Starting phenix.refine on Mon May 20 17:17:06 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4iy2.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4iy2/4iy2.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=True secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4iy2/4iy2.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4iy2/4iy2.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4iy2.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4iy2.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 { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { 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 "A PHE 560": "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: 4856 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2428 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 144} Chain: "C" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2428 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 144} Time building chain proxies: 1.66, per 1000 atoms: 0.34 Number of scatterers: 4856 At special positions: 0 Unit cell: (102.513, 104.593, 105.694, 90, 90, 90) Space group: I 21 21 21 (No. 24) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Se 12 33.99 S 4 16.00 O 482 8.00 N 382 7.00 C 1558 6.00 H 2418 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: 2.53 Conformation dependent library (CDL) restraints added in 560.0 milliseconds 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 576 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.19: 2414 1.19 - 1.39: 976 1.39 - 1.60: 1480 1.60 - 1.81: 3 1.81 - 2.02: 25 Bond restraints: 4898 Sorted by residual: bond pdb=" N VAL C 572 " pdb=" H VAL C 572 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N MSE A 470 " pdb=" H MSE A 470 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N CYS A 456 " pdb=" H CYS A 456 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N VAL A 449 " pdb=" H VAL A 449 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" ND2 ASN C 468 " pdb="HD21 ASN C 468 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 4893 not shown) Histogram of bond angle deviations from ideal: 96.68 - 103.60: 39 103.60 - 110.52: 4917 110.52 - 117.44: 1798 117.44 - 124.36: 2024 124.36 - 131.29: 120 Bond angle restraints: 8898 Sorted by residual: angle pdb=" C HIS A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta sigma weight residual 119.76 125.62 -5.86 1.03e+00 9.43e-01 3.23e+01 angle pdb=" C HIS C 520 " pdb=" N PRO C 521 " pdb=" CA PRO C 521 " ideal model delta sigma weight residual 119.78 124.36 -4.58 1.03e+00 9.43e-01 1.98e+01 angle pdb=" C ASP A 558 " pdb=" N PRO A 559 " pdb=" CA PRO A 559 " ideal model delta sigma weight residual 119.76 123.72 -3.96 1.00e+00 1.00e+00 1.57e+01 angle pdb=" C VAL C 497 " pdb=" N LYS C 498 " pdb=" CA LYS C 498 " ideal model delta sigma weight residual 120.38 125.51 -5.13 1.37e+00 5.33e-01 1.40e+01 angle pdb=" N ASP A 493 " pdb=" CA ASP A 493 " pdb=" C ASP A 493 " ideal model delta sigma weight residual 108.74 113.88 -5.14 1.38e+00 5.25e-01 1.39e+01 ... (remaining 8893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 2041 16.89 - 33.77: 153 33.77 - 50.65: 67 50.65 - 67.54: 24 67.54 - 84.42: 3 Dihedral angle restraints: 2288 sinusoidal: 1262 harmonic: 1026 Sorted by residual: dihedral pdb=" C VAL C 572 " pdb=" N VAL C 572 " pdb=" CA VAL C 572 " pdb=" CB VAL C 572 " ideal model delta harmonic sigma weight residual -122.00 -129.82 7.82 0 2.50e+00 1.60e-01 