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/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=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/4iy2.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4iy2.pdb" 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" } 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 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: 0.98, per 1000 atoms: 0.20 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: 1.04 Conformation dependent library (CDL) restraints added in 204.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 576 Time building geometry restraints manager: 1.22 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 { 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 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 11.769747 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 0.2657 0.2972 0.0316 0.015 1.3 14.0 1.0 6.1 0 5.885 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 26.57 29.72 3.16 5.478 103.625 0.161 0.086 26.63 29.62 3.00 5.086 104.039 0.005 0.086 26.42 29.48 3.06 5.110 104.065 0.020 0.085 25.69 28.93 3.24 6.209 104.728 0.080 0.081 24.86 28.72 3.87 8.491 105.087 0.161 0.078 24.77 28.69 3.92 8.400 104.844 0.241 0.077 24.69 28.66 3.96 8.630 104.858 0.322 0.077 24.53 28.61 4.08 9.284 105.094 0.402 0.076 24.38 28.57 4.19 10.074 105.402 0.482 0.076 24.34 28.57 4.23 10.298 105.451 0.563 0.075 24.34 28.57 4.24 10.286 105.407 0.643 0.076 23.98 28.56 4.58 12.989 106.501 0.724 0.074 23.97 28.63 4.66 13.184 106.539 0.804 0.074 max suggested for this run: 20.73 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.724 Accepted refinement result: 23.98 28.56 4.58 12.989 106.501 0.724 0.074 Individual atomic B min max mean iso aniso Overall: 61.58 252.75 110.61 13.28 2438 0 Protein: 61.58 252.75 110.61 13.28 2438 0 Chain A: 65.97 252.75 110.82 N/A 1219 0 Chain C: 61.58 244.03 110.40 N/A 1219 0 Histogram: Values Number of atoms 61.58 - 80.70 163 80.70 - 99.81 845 99.81 - 118.93 745 118.93 - 138.05 295 138.05 - 157.16 146 157.16 - 176.28 199 176.28 - 195.40 40 195.40 - 214.52 3 214.52 - 233.63 0 233.63 - 252.75 2 =========================== Idealize ADP of riding H ========================== r_work=0.2398 r_free=0.2856 r_work=0.2384 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= 0.2384 r_free= 0.2833 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.072978 | | target function (ls_wunit_k1) not normalized (work): 462.678468 | | target function (ls_wunit_k1) not normalized (free): 26.209352 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2405 0.2384 0.2833 n_refl.: 6654 re-set all scales: r(all,work,free)=0.5538 0.5537 0.5409 n_refl.: 6654 remove outliers: r(all,work,free)=0.5538 0.5537 0.5409 n_refl.: 6654 overall B=-6.01 to atoms: r(all,work,free)=0.5347 0.5345 0.5233 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2382 0.2360 0.2842 n_refl.: 6654 remove outliers: r(all,work,free)=0.2382 0.2360 0.2842 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 0.4337 1138.032 972.682 1.336 1.013 0.359 15.485-12.238 97.00 96 1 0.1926 1140.705 1162.388 1.341 1.014 0.343 12.212-9.617 100.00 192 10 0.1450 1221.771 1179.513 1.281 1.013 0.298 9.605-7.558 100.00 374 15 0.1762 