Starting phenix.refine on Wed Apr 10 15:59:19 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 6ZM8_complete.pdb Found miller_array, 6ZM8.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_adp=true optimize_xyz=true hydrogens.refine=riding nproc=20 main.max_number_of_iterations=50 main.number_of_m=5 refine.adp.individual.aniso=not element H refine.adp.individual.iso=element H Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "6ZM8_complete.pdb" } default_model = "6ZM8_complete.pdb" miller_array { file = "6ZM8.mtz" } default_miller_array = "6ZM8.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 { adp { individual { isotropic = element H anisotropic = not element H } } } main { number_of_macro_cycles = 5 max_number_of_iterations = 50 nproc = 20 } hydrogens { refine = individual *riding Auto } 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: 4197 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3129 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "A" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 1068 Classifications: {'water': 356} Link IDs: {None: 355} Time building chain proxies: 0.74, per 1000 atoms: 0.18 Number of scatterers: 4197 At special positions: 0 Unit cell: (34.087, 77.272, 35.728, 90, 104.195, 90) Space group: P 1 21 1 (No. 4) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 664 8.00 N 285 7.00 C 1039 6.00 H 2205 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 144 " distance=2.02 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: 1.57 Conformation dependent library (CDL) restraints added in 98.8 milliseconds Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.04: 1091 1.04 - 1.24: 1289 1.24 - 1.44: 658 1.44 - 1.63: 853 1.63 - 1.83: 6 Bond restraints: 3897 Sorted by residual: bond pdb=" C PRO A 100 " pdb=" O PRO A 100 " ideal model delta sigma weight residual 1.236 1.106 0.130 1.23e-02 6.61e+03 1.12e+02 bond pdb=" CA PRO A 100 " pdb=" C PRO A 100 " ideal model delta sigma weight residual 1.519 1.649 -0.129 1.30e-02 5.92e+03 9.90e+01 bond pdb=" NH2 ARG A 130 " pdb="HH21 ARG A 130 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH2 ARG A 154 " pdb="HH21 ARG A 154 " 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 48 " pdb=" H GLY A 48 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 3892 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.64: 558 106.64 - 113.83: 3167 113.83 - 121.02: 1426 121.02 - 128.21: 828 128.21 - 135.40: 30 Bond angle restraints: 6009 Sorted by residual: angle pdb=" CA PRO A 100 " pdb=" C PRO A 100 " pdb=" O PRO A 100 " ideal model delta sigma weight residual 118.98 104.84 14.14 1.22e+00 6.72e-01 1.34e+02 angle pdb=" CA ASN A 101 " pdb=" CB ASN A 101 " pdb=" CG ASN A 101 " ideal model delta sigma weight residual 112.60 101.43 11.17 1.00e+00 1.00e+00 1.25e+02 angle pdb=" N PRO A 100 " pdb=" CA PRO A 100 " pdb=" C PRO A 100 " ideal model delta sigma weight residual 114.35 101.55 12.80 1.25e+00 6.40e-01 1.05e+02 angle pdb=" OE1 GLN A 143 " pdb=" CD GLN A 143 " pdb=" NE2 GLN A 143 " ideal model delta sigma weight residual 122.60 115.32 7.28 1.00e+00 1.00e+00 5.30e+01 angle pdb=" N GLY A 207 " pdb=" CA GLY A 207 " pdb=" C GLY A 207 " ideal model delta sigma weight residual 115.67 104.71 10.96 1.59e+00 3.96e-01 4.75e+01 ... (remaining 6004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 1063 17.57 - 35.15: 76 35.15 - 52.72: 23 52.72 - 70.29: 14 70.29 - 87.87: 1 Dihedral angle restraints: 1177 sinusoidal: 774 harmonic: 403 Sorted by residual: dihedral pdb=" CA PHE A 54 " pdb=" C PHE A 54 " pdb=" N ILE A 55 " pdb=" CA ILE A 55 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA PRO A 12 " pdb=" C PRO A 12 " pdb=" N THR A 13 " pdb=" CA THR A 13 " ideal model delta harmonic sigma weight residual -180.00 -160.02 -19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASN A 192 " pdb=" C ASN A 192 " pdb=" N TRP A 193 " pdb=" CA TRP A 193 " ideal model delta harmonic sigma weight residual 180.00 162.29 17.71 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 1174 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.078: 133 0.078 - 0.154: 66 0.154 - 0.231: 16 0.231 - 0.307: 8 0.307 - 0.383: 2 Chirality restraints: 225 Sorted by residual: chirality pdb=" CA PRO A 100 " pdb=" N PRO A 100 " pdb=" C PRO A 100 " pdb=" CB PRO A 100 " both_signs ideal model delta sigma weight residual False 2.72 3.10 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CB THR A 36 " pdb=" CA THR A 36 " pdb=" OG1 THR A 36 " pdb=" CG2 THR A 36 " both_signs ideal model delta sigma weight residual False 2.55 2.88 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA THR A 104 " pdb=" N THR A 104 " pdb=" C THR A 104 " pdb=" CB THR A 104 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 222 not shown) Planarity restraints: 502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 46 " 0.151 2.00e-02 2.50e+03 6.61e-02 1.31e+02 pdb=" CG TYR A 46 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A 46 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 46 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 46 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 46 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 46 " 0.031 2.00e-02 2.50e+03 pdb=" OH TYR A 46 " 0.117 2.00e-02 2.50e+03 pdb=" HD1 TYR A 46 " -0.077 2.00e-02 2.50e+03 pdb=" HD2 TYR A 46 " -0.056 2.00e-02 2.50e+03 pdb=" HE1 TYR A 46 " -0.031 2.00e-02 2.50e+03 pdb=" HE2 TYR A 46 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 185 " -0.156 2.00e-02 2.50e+03 6.33e-02 1.20e+02 pdb=" CG TYR A 185 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 185 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A 185 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 185 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 185 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 