9.78e+00 dihedral pdb=" C VAL A 572 " pdb=" N VAL A 572 " pdb=" CA VAL A 572 " pdb=" CB VAL A 572 " ideal model delta harmonic sigma weight residual -122.00 -129.79 7.79 0 2.50e+00 1.60e-01 9.71e+00 dihedral pdb=" CB GLU C 574 " pdb=" CG GLU C 574 " pdb=" CD GLU C 574 " pdb=" OE1 GLU C 574 " ideal model delta sinusoidal sigma weight residual 0.00 -84.42 84.42 1 3.00e+01 1.11e-03 9.63e+00 ... (remaining 2285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 198 0.044 - 0.088: 121 0.088 - 0.132: 47 0.132 - 0.176: 17 0.176 - 0.220: 7 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA GLU C 556 " pdb=" N GLU C 556 " pdb=" C GLU C 556 " pdb=" CB GLU C 556 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLU A 556 " pdb=" N GLU A 556 " pdb=" C GLU A 556 " pdb=" CB GLU A 556 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE A 573 " pdb=" N ILE A 573 " pdb=" C ILE A 573 " pdb=" CB ILE A 573 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 387 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 523 " 0.023 2.00e-02 2.50e+03 1.27e-02 3.64e+00 pdb=" CG HIS A 523 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS A 523 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 HIS A 523 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS A 523 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 523 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 HIS A 523 " -0.013 2.00e-02 2.50e+03 pdb=" HE1 HIS A 523 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 HIS A 523 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 538 " 0.004 2.00e-02 2.50e+03 7.38e-03 1.63e+00 pdb=" CG PHE A 538 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE A 538 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 538 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 538 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 538 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 538 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 538 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 PHE A 538 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 538 " -0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE A 538 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 538 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 467 " -0.012 2.00e-02 2.50e+03 7.27e-03 1.59e+00 pdb=" CG PHE A 467 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE A 467 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 467 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 467 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 467 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 467 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 467 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE A 467 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 467 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 467 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 467 " -0.001 2.00e-02 2.50e+03 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.03: 257 2.03 - 2.72: 7497 2.72 - 3.41: 16347 3.41 - 4.11: 22074 4.11 - 4.80: 34986 Nonbonded interactions: 81161 Sorted by model distance: nonbonded pdb=" HA ASP A 504 " pdb=" HE2 PHE C 467 " model vdw 1.334 2.270 nonbonded pdb=" HE2 PHE A 467 " pdb=" HA ASP C 504 " model vdw 1.337 2.270 nonbonded pdb=" O GLU C 485 " pdb="HD22 ASN C 490 " model vdw 1.340 1.850 nonbonded pdb=" O GLU A 485 " pdb="HD22 ASN A 490 " model vdw 1.343 1.850 