 0.014 1.4 16.0 0.3 9.8 0 10.000 0.2386 0.3139 0.0754 0.011 1.2 10.8 0.2 7.6 0 6.682 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2844 0.3123 0.0279 0.002 0.5 0.3 0.0 0.2 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2844 r_free=0.3123 230 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 1.626 outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.8284 time to fit residues: 2.7211 After: r_work=0.2847 r_free=0.3124 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 28.47 31.24 2.77 3.255 86.699 0.141 0.082 28.36 31.22 2.87 3.525 86.938 0.004 0.081 28.09 31.08 2.99 3.573 86.939 0.018 0.079 26.89 30.52 3.64 5.974 87.550 0.071 0.072 26.26 30.20 3.94 7.076 87.708 0.141 0.068 25.94 30.04 4.10 7.990 87.901 0.212 0.067 25.76 29.93 4.17 8.640 88.052 0.282 0.066 25.55 29.84 4.28 9.486 88.322 0.353 0.064 25.28 29.73 4.46 10.786 88.793 0.423 0.063 25.18 29.67 4.50 11.275 88.928 0.494 0.063 25.10 29.64 4.54 11.721 89.050 0.564 0.062 25.01 29.60 4.60 12.236 89.206 0.635 0.062 24.95 29.59 4.64 12.584 89.302 0.706 0.061 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.706 Accepted refinement result: 24.95 29.59 4.64 12.584 89.302 0.706 0.061 Individual atomic B min max mean iso aniso Overall: 25.27 265.26 91.95 11.99 4749 0 Protein: 25.27 265.26 91.95 11.99 4749 0 Chain A: 25.27 167.78 90.73 N/A 1583 0 Chain B: 34.24 162.01 84.76 N/A 1583 0 Chain C: 35.83 265.26 100.34 N/A 1583 0 Histogram: Values Number of atoms 25.27 - 49.27 203 49.27 - 73.27 1210 73.27 - 97.27 1454 97.27 - 121.27 1071 121.27 - 145.27 640 145.27 - 169.27 129 169.27 - 193.27 23 193.27 - 217.27 11 217.27 - 241.26 5 241.26 - 265.26 3 =========================== Idealize ADP of riding H ========================== r_work=0.2495 r_free=0.2959 r_work=0.2463 r_free=0.2935 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2463 r_free= 0.2935 coordinate error (max.-lik. estimate): 0.51 A | | | | normalized target function (ls_wunit_k1) (work): 0.059742 | | target function (ls_wunit_k1) not normalized (work): 721.797646 | | target function (ls_wunit_k1) not normalized (free): 52.141702 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2486 0.2463 0.2935 n_refl.: 12705 re-set all scales: r(all,work,free)=0.4821 0.4837 0.4436 n_refl.: 12705 remove outliers: r(all,work,free)=0.4821 0.4837 0.4436 n_refl.: 12705 overall B=-0.07 to atoms: r(all,work,free)=0.4819 0.4835 0.4435 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2465 0.2441 0.2926 n_refl.: 12705 remove outliers: r(all,work,free)=0.2465 0.2441 0.2926 n_refl.: 12705 ======================== 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 32.244-17.658 90.00 95 4 0.2235 1603.082 1604.017 1.335 1.079 0.430 17.650-14.285 98.02 94 5 0.1517 1690.058 1668.720 1.080 1.078 0.383 14.282-11.568 95.90 180 7 0.1396 1673.227 1657.261 1.163 1.063 0.362 11.530-9.354 97.49 335 14 0.2041 906.394 895.260 1.128 1.053 0.347 9.349-7.570 98.64 624 29 0.2311 679.069 659.784 0.908 1.034 0.300 7.566-6.123 98.85 1143 56 0.2553 527.517 508.520 0.910 1.008 0.260 6.123-4.955 97.48 2111 97 0.2641 468.344 452.744 1.016 0.964 0.250 4.954-4.009 97.40 3921 193 0.2206 651.812 646.536 1.237 0.903 0.170 4.009-3.554 