185 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR A 185 " -0.096 2.00e-02 2.50e+03 pdb=" HD1 TYR A 185 " 0.068 2.00e-02 2.50e+03 pdb=" HD2 TYR A 185 " 0.074 2.00e-02 2.50e+03 pdb=" HE1 TYR A 185 " 0.029 2.00e-02 2.50e+03 pdb=" HE2 TYR A 185 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 140 " 0.080 2.00e-02 2.50e+03 4.49e-02 8.07e+01 pdb=" CG TRP A 140 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A 140 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 140 " -0.041 2.00e-02 2.50e+03 pdb=" NE1 TRP A 140 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TRP A 140 " -0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP A 140 " -0.045 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 140 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 140 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 140 " 0.031 2.00e-02 2.50e+03 pdb=" HD1 TRP A 140 " 0.048 2.00e-02 2.50e+03 pdb=" HE1 TRP A 140 " -0.033 2.00e-02 2.50e+03 pdb=" HE3 TRP A 140 " -0.088 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 140 " -0.029 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 140 " 0.031 2.00e-02 2.50e+03 pdb=" HH2 TRP A 140 " 0.083 2.00e-02 2.50e+03 ... (remaining 499 not shown) Histogram of nonbonded interaction distances: 0.98 - 1.70: 38 1.70 - 2.43: 2779 2.43 - 3.15: 14999 3.15 - 3.88: 23943 3.88 - 4.60: 36506 Warning: very small nonbonded interaction distances. Nonbonded interactions: 78265 Sorted by model distance: nonbonded pdb=" HG1 THR A 32 " pdb=" HD1 HIS A 60 " model vdw 0.979 2.100 nonbonded pdb=" O HOH A 394 " pdb=" O HOH A 409 " model vdw 0.995 2.200 nonbonded pdb=" H2 HOH A 569 " pdb=" O HOH A 589 " model vdw 1.435 1.850 nonbonded pdb=" H1 HOH A 569 " pdb=" O HOH A 589 " model vdw 1.436 1.850 nonbonded pdb=" O HOH A 344 " pdb=" O HOH A 541 " model vdw 1.456 2.200 ... (remaining 78260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 4 15.96 3 O 664 7.98 3 N 285 6.98 3 C 1039 5.99 3 H 2205 1.00 3 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 ===================== n_use = 4197 n_use_u_iso = 2205 n_use_u_aniso = 1992 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 = 4197 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4197 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 2205 aniso = 1992) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (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 { adp { individual { isotropic = element H anisotropic = not element H } } } main { number_of_macro_cycles = 5 max_number_of_iterations = 50 nproc = 20 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "6ZM8_complete_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2205 occupancy sum: 2205.00 (% of total atoms 52.54) Rotatable: count: 325 occupancy sum: 325.00 (% of total atoms 7.74) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.78 - 38.64 A, n_refl.=200663 (all), 4.98 % free)-----------| | | | r_work= 0.1768 r_free= 0.1641 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 1.774229 | | target function (ml) not normalized (work): 338276.194204 | | target function (ml) not normalized (free): 18238.393483 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.64 - 2.42 1.00 6457 383 0.1960 0.1965 4.3725 4.251| | 2: 2.42 - 1.92 1.00 6506 311 0.1506 0.1385 3.3732 3.391| | 3: 1.92 - 1.68 1.00 6469 320 0.1572 0.1458 2.9219 3.0064| | 4: 1.68 - 1.53 1.00 6449 322 0.1581 0.1468 2.5984 2.6776| | 5: 1.53 - 1.42 1.00 6404 359 0.1617 0.1293 2.3781 2.3974| | 6: 1.42 - 1.33 1.00 6458 321 0.1610 0.1413 2.2257 2.3339| | 7: 1.33 - 1.27 1.00 6394 370 0.1602 0.1335 2.1408 2.2388| | 8: 1.27 - 1.21 1.00 6418 353 0.1589 0.1235 2.0071 2.027| | 9: 1.21 - 1.17 1.00 6361 370 0.1607 0.1314 1.973 2.0694| | 10: 1.17 - 1.12 1.00 6436 324 0.1636 0.1317 1.945 2.0986| | 11: 1.12 - 1.09 1.00 6449 319 0.1648 0.1358 1.837 1.8834| | 12: 1.09 - 1.06 1.00 6419 314 0.1681 0.1351 1.7549 1.8716| | 13: 1.06 - 1.03 1.00 6419 327 0.1689 0.1527 1.6613 1.7688| | 14: 1.03 - 1.01 1.00 6415 346 0.1702 0.1465 1.5934 1.6913| | 15: 1.01 - 0.98 1.00 6439 321 0.1709 0.1656 1.5056 1.6269| | 16: 0.98 - 0.96 1.00 6411 338 0.1720 0.1533 1.4406 1.4588| | 17: 0.96 - 0.94 1.00 6358 387 0.1806 0.1622 1.4251 1.4974| | 18: 0.94 - 0.92 1.00 6473 322 0.1843 0.1831 1.3992 1.459| | 19: 0.92 - 0.91 1.00 6401 335 0.1857 0.1871 1.3627 1.3961| | 20: 0.91 - 0.89 1.00 6354 339 0.1976 0.1864 1.318 1.2672| | 21: 0.89 - 0.88 1.00 6389 369 0.2034 0.2037 1.2887 1.3172| | 22: 0.88 - 0.86 1.00 6463 354 0.2219 0.2148 1.287 1.2672| | 23: 0.86 - 0.85 1.00 6332 321 0.2356 0.2556 1.2609 1.3043| | 24: 0.85 - 0.84 1.00 6442 349 0.2494 0.2638 1.2258 1.2649| | 25: 0.84 - 0.83 1.00 6387 320 0.2719 0.2758 1.1978 1.24| | 26: 0.83 - 0.82 0.99 6426 322 0.2875 0.2848 1.1628 1.1342| | 27: 0.82 - 0.81 0.99 6344 346 0.3073 0.2990 1.1351 1.1012| | 28: 0.81 - 0.80 0.96 6170 310 0.3305 0.3476 1.1034 1.0995| | 29: 0.80 - 0.79 0.90 5798 271 0.3447 0.3610 1.0575 1.0573| | 30: 0.79 - 0.78 0.84 5420 259 0.3626 0.3783 0.98907 0.97653| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 38.64 - 2.42 6457 383 0.85 21.60 0.91 0.30 994.71| | 2: 2.42 - 1.92 6506 311 0.94 12.14 1.10 0.33 140.90| | 3: 1.92 - 1.68 6469 320 0.94 12.15 1.12 0.34 55.39| | 4: 1.68 - 1.53 6449 322 0.95 10.10 1.14 0.35 26.48| | 5: 1.53 - 1.42 6404 359 0.96 8.77 1.15 0.35 15.21| | 6: 1.42 - 1.33 6458 321 0.95 10.00 1.15 0.35 13.12| | 7: 1.33 - 1.27 6394 370 0.95 10.00 1.15 0.34 10.84| | 8: 1.27 - 1.21 6418 353 0.96 8.67 1.16 0.35 7.85| | 9: 1.21 - 1.17 6361 370 0.96 8.92 1.16 0.35 7.52| | 10: 1.17 - 1.12 6436 324 0.95 9.42 1.17 0.35 7.30| | 11: 1.12 - 1.09 6449 319 0.96 8.49 1.17 0.35 5.14| | 12: 1.09 - 1.06 6419 314 0.95 10.18 1.17 0.35 5.01| | 13: 1.06 - 1.03 6419 327 0.94 11.29 1.17 0.35 4.51| | 14: 1.03 - 1.01 6415 346 0.95 10.93 1.17 0.35 3.61| | 15: 1.01 - 0.98 