nonbonded pdb="HH22 ARG A 550 " pdb=" OE1 GLU A 554 " model vdw 1.350 1.850 ... (remaining 81156 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 Se 12 33.79 1 S 4 15.91 1 O 482 7.97 1 N 382 6.97 1 C 1558 5.97 1 H 2418 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: 2418 of 4856 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 4856 n_use_u_iso = 4856 n_use_u_aniso = 0 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 = 4856 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4856 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4856 aniso = 0) 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 { ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "4iy2_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2418 occupancy sum: 2418.00 (% of total atoms 49.89) Rotatable: count: 714 occupancy sum: 714.00 (% of total atoms 14.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.60 - 42.85 A, n_refl.=6670 (all), 4.74 % free)-------------| | | | r_work= 0.6305 r_free= 0.6362 coordinate error (max.-lik. estimate): 0.17 A | | | | normalized target function (ml) (work): 6.476566 | | target function (ml) not normalized (work): 41152.101576 | | target function (ml) not normalized (free): 2067.378995 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 42.85 - 4.54 1.00 3313 159 0.5995 0.6281 7.0436 7.1411| | 2: 4.54 - 3.60 0.95 3041 157 0.6997 0.6514 5.8588 5.936| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 42.85 - 4.54 3313 159 0.29 67.64 0.94 0.33 277885.05| | 2: 4.54 - 3.60 3041 157 0.70 35.82 3.03 0.97 23390.81| |alpha: min = 0.33 max = 0.97 mean = 0.63| |beta: min = 23390.81 max = 277885.05 mean = 156085.09| |figures of merit: min = 0.00 max = 1.00 mean = 0.48| |phase err.(work): min = 0.00 max = 89.99 mean = 52.41| |phase err.(test): min = 0.00 max = 89.77 mean = 51.68| |-----------------------------------------------------------------------------| ----------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 : 0.008 0.080 2480 Z= 0.422 Angle : 1.169 6.740 3354 Z= 0.826 Chirality : 0.068 0.220 390 Planarity : 0.002 0.016 436 Dihedral : 15.008 84.424 936 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.76 % Allowed : 5.40 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -0.97 (0.44), residues: 300 helix: -1.35 (0.39), residues: 120 sheet: -2.25 (0.57), residues: 36 loop : 0.76 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 454 TYR 0.007 0.001 TYR A 518 PHE 0.016 0.003 PHE A 467 HIS 0.006 0.002 HIS A 523 Individual atomic B min max mean iso aniso Overall: 80.79 182.44 119.09 7.70 2438 0 Protein: 80.79 182.44 119.09 7.70 2438 0 Chain A: 85.18 181.31 119.19 N/A 1219 0 Chain C: 80.79 182.44 119.00 N/A 1219 0 Histogram: Values Number of atoms 80.79 - 90.96 131 90.96 - 101.12 407 101.12 - 111.28 688 111.28 - 121.45 445 121.45 - 131.62 247 131.62 - 141.78 122 141.78 - 151.94 59 151.94 - 162.11 62 162.11 - 172.27 71 172.27 - 182.44 206 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.60 - 42.85 A, n_refl.=6670 (all), 4.74 % free)-------------| | | | r_work= 0.6305 r_free= 0.6362 coordinate error (max.