97.79 3579 218 0.3148 393.168 360.460 1.226 0.843 0.140 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.1910 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2441 r_free=0.2926 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN Total number of N/Q/H flips: 1 r_work=0.2441 r_free=0.2926 ========================= Local real-space refinement ========================= Before: r_work=0.2441 r_free=0.2926 246 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.494 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9173 After: r_work=0.2441 r_free=0.2926 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.537244 wxc_scale = 0.030 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.034940 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2536 0.2990 0.0455 0.001 0.4 1.0 0.0 0.0 0 0.010 0.2475 0.2985 0.0510 0.001 0.4 0.5 0.0 0.0 0 0.031 0.2406 0.2956 0.0551 0.001 0.4 0.5 0.0 0.0 0 0.063 0.2370 0.2958 0.0587 0.001 0.4 0.5 0.0 0.2 0 0.094 0.2346 0.2938 0.0592 0.002 0.4 0.9 0.0 0.4 0 0.125 0.2331 0.2932 0.0601 0.002 0.5 0.8 0.0 0.4 0 0.157 0.2321 0.2920 0.0599 0.002 0.5 0.6 0.0 0.4 0 0.188 0.2308 0.2918 0.0610 0.002 0.5 0.8 0.0 0.4 0 0.219 0.2360 0.2953 0.0593 0.001 0.4 0.8 0.0 0.2 0 0.104 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2536 0.2990 0.0455 0.001 0.4 1.0 0.0 0.0 0 0.010 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2536 r_free=0.2990 258 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.613 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4499 After: r_work=0.2536 r_free=0.2990 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.36 29.90 4.55 16.054 101.169 0.035 6.575 28.73 31.19 2.46 14.124 106.142 0.001 6.652 28.51 31.11 2.60 14.013 106.788 0.004 6.638 26.62 29.95 3.32 15.360 103.099 0.017 6.582 25.91 29.69 3.77 16.182 102.344 0.035 6.556 25.31 29.51 4.20 16.379 101.644 0.052 6.545 25.12 29.59 4.47 16.839 102.108 0.070 6.535 24.96 29.61 4.66 17.243 102.301 0.087 6.530 24.84 29.58 4.73 17.410 102.215 0.105 6.528 24.75 29.57 4.83 17.722 102.384 0.122 6.525 24.67 29.56 4.88 18.028 102.539 0.140 6.523 24.61 29.56 4.95 18.311 102.684 0.157 6.521 24.56 29.56 5.00 18.608 102.833 0.175 6.519 max suggested for this run: 20.23 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.052 Accepted refinement result: 25.31 29.51 4.20 16.379 101.644 0.052 6.545 Individual atomic B min max mean iso aniso Overall: 31.62 260.19 92.81 11.44 4749 0 Protein: 31.62 260.19 92.81 11.44 4749 0 Chain A: 31.62 167.06 90.84 N/A 1583 0 Chain B: 33.82 164.93 85.65 N/A 1583 0 Chain C: 37.85 260.19 101.94 N/A 1583 0 Histogram: Values Number of atoms 31.62 - 54.48 275 54.48 - 77.33 1388 77.33 - 100.19 1376 100.19 - 123.05 908 123.05 - 145.91 600 145.91 - 168.76 161 168.76 - 191.62 22 191.62 - 214.48 11 214.48 - 237.34 5 237.34 - 260.19 3 =========================== Idealize ADP of riding H ========================== r_work=0.2531 r_free=0.2951 r_work=0.2537 r_free=0.2946 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2537 r_free= 0.2946 coordinate error (max.