6439 321 0.94 12.42 1.15 0.35 3.30| | 16: 0.98 - 0.96 6411 338 0.94 11.91 1.14 0.35 2.58| | 17: 0.96 - 0.94 6358 387 0.93 13.35 1.14 0.34 2.44| | 18: 0.94 - 0.92 6473 322 0.92 14.95 1.13 0.33 2.54| | 19: 0.92 - 0.91 6401 335 0.91 16.02 1.10 0.33 2.39| | 20: 0.91 - 0.89 6354 339 0.92 16.11 1.08 0.32 1.99| | 21: 0.89 - 0.88 6389 369 0.91 17.33 1.06 0.32 1.89| | 22: 0.88 - 0.86 6463 354 0.89 19.17 1.05 0.31 1.92| | 23: 0.86 - 0.85 6332 321 0.87 21.83 1.02 0.30 2.05| | 24: 0.85 - 0.84 6442 349 0.83 25.34 1.01 0.28 2.26| | 25: 0.84 - 0.83 6387 320 0.82 26.25 0.96 0.28 2.08| | 26: 0.83 - 0.82 6426 322 0.81 26.96 0.94 0.27 1.93| | 27: 0.82 - 0.81 6344 346 0.81 27.05 0.92 0.27 1.72| | 28: 0.81 - 0.80 6170 310 0.78 29.76 0.88 0.25 1.79| | 29: 0.80 - 0.79 5798 271 0.74 34.04 0.87 0.23 1.90| | 30: 0.79 - 0.78 5420 259 0.70 37.01 0.83 0.21 1.86| |alpha: min = 0.20 max = 0.35 mean = 0.32| |beta: min = 1.69 max = 1565.65 mean = 45.11| |figures of merit: min = 0.00 max = 1.00 mean = 0.90| |phase err.(work): min = 0.00 max = 89.97 mean = 16.55| |phase err.(test): min = 0.00 max = 89.05 mean = 16.56| |-----------------------------------------------------------------------------| ----------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 : 0.014 0.130 1692 Z= 0.903 Angle : 1.522 14.143 2310 Z= 1.052 Chirality : 0.104 0.383 225 Planarity : 0.016 0.086 304 Dihedral : 13.057 87.866 566 Min Nonbonded Distance : 0.995 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.62 % Allowed : 1.24 % Favored : 98.14 % Cbeta Deviations : 0.54 % 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: -0.14 (0.54), residues: 206 helix: 1.37 (0.57), residues: 74 sheet: -0.92 (0.69), residues: 42 loop : -0.84 (0.59), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.006 ARG A 202 TYR 0.117 0.022 TYR A 185 PHE 0.072 0.017 PHE A 54 TRP 0.058 0.019 TRP A 173 HIS 0.014 0.006 HIS A 60 Individual atomic B min max mean iso aniso Overall: 4.29 139.17 11.70 4.81 0 1992 Protein: 4.29 139.17 8.42 4.81 0 1636 Water: 5.90 111.17 26.81 N/A 0 356 Chain A: 4.29 139.17 11.70 N/A 0 1992 Histogram: Values Number of atoms 4.29 - 17.78 1689 17.78 - 31.27 163 31.27 - 44.76 98 44.76 - 58.24 27 58.24 - 71.73 7 71.73 - 85.22 3 85.22 - 98.71 2 98.71 - 112.20 1 112.20 - 125.69 1 125.69 - 139.17 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 0.78 - 38.64 A, n_refl.=200663 (all), 4.98 % free)-----------| | | | r_work= 0.1768 r_free= 0.1641 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 1.774229 | | target function (ml) not normalized (work): 338276.194204 | | target function (ml) not normalized (free): 18238.393483 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1758 0.1768 0.1641 n_refl.: 200663 re-set all scales: r(all,work,free)=0.1758 0.1768 0.1641 n_refl.: 200663 remove outliers: r(all,work,free)=0.1758 0.1768 0.1641 n_refl.: 200650 overall B=0.09 to atoms: r(all,work,free)=0.1797 0.1807 0.1664 n_refl.: 200650 bulk-solvent and scaling: r(all,work,free)=0.1343 0.1338 0.1437 n_refl.: 200650 remove outliers: r(all,work,free)=0.1340 0.1335 0.1435 n_refl.: 200604 ======================== 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 38.636-10.170 99.01 94 6 0.1754 276.415 271.544 0.879 1.017 0.390 10.167-7.973 99.01 98 2 0.1866 240.645 227.720 0.910 1.018 0.408 7.970-6.248 99.54 206 11 0.2018 202.703 194.023 0.893 1.016 0.408 6.247-4.898 99.54 395 37 0.1793 242.578 235.658 0.914 1.016 0.372 4.897-3.840 99.66 838 50 0.1458 305.208 299.247 0.935 1.014 0.346 3.839-3.010 99.68 1748 112 0.1439 276.993 270.742 0.943 1.011 0.091 3.009-2.359 99.77 3641 184 0.1418 184.712 181.826 0.948 1.007 0.005 2.359-1.850 99.95 7566 372 0.1238 138.106 136.372 1.007 1.000 0.000 1.849-1.450 99.94 15595 806 0.1133 77.891 76.969 1.049 0.988 0.000 1.450-1.137 99.90 32229 1745 0.0997 48.819 48.432 1.093 0.968 0.000 1.136-0.891 99.91 66882 3493 0.1225 23.929 23.853 1.144 0.936 0.000 0.891-0.780 96.83 61314 3180 0.2799 9.174 8.243 0.983 0.902 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=0.4158 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1335 r_free=0.1435 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1335 r_free=0.1435 ========================= Local real-space refinement ========================= Before: r_work=0.1335 r_free=0.1435 21 residues out of total 159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.136 outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 2.1041 time to fit residues: 42.7778 After: r_work=0.1333 r_free=0.1436 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.612106 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 761.823564 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1639 0.1708 0.0069 0.002 0.5 1.9 0.0 0.0 0 0.125 0.1590 0.1661 0.0072 0.002 0.5 1.9 0.0 0.0 0 0.250 0.1536 0.1613 0.0076 0.002 0.6 2.2 0.0 0.0 0 0.500 0.1467 0.1549 0.0082 0.003 0.6 1.9 0.0 0.0 0 1.000 0.1417 0.1503 0.0086 0.003 0.6 1.9 0.0 0.0 0 2.000 0.1397 0.1490 0.0093 0.004 0.7 1.9 0.0 0.0 0 3.000 0.1382 0.1481 0.0099 0.004 0.7 1.9 0.0 0.0 0 4.000 0.1375 0.1482 0.0107 0.005 0.7 1.9 0.0 0.0 0 5.000 0.1363 0.1473 0.0110 0.005 0.8 1.9 0.0 0.0 0 6.000 0.1361 0.1478 0.0117 0.005 0.8 1.9 0.0 0.0 0 7.000 0.1353 0.1473 0.0120 0.006 0.8 1.9 0.0 0.0 0 8.000 0.1349 0.1472 0.0123 0.006 0.8 1.9 0.0 0.0 0 9.000 0.1346 0.1472 0.0126 0.007 0.8 1.9 0.0 0.0 0 10.000 0.1348 0.1474 0.0127 0.007 0.8 1.9 0.0 0.0 0 9.806 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1346 0.1472 0.0126 0.007 0.8 1.9 0.0 0.0 0 10.