-lik. estimate): 0.17 A | | | | normalized target function (ml) (work): 6.476566 | | target function (ml) not normalized (work): 41152.101576 | | target function (ml) not normalized (free): 2067.378995 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.6313 0.6305 0.6362 n_refl.: 6670 re-set all scales: r(all,work,free)=0.6313 0.6305 0.6362 n_refl.: 6670 remove outliers: r(all,work,free)=0.6040 0.6042 0.5817 n_refl.: 6654 overall B=-14.21 to atoms: r(all,work,free)=0.5615 0.5617 0.5404 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2925 0.2929 0.2829 n_refl.: 6654 remove outliers: r(all,work,free)=0.2925 0.2929 0.2829 n_refl.: 6654 ======================== 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 36.793-15.524 96.91 93 1 0.5073 3051.792 2508.221 1.225 0.998 0.351 15.485-12.238 97.00 96 1 0.2476 3058.961 3020.909 1.312 1.001 0.336 12.212-9.617 100.00 192 10 0.2091 3276.350 3135.582 1.304 1.002 0.299 9.605-7.558 100.00 374 15 0.2628 2059.388 1987.213 1.306 0.995 0.295 7.551-5.945 99.50 761 39 0.3183 1127.282 1051.045 1.060 0.987 0.250 5.945-4.677 99.31 1515 77 0.2774 988.552 902.197 0.990 0.970 0.183 4.676-3.603 95.60 3309 171 0.3058 695.546 649.590 1.087 0.946 0.112 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.7331 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 11.700662 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.160797 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 0.2664 0.2975 0.0311 0.015 1.3 12.4 0.0 5.8 0 5.850 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 26.64 29.75 3.11 5.478 103.625 0.161 0.087 26.70 29.62 2.92 5.086 104.039 0.005 0.087 26.49 29.47 2.98 5.115 104.064 0.020 0.086 25.76 28.92 3.17 6.222 104.716 0.080 0.082 24.93 28.68 3.75 8.609 105.122 0.161 0.079 24.83 28.73 3.90 8.550 104.879 0.241 0.078 24.82 28.76 3.94 8.548 104.775 0.322 0.078 24.57 28.64 4.07 9.664 105.238 0.402 0.077 24.49 28.62 4.13 10.005 105.357 0.482 0.077 24.45 28.60 4.16 10.197 105.393 0.563 0.076 24.41 28.58 4.17 10.391 105.438 0.643 0.076 24.18 28.68 4.50 11.997 106.095 0.724 0.075 24.07 28.75 4.68 13.119 106.515 0.804 0.075 max suggested for this run: 20.73 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.643 Accepted refinement result: 24.41 28.58 4.17 10.391 105.438 0.643 0.076 Individual atomic B min max mean iso aniso Overall: 62.09 238.39 108.49 11.31 2438 0 Protein: 62.09 238.39 108.49 11.31 2438 0 Chain A: 65.97 233.74 108.63 N/A 1219 0 Chain C: 62.09 238.39 108.35 N/A 1219 0 Histogram: Values Number of atoms 62.09 - 79.72 155 79.72 - 97.35 832 97.35 - 114.98 756 114.98 - 132.61 288 132.61 - 150.24 133 150.24 - 167.87 208 167.87 - 185.50 61 185.50 - 203.13 3 203.13 - 220.76 0 220.76 - 238.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.2441 r_free=0.2858 r_work=0.2426 r_free=0.2833 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.60 - 36.79 A, n_refl.=6654 (all), 4.72 % free)-------------| | | | r_work= 0.2426 r_free= 0.2833 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ls_wunit_k1) (work): 0.075330 | | target function (ls_wunit_k1) not normalized (work): 477.589655 | | target function (ls_wunit_k1) not normalized (free): 26.294693 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2445 0.2426 0.2833 n_refl.: 6654 re-set all scales: r(all,work,free)=0.5491 0.5489 0.5384 n_refl.: 6654 remove outliers: r(all,work,free)=0.5491 0.5489 0.5384 n_refl.: 6654 overall B=0.00 to atoms: r(all,work,free)=0.5491 0.5489 0.5384 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2414 0.2394 0.2843 n_refl.: 6654 remove outliers: r(all,work,free)=0.2414 0.2394 0.2843 n_refl.: 6654 ======================== 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 36.793-15.524 96.91 93 1 0.4406 1151.171 988.454 1.249 1.063 0.358 15.485-12.238 97.00 96 1 0.1978 1153.875 