Starting phenix.refine on Mon May 20 17:16:28 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4xcr.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4xcr/4xcr.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 ramachandran_plot_restraints.enabled=False secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4xcr.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4xcr.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4xcr/4xcr.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4xcr/4xcr.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 } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1543 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1543 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Time building chain proxies: 0.60, per 1000 atoms: 0.19 Number of scatterers: 3086 At special positions: 0 Unit cell: (70.8199, 70.8199, 70.01, 90, 90, 120) Space group: P 65 (No. 170) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 308 8.00 N 280 7.00 C 954 6.00 H 1544 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: 0.71 Conformation dependent library (CDL) restraints added in 107.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 360 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.10: 1544 1.10 - 1.21: 0 1.21 - 1.33: 308 1.33 - 1.44: 336 1.44 - 1.56: 918 Bond restraints: 3106 Sorted by residual: bond pdb=" N GLY A 104 " pdb=" H GLY A 104 " 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 93 " pdb=" H ALA A 93 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N HIS B 48 " pdb=" H HIS B 48 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLY A 10 " pdb=" H GLY A 10 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N SER B 103 " pdb=" H SER B 103 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 3101 not shown) Histogram of bond angle deviations from ideal: 102.64 - 108.90: 1201 108.90 - 115.16: 2931 115.16 - 121.42: 737 121.42 - 127.67: 747 127.67 - 133.93: 16 Bond angle restraints: 5632 Sorted by residual: angle pdb=" N HIS A 46 " pdb=" CA HIS A 46 " pdb=" C HIS A 46 " ideal model delta sigma weight residual 108.79 114.62 -5.83 1.53e+00 4.27e-01 1.45e+01 angle pdb=" N ALA B 50 " pdb=" CA ALA B 50 " pdb=" C ALA B 50 " ideal model delta sigma weight residual 108.13 114.63 -6.50 1.72e+00 3.38e-01 1.43e+01 angle pdb=" N HIS B 46 " pdb=" CA HIS B 46 " pdb=" C HIS B 46 " ideal model delta sigma weight residual 109.07 115.09 -6.02 1.61e+00 3.86e-01 1.40e+01 angle pdb=" N THR A 86 " pdb=" CA THR A 86 " pdb=" C THR A 86 " ideal model delta sigma weight residual 108.96 114.59 -5.63 1.59e+00 3.96e-01 1.26e+01 angle pdb=" N ALA A 109 " pdb=" CA ALA A 109 " pdb=" C ALA A 109 " ideal model delta sigma weight residual 112.93 108.80 4.13 1.33e+00 5.65e-01 9.65e+00 ... (remaining 5627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 1281 17.29 - 34.57: 82 34.57 - 51.86: 49 51.86 - 69.15: 16 69.15 - 86.44: 2 Dihedral angle restraints: 1430 sinusoidal: 788 harmonic: 642 Sorted by residual: dihedral pdb=" CA HIS B 46 " pdb=" C HIS B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LEU B 101 " pdb=" C LEU B 101 " pdb=" N ALA B 102 " pdb=" CA ALA B 102 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ILE B 69 " pdb=" C ILE B 69 " pdb=" N GLU B 70 " pdb=" CA GLU B 70 " ideal model delta harmonic sigma weight residual 180.00 163.32 16.68 