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1346 r_free=0.1472 25 residues out of total 159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.241 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2297 After: r_work=0.1346 r_free=0.1472 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.46 14.72 1.26 3.170 13.333 761.824 0.020 13.47 14.72 1.26 2.927 13.334 22.855 0.020 13.41 14.75 1.34 2.566 13.350 95.228 0.020 13.68 15.37 1.69 3.828 13.904 380.912 0.018 14.24 15.99 1.74 2.802 13.316 761.824 0.019 14.34 16.26 1.92 2.820 13.422 1142.735 0.019 13.46 15.14 1.68 4.484 14.061 1523.647 0.017 13.51 15.29 1.77 4.465 14.033 1904.559 0.017 13.60 15.40 1.81 4.610 14.070 2285.471 0.017 13.56 15.41 1.85 5.138 14.203 2666.382 0.017 13.61 15.46 1.84 5.001 14.180 3047.294 0.017 13.44 15.28 1.84 5.309 14.250 3428.206 0.016 13.62 15.56 1.94 5.176 14.217 3809.118 0.016 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 22.855 Accepted refinement result: 13.47 14.72 1.26 2.927 13.334 22.855 0.020 Individual atomic B min max mean iso aniso Overall: 4.39 135.23 11.80 4.44 0 1992 Protein: 4.39 135.23 8.51 4.44 0 1636 Water: 5.98 111.26 26.90 N/A 0 356 Chain A: 4.39 135.23 11.80 N/A 0 1992 Histogram: Values Number of atoms 4.39 - 17.47 1685 17.47 - 30.56 160 30.56 - 43.64 97 43.64 - 56.72 32 56.72 - 69.81 9 69.81 - 82.89 4 82.89 - 95.98 2 95.98 - 109.06 0 109.06 - 122.15 2 122.15 - 135.23 1 =========================== Idealize ADP of riding H ========================== r_work=0.1347 r_free=0.1472 r_work=0.1343 r_free=0.1469 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 0.78 - 38.64 A, n_refl.=200604 (all), 4.98 % free)-----------| | | | r_work= 0.1343 r_free= 0.1469 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.019928 | | target function (ls_wunit_k1) not normalized (work): 3798.369541 | | target function (ls_wunit_k1) not normalized (free): 267.875878 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1349 0.1343 0.1469 n_refl.: 200604 re-set all scales: r(all,work,free)=0.1789 0.1796 0.1700 n_refl.: 200604 remove outliers: r(all,work,free)=0.1789 0.1796 0.1700 n_refl.: 200604 overall B=0.00 to atoms: r(all,work,free)=0.1789 0.1796 0.1700 n_refl.: 200604 bulk-solvent and scaling: r(all,work,free)=0.1347 0.1340 0.1467 n_refl.: 200604 remove outliers: r(all,work,free)=0.1347 0.1340 0.1467 n_refl.: 200603 ======================== 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 38.636-10.170 99.01 94 6 0.1641 276.415 271.783 0.851 1.015 0.390 10.167-7.973 99.01 98 2 0.1648 240.645 230.883 0.890 1.015 0.401 7.970-6.248 99.54 206 11 0.1822 202.703 195.089 0.858 1.014 0.401 6.247-4.898 99.54 395 37 0.1573 242.578 237.189 0.875 1.014 0.388 4.897-3.840 99.66 838 50 0.1211 305.208 301.503 0.897 1.012 0.380 3.839-3.010 99.68 1748 112 0.1244 276.993 272.681 0.912 1.010 0.087 3.009-2.359 99.77 3641 184 0.1269 184.712 182.421 0.917 1.006 0.010 2.359-1.850 99.95 7566 372 0.1200 138.106 136.443 0.976 1.000 0.000 1.849-1.450 99.94 15595 806 0.1168 77.891 76.883 1.005 0.990 0.000 1.450-1.137 99.90 32229 1745 0.1092 48.819 48.347 1.051 0.974 0.000 1.136-0.891 99.91 66881 3493 0.1324 23.929 23.840 1.102 0.948 0.000 0.891-0.780 96.83 61314 3180 0.2843 9.174 8.272 0.945 0.919 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=0.3644 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1340 r_free=0.1467 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1340 r_free=0.1467 ========================= Local real-space refinement ========================= Before: r_work=0.1340 r_free=0.1467 27 residues out of total 159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.257 outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 2.4459 time to fit residues: 67.1813 After: r_work=0.1341 r_free=0.1464 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.573227 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 575.918945 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1756 0.1852 0.0096 0.002 0.5 0.6 0.0 0.0 0 0.125 0.1652 0.1750 0.0097 0.002 0.5 1.0 0.0 0.0 0 0.250 0.1552 0.1653 0.0100 0.002 0.5 1.3 0.0 0.0 0 0.500 0.1462 0.1566 0.0105 0.002 0.6 1.6 0.0 0.0 0 1.000 0.1408 0.1519 0.0111 0.003 0.6 1.6 0.0 0.0 0 2.000 0.1379 0.1496 0.0116 0.003 0.7 1.6 0.0 0.0 0 3.000 0.1366 0.1487 0.0121 0.004 0.7 1.6 0.0 0.0 0 4.000 0.1355 0.1481 0.0126 0.004 0.7 1.6 0.0 0.0 0 5.000 0.1348 0.1478 0.0130 0.005 0.8 1.6 0.0 0.0 0 6.000 0.1343 0.1477 0.0134 0.005 0.8 1.6 0.0 0.0 0 7.000 0.1339 0.1477 0.0138 0.006 0.8 1.6 0.0 0.0 0 8.000 0.1337 0.1479 0.0142 0.006 0.8 1.6 0.0 0.0 0 9.000 0.1334 0.1478 0.0144 0.007 0.8 1.6 0.0 0.0 0 10.000 0.1336 0.1480 0.0144 0.007 0.8 1.6 0.0 0.0 0 9.787 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1339 0.1477 0.0138 0.006 0.8 1.6 0.0 0.0 0 8.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1339 r_free=0.1477 26 residues out of total 159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.257 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1342 After: r_work=0.1339 r_free=0.1477 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.39 14.77 1.38 4.162 14.878 575.919 0.020 13.39 14.77 1.38 4.139 14.878 17.278 0.020 13.41 14.85 1.44 3.774 14.900 71.990 0.020 13.63 15.42 1.79 3.909 15.382 287.959 0.018 13.46 15.29 1.83 4.231 15.592 575.919 0.017 13.37 15.08 1.72 4.244 15.616 863.878 0.017 13.35 15.08 1.73 4.381 15.641 1151.838 0.017 13.33 15.03 1.69 4.288 15.596 1439.797 0.017 13.16 14.96 1.80 4.130 15.501 1727.757 0.016 13.41 15.26 1.85 4.593 15.681 2015.716 0.016 13.41 15.23 1.82 4.680 15.715 2303.676 0.016 13.28 15.16 1.88 4.359 15.586 2591.635 0.016 13.54 15.49 1.94 4.807 15.745 2879.595 0.016 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 17.278 Accepted refinement result: 13.39 14.77 1.38 4.139 14.878 17.278 0.020 Individual atomic B min max mean iso aniso Overall: 4.39 134.57 11.80 4.38 0 1992 Protein: 4.39 134.57 8.51 4.38 0 1636 Water: 5.98 111.26 26.91 N/A 0 356 Chain A: 4.39 134.57 11.80 N/A 0 1992 Histogram: Values Number of atoms 4.39 - 17.41 1682 17.41 - 30.43 162 30.43 - 43.44 98 43.44 - 56.46 32 56.46 - 69.48 9 69.48 - 82.50 3 82.50 - 95.52 3 95.52 - 108.54 0 108.54 - 121.56 2 121.56 - 134.57 1 =========================== Idealize ADP of riding H ========================== r_work=0.1339 r_free=0.1477 r_work=0.1339 r_free=0.1477 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 0.78 - 38.64 A, n_refl.