1183.420 1.272 1.059 0.340 12.212-9.617 100.00 192 10 0.1469 1235.877 1194.682 1.225 1.051 0.300 9.605-7.558 100.00 374 15 0.1852 776.825 777.965 1.268 1.032 0.290 7.551-5.945 99.50 761 39 0.2496 425.224 407.786 1.028 1.002 0.240 5.945-4.677 99.31 1515 77 0.2201 372.893 357.775 1.013 0.951 0.170 4.676-3.603 95.60 3309 171 0.2713 262.368 249.612 1.225 0.870 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=1.2422 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.920391 wxc_scale = 0.068 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.046963 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 0.2580 0.2854 0.0274 0.002 0.5 3.1 0.0 4.3 0 0.027 0.2538 0.2878 0.0341 0.003 0.5 3.5 0.0 4.0 0 0.080 0.2497 0.2887 0.0390 0.003 0.5 3.7 0.0 4.0 0 0.160 0.2458 0.2916 0.0458 0.004 0.6 5.2 0.0 3.6 0 0.240 0.2432 0.2902 0.0469 0.005 0.6 6.4 0.0 4.0 0 0.320 0.2410 0.2908 0.0498 0.006 0.7 7.6 0.0 5.0 0 0.400 0.2401 0.2906 0.0505 0.006 0.7 7.8 0.0 5.0 0 0.480 0.2389 0.2913 0.0525 0.007 0.8 10.7 0.0 5.4 0 0.560 0.2443 0.2909 0.0466 0.004 0.6 5.4 0.0 3.6 0 0.267 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2580 0.2854 0.0274 0.002 0.5 3.1 0.0 4.3 0 0.027 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.80 28.54 2.74 17.294 117.886 0.047 6.209 29.72 30.49 0.76 15.011 125.275 0.001 6.273 28.79 29.58 0.79 14.514 124.199 0.006 6.247 26.71 27.97 1.25 15.686 122.894 0.023 6.182 25.32 27.50 2.17 16.971 121.504 0.047 6.150 24.87 27.47 2.60 18.025 121.521 0.070 6.139 24.69 27.50 2.82 18.260 121.027 0.094 6.139 24.56 27.49 2.92 18.730 121.139 0.117 6.136 24.49 27.55 3.06 19.035 121.192 0.141 6.134 24.43 27.55 3.11 19.383 121.331 0.164 6.133 24.39 27.57 3.19 19.696 121.460 0.188 6.131 24.34 27.56 3.22 20.184 121.718 0.211 6.129 24.33 27.57 3.24 20.165 121.643 0.235 6.130 max suggested for this run: 23.58 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.070 Accepted refinement result: 24.87 27.47 2.60 18.025 121.521 0.070 6.139 Individual atomic B min max mean iso aniso Overall: 60.26 260.99 115.73 16.60 2438 0 Protein: 60.26 260.99 115.73 16.60 2438 0 Chain A: 60.99 258.70 115.73 N/A 1219 0 Chain C: 60.26 260.99 115.73 N/A 1219 0 Histogram: Values Number of atoms 60.26 - 80.33 125 80.33 - 100.40 696 100.40 - 120.48 767 120.48 - 140.55 376 140.55 - 160.62 274 160.62 - 180.70 151 180.70 - 200.77 41 200.77 - 220.84 6 220.84 - 240.91 0 240.91 - 260.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.2487 r_free=0.2747 r_work=0.2488 r_free=0.2735 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.60 - 36.79 A, n_refl.=6654 (all), 4.72 % free)-------------| | | | r_work= 0.2488 r_free= 0.2735 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 6.134638 | | target function (ml) not normalized (work): 38893.605959 | | target function (ml) not normalized (free): 1944.819749 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2499 0.2488 0.2735 n_refl.: 6654 re-set all scales: r(all,work,free)=0.5740 0.5744 0.5471 n_refl.: 6654 remove outliers: r(all,work,free)=0.5740 0.5744 0.5471 n_refl.: 6654 overall B=-10.22 to atoms: r(all,work,free)=0.5415 0.5418 0.5159 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2522 0.2510 0.2794 n_refl.: 6654 remove outliers: r(all,work,free)=0.2522 0.2510 0.2794 n_refl.: 6654 ======================== 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 36.793-15.524 96.91 93 1 0.4485 1151.171 1091.672 1.550 0.972 0.355 15.485-12.238 97.00 96 1 0.2237 1153.875 