767.958 767.481 1.296 1.007 0.286 7.551-5.945 99.50 761 39 0.2449 420.370 404.007 1.039 0.999 0.248 5.945-4.677 99.31 1515 77 0.2163 368.637 355.140 0.967 0.983 0.180 4.676-3.603 95.60 3309 171 0.2709 259.373 250.644 1.080 0.961 0.088 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.4779 ============================ 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 = 3.928973 wxc_scale = 0.057 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.049831 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 0.2541 0.2865 0.0325 0.002 0.5 2.5 0.0 4.3 0 0.022 0.2511 0.2869 0.0358 0.003 0.5 2.5 0.0 4.0 0 0.067 0.2465 0.2881 0.0416 0.003 0.5 3.3 0.0 4.3 0 0.134 0.2451 0.2883 0.0433 0.004 0.6 3.5 0.3 4.3 0 0.201 0.2425 0.2903 0.0478 0.004 0.6 4.9 0.7 4.3 0 0.269 0.2401 0.2899 0.0497 0.005 0.7 7.0 0.7 4.7 0 0.336 0.2390 0.2899 0.0510 0.006 0.7 7.6 0.7 4.7 0 0.403 0.2387 0.2944 0.0557 0.006 0.7 9.5 1.0 4.7 0 0.470 0.2437 0.2877 0.0440 0.004 0.6 4.1 0.3 4.3 0 0.224 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2511 0.2869 0.0358 0.003 0.5 2.5 0.0 4.0 0 0.067 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.11 28.69 3.58 18.266 114.255 0.050 6.182 28.91 29.91 1.00 15.463 121.692 0.001 6.240 28.24 29.27 1.03 15.086 121.039 0.006 6.219 26.36 27.92 1.56 16.133 119.194 0.025 6.161 25.24 27.33 2.10 17.860 118.243 0.050 6.129 24.59 27.42 2.83 18.354 117.542 0.075 6.119 24.37 27.42 3.05 19.054 117.609 0.100 6.114 24.25 27.53 3.28 19.125 117.222 0.125 6.115 24.16 27.53 3.37 19.563 117.410 0.149 6.112 24.10 27.55 3.45 19.798 117.442 0.174 6.112 24.06 27.56 3.50 20.094 117.570 0.199 6.111 24.02 27.56 3.54 20.428 117.746 0.224 6.109 24.00 27.56 3.57 20.663 117.850 0.249 6.108 max suggested for this run: 22.85 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.050 Accepted refinement result: 25.24 27.33 2.10 17.860 118.243 0.050 6.129 Individual atomic B min max mean iso aniso Overall: 54.25 251.77 112.54 15.02 2438 0 Protein: 54.25 251.77 112.54 15.02 2438 0 Chain A: 59.62 245.77 112.58 N/A 1219 0 Chain C: 54.25 251.77 112.51 N/A 1219 0 Histogram: Values Number of atoms 54.25 - 74.00 62 74.00 - 93.76 537 93.76 - 113.51 905 113.51 - 133.26 436 133.26 - 153.01 282 153.01 - 172.76 149 172.76 - 192.51 58 192.51 - 212.27 6 212.27 - 232.02 1 232.02 - 251.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.2524 r_free=0.2733 r_work=0.2538 r_free=0.2724 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.60 - 36.79 A, n_refl.=6654 (all), 4.72 % free)-------------| | | | r_work= 0.2538 r_free= 0.2724 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 6.128352 | | target function (ml) not normalized (work): 38853.753547 | | target function (ml) not normalized (free): 1943.632293 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2546 0.2538 0.2724 n_refl.: 6654 re-set all scales: r(all,work,free)=0.5681 0.5685 0.5404 n_refl.: 6654 remove outliers: r(all,work,free)=0.5681 0.5685 0.5404 n_refl.: 6654 overall B=-6.58 to atoms: r(all,work,free)=0.5473 0.5477 0.5203 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2554 0.2543 0.2797 n_refl.: 6654 remove outliers: r(all,work,free)=0.2554 0.2543 0.2797 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 0.4482 1138.032 1065.821 