=200603 (all), 4.98 % free)-----------| | | | r_work= 0.1339 r_free= 0.1477 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.019784 | | target function (ls_wunit_k1) not normalized (work): 3770.853960 | | target function (ls_wunit_k1) not normalized (free): 269.967244 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1346 0.1339 0.1477 n_refl.: 200603 re-set all scales: r(all,work,free)=0.1788 0.1795 0.1709 n_refl.: 200603 remove outliers: r(all,work,free)=0.1788 0.1795 0.1709 n_refl.: 200603 overall B=0.00 to atoms: r(all,work,free)=0.1788 0.1795 0.1709 n_refl.: 200603 bulk-solvent and scaling: r(all,work,free)=0.1346 0.1339 0.1476 n_refl.: 200603 remove outliers: r(all,work,free)=0.1346 0.1339 0.1476 n_refl.: 200603 ======================== 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 38.636-10.170 99.01 94 6 0.1616 243.035 238.741 0.848 1.016 0.390 10.167-7.973 99.01 98 2 0.1614 211.585 203.237 0.886 1.017 0.410 7.970-6.248 99.54 206 11 0.1773 178.224 171.916 0.858 1.015 0.410 6.247-4.898 99.54 395 37 0.1565 213.284 208.556 0.871 1.015 0.395 4.897-3.840 99.66 838 50 0.1205 268.351 265.009 0.892 1.014 0.390 3.839-3.010 99.68 1748 112 0.1226 243.543 239.847 0.909 1.011 0.082 3.009-2.359 99.77 3641 184 0.1270 162.406 160.407 0.914 1.007 0.000 2.359-1.850 99.95 7566 372 0.1214 121.429 119.971 0.974 1.000 0.000 1.849-1.450 99.94 15595 806 0.1166 68.485 67.636 1.004 0.990 0.000 1.450-1.137 99.90 32229 1745 0.1090 42.924 42.523 1.051 0.972 0.000 1.136-0.891 99.91 66881 3493 0.1318 21.040 20.950 1.103 0.944 0.000 0.891-0.780 96.83 61314 3180 0.2840 8.066 7.250 0.947 0.913 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=0.3779 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1339 r_free=0.1476 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1339 r_free=0.1476 ========================= Local real-space refinement ========================= Before: r_work=0.1339 r_free=0.1476 27 residues out of total 159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.118 outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 1.8420 time to fit residues: 50.4986 After: r_work=0.1339 r_free=0.1473 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.468293 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.734092 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1369 0.1469 0.0100 0.003 0.7 1.6 0.0 0.0 0 0.073 0.1326 0.1430 0.0104 0.004 0.8 1.6 0.0 0.0 0 0.220 0.1310 0.1414 0.0104 0.005 0.9 1.6 0.0 0.0 0 0.440 0.1302 0.1409 0.0107 0.006 0.9 1.6 0.0 0.0 0 0.661 0.1298 0.1407 0.0108 0.006 0.9 1.6 0.0 0.0 0 0.881 0.1295 0.1406 0.0111 0.007 1.0 1.6 0.0 0.0 0 1.101 0.1293 0.1405 0.0112 0.007 1.0 1.6 0.0 0.0 0 1.321 0.1292 0.1405 0.0113 0.008 1.0 1.6 0.0 0.0 0 1.542 0.1300 0.1408 0.0107 0.006 0.9 1.6 0.0 0.0 0 0.734 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1292 0.1405 0.0113 0.008 1.0 1.6 0.0 0.0 0 1.542 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1292 r_free=0.1405 25 residues out of total 159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.131 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1118 After: r_work=0.1292 r_free=0.1405 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.92 14.05 1.13 4.137 14.877 13.734 2.765 12.92 14.05 1.13 4.133 14.877 0.412 2.765 12.91 14.04 1.13 4.033 14.878 1.717 2.764 12.82 14.00 1.18 3.894 14.890 6.867 2.754 12.81 14.01 1.20 4.001 14.887 13.734 2.752 12.86 14.06 1.20 4.033 14.886 20.601 2.758 12.73 13.94 1.21 4.052 14.885 27.468 2.745 12.78 14.04 1.26 4.025 14.893 34.335 2.751 12.73 14.00 1.26 4.022 14.895 41.202 2.747 12.70 13.96 1.26 4.028 14.895 48.069 2.743 12.69 13.97 1.28 4.028 14.897 54.936 2.744 12.67 13.94 1.28 4.030 14.898 61.803 2.741 12.65 13.92 1.27 4.034 14.899 68.670 2.740 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 68.670 Accepted refinement result: 12.65 13.92 1.27 4.034 14.899 68.670 2.740 Individual atomic B min max mean iso aniso Overall: 4.34 130.71 11.84 4.13 0 1992 Protein: 4.34 130.71 8.56 4.13 0 1636 Water: 5.93 111.26 26.91 N/A 0 356 Chain A: 4.34 130.71 11.84 N/A 0 1992 Histogram: Values Number of atoms 4.34 - 16.98 1666 16.98 - 29.62 174 29.62 - 42.25 98 42.25 - 54.89 31 54.89 - 67.53 13 67.53 - 80.16 4 80.16 - 92.80 3 92.80 - 105.44 0 105.44 - 118.08 2 118.08 - 130.71 1 =========================== Idealize ADP of riding H ========================== r_work=0.1265 r_free=0.1392 r_work=0.1265 r_free=0.1392 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 0.78 - 38.64 A, n_refl.=200603 (all), 4.98 % free)-----------| | | | r_work= 0.1265 r_free= 0.1392 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 2.739476 | | target function (ml) not normalized (work): 522157.764451 | | target function (ml) not normalized (free): 28220.912479 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1271 0.1265 0.1392 n_refl.: 200603 re-set all scales: r(all,work,free)=0.1760 0.1770 0.1632 n_refl.: 200603 remove outliers: r(all,work,free)=0.1760 0.1770 0.1632 n_refl.: 200603 overall B=0.00 to atoms: r(all,work,free)=0.1760 0.1770 0.1632 n_refl.: 200603 bulk-solvent and scaling: r(all,work,free)=0.1276 0.1269 0.1398 n_refl.: 200603 remove outliers: r(all,work,free)=0.1275 0.1269 0.1397 n_refl.: 200595 ======================== 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 38.636-10.170 99.01 94 6 0.1707 243.035 237.984 0.861 1.004 0.390 10.167-7.973 99.01 98 2 0.1772 211.585 202.072 0.903 1.005 0.410 7.970-6.248 99.54 206 11 0.1910 178.224 170.895 0.878 1.003 0.410 6.247-4.898 99.54 395 37 0.1729 213.284 207.747 0.888 1.004 0.357 4.897-3.840 99.66 838 50 0.1334 