1121.257 1.306 0.977 0.329 12.212-9.617 100.00 192 10 0.1671 1235.877 1183.941 1.341 0.980 0.311 9.605-7.558 100.00 374 15 0.2288 776.825 747.904 1.317 0.979 0.301 7.551-5.945 99.50 761 39 0.2876 425.224 396.332 1.051 0.979 0.244 5.945-4.677 99.31 1515 77 0.2447 372.893 346.501 0.957 0.976 0.165 4.676-3.603 95.60 3309 171 0.2504 262.368 251.370 1.037 0.975 0.094 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.8316 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2510 r_free=0.2794 After: r_work=0.2510 r_free=0.2794 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.557947 wxc_scale = 0.025 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.045613 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 0.2511 0.2798 0.0287 0.002 0.5 3.1 0.0 4.3 0 0.009 0.2510 0.2797 0.0286 0.002 0.5 3.1 0.0 4.3 0 0.026 0.2509 0.2796 0.0286 0.002 0.5 3.1 0.0 4.3 0 0.052 0.2508 0.2796 0.0287 0.002 0.5 3.1 0.0 4.3 0 0.079 0.2506 0.2795 0.0289 0.002 0.5 3.1 0.0 4.3 0 0.105 0.2505 0.2794 0.0289 0.002 0.5 3.1 0.0 4.3 0 0.131 0.2503 0.2794 0.0291 0.002 0.5 3.1 0.0 4.3 0 0.157 0.2501 0.2793 0.0292 0.003 0.5 3.1 0.0 4.3 0 0.183 0.2508 0.2796 0.0288 0.002 0.5 3.1 0.0 4.3 0 0.087 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2505 0.2794 0.0289 0.002 0.5 3.1 0.0 4.3 0 0.131 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.05 27.94 2.89 20.147 115.407 0.046 6.155 29.10 29.44 0.34 16.564 123.122 0.001 6.253 28.16 28.79 0.63 16.086 121.630 0.006 6.235 26.77 28.10 1.33 16.523 119.686 0.023 6.201 25.47 27.56 2.10 17.164 118.496 0.046 6.167 24.59 27.41 2.82 17.930 118.251 0.068 6.142 24.16 27.45 3.29 18.975 118.532 0.091 6.127 24.16 27.55 3.39 19.638 117.187 0.114 6.128 24.07 27.58 3.51 20.041 117.253 0.137 6.125 24.01 27.61 3.60 20.365 117.327 0.160 6.122 23.83 27.59 3.76 20.966 117.920 0.182 6.117 23.79 27.60 3.82 21.290 118.049 0.205 6.116 23.77 27.63 3.86 21.532 118.121 0.228 6.115 max suggested for this run: 23.08 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.068 Accepted refinement result: 24.59 27.41 2.82 17.930 118.251 0.068 6.142 Individual atomic B min max mean iso aniso Overall: 45.04 256.15 111.18 15.48 2438 0 Protein: 45.04 256.15 111.18 15.48 2438 0 Chain A: 54.04 246.68 111.26 N/A 1219 0 Chain C: 45.04 256.15 111.09 N/A 1219 0 Histogram: Values Number of atoms 45.04 - 66.15 31 66.15 - 87.26 359 87.26 - 108.37 948 108.37 - 129.49 582 129.49 - 150.60 284 150.60 - 171.71 141 171.71 - 192.82 80 192.82 - 213.93 11 213.93 - 235.04 0 235.04 - 256.15 2 =========================== Idealize ADP of riding H ========================== r_work=0.2459 r_free=0.2741 r_work=0.2459 r_free=0.2746 ----------X-ray data---------- |--(resolution: 3.60 - 36.79 A, n_refl.=6654 (all), 4.72 % free)-------------| | | | r_work= 0.2459 r_free= 0.2746 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 6.143691 | | target function (ml) not normalized (work): 38951.000419 | | target function (ml) not normalized (free): 1947.588940 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 36.79 - 4.54 0.99 3304 158 0.2444 0.2705 6.5177 6.5266| | 2: 4.54 - 3.60 0.95 3036 156 0.2493 0.2826 5.7367 5.8742| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 36.79 - 4.54 3304 158 0.75 30.19 0.99 1.01 69056.67| | 2: 4.54 - 3.60 3036 156 0.79 28.11 1.05 0.98 18640.17| |alpha: min = 0.98 max = 1.01 mean = 1.00| |beta: min = 18640.17 max = 69056.67 mean = 44914.00| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 89.97 mean = 29.20| |phase err.