-lik. estimate): 0.59 A | | | | normalized target function (ml) (work): 6.543532 | | target function (ml) not normalized (work): 79058.947743 | | target function (ml) not normalized (free): 4140.858444 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2557 0.2537 0.2946 n_refl.: 12705 re-set all scales: r(all,work,free)=0.4881 0.4897 0.4457 n_refl.: 12705 remove outliers: r(all,work,free)=0.4881 0.4897 0.4457 n_refl.: 12705 overall B=-0.41 to atoms: r(all,work,free)=0.4868 0.4885 0.4449 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2555 0.2535 0.2961 n_refl.: 12705 remove outliers: r(all,work,free)=0.2555 0.2535 0.2961 n_refl.: 12705 ======================== 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 32.244-17.658 90.00 95 4 0.2307 1603.082 1593.040 1.250 1.088 0.430 17.650-14.285 98.02 94 5 0.1514 1690.058 1656.072 1.002 1.087 0.380 14.282-11.568 95.90 180 7 0.1486 1673.227 1637.399 1.099 1.072 0.365 11.530-9.354 97.49 335 14 0.2103 906.394 887.364 1.084 1.061 0.360 9.349-7.570 98.64 624 29 0.2345 679.069 651.554 0.869 1.041 0.300 7.566-6.123 98.85 1143 56 0.2651 527.517 502.155 0.861 1.013 0.248 6.123-4.955 97.48 2111 97 0.2812 468.344 445.100 0.982 0.966 0.227 4.954-4.009 97.40 3921 193 0.2300 651.812 642.712 1.195 0.900 0.171 4.009-3.554 97.79 3579 218 0.3227 393.168 356.625 1.191 0.836 0.131 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.2772 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2535 r_free=0.2961 After: r_work=0.2535 r_free=0.2961 ================================== NQH flips ================================== r_work=0.2535 r_free=0.2961 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 71 ASN A 179 GLN B 61 ASN B 71 ASN C 61 ASN Total number of N/Q/H flips: 6 r_work=0.2535 r_free=0.2965 ========================= Local real-space refinement ========================= Before: r_work=0.2535 r_free=0.2965 267 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 0.979 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9262 After: r_work=0.2535 r_free=0.2965 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.808566 wxc_scale = 0.024 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.035684 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2536 0.2968 0.0432 0.001 0.4 0.9 0.0 0.0 0 0.009 0.2536 0.2968 0.0432 0.001 0.4 0.9 0.0 0.0 0 0.028 0.2535 0.2968 0.0433 0.001 0.4 0.9 0.0 0.0 0 0.056 0.2533 0.2966 0.0434 0.001 0.4 0.9 0.0 0.0 0 0.084 0.2530 0.2966 0.0437 0.001 0.4 0.9 0.0 0.0 0 0.112 0.2526 0.2967 0.0441 0.002 0.4 0.9 0.0 0.0 0 0.140 0.2519 0.2967 0.0448 0.002 0.4 0.9 0.0 0.0 0 0.167 0.2504 0.2957 0.0453 0.003 0.5 0.9 0.0 0.0 0 0.195 0.2532 0.2967 0.0435 0.001 0.4 0.9 0.0 0.0 0 0.093 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2504 0.2957 0.0453 0.003 0.5 0.9 0.0 0.0 0 0.195 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2504 r_free=0.2957 264 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 0.585 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4329 After: r_work=0.2504 r_free=0.2957 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.04 29.57 4.53 15.927 101.805 0.036 6.541 29.29 31.77 2.48 14.314 108.390 0.001 6.669 28.48 31.06 2.59 13.572 108.370 0.004 6.641 26.58 29.82 3.23 14.852 103.919 0.018 6.587 25.54 29.16 3.62 15.396 102.728 0.036 6.550 24.69 28.96 