268.351 265.697 0.909 1.004 0.313 3.839-3.010 99.68 1748 112 0.1339 243.543 239.075 0.922 1.003 0.134 3.009-2.359 99.77 3641 184 0.1357 162.406 159.854 0.925 1.003 0.100 2.359-1.850 99.95 7566 372 0.1201 121.429 119.772 0.980 1.002 0.000 1.849-1.450 99.93 15594 806 0.1063 68.480 67.560 1.006 1.000 0.000 1.450-1.137 99.88 32224 1744 0.0925 42.918 42.542 1.037 0.996 0.000 1.136-0.891 99.91 66880 3493 0.1169 21.040 21.109 1.073 0.991 0.000 0.891-0.780 96.83 61314 3180 0.2731 8.066 7.390 0.902 0.985 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=0.2943 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1269 r_free=0.1397 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1269 r_free=0.1397 ========================= Local real-space refinement ========================= Before: r_work=0.1269 r_free=0.1397 27 residues out of total 159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.116 outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 1.9599 time to fit residues: 53.6914 After: r_work=0.1273 r_free=0.1400 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.358339 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 12.370549 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1339 0.1445 0.0106 0.003 0.7 1.6 0.0 0.0 0 0.068 0.1298 0.1412 0.0114 0.004 0.8 1.6 0.0 0.0 0 0.204 0.1283 0.1401 0.0118 0.005 0.8 1.6 0.0 0.0 0 0.408 0.1277 0.1397 0.0120 0.005 0.9 1.6 0.0 0.0 0 0.611 0.1273 0.1396 0.0123 0.006 0.9 1.9 0.0 0.0 0 0.815 0.1270 0.1395 0.0125 0.007 0.9 1.9 0.0 0.0 0 1.019 0.1268 0.1395 0.0126 0.007 1.0 1.9 0.0 0.0 0 1.223 0.1267 0.1394 0.0128 0.007 1.0 1.9 0.0 0.0 0 1.426 0.1276 0.1397 0.0121 0.006 0.9 1.9 0.0 0.0 0 0.679 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1267 0.1394 0.0128 0.007 1.0 1.9 0.0 0.0 0 1.426 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1267 r_free=0.1394 27 residues out of total 159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.122 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1030 After: r_work=0.1267 r_free=0.1394 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.67 13.94 1.28 4.024 14.931 12.371 2.741 12.67 13.93 1.26 3.968 14.931 0.371 2.741 12.67 13.92 1.25 3.937 14.932 1.546 2.740 12.65 13.89 1.23 3.926 14.933 6.185 2.737 12.68 13.90 1.22 3.933 14.935 12.371 2.740 12.65 13.88 1.23 3.952 14.934 18.556 2.736 12.64 13.88 1.24 3.973 14.934 24.741 2.735 12.64 13.87 1.23 3.966 14.935 30.926 2.735 12.64 13.87 1.23 3.971 14.935 37.112 2.735 12.64 13.85 1.21 3.955 14.937 43.297 2.734 12.63 13.84 1.21 3.960 14.937 49.482 2.734 12.62 13.80 1.19 3.935 14.939 55.667 2.732 12.62 13.80 1.18 3.938 14.940 61.853 2.732 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 61.853 Accepted refinement result: 12.62 13.80 1.18 3.938 14.940 61.853 2.732 Individual atomic B min max mean iso aniso Overall: 4.37 127.58 11.86 3.92 0 1992 Protein: 4.37 127.58 8.58 3.92 0 1636 Water: 5.98 111.25 26.92 N/A 0 356 Chain A: 4.37 127.58 11.86 N/A 0 1992 Histogram: Values Number of atoms 4.37 - 16.69 1659 16.69 - 29.01 171 29.01 - 41.33 103 41.33 - 53.65 34 53.65 - 65.97 15 65.97 - 78.29 4 78.29 - 90.61 3 90.61 - 102.94 0 102.94 - 115.26 2 115.26 - 127.58 1 =========================== Idealize ADP of riding H ========================== r_work=0.1262 r_free=0.1380 r_work=0.1262 r_free=0.1380 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 0.78 - 38.64 A, n_refl.=200595 (all), 4.98 % free)-----------| | | | r_work= 0.1262 r_free= 0.1380 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 2.732226 | | target function (ml) not normalized (work): 520756.764280 | | target function (ml) not normalized (free): 28075.548484 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1268 0.1262 0.1380 n_refl.: 200595 re-set all scales: r(all,work,free)=0.1769 0.1780 0.1626 n_refl.: 200595 remove outliers: r(all,work,free)=0.1769 0.1780 0.1626 n_refl.: 200595 overall B=0.00 to atoms: r(all,work,free)=0.1769 0.1780 0.1626 n_refl.: 200595 bulk-solvent and scaling: r(all,work,free)=0.1265 0.1259 0.1378 n_refl.: 200595 remove outliers: r(all,work,free)=0.1265 0.1259 0.1378 n_refl.: 200593 ======================== 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 38.636-10.170 99.01 94 6 0.1720 243.035 237.507 0.859 1.003 0.390 10.167-7.973 99.01 98 2 0.1768 211.585 202.030 0.900 1.004 0.410 7.970-6.248 99.54 206 11 0.1932 178.224 170.511 0.873 1.002 0.410 6.247-4.898 99.54 395 37 0.1726 213.284 207.645 0.886 1.004 0.360 4.897-3.840 99.66 838 50 0.1351 268.351 265.596 0.907 1.003 0.317 3.839-3.010 99.68 1748 112 0.1344 243.543 238.884 0.919 1.003 0.139 3.009-2.359 99.77 3641 184 0.1351 162.406 159.784 0.923 1.003 0.053 2.359-1.850 99.95 7566 372 0.1187 121.429 119.834 0.978 1.002 0.000 1.849-1.450 99.93 15594 806 0.1044 68.480 67.635 1.005 1.001 0.000 1.450-1.137 99.88 32223 1744 0.0903 42.917 42.585 1.038 0.999 0.000 1.136-0.891 99.91 66879 3493 0.1159 21.039 21.091 1.073 0.997 0.000 0.891-0.780 96.83 61314 3180 0.2742 8.066 7.342 0.899 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=0.2797 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1259 r_free=0.1378 After: r_work=0.1260 r_free=0.1378 ================================== NQH flips ================================== r_work=0.1260 r_free=0.1378 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1260 r_free=0.1378 ========================= Local real-space refinement ========================= Before: r_work=0.1260 r_free=0.1378 31 residues out of total 159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.128 outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 1.6623 time to fit residues: 52.3686 After: r_work=0.1261 r_free=0.1378 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.380808 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 10.876012 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1329 