(test): min = 0.00 max = 89.56 mean = 29.20| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2472 0.2459 0.2746 n_refl.: 6654 re-set all scales: r(all,work,free)=0.5617 0.5620 0.5389 n_refl.: 6654 remove outliers: r(all,work,free)=0.5617 0.5620 0.5389 n_refl.: 6654 overall B=-6.05 to atoms: r(all,work,free)=0.5424 0.5427 0.5207 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2470 0.2455 0.2786 n_refl.: 6654 remove outliers: r(all,work,free)=0.2470 0.2455 0.2786 n_refl.: 6654 ======================== 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 36.793-15.524 96.91 93 1 0.4468 1151.171 1089.210 1.546 0.975 0.354 15.485-12.238 97.00 96 1 0.2223 1153.875 1103.123 1.299 0.981 0.333 12.212-9.617 100.00 192 10 0.1618 1235.877 1188.958 1.375 0.983 0.319 9.605-7.558 100.00 374 15 0.2220 776.825 750.190 1.334 0.982 0.307 7.551-5.945 99.50 761 39 0.2729 425.224 399.661 1.050 0.982 0.238 5.945-4.677 99.31 1515 77 0.2335 372.893 350.222 0.967 0.978 0.169 4.676-3.603 95.60 3309 171 0.2517 262.368 252.789 1.062 0.977 0.110 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.4964 ================= 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 : 0.6305 0.6362 0.008 1.169 80.8 182.4 119.1 0 0.000 1_bss: 0.2929 0.2829 0.008 1.169 66.6 168.2 104.9 0 0.000 1_settarget: 0.2929 0.2829 0.008 1.169 66.6 168.2 104.9 0 0.000 1_updatephipsi: 0.2929 0.2829 0.008 1.169 66.6 168.2 104.9 0 0.000 1_weight: 0.2929 0.2829 0.008 1.169 66.6 168.2 104.9 0 0.000 1_xyzrec: 0.2664 0.2975 0.015 1.304 66.6 168.2 104.9 0 0.283 1_adp: 0.2441 0.2858 0.015 1.304 62.1 238.4 108.5 0 0.283 1_regHadp: 0.2426 0.2833 0.015 1.304 62.1 238.4 108.5 0 0.283 2_bss: 0.2394 0.2843 0.015 1.304 62.1 238.4 108.5 0 0.283 2_settarget: 0.2394 0.2843 0.015 1.304 62.1 238.4 108.5 0 0.283 2_updatephipsi: 0.2394 0.2843 0.015 1.304 62.1 238.4 108.5 0 0.283 2_updatecdl: 0.2394 0.2843 0.015 1.332 62.1 238.4 108.5 0 0.283 2_weight: 0.2394 0.2843 0.015 1.332 62.1 238.4 108.5 0 0.283 2_xyzrec: 0.2580 0.2854 0.002 0.480 62.1 238.4 108.5 0 0.257 2_adp: 0.2487 0.2747 0.002 0.480 60.3 261.0 115.7 0 0.257 2_regHadp: 0.2488 0.2735 0.002 0.480 60.3 261.0 115.7 0 0.257 3_bss: 0.2510 0.2794 0.002 0.480 50.0 250.8 105.5 0 0.257 3_settarget: 0.2510 0.2794 0.002 0.480 50.0 250.8 105.5 0 0.257 3_updatephipsi: 0.2510 0.2794 0.002 0.480 50.0 250.8 105.5 0 0.257 3_updatecdl: 0.2510 0.2794 0.002 0.517 50.0 250.8 105.5 0 0.257 3_setrh: 0.2510 0.2794 0.002 0.517 50.0 250.8 105.5 0 0.257 3_weight: 0.2510 0.2794 0.002 0.517 50.0 250.8 105.5 0 0.257 3_xyzrec: 0.2505 0.2794 0.002 0.481 50.0 250.8 105.5 0 0.257 3_adp: 0.2459 0.2741 0.002 0.481 45.0 256.2 111.2 0 0.257 3_regHadp: 0.2459 0.2746 0.002 0.481 45.0 256.2 111.2 0 0.257 end: 0.2455 0.2786 0.002 0.481 39.0 250.1 105.1 0 0.257 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/4iy2_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/4iy2_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.1600 Refinement macro-cycles (run) : 197.0200 Write final files (write_after_run_outputs) : 19.5600 Total : 223.7400 Total CPU time: 4.28 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:30:38 PDT -0700 (1716251438.36 s) Start R-work = 0.2929, R-free = 0.2829 Final R-work = 0.2455, R-free = 0.2786 =============================================================================== Job complete usr+sys time: 273.73 seconds wall clock time: 14 minutes 5.37 seconds (845.37 seconds total)