Starting phenix.refine on Mon May 20 17:17:36 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=True 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 { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 4856 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2428 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 144} Chain: "C" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2428 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 144} Time building chain proxies: 1.71, per 1000 atoms: 0.35 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: 3.45 Conformation dependent library (CDL) restraints added in 767.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 4 sheets defined 36.8% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 431 through 442 removed outlier: 4.526A pdb=" N ARG A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 468 through 476 removed outlier: 3.574A pdb=" N MSE A 474 " --> pdb=" O SER A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 500 Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 532 through 539 removed outlier: 3.513A pdb=" N LYS A 539 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 577 Processing helix chain 'C' and resid 431 through 442 removed outlier: 4.517A pdb=" N ARG C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 448 No H-bonds generated for 'chain 'C' and resid 446 through 448' Processing helix chain 'C' and resid 453 through 455 No H-bonds generated for 'chain 'C' and resid 453 through 455' Processing helix chain 'C' and resid 468 through 476 removed outlier: 3.543A pdb=" N MSE C 474 " --> pdb=" O SER C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 500 Processing helix chain 'C' and resid 505 through 507 No H-bonds generated for 'chain 'C' and resid 505 through 507' Processing helix chain 'C' and resid 511 through 518 Processing helix chain 'C' and resid 532 through 539 removed outlier: 3.519A pdb=" N LYS C 539 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 577 Processing sheet with id= A, first strand: chain 'A' and resid 524 through 526 removed outlier: 7.505A pdb=" N VAL A 525 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE A 547 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 565 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG A 550 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL A 563 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN A 552 " --> pdb=" O TYR A 561 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR A 561 " --> pdb=" O ASN A 552 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 480 through 484 Processing sheet with id= C, first strand: chain 'C' and resid 524 through 526 removed outlier: 7.590A pdb=" N VAL C 525 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE C 547 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY C 565 " --> pdb=" O VAL C 548 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG C 550 " --> pdb=" O VAL C 563 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL C 563 " --> pdb=" O ARG C 550 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN C 552 " --> pdb=" O TYR C 561 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR C 561 " --> pdb=" O ASN C 552 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 480 through 484 66 hydrogen bonds defined for protein. 138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 2.22 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: 221 2.03 - 2.72: 7474 2.72 - 3.41: 16274 3.41 - 4.11: 21898 4.11 - 4.80: 34964 Nonbonded interactions: 80831 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 80826 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 { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 431 through 442 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 446 through 448 helix_type = alpha pi *3_10 unknown } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 453 through 455 helix_type = alpha pi *3_10 unknown } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 468 through 476 helix_type = alpha pi *3_10 unknown } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 497 through 500 helix_type = alpha pi *3_10 unknown } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 505 through 507 helix_type = alpha pi *3_10 unknown } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 511 through 518 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 532 through 539 helix_type = alpha pi *3_10 unknown } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 569 through 577 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'C' and resid 431 through 442 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'C' and resid 446 through 448 helix_type = alpha pi *3_10 unknown } helix { serial_number = "12" helix_identifier = "12" selection = chain 'C' and resid 453 through 455 helix_type = alpha pi *3_10 unknown } helix { serial_number = "13" helix_identifier = "13" selection = chain 'C' and resid 468 through 476 helix_type = alpha pi *3_10 unknown } helix { serial_number = "14" helix_identifier = "14" selection = chain 'C' and resid 497 through 500 helix_type = alpha pi *3_10 unknown } helix { serial_number = "15" helix_identifier = "15" selection = chain 'C' and resid 505 through 507 helix_type = alpha pi *3_10 unknown } helix { serial_number = "16" helix_identifier = "16" selection = chain 'C' and resid 511 through 518 } helix { serial_number = "17" helix_identifier = "17" selection = chain 'C' and resid 532 through 539 helix_type = alpha pi *3_10 unknown } helix { serial_number = "18" helix_identifier = "18" selection = chain 'C' and resid 569 through 577 } sheet { first_strand = chain 'A' and resid 524 through 526 sheet_id = " A" strand { selection = chain 'A' and resid 545 through 552 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 547 and name N bond_start_previous = chain 'A' and resid 525 and name O } strand { selection = chain 'A' and resid 560 through 568 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 567 and name N bond_start_previous = chain 'A' and resid 546 and name O } } sheet { first_strand = chain 'A' and resid 480 through 484 sheet_id = " B" strand { selection = chain 'A' and resid 491 through 496 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 495 and name N bond_start_previous = chain 'A' and resid 481 and name O } } sheet { first_strand = chain 'C' and resid 524 through 526 sheet_id = " C" strand { selection = chain 'C' and resid 545 through 552 sense = *parallel antiparallel unknown bond_start_current = chain 'C' and resid 547 and name N bond_start_previous = chain 'C' and resid 525 and name O } strand { selection = chain 'C' and resid 560 through 568 sense = parallel *antiparallel unknown bond_start_current = chain 'C' and resid 567 and name N bond_start_previous = chain 'C' and resid 546 and name O } } sheet { first_strand = chain 'C' and resid 480 through 484 sheet_id = " D" strand { selection = chain 'C' and resid 491 through 496 sense = parallel *antiparallel unknown bond_start_current = chain 'C' and resid 495 and name N bond_start_previous = chain 'C' and resid 481 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "4iy2_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2418 occupancy sum: 2418.00 (% of total atoms 49.89) Rotatable: count: 714 occupancy sum: 714.00 (% of total atoms 14.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.60 - 42.85 A, n_refl.=6670 (all), 4.74 % free)-------------| | | | r_work= 0.6305 r_free= 0.6362 coordinate error (max.-lik. estimate): 0.17 A | | | | normalized target function (ml) (work): 6.476566 | | target function (ml) not normalized (work): 41152.101576 | | target function (ml) not normalized (free): 2067.378995 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 42.85 - 4.54 1.00 3313 159 0.5995 0.6281 7.0436 7.1411| | 2: 4.54 - 3.60 0.95 3041 157 0.6997 0.6514 5.8588 5.936| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 42.85 - 4.54 3313 159 0.29 67.64 0.94 0.33 277885.05| | 2: 4.54 - 3.60 3041 157 0.70 35.82 3.03 0.97 23390.81| |alpha: min = 0.33 max = 0.97 mean = 0.63| |beta: min = 23390.81 max = 277885.05 mean = 156085.09| |figures of merit: min = 0.00 max = 1.00 mean = 0.48| |phase err.(work): min = 0.00 max = 89.99 mean = 52.41| |phase err.(test): min = 0.00 max = 89.77 mean = 51.68| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 2480 Z= 0.511 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 = 11.753209 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 0.2658 0.2994 0.0337 0.015 1.2 14.8 1.7 5.4 0 5.877 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 26.58 29.94 3.37 5.478 103.625 0.161 0.086 26.63 29.88 3.24 5.087 104.039 0.005 0.086 26.43 29.70 3.28 5.107 104.059 0.020 0.085 25.71 29.24 3.53 6.169 104.681 0.080 0.082 24.90 29.12 4.22 8.464 105.028 0.161 0.078 24.79 29.01 4.22 8.482 104.841 0.241 0.078 24.73 28.97 4.24 8.613 104.801 0.322 0.077 24.57 28.88 4.31 9.319 105.054 0.402 0.077 24.46 28.86 4.40 9.858 105.247 0.482 0.076 24.38 28.84 4.46 10.241 105.364 0.563 0.076 24.39 28.85 4.46 10.176 105.292 0.643 0.076 24.10 28.82 4.71 12.151 106.102 0.724 0.075 24.06 28.86 4.80 12.817 106.320 0.804 0.075 max suggested for this run: 20.73 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.724 Accepted refinement result: 24.10 28.82 4.71 12.151 106.102 0.724 0.075 Individual atomic B min max mean iso aniso Overall: 61.58 253.96 109.81 12.76 2438 0 Protein: 61.58 253.96 109.81 12.76 2438 0 Chain A: 65.97 253.96 109.83 N/A 1219 0 Chain C: 61.58 253.63 109.79 N/A 1219 0 Histogram: Values Number of atoms 61.58 - 80.82 171 80.82 - 100.05 884 100.05 - 119.29 751 119.29 - 138.53 261 138.53 - 157.77 137 157.77 - 177.01 199 177.01 - 196.24 30 196.24 - 215.48 3 215.48 - 234.72 0 234.72 - 253.