1.514 0.974 0.354 15.485-12.238 97.00 96 1 0.2221 1140.705 1103.313 1.293 0.980 0.328 12.212-9.617 100.00 192 10 0.1623 1221.771 1173.937 1.340 0.983 0.309 9.605-7.558 100.00 374 15 0.2252 767.958 740.269 1.323 0.981 0.297 7.551-5.945 99.50 761 39 0.2905 420.370 391.924 1.069 0.981 0.249 5.945-4.677 99.31 1515 77 0.2500 368.637 341.286 0.964 0.977 0.160 4.676-3.603 95.60 3309 171 0.2584 259.373 247.403 1.054 0.975 0.089 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.9747 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2543 r_free=0.2797 After: r_work=0.2543 r_free=0.2797 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.710687 wxc_scale = 0.027 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.044594 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 0.2545 0.2797 0.0252 0.002 0.5 2.3 0.0 4.0 0 0.010 0.2544 0.2798 0.0254 0.003 0.5 2.3 0.0 4.0 0 0.030 0.2542 0.2797 0.0255 0.003 0.5 2.3 0.0 4.0 0 0.061 0.2541 0.2798 0.0257 0.003 0.5 2.3 0.0 4.0 0 0.091 0.2540 0.2797 0.0257 0.003 0.5 2.3 0.0 4.0 0 0.121 0.2538 0.2797 0.0258 0.003 0.5 2.3 0.0 4.0 0 0.152 0.2535 0.2797 0.0262 0.003 0.5 2.7 0.0 4.0 0 0.182 0.2532 0.2791 0.0259 0.004 0.5 2.7 0.0 4.0 0 0.212 0.2541 0.2796 0.0255 0.003 0.5 2.3 0.0 4.0 0 0.101 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2545 0.2797 0.0252 0.002 0.5 2.3 0.0 4.0 0 0.010 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.45 27.97 2.52 19.103 115.520 0.045 6.146 29.38 29.53 0.15 16.047 123.416 0.001 6.242 29.06 29.35 0.29 16.347 123.030 0.006 6.238 26.35 28.22 1.87 16.005 119.080 0.022 6.177 24.80 27.93 3.13 16.984 118.614 0.045 6.136 24.16 27.75 3.58 18.426 118.058 0.067 6.115 23.89 27.71 3.82 19.473 118.202 0.089 6.106 23.77 27.78 4.01 20.237 118.403 0.111 6.101 23.70 27.82 4.11 20.877 118.610 0.134 6.099 23.67 27.89 4.22 21.424 118.810 0.156 6.097 23.64 27.94 4.30 21.901 119.006 0.178 6.096 23.62 27.96 4.34 22.318 119.188 0.201 6.095 23.61 27.98 4.37 22.692 119.350 0.223 6.094 max suggested for this run: 23.10 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.089 Accepted refinement result: 23.89 27.71 3.82 19.473 118.202 0.089 6.106 Individual atomic B min max mean iso aniso Overall: 44.15 267.98 111.30 19.42 2438 0 Protein: 44.15 267.98 111.30 19.42 2438 0 Chain A: 51.67 267.98 111.33 N/A 1219 0 Chain C: 44.15 264.99 111.27 N/A 1219 0 Histogram: Values Number of atoms 44.15 - 66.53 52 66.53 - 88.91 488 88.91 - 111.30 847 111.30 - 133.68 543 133.68 - 156.07 310 156.07 - 178.45 144 178.45 - 200.83 44 200.83 - 223.22 8 223.22 - 245.60 0 245.60 - 267.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.2389 r_free=0.2771 r_work=0.2379 r_free=0.2759 ----------X-ray data---------- |--(resolution: 3.60 - 36.79 A, n_refl.=6654 (all), 4.72 % free)-------------| | | | r_work= 0.2379 r_free= 0.2759 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ml) (work): 6.102753 | | target function (ml) not normalized (work): 38691.456472 | | target function (ml) not normalized (free): 1944.734623 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2412 0.2697 6.4916 6.5175| | 2: 4.54 - 3.60 0.95 3036 156 0.2307 0.2882 5.6796 5.8652| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.74 30.43 1.00 0.99 67648.39| | 2: 4.54 - 3.60 3036 156 0.79 27.95 1.02 0.93 17884.67| |alpha: min = 0.93 max = 0.99 mean = 0.96| |beta: min = 17884.67 max = 67648.39 mean = 43818.32| |figures of merit: min = 0.00 max = 1.00 mean = 0.76| |phase err.