0.1431 0.0102 0.004 0.7 2.6 0.0 0.0 0 0.069 0.1289 0.1398 0.0109 0.004 0.8 2.2 0.0 0.0 0 0.207 0.1279 0.1390 0.0111 0.005 0.9 1.9 0.0 0.0 0 0.414 0.1271 0.1384 0.0113 0.005 0.9 1.9 0.0 0.0 0 0.621 0.1264 0.1379 0.0115 0.006 1.0 1.9 0.0 0.0 0 0.828 0.1261 0.1378 0.0117 0.007 1.0 1.9 0.0 0.0 0 1.036 0.1260 0.1377 0.0117 0.007 1.0 1.9 0.0 0.0 0 1.243 0.1260 0.1377 0.0118 0.008 1.0 1.9 0.0 0.0 0 1.450 0.1267 0.1381 0.0114 0.006 0.9 1.9 0.0 0.0 0 0.690 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1260 0.1377 0.0118 0.008 1.0 1.9 0.0 0.0 0 1.450 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1260 r_free=0.1377 31 residues out of total 159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.120 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1017 After: r_work=0.1260 r_free=0.1377 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.60 13.77 1.18 3.930 14.951 10.876 2.734 12.60 13.77 1.18 3.930 14.951 0.326 2.734 12.60 13.77 1.17 3.910 14.951 1.360 2.734 12.60 13.76 1.17 3.872 14.952 5.438 2.733 12.60 13.77 1.17 3.900 14.952 10.876 2.733 12.61 13.78 1.17 3.907 14.952 16.314 2.734 12.60 13.78 1.18 3.893 14.953 21.752 2.732 12.59 13.78 1.19 3.900 14.953 27.190 2.731 12.61 13.82 1.20 3.873 14.956 32.628 2.733 12.60 13.80 1.20 3.890 14.955 38.066 2.732 12.60 13.82 1.21 3.881 14.957 43.504 2.731 12.61 13.83 1.22 3.881 14.958 48.942 2.732 12.60 13.82 1.22 3.887 14.958 54.380 2.731 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.438 Accepted refinement result: 12.60 13.76 1.17 3.872 14.952 5.438 2.733 Individual atomic B min max mean iso aniso Overall: 4.40 125.50 11.86 3.77 0 1992 Protein: 4.40 125.50 8.59 3.77 0 1636 Water: 5.99 111.25 26.92 N/A 0 356 Chain A: 4.40 125.50 11.86 N/A 0 1992 Histogram: Values Number of atoms 4.40 - 16.51 1654 16.51 - 28.62 174 28.62 - 40.73 102 40.73 - 52.84 36 52.84 - 64.95 16 64.95 - 77.06 3 77.06 - 89.17 4 89.17 - 101.28 0 101.28 - 113.39 1 113.39 - 125.50 2 =========================== Idealize ADP of riding H ========================== r_work=0.1260 r_free=0.1376 r_work=0.1260 r_free=0.1377 ----------X-ray data---------- |--(resolution: 0.78 - 38.64 A, n_refl.=200593 (all), 4.98 % free)-----------| | | | r_work= 0.1260 r_free= 0.1377 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 2.732890 | | target function (ml) not normalized (work): 520877.934051 | | target function (ml) not normalized (free): 28072.860047 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.64 - 2.42 1.00 6454 383 0.1408 0.1508 4.9798 5.0561| | 2: 2.42 - 1.92 1.00 6506 311 0.1201 0.1269 4.3957 4.3945| | 3: 1.92 - 1.68 1.00 6468 320 0.1148 0.1393 3.9265 4.0606| | 4: 1.68 - 1.53 1.00 6448 322 0.1023 0.1144 3.5768 3.667| | 5: 1.53 - 1.42 1.00 6403 359 0.0967 0.1048 3.3346 3.4167| | 6: 1.42 - 1.33 1.00 6456 321 0.0973 0.1128 3.1885 3.3141| | 7: 1.33 - 1.27 1.00 6393 369 0.0926 0.1078 3.071 3.2254| | 8: 1.27 - 1.21 1.00 6415 353 0.0866 0.0900 2.9281 2.9588| | 9: 1.21 - 1.17 1.00 6357 370 0.0857 0.0999 2.8887 3.0405| | 10: 1.17 - 1.12 1.00 6424 323 0.0857 0.0920 2.8164 2.8788| | 11: 1.12 - 1.09 1.00 6445 319 0.0938 0.1026 2.7347 2.8321| | 12: 1.09 - 1.06 1.00 6416 313 0.0939 0.1018 2.6429 2.7659| | 13: 1.06 - 1.03 1.00 6418 327 0.0941 0.1117 2.5452 2.7228| | 14: 1.03 - 1.01 1.00 6413 345 0.0966 0.1082 2.4766 2.5473| | 15: 1.01 - 0.98 1.00 6436 321 0.1047 0.1244 2.3969 2.5343| | 16: 0.98 - 0.96 1.00 6409 338 0.1156 0.1304 2.3544 2.4168| | 17: 0.96 - 0.94 1.00 6356 387 0.1322 0.1609 2.3408 2.4676| | 18: 0.94 - 0.92 1.00 6472 322 0.1488 0.1609 2.3354 2.3687| | 19: 0.92 - 0.91 1.00 6398 335 0.1778 0.1843 2.3325 2.3973| | 20: 0.91 - 0.89 1.00 6353 339 0.2044 0.2305 2.2912 2.3024| | 21: 0.89 - 0.88 1.00 6387 369 0.2121 0.2307 2.3907 2.4949| | 22: 0.88 - 0.86 1.00 6461 354 0.2246 0.2170 2.2888 2.2619| | 23: 0.86 - 0.85 1.00 6331 321 0.2345 0.2505 2.2793 2.3499| | 24: 0.85 - 0.84 1.00 6438 348 0.2474 0.2611 2.2538 2.3011| | 25: 0.84 - 0.83 1.00 6382 320 0.2697 0.2675 2.2372 2.2698| | 26: 0.83 - 0.82 0.99 6426 322 0.2853 0.2828 2.2115 2.2052| | 27: 0.82 - 0.81 0.99 6344 346 0.3103 0.3095 2.1891 2.1816| | 28: 0.81 - 0.80 0.96 6170 310 0.3355 0.3381 2.1589 2.1633| | 29: 0.80 - 0.79 0.90 5797 271 0.3561 0.3536 2.1157 2.1043| | 30: 0.79 - 0.78 0.84 5420 259 0.3835 0.3819 2.0526 2.0504| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 38.64 - 2.42 6454 383 0.92 14.09 1.00 1.00 3498.95| | 2: 2.42 - 1.92 6506 311 0.94 11.44 1.00 0.99 1076.98| | 3: 1.92 - 1.68 6468 320 0.94 11.65 1.00 0.99 435.73| | 4: 1.68 - 1.53 6448 322 0.95 9.21 1.00 1.01 194.62| | 5: 1.53 - 1.42 6403 359 0.96 8.22 1.01 1.00 115.15| | 6: 1.42 - 1.33 6456 321 0.96 9.06 1.01 1.01 95.54| | 7: 1.33 - 1.27 6393 369 0.96 8.60 1.00 0.99 73.84| | 8: 1.27 - 1.21 6415 353 0.96 7.24 1.00 0.99 51.75| | 9: 1.21 - 1.17 6357 370 0.96 7.41 0.99 0.98 49.37| | 10: 1.17 - 1.12 6424 323 0.97 7.14 1.01 0.99 42.08| | 11: 1.12 - 1.09 6445 319 0.97 7.07 1.04 1.03 33.52| | 12: 1.09 - 1.06 6416 313 0.96 8.32 1.03 1.02 31.66| | 13: 1.06 - 1.03 6418 327 0.96 9.00 1.02 1.01 27.13| | 14: 1.03 - 1.01 6413 345 0.96 8.71 1.01 1.00 21.82| | 15: 1.01 - 0.98 6436 321 0.96 9.69 0.99 0.99 19.48| | 16: 0.98 - 0.96 6409 338 0.95 10.10 0.97 0.97 17.01| | 17: 0.96 - 0.94 6356 387 0.94 11.80 0.95 0.93 16.87| | 18: 0.94 - 0.92 6472 322 0.94 12.86 0.93 0.92 16.62| | 19: 0.92 - 0.91 6398 335 0.93 14.26 0.90 0.90 16.40| | 20: 0.91 - 0.89 6353 339 0.92 15.44 0.88 0.86 15.39| | 21: 0.89 - 0.88 6387 369 0.89 19.05 1.07 0.97 16.65| | 22: 0.88 - 0.86 6461 354 0.89 19.15 1.10 1.07 15.60| | 23: 0.86 - 0.85 6331 321 0.87 21.29 1.06 1.02 16.14| | 24: 0.85 - 0.84 6438 348 0.83 25.10 1.04 0.97 18.15| | 25: 0.84 - 0.83 6382 320 0.82 26.78 0.99 0.94 17.34| | 26: 0.83 - 0.82 6426 322 0.81 27.77 0.96 0.91 16.46| | 27: 0.82 - 0.81 6344 346 0.79 29.21 0.93 0.88 15.82| | 28: 0.81 - 0.80 6170 310 0.76 31.53 0.88 0.82 15.96| | 29: 0.80 - 0.79 5797 271 0.72 35.01 0.85 0.75 16.26| | 30: 0.79 - 0.78 5420 259 0.67 39.41 0.80 0.66 16.63| |alpha: min = 0.62 max = 1.08 mean = 0.96| |beta: min = 14.80 max = 4735.95 mean = 203.65| |figures of merit: min = 0.00 max = 1.00 mean = 0.90| |phase err.