4.27 15.877 102.401 0.054 6.524 24.33 28.97 4.64 16.653 102.549 0.071 6.513 24.16 29.06 4.90 17.255 102.713 0.089 6.507 24.05 29.11 5.06 17.710 102.865 0.107 6.504 23.98 29.15 5.17 18.081 103.019 0.125 6.501 23.92 29.16 5.24 18.410 103.171 0.143 6.500 23.88 29.19 5.32 18.710 103.318 0.161 6.498 23.84 29.21 5.37 18.982 103.454 0.178 6.498 max suggested for this run: 20.36 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.054 Accepted refinement result: 24.69 28.96 4.27 15.877 102.401 0.054 6.524 Individual atomic B min max mean iso aniso Overall: 32.75 254.78 93.57 12.12 4749 0 Protein: 32.75 254.78 93.57 12.12 4749 0 Chain A: 32.75 180.92 90.40 N/A 1583 0 Chain B: 34.59 167.34 86.69 N/A 1583 0 Chain C: 36.71 254.78 103.62 N/A 1583 0 Histogram: Values Number of atoms 32.75 - 54.95 291 54.95 - 77.15 1341 77.15 - 99.36 1373 99.36 - 121.56 845 121.56 - 143.76 580 143.76 - 165.97 249 165.97 - 188.17 52 188.17 - 210.37 11 210.37 - 232.58 4 232.58 - 254.78 3 =========================== Idealize ADP of riding H ========================== r_work=0.2469 r_free=0.2896 r_work=0.2468 r_free=0.2892 ----------X-ray data---------- |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2468 r_free= 0.2892 coordinate error (max.-lik. estimate): 0.58 A | | | | normalized target function (ml) (work): 6.523538 | | target function (ml) not normalized (work): 78817.380517 | | target function (ml) not normalized (free): 4132.553374 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.24 - 5.63 0.98 3159 150 0.2252 0.2506 6.6796 6.7953| | 2: 5.63 - 4.48 0.97 3003 139 0.2320 0.2681 6.5511 6.7178| | 3: 4.48 - 3.91 0.98 2973 158 0.2357 0.2783 6.5371 6.7199| | 4: 3.91 - 3.55 0.98 2947 176 0.3331 0.4025 6.3145 6.3508| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 32.24 - 5.63 3159 150 0.76 28.72 0.99 1.03 109938.77| | 2: 5.63 - 4.48 3003 139 0.70 34.95 1.05 1.01 99980.90| | 3: 4.48 - 3.91 2973 158 0.73 31.92 0.97 0.93 87349.32| | 4: 3.91 - 3.55 2947 176 0.60 43.62 0.97 0.78 72044.05| |alpha: min = 0.78 max = 1.03 mean = 0.94| |beta: min = 72044.05 max = 109938.77 mean = 92662.02| |figures of merit: min = 0.00 max = 1.00 mean = 0.70| |phase err.(work): min = 0.00 max = 89.93 mean = 34.69| |phase err.(test): min = 0.00 max = 89.03 mean = 35.58| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2488 0.2468 0.2892 n_refl.: 12705 re-set all scales: r(all,work,free)=0.4877 0.4895 0.4440 n_refl.: 12705 remove outliers: r(all,work,free)=0.4877 0.4895 0.4440 n_refl.: 12705 overall B=0.22 to atoms: r(all,work,free)=0.4884 0.4902 0.4445 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2482 0.2462 0.2885 n_refl.: 12705 remove outliers: r(all,work,free)=0.2482 0.2462 0.2885 n_refl.: 12705 ======================== 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 32.244-17.658 90.00 95 4 0.2376 1603.082 1603.740 1.199 1.114 0.430 17.650-14.285 98.02 94 5 0.1473 1690.058 1674.553 0.962 1.112 0.380 14.282-11.568 95.90 180 7 0.1421 1673.227 1654.742 1.057 1.094 0.365 11.530-9.354 97.49 335 14 0.2078 906.394 894.183 1.045 1.081 0.360 9.349-7.570 98.64 624 29 0.2302 679.069 655.637 0.840 1.058 0.300 7.566-6.123 98.85 1143 56 0.2601 527.517 