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 1427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 152 0.034 - 0.067: 46 0.067 - 0.101: 23 0.101 - 0.135: 17 0.135 - 0.168: 6 Chirality restraints: 244 Sorted by residual: chirality pdb=" CA VAL B 47 " pdb=" N VAL B 47 " pdb=" C VAL B 47 " pdb=" CB VAL B 47 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA ILE A 18 " pdb=" N ILE A 18 " pdb=" C ILE A 18 " pdb=" CB ILE A 18 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE B 18 " pdb=" N ILE B 18 " pdb=" C ILE B 18 " pdb=" CB ILE B 18 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.19e-01 ... (remaining 241 not shown) Planarity restraints: 494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 20 " -0.000 2.00e-02 2.50e+03 4.94e-03 7.31e-01 pdb=" CG PHE B 20 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 20 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 20 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE B 20 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE B 20 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 PHE B 20 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 45 " 0.004 2.00e-02 2.50e+03 4.84e-03 7.02e-01 pdb=" CG PHE A 45 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 45 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 45 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 45 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 45 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 45 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 45 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE A 45 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 45 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE A 45 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 45 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 20 " 0.003 2.00e-02 2.50e+03 3.91e-03 4.58e-01 pdb=" CG PHE A 20 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE A 20 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 20 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 20 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 20 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 20 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 20 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE A 20 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 20 " 0.000 2.00e-02 2.50e+03 pdb=" HZ PHE A 20 " -0.001 2.00e-02 2.50e+03 ... (remaining 491 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.08: 168 2.08 - 2.69: 4385 2.69 - 3.29: 8530 3.29 - 3.90: 10967 3.90 - 4.50: 16312 Nonbonded interactions: 40362 Sorted by model distance: nonbonded pdb=" H GLY A 96 " pdb="HD21 ASN B 26 " model vdw sym.op. 1.477 2.100 -x+1,-y+1,z+1/2 nonbonded pdb=" O ALA B 4 " pdb=" H PHE B 20 " model vdw 1.502 1.850 nonbonded pdb=" OE2 GLU A 21 " pdb=" HE1 TRP A 32 " model vdw 1.545 1.850 nonbonded pdb=" O LEU B 42 " pdb=" H GLY B 94 " model vdw 1.609 1.850 nonbonded pdb=" H VAL A 47 " pdb=" O GLY A 52 " model vdw 1.623 1.850 ... (remaining 40357 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: 4 Type Number sf(0) Gaussians O 308 7.97 1 N 280 6.97 1 C 954 5.97 1 H 1544 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: 1544 of 3086 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3086 n_use_u_iso = 1544 n_use_u_aniso = 1542 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 = 3086 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3086 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1544 aniso = 1542) 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 { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "4xcr_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1544 occupancy sum: 1544.00 (% of total atoms 50.09) Rotatable: count: 506 occupancy sum: 506.00 (% of total atoms 16.41) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.60 - 46.13 A, n_refl.=2197 (all), 9.97 % free)-------------| | | | r_work= 0.4859 r_free= 0.4533 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 6.422387 | | target function (ml) not normalized (work): 12703.482032 | | target function (ml) not normalized (free): 1443.643012 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 46.13 - 4.54 0.92 985 109 0.4372 0.4517 6.651 6.749| | 2: 4.53 - 3.60 0.94 993 110 0.5457 0.4551 6.1956 6.4364| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 46.13 - 4.54 985 109 0.66 38.01 0.84 0.99 177349.34| | 2: 4.53 - 3.60 993 110 0.87 20.59 2.01 1.79 35225.25| |alpha: min = 0.37 max = 2.03 mean = 1.39| |beta: min = 27468.29 max = 448438.04 mean = 105999.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 90.00 mean = 29.26| |phase err.(test): min = 0.00 max = 89.63 mean = 29.40| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 1562 Z= 0.320 Angle : 1.074 6.499 2110 Z= 0.704 Chirality : 0.052 0.168 244 Planarity : 0.002 0.012 280 Dihedral : 14.220 86.435 540 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.93 % Allowed : 8.33 % Favored : 90.74 % Rotamer: Outliers : 3.85 % Allowed : 7.69 % Favored : 88.46 % 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: -4.86 (0.40), residues: 216 helix: None (None), residues: 0 sheet: -2.78 (0.43), residues: 94 loop : -3.71 (0.33), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 100 PHE 0.009 0.003 PHE A 45 TRP 0.004 0.001 TRP B 32 HIS 0.002 0.001 HIS B 80 Individual atomic B min max mean iso aniso Overall: 42.38 96.62 61.74 1.86 1542 0 Protein: 42.38 96.62 61.74 1.86 1542 0 Chain A: 42.38 92.35 59.13 N/A 771 0 Chain B: 46.95 96.62 64.36 N/A 771 0 Histogram: Values Number of atoms 42.38 - 47.80 75 47.80 - 53.23 307 53.23 - 58.65 306 58.65 - 64.08 257 64.08 - 69.50 241 69.50 - 74.92 185 74.92 - 80.35 96 80.35 - 85.77 43 85.77 - 91.20 25 91.20 - 96.62 7 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.60 - 46.13 A, n_refl.=2197 (all), 9.97 % free)-------------| | | | r_work= 0.4859 r_free= 0.4533 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 6.422387 | | target function (ml) not normalized (work): 12703.482032 | | target function (ml) not normalized (free): 1443.643012 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3070 percent. r_work = 0.4990 r_free = 0.4731 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4964 0.4990 0.4731 n_refl.: 2197 re-set all scales: r(all,work,free)=0.4964 0.4990 0.4731 n_refl.: 2197 remove outliers: r(all,work,free)=0.4926 0.4948 0.4731 n_refl.: 2192 overall B=-12.88 to atoms: r(all,work,free)=0.4430 0.4444 0.4361 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2094 0.2035 0.2627 n_refl.: 2192 remove outliers: r(all,work,free)=0.2094 0.2035 0.2627 n_refl.: 2192 ======================== 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 46.133-10.115 85.45 