(work): min = 0.00 max = 90.00 mean = 15.64| |phase err.(test): min = 0.00 max = 89.73 mean = 15.69| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1266 0.1260 0.1377 n_refl.: 200593 re-set all scales: r(all,work,free)=0.1774 0.1785 0.1629 n_refl.: 200593 remove outliers: r(all,work,free)=0.1774 0.1785 0.1629 n_refl.: 200593 overall B=0.00 to atoms: r(all,work,free)=0.1774 0.1785 0.1629 n_refl.: 200593 bulk-solvent and scaling: r(all,work,free)=0.1265 0.1260 0.1375 n_refl.: 200593 remove outliers: r(all,work,free)=0.1265 0.1260 0.1375 n_refl.: 200593 ======================== 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 38.636-10.170 99.01 94 6 0.1720 243.035 238.315 0.857 1.005 0.390 10.167-7.973 99.01 98 2 0.1772 211.585 201.060 0.892 1.006 0.404 7.970-6.248 99.54 206 11 0.1937 178.224 170.534 0.869 1.004 0.405 6.247-4.898 99.54 395 37 0.1726 213.284 207.508 0.882 1.005 0.385 4.897-3.840 99.66 838 50 0.1349 268.351 264.319 0.898 1.005 0.321 3.839-3.010 99.68 1748 112 0.1344 243.543 238.919 0.917 1.004 0.177 3.009-2.359 99.77 3641 184 0.1350 162.406 159.892 0.919 1.004 0.111 2.359-1.850 99.95 7566 372 0.1191 121.429 119.985 0.976 1.003 0.000 1.849-1.450 99.93 15594 806 0.1049 68.480 67.737 1.004 1.001 0.000 1.450-1.137 99.88 32223 1744 0.0905 42.917 42.621 1.038 0.998 0.000 1.136-0.891 99.91 66879 3493 0.1154 21.039 21.045 1.073 0.993 0.000 0.891-0.780 96.83 61314 3180 0.2741 8.066 7.294 0.899 0.988 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=0.2969 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.1768 0.1641 0.014 1.522 4.3 139.2 11.7 1068 0.000 1_bss: 0.1335 0.1435 0.014 1.522 4.4 139.3 11.8 1068 0.000 1_settarget: 0.1335 0.1435 0.014 1.522 4.4 139.3 11.8 1068 0.000 1_nqh: 0.1335 0.1435 0.014 1.522 4.4 139.3 11.8 1068 0.000 1_realsrl: 0.1333 0.1436 0.014 1.522 4.4 139.3 11.8 1068 0.018 1_weight: 0.1333 0.1436 0.014 1.522 4.4 139.3 11.8 1068 0.018 1_xyzrec: 0.1346 0.1472 0.007 0.844 4.4 139.3 11.8 1068 0.113 1_realsrl2: 0.1346 0.1472 0.007 0.844 4.4 139.3 11.8 1068 0.113 1_adp: 0.1347 0.1472 0.007 0.844 4.4 135.2 11.8 1068 0.113 1_regHadp: 0.1343 0.1469 0.007 0.844 4.4 135.2 11.8 1068 0.113 2_bss: 0.1340 0.1467 0.007 0.844 4.4 135.2 11.8 1068 0.113 2_settarget: 0.1340 0.1467 0.007 0.844 4.4 135.2 11.8 1068 0.113 2_updatecdl: 0.1340 0.1467 0.007 0.846 4.4 135.2 11.8 1068 0.113 2_nqh: 0.1340 0.1467 0.007 0.846 4.4 135.2 11.8 1068 0.113 2_realsrl: 0.1341 0.1464 0.007 0.846 4.4 135.2 11.8 1068 0.116 2_weight: 0.1341 0.1464 0.007 0.846 4.4 135.2 11.8 1068 0.116 2_xyzrec: 0.1339 0.1477 0.006 0.801 4.4 135.2 11.8 1068 0.129 2_realsrl2: 0.1339 0.1477 0.006 0.801 4.4 135.2 11.8 1068 0.129 2_adp: 0.1339 0.1477 0.006 0.801 4.4 134.6 11.8 1068 0.129 2_regHadp: 0.1339 0.1477 0.006 0.801 4.4 134.6 11.8 1068 0.129 3_bss: 0.1339 0.1476 0.006 0.801 4.4 134.6 11.8 1068 0.129 3_settarget: 0.1339 0.1476 0.006 0.801 4.4 134.6 11.8 1068 0.129 3_updatecdl: 0.1339 0.1476 0.006 0.803 4.4 134.6 11.8 1068 0.129 3_nqh: 0.1339 0.1476 0.006 0.803 4.4 134.6 11.8 1068 0.129 3_realsrl: 0.1339 0.1473 0.006 0.803 4.4 134.6 11.8 1068 0.129 3_weight: 0.1339 0.1473 0.006 0.803 4.4 134.6 11.8 1068 0.129 3_xyzrec: 0.1292 0.1405 0.008 1.018 4.4 134.6 11.8 1068 0.113 3_realsrl2: 0.1292 0.1405 0.008 1.018 4.4 134.6 11.8 1068 0.113 3_adp: 0.1265 0.1392 0.008 1.018 4.3 130.7 11.8 1068 0.113 3_regHadp: 0.1265 0.1392 0.008 1.018 4.3 130.7 11.8 1068 0.113 4_bss: 0.1269 0.1397 0.008 1.018 4.3 130.7 11.8 1068 0.113 4_settarget: 0.1269 0.1397 0.008 1.018 4.3 130.7 11.8 1068 0.113 4_updatecdl: 0.1269 0.1397 0.008 1.020 4.3 130.7 11.8 1068 0.113 4_nqh: 0.1269 0.1397 0.008 1.020 4.3 130.7 11.8 1068 0.113 4_realsrl: 0.1273 0.1400 0.008 1.020 4.3 130.7 11.8 1068 0.116 4_weight: 0.1273 0.1400 0.008 1.020 4.3 130.7 11.8 1068 0.116 4_xyzrec: 0.1267 0.1394 0.007 0.989 4.3 130.7 11.8 1068 0.113 4_realsrl2: 0.1267 0.1394 0.007 0.989 4.3 130.7 11.8 1068 0.113 4_adp: 0.1262 0.1380 0.007 0.989 4.4 127.6 11.9 1068 0.113 4_regHadp: 0.1262 0.1380 0.007 0.989 4.4 127.6 11.9 1068 0.113 5_bss: 0.1259 0.1378 0.007 0.989 4.4 127.6 11.9 1068 0.113 5_settarget: 0.1259 0.1378 0.007 0.989 4.4 127.6 11.9 1068 0.113 5_updatecdl: 0.1259 0.1378 0.007 0.989 4.4 127.6 11.9 1068 0.113 5_setrh: 0.1260 0.1378 0.007 0.989 4.4 127.6 11.9 1068 0.112 5_nqh: 0.1260 0.1378 0.007 0.989 4.4 127.6 11.9 1068 0.112 5_realsrl: 0.1261 0.1378 0.007 0.989 4.4 127.6 11.9 1068 0.113 5_weight: 0.1261 0.1378 0.007 0.989 4.4 127.6 11.9 1068 0.113 5_xyzrec: 0.1260 0.1377 0.008 1.003 4.4 127.6 11.9 1068 0.112 5_realsrl2: 0.1260 0.1377 0.008 1.003 4.4 127.6 11.9 1068 0.112 5_adp: 0.1260 0.1376 0.008 1.003 4.4 125.5 11.9 1068 0.112 5_regHadp: 0.1260 0.1377 0.008 1.003 4.4 125.5 11.9 1068 0.112 end: 0.1260 0.1375 0.008 1.003 4.4 125.5 11.9 1068 0.112 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/6ZM8_complete_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/6ZM8_complete_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.5200 Refinement macro-cycles (run) : 2206.1000 Write final files (write_after_run_outputs) : 110.3100 Total : 2318.9300 Total CPU time: 39.02 minutes =========================== phenix.refine: finished =========================== # Date 2024-04-10 Time 16:56:03 PDT -0700 (1712793363.75 s) Start R-work = 0.1335, R-free = 0.1435 Final R-work = 0.1260, R-free = 0.1375 =============================================================================== Job complete usr+sys time: 2539.38 seconds wall clock time: 60 minutes 3.98 seconds (3603.98 seconds total)