503.826 0.842 1.025 0.250 6.123-4.955 97.48 2111 97 0.2712 468.344 445.013 1.002 0.972 0.250 4.954-4.009 97.40 3921 193 0.2196 651.812 639.878 1.186 0.895 0.170 4.009-3.554 97.79 3579 218 0.3172 393.168 354.499 1.188 0.819 0.139 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=0.0244 ================= 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) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.4648 0.3724 0.017 1.564 49.6 289.8 106.4 0 0.000 1_bss: 0.2820 0.3031 0.017 1.564 30.1 270.3 86.8 0 0.000 1_settarget: 0.2820 0.3031 0.017 1.564 30.1 270.3 86.8 0 0.000 1_updatephipsi: 0.2820 0.3031 0.017 1.564 30.1 270.3 86.8 0 0.000 1_nqh: 0.2820 0.3031 0.017 1.564 30.1 270.3 86.8 0 0.000 1_realsrl: 0.2823 0.3034 0.017 1.564 30.1 270.3 86.8 0 0.009 1_weight: 0.2823 0.3034 0.017 1.564 30.1 270.3 86.8 0 0.009 1_xyzrec: 0.2844 0.3123 0.002 0.454 30.1 270.3 86.8 0 0.173 1_realsrl2: 0.2847 0.3124 0.002 0.454 30.1 270.3 86.8 0 0.173 1_adp: 0.2495 0.2959 0.002 0.454 25.3 265.3 91.9 0 0.173 1_regHadp: 0.2463 0.2935 0.002 0.454 25.3 265.3 91.9 0 0.173 2_bss: 0.2441 0.2926 0.002 0.454 25.2 265.2 91.9 0 0.173 2_settarget: 0.2441 0.2926 0.002 0.454 25.2 265.2 91.9 0 0.173 2_updatephipsi: 0.2441 0.2926 0.002 0.454 25.2 265.2 91.9 0 0.173 2_updatecdl: 0.2441 0.2926 0.002 0.471 25.2 265.2 91.9 0 0.173 2_nqh: 0.2441 0.2926 0.002 0.471 25.2 265.2 91.9 0 0.174 2_realsrl: 0.2441 0.2926 0.002 0.471 25.2 265.2 91.9 0 0.174 2_weight: 0.2441 0.2926 0.002 0.471 25.2 265.2 91.9 0 0.174 2_xyzrec: 0.2536 0.2990 0.001 0.395 25.2 265.2 91.9 0 0.214 2_realsrl2: 0.2536 0.2990 0.001 0.395 25.2 265.2 91.9 0 0.214 2_adp: 0.2531 0.2951 0.001 0.395 31.6 260.2 92.8 0 0.214 2_regHadp: 0.2537 0.2946 0.001 0.395 31.6 260.2 92.8 0 0.214 3_bss: 0.2535 0.2961 0.001 0.395 31.2 259.8 92.4 0 0.214 3_settarget: 0.2535 0.2961 0.001 0.395 31.2 259.8 92.4 0 0.214 3_updatephipsi: 0.2535 0.2961 0.001 0.395 31.2 259.8 92.4 0 0.214 3_updatecdl: 0.2535 0.2961 0.001 0.407 31.2 259.8 92.4 0 0.214 3_setrh: 0.2535 0.2961 0.001 0.407 31.2 259.8 92.4 0 0.214 3_nqh: 0.2535 0.2965 0.001 0.407 31.2 259.8 92.4 0 0.220 3_realsrl: 0.2535 0.2965 0.001 0.407 31.2 259.8 92.4 0 0.220 3_weight: 0.2535 0.2965 0.001 0.407 31.2 259.8 92.4 0 0.220 3_xyzrec: 0.2504 0.2957 0.003 0.468 31.2 259.8 92.4 0 0.219 3_realsrl2: 0.2504 0.2957 0.003 0.468 31.2 259.8 92.4 0 0.219 3_adp: 0.2469 0.2896 0.003 0.468 32.7 254.8 93.6 0 0.219 3_regHadp: 0.2468 0.2892 0.003 0.468 32.7 254.8 93.6 0 0.219 end: 0.2462 0.2885 0.003 0.468 33.0 255.0 93.8 0 0.219 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/4yei_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/4yei_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.4300 Refinement macro-cycles (run) : 404.1100 Write final files (write_after_run_outputs) : 18.4800 Total : 430.0200 Total CPU time: 7.68 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:38 PDT -0700 (1716251738.99 s) Start R-work = 0.2820, R-free = 0.3031 Final R-work = 0.2462, R-free = 0.2885 =============================================================================== Job complete usr+sys time: 482.07 seconds wall clock time: 20 minutes 35.64 seconds (1235.64 seconds total)