84 10 0.1851 812.492 781.541 1.249 1.028 0.367 10.083-8.012 89.47 92 10 0.2086 541.003 524.203 1.179 1.018 0.365 8.010-6.369 94.31 180 19 0.2300 513.402 486.339 1.059 1.011 0.363 6.360-5.059 92.00 354 37 0.1977 502.797 476.188 0.934 1.003 0.366 5.057-4.020 93.59 707 82 0.1974 525.069 501.856 0.990 0.990 0.283 4.017-3.602 94.20 556 61 0.2122 381.422 353.384 1.010 0.980 0.255 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.8283 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.695683 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.265339 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 0.2163 0.2806 0.0643 0.002 0.4 1.9 0.9 3.8 0 0.125 0.2087 0.2784 0.0698 0.002 0.4 1.9 0.9 4.5 0 0.250 0.2004 0.2811 0.0807 0.002 0.5 3.2 0.9 4.5 0 0.500 0.1909 0.2827 0.0917 0.003 0.5 4.2 0.9 3.8 0 1.000 0.1833 0.2887 0.1054 0.005 0.7 6.8 0.9 5.8 0 2.000 0.1788 0.2909 0.1121 0.006 0.8 9.7 1.4 6.4 0 3.000 0.1758 0.2930 0.1172 0.008 0.9 12.3 1.4 7.1 0 4.000 0.1731 0.2900 0.1169 0.009 1.0 13.0 1.4 7.1 0 5.000 0.1703 0.2992 0.1288 0.011 1.1 14.3 1.9 9.0 0 6.000 0.1676 0.3006 0.1330 0.012 1.2 15.9 2.3 9.0 0 7.000 0.1656 0.2996 0.1340 0.013 1.3 16.9 2.3 9.6 0 8.000 0.1639 0.3010 0.1371 0.014 1.4 18.5 2.3 9.6 0 9.000 0.1630 0.3049 0.1419 0.015 1.5 19.8 2.3 9.6 0 10.000 0.1684 0.3024 0.1341 0.012 1.2 15.9 2.8 9.0 0 6.848 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2087 0.2784 0.0698 0.002 0.4 1.9 0.9 4.5 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.87 27.84 6.98 8.919 45.386 0.265 0.057 21.14 28.46 7.32 8.127 45.900 0.008 0.058 20.16 28.08 7.92 8.607 45.726 0.033 0.054 19.55 27.75 8.20 9.225 45.513 0.133 0.051 18.82 27.58 8.76 9.972 45.789 0.265 0.047 17.63 27.47 9.84 12.285 46.652 0.398 0.042 17.40 27.50 10.11 12.948 46.899 0.531 0.041 17.24 27.52 10.29 13.449 47.089 0.663 0.040 17.03 27.53 10.50 14.123 47.381 0.796 0.039 16.92 27.56 10.64 14.500 47.527 0.929 0.038 16.45 27.66 11.22 16.125 48.263 1.061 0.037 16.35 27.71 11.36 16.528 48.415 1.194 0.036 16.24 27.73 11.49 16.993 48.601 1.327 0.036 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.008 Accepted refinement result: 21.14 28.46 7.32 8.127 45.900 0.008 0.058 Individual atomic B min max mean iso aniso Overall: 35.27 78.74 49.90 1.32 1542 0 Protein: 35.27 78.74 49.90 1.32 1542 0 Chain A: 35.27 74.47 47.68 N/A 771 0 Chain B: 36.64 78.74 52.11 N/A 771 0 Histogram: Values Number of atoms 35.27 - 39.62 185 39.62 - 43.97 265 43.97 - 48.31 229 48.31 - 52.66 275 52.66 - 57.01 301 57.01 - 61.35 148 61.35 - 65.70 86 65.70 - 70.05 24 70.05 - 74.40 19 74.40 - 78.74 10 =========================== Idealize ADP of riding H ========================== r_work=0.2114 r_free=0.2846 r_work=0.2109 r_free=0.2811 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.2109 r_free= 0.2811 coordinate error (max.-lik. estimate): 0.46 A | | | | normalized target function (ls_wunit_k1) (work): 0.058263 | | target function (ls_wunit_k1) not normalized (work): 114.952697 | | target function (ls_wunit_k1) not normalized (free): 22.939042 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2178 0.2109 0.2811 n_refl.: 2192 re-set all scales: r(all,work,free)=0.4483 0.4491 0.4488 n_refl.: 2192 remove outliers: r(all,work,free)=0.4483 0.4491 0.4488 n_refl.: 2192 overall B=1.58 to atoms: r(all,work,free)=0.4542 0.4552 0.4525 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2164 