(work): min = 0.00 max = 90.00 mean = 29.24| |phase err.(test): min = 0.00 max = 88.78 mean = 29.05| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2396 0.2379 0.2759 n_refl.: 6654 re-set all scales: r(all,work,free)=0.5595 0.5599 0.5331 n_refl.: 6654 remove outliers: r(all,work,free)=0.5595 0.5599 0.5331 n_refl.: 6654 overall B=-2.35 to atoms: r(all,work,free)=0.5519 0.5523 0.5259 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2401 0.2381 0.2816 n_refl.: 6654 remove outliers: r(all,work,free)=0.2401 0.2381 0.2816 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 0.4548 1138.032 937.772 1.282 0.957 0.354 15.485-12.238 97.00 96 1 0.2138 1140.705 1152.941 1.342 0.965 0.331 12.212-9.617 100.00 192 10 0.1564 1221.771 1167.928 1.300 0.968 0.306 9.605-7.558 100.00 374 15 0.2112 767.958 759.325 1.328 0.970 0.292 7.551-5.945 99.50 761 39 0.2696 420.370 397.884 1.066 0.974 0.243 5.945-4.677 99.31 1515 77 0.2351 368.637 348.262 0.958 0.977 0.164 4.676-3.603 95.60 3309 171 0.2354 259.373 250.382 1.036 0.988 0.079 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=0.8615 ================= 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_weight: 0.2929 0.2829 0.008 1.169 66.6 168.2 104.9 0 0.000 1_xyzrec: 0.2657 0.2972 0.015 1.305 66.6 168.2 104.9 0 0.283 1_adp: 0.2398 0.2856 0.015 1.305 61.6 252.8 110.6 0 0.283 1_regHadp: 0.2384 0.2833 0.015 1.305 61.6 252.8 110.6 0 0.283 2_bss: 0.2360 0.2842 0.015 1.305 55.6 246.7 104.6 0 0.283 2_settarget: 0.2360 0.2842 0.015 1.305 55.6 246.7 104.6 0 0.283 2_updatecdl: 0.2360 0.2842 0.015 1.349 55.6 246.7 104.6 0 0.283 2_weight: 0.2360 0.2842 0.015 1.349 55.6 246.7 104.6 0 0.283 2_xyzrec: 0.2511 0.2869 0.003 0.519 55.6 246.7 104.6 0 0.264 2_adp: 0.2524 0.2733 0.003 0.519 54.3 251.8 112.5 0 0.264 2_regHadp: 0.2538 0.2724 0.003 0.519 54.3 251.8 112.5 0 0.264 3_bss: 0.2543 0.2797 0.003 0.519 47.7 245.2 106.0 0 0.264 3_settarget: 0.2543 0.2797 0.003 0.519 47.7 245.2 106.0 0 0.264 3_updatecdl: 0.2543 0.2797 0.003 0.573 47.7 245.2 106.0 0 0.264 3_setrh: 0.2543 0.2797 0.003 0.573 47.7 245.2 106.0 0 0.264 3_weight: 0.2543 0.2797 0.003 0.573 47.7 245.2 106.0 0 0.264 3_xyzrec: 0.2545 0.2797 0.002 0.512 47.7 245.2 106.0 0 0.264 3_adp: 0.2389 0.2771 0.002 0.512 44.1 268.0 111.3 0 0.264 3_regHadp: 0.2379 0.2759 0.002 0.512 44.1 268.0 111.3 0 0.264 end: 0.2381 0.2816 0.002 0.512 41.8 265.6 108.9 0 0.264 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/4iy2_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/4iy2_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.4400 Refinement macro-cycles (run) : 183.7500 Write final files (write_after_run_outputs) : 18.9700 Total : 208.1600 Total CPU time: 3.80 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:28:09 PDT -0700 (1716251289.64 s) Start R-work = 0.2929, R-free = 0.2829 Final R-work = 0.2381, R-free = 0.2816 =============================================================================== Job complete usr+sys time: 244.90 seconds wall clock time: 12 minutes 25.66 seconds (745.66 seconds total)