0.2098 0.2763 n_refl.: 2192 remove outliers: r(all,work,free)=0.2164 0.2098 0.2763 n_refl.: 2192 ======================== 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 46.133-10.115 85.45 84 10 0.1797 487.485 475.727 1.244 1.069 0.373 10.083-8.012 89.47 92 10 0.1990 324.595 318.230 1.174 1.048 0.374 8.010-6.369 93.43 180 19 0.2286 308.035 298.244 1.066 1.030 0.377 6.360-5.059 92.00 354 37 0.2065 301.672 286.784 0.948 1.007 0.375 5.057-4.020 93.48 707 82 0.2074 315.035 299.409 1.025 0.969 0.284 4.017-3.602 94.20 556 61 0.2194 228.848 208.835 1.057 0.935 0.263 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=7.0946 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.103864 wxc_scale = 0.027 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.042278 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 0.2302 0.2851 0.0549 0.002 0.4 1.6 1.4 3.2 0 0.006 0.2172 0.2776 0.0603 0.001 0.4 2.3 1.4 3.2 0 0.017 0.2089 0.2788 0.0699 0.002 0.4 2.3 1.4 3.2 0 0.034 0.2033 0.2762 0.0729 0.002 0.4 3.2 1.4 3.2 0 0.051 0.2006 0.2760 0.0754 0.002 0.4 2.9 0.9 3.8 0 0.068 0.1982 0.2770 0.0788 0.002 0.4 3.2 0.9 3.8 0 0.085 0.1959 0.2763 0.0803 0.002 0.5 2.9 0.9 3.8 0 0.102 0.1941 0.2780 0.0839 0.002 0.5 2.9 0.9 3.8 0 0.119 0.2018 0.2756 0.0738 0.002 0.4 3.6 1.4 3.2 0 0.057 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2018 0.2756 0.0738 0.002 0.4 3.6 1.4 3.2 0 0.057 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.18 27.56 7.38 7.148 56.243 0.042 5.638 20.70 28.10 7.40 7.194 57.433 0.001 5.657 18.89 27.38 8.48 7.279 57.038 0.005 5.572 17.37 27.10 9.74 8.777 57.253 0.021 5.488 17.06 27.12 10.07 9.504 57.391 0.042 5.467 16.79 27.11 10.32 10.281 57.713 0.063 5.449 16.60 27.09 10.49 10.939 57.966 0.085 5.436 16.48 27.10 10.62 11.459 58.155 0.106 5.428 16.39 27.11 10.72 11.894 58.309 0.127 5.421 16.33 27.11 10.79 12.248 58.432 0.148 5.416 16.28 27.11 10.84 12.549 58.535 0.169 5.413 16.24 27.12 10.88 12.794 58.618 0.190 5.410 16.17 27.13 10.96 13.274 58.773 0.211 5.405 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.001 Accepted refinement result: 20.70 28.10 7.40 7.194 57.433 0.001 5.657 Individual atomic B min max mean iso aniso Overall: 40.87 75.32 53.85 1.41 1542 0 Protein: 40.87 75.32 53.85 1.41 1542 0 Chain A: 40.87 71.05 52.31 N/A 771 0 Chain B: 44.28 75.32 55.40 N/A 771 0 Histogram: Values Number of atoms 40.87 - 44.32 6 44.32 - 47.76 122 47.76 - 51.21 357 51.21 - 54.65 466 54.65 - 58.10 316 58.10 - 61.54 175 61.54 - 64.99 60 64.99 - 68.43 16 68.43 - 71.88 18 71.88 - 75.32 6 =========================== Idealize ADP of riding H ========================== r_work=0.2070 r_free=0.2810 r_work=0.2077 r_free=0.2813 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.2077 r_free= 0.2813 coordinate error (max.-lik. estimate): 0.48 A | | | | normalized target function (ml) (work): 5.659582 | | target function (ml) not normalized (work): 11166.355696 | | target function (ml) not normalized (free): 1328.293027 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2151 0.2077 0.2813 n_refl.: 2192 re-set all scales: r(all,work,free)=0.4682 0.4686 0.4708 n_refl.: 2192 remove outliers: r(all,work,free)=0.4682 0.4686 0.4708 n_refl.: 2192 overall B=0.00 to atoms: r(all,work,free)=0.4682 0.4686 0.4708 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2131 0.2058 0.2788 n_refl.: 2192 remove outliers: r(all,work,free)=0.2131 0.2058 0.2788 n_refl.: 2192 ======================== 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 46.133-10.115 85.45 84 10 0.1846 487.485 470.635 1.111 1.134 0.371 10.083-8.012 89.47 92 10 0.2091 324.595 313.058 1.039 1.102 0.373 8.010-6.369 93.43 180 19 0.2389 308.035 292.481 0.966 1.072 0.374 6.360-5.059 92.00 354 37 0.2077 301.672 284.448 0.901 1.029 0.370 5.057-4.020 93.48 707 82 0.1989 315.035 301.659 1.045 0.960 0.293 4.017-3.602 94.20 556 61 0.2079 228.848 214.330 1.125 0.894 0.280 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=1.8772 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2058 r_free=0.2788 After: r_work=0.2058 r_free=0.2788 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.021375 wxc_scale = 0.031 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.036782 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 0.2065 0.2789 0.0725 0.002 0.4 3.6 1.4 3.2 0 0.006 0.2062 0.2788 0.0726 0.002 0.4 3.6 1.4 3.2 0 0.019 0.2060 0.2787 0.0726 0.002 0.4 3.6 1.4 3.2 0 0.038 0.2058 0.2788 0.0730 0.002 0.4 3.6 1.4 3.2 0 0.057 0.2056 0.2788 0.0732 0.002 0.4 3.6 1.4 3.2 0 0.075 0.2054 0.2789 0.0735 0.002 0.4 3.6 1.4 3.2 0 0.094 0.2052 0.2789 0.0738 0.002 0.4 3.6 1.4 3.2 0 0.113 0.2046 0.2788 0.0742 0.003 0.4 3.6 1.4 3.2 0 0.132 0.2058 0.2788 0.0730 0.002 0.4 3.6 1.4 3.2 0 0.063 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2060 0.2787 0.0726 0.002 0.4 3.6 1.4 3.2 0 0.038 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.60 27.87 7.26 7.692 59.233 0.037 5.655 20.55 27.76 7.21 7.822 59.290 0.001 5.653 19.68 27.71 8.03 7.997 59.276 0.005 5.610 17.64 26.69 9.05 9.175 60.427 0.018 5.501 17.29 26.83 9.53 9.853 60.480 0.037 5.479 17.02 26.73 9.72 10.573 60.754 0.055 5.461 16.82 26.65 9.83 11.203 61.002 0.074 5.447 16.68 26.63 9.95 11.723 61.196 0.092 5.438 16.58 26.61 10.03 12.147 61.349 0.110 5.431 16.50 26.59 10.09 12.504 61.474 0.129 5.426 16.44 26.59 10.14 12.838 61.592 0.147 5.422 16.39 26.57 10.19 13.138 61.698 0.166 5.418 16.36 26.56 10.20 13.326 61.763 0.184 5.416 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.001 Accepted refinement result: 20.55 27.76 7.21 7.822 59.290 0.001 5.653 Individual atomic B min max mean iso aniso Overall: 44.78 71.99 53.97 0.71 1542 0 Protein: 44.78 71.99 53.97 0.71 1542 0 Chain A: 44.78 66.05 52.47 N/A 771 0 Chain B: 47.78 71.99 55.46 N/A 771 0 Histogram: Values Number of atoms 44.78 - 47.50 45 47.50 - 50.22 278 50.22 - 52.94 359 52.94 - 55.66 415 55.66 - 58.38 205 58.38 - 61.11 146 61.11 - 63.83 57 63.83 - 66.55 17 66.55 - 69.27 8 69.27 - 71.99 12 =========================== Idealize ADP of riding H ========================== r_work=0.2055 r_free=0.2776 r_work=0.2054 r_free=0.2777 ----------X-ray data---------- |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.2054 r_free= 0.2777 coordinate error (max.-lik. estimate): 0.48 A | | | | normalized target function (ml) (work): 5.653271 | | target function (ml) not normalized (work): 11153.904520 | | target function (ml) not normalized (free): 1328.595707 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 46.13 - 4.54 0.92 980 109 0.2033 0.2858 5.7464 6.1322| | 2: 4.53 - 3.60 0.94 993 110 0.2079 0.2681 5.5613 6.0017| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 46.13 - 4.54 980 109 0.88 18.91 1.00 1.05 15115.34| | 2: 4.53 - 3.60 993 110 0.91 16.81 1.00 1.03 9112.98| |alpha: min = 0.96 max = 1.08 mean = 1.04| |beta: min = 6677.69 max = 20277.86 mean = 12094.38| |figures of merit: min = 0.00 max = 1.00 mean = 0.89| |phase err.(work): min = 0.00 max = 90.00 mean = 17.85| |phase err.(test): min = 0.00 max = 78.18 mean = 16.97| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2127 0.2054 0.2777 n_refl.: 2192 re-set all scales: r(all,work,free)=0.4691 0.4694 0.4716 n_refl.: 2192 remove outliers: r(all,work,free)=0.4691 0.4694 0.4716 n_refl.: 2192 overall B=0.00 to atoms: r(all,work,free)=0.4691 0.4694 0.4716 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2126 0.2053 0.2786 n_refl.: 2192 remove outliers: r(all,work,free)=0.2126 0.2053 0.2786 n_refl.: 2192 ======================== 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 46.133-10.115 85.45 84 10 0.1820 487.485 475.032 1.154 1.135 0.376 10.083-8.012 89.47 92 10 0.2100 324.595 314.401 1.074 1.103 0.380 8.010-6.369 93.43 180 19 0.2359 308.035 294.310 0.995 1.072 0.380 6.360-5.059 92.00 354 37 0.2075 301.672 285.373 0.916 1.029 0.370 5.057-4.020 93.48 707 82 0.1991 315.035 300.529 1.052 0.959 0.270 4.017-3.602 94.20 556 61 0.2066 228.848 212.114 1.135 0.893 0.270 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=3.6094 ================= 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 : 0.4859 0.4533 0.005 1.074 42.4 96.6 61.7 0 0.000 1_bss: 0.2035 0.2627 0.005 1.074 29.5 83.7 48.9 0 0.000 1_settarget: 0.2035 0.2627 0.005 1.074 29.5 83.7 48.9 0 0.000 1_weight: 0.2035 0.2627 0.005 1.074 29.5 83.7 48.9 0 0.000 1_xyzrec: 0.2087 0.2784 0.002 0.421 29.5 83.7 48.9 0 0.148 1_adp: 0.2114 0.2846 0.002 0.421 35.3 78.7 49.9 0 0.148 1_regHadp: 0.2109 0.2811 0.002 0.421 35.3 78.7 49.9 0 0.148 2_bss: 0.2098 0.2763 0.002 0.421 36.8 80.3 51.5 0 0.148 2_settarget: 0.2098 0.2763 0.002 0.421 36.8 80.3 51.5 0 0.148 2_updatecdl: 0.2098 0.2763 0.002 0.484 36.8 80.3 51.5 0 0.148 2_weight: 0.2098 0.2763 0.002 0.484 36.8 80.3 51.5 0 0.148 2_xyzrec: 0.2018 0.2756 0.002 0.402 36.8 80.3 51.5 0 0.195 2_adp: 0.2070 0.2810 0.002 0.402 40.9 75.3 53.9 0 0.195 2_regHadp: 0.2077 0.2813 0.002 0.402 40.9 75.3 53.9 0 0.195 3_bss: 0.2058 0.2788 0.002 0.402 40.9 75.3 53.9 0 0.195 3_settarget: 0.2058 0.2788 0.002 0.402 40.9 75.3 53.9 0 0.195 3_updatecdl: 0.2058 0.2788 0.002 0.457 40.9 75.3 53.9 0 0.195 3_setrh: 0.2058 0.2788 0.002 0.457 40.9 75.3 53.9 0 0.195 3_weight: 0.2058 0.2788 0.002 0.457 40.9 75.3 53.9 0 0.195 3_xyzrec: 0.2060 0.2787 0.002 0.417 40.9 75.3 53.9 0 0.195 3_adp: 0.2055 0.2776 0.002 0.417 44.8 72.0 54.0 0 0.195 3_regHadp: 0.2054 0.2777 0.002 0.417 44.8 72.0 54.0 0 0.195 end: 0.2053 0.2786 0.002 0.417 44.8 72.0 54.0 0 0.195 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/4xcr_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/4xcr_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3000 Refinement macro-cycles (run) : 92.9000 Write final files (write_after_run_outputs) : 13.4400 Total : 109.6400 Total CPU time: 2.11 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:22:21 PDT -0700 (1716250941.99 s) Start R-work = 0.2035, R-free = 0.2627 Final R-work = 0.2053, R-free = 0.2786 =============================================================================== Job complete usr+sys time: 134.39 seconds wall clock time: 6 minutes 22.27 seconds (382.27 seconds total)