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.2410 r_free=0.2882 r_work=0.2397 r_free=0.2858 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.60 - 36.79 A, n_refl.=6654 (all), 4.72 % free)-------------| | | | r_work= 0.2397 r_free= 0.2858 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ls_wunit_k1) (work): 0.073804 | | target function (ls_wunit_k1) not normalized (work): 467.914872 | | target function (ls_wunit_k1) not normalized (free): 25.852290 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2418 0.2397 0.2858 n_refl.: 6654 re-set all scales: r(all,work,free)=0.5520 0.5518 0.5401 n_refl.: 6654 remove outliers: r(all,work,free)=0.5520 0.5518 0.5401 n_refl.: 6654 overall B=0.00 to atoms: r(all,work,free)=0.5520 0.5518 0.5401 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2384 0.2361 0.2869 n_refl.: 6654 remove outliers: r(all,work,free)=0.2384 0.2361 0.2869 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 0.4403 1147.286 988.520 1.199 1.074 0.358 15.485-12.238 97.00 96 1 0.1956 1149.981 1177.690 1.219 1.069 0.340 12.212-9.617 100.00 192 10 0.1460 1231.706 1193.689 1.176 1.059 0.300 9.605-7.558 100.00 374 15 0.1781 774.203 775.999 1.227 1.037 0.290 7.551-5.945 99.50 761 39 0.2439 423.788 406.654 1.007 1.003 0.240 5.945-4.677 99.31 1515 77 0.2157 371.634 357.844 0.989 0.945 0.160 4.676-3.603 95.60 3309 171 0.2696 261.483 249.054 1.236 0.852 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=0.0728 ============================ 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 = 3.939952 wxc_scale = 0.063 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.045650 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 0.2586 0.2911 0.0325 0.003 0.5 3.1 0.3 4.3 0 0.025 0.2538 0.2890 0.0352 0.003 0.5 3.1 0.3 4.3 0 0.074 0.2473 0.2890 0.0416 0.004 0.6 4.5 0.0 4.3 0 0.148 0.2439 0.2915 0.0476 0.004 0.6 5.8 0.0 4.3 0 0.223 0.2420 0.2932 0.0512 0.005 0.7 6.4 0.0 4.3 0 0.297 0.2400 0.2955 0.0555 0.006 0.7 7.4 0.3 4.7 0 0.371 0.2385 0.2969 0.0584 0.006 0.7 8.7 1.0 4.7 0 0.445 0.2366 0.2956 0.0591 0.007 0.8 10.3 1.3 5.0 0 0.519 0.2434 0.2921 0.0486 0.005 0.6 6.2 0.0 4.3 0 0.247 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2538 0.2890 0.0352 0.003 0.5 3.1 0.3 4.3 0 0.074 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.38 28.90 3.52 17.973 119.356 0.046 6.189 29.34 30.65 1.31 15.494 126.773 0.001 6.252 28.49 29.93 1.44 15.084 125.739 0.006 6.229 26.48 28.45 1.97 16.077 123.815 0.023 6.170 25.47 27.76 2.30 17.821 123.409 0.046 6.137 24.80 27.94 3.14 18.022 121.950 0.068 6.133 24.60 27.85 3.26 18.621 122.101 0.091 6.128 24.47 27.84 3.37 19.114 122.249 0.114 6.126 24.38 27.82 3.44 19.486 122.369 0.137 6.124 24.32 27.78 3.46 19.880 122.555 0.160 6.122 24.28 27.75 3.47 20.127 122.638 0.183 6.121 24.24 27.73 3.49 20.442 122.789 0.205 6.119 24.21 27.73 3.51 20.641 122.866 0.228 6.119 max suggested for this run: 23.87 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.228 Accepted refinement result: 24.21 27.73 3.51 20.641 122.866 0.228 6.119 Individual atomic B min max mean iso aniso Overall: 56.58 281.29 116.81 21.23 2438 0 Protein: 56.58 281.29 116.81 21.23 2438 0 Chain A: 60.99 279.62 116.87 N/A 1219 0 Chain C: 56.58 281.29 116.74 N/A 1219 0 Histogram: Values Number of atoms 56.58 - 79.05 141 79.05 - 101.52 748 101.52 - 123.99 702 123.99 - 146.46 401 146.46 - 168.93 300 168.93 - 191.41 116 191.41 - 213.88 25 213.88 - 236.35 3 236.35 - 258.82 0 258.82 - 281.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.2421 r_free=0.2773 r_work=0.2420 r_free=0.2765 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.60 - 36.79 A, n_refl.=6654 (all), 4.72 % free)-------------| | | | r_work= 0.2420 r_free= 0.2765 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 6.115301 | | target function (ml) not normalized (work): 38771.006372 | | target function (ml) not normalized (free): 1950.798648 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2435 0.2420 0.2765 n_refl.: 6654 re-set all scales: r(all,work,free)=0.5745 0.5749 0.5473 n_refl.: 6654 remove outliers: r(all,work,free)=0.5745 0.5749 0.5473 n_refl.: 6654 overall B=-10.55 to atoms: r(all,work,free)=0.5409 0.5413 0.5145 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2462 0.2444 0.2834 n_refl.: 6654 remove outliers: r(all,work,free)=0.2462 0.2444 0.2834 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 0.4570 1147.286 1069.208 1.507 0.973 0.355 15.485-12.238 97.00 96 1 0.2193 1149.981 1115.193 1.300 0.979 0.330 12.212-9.617 100.00 192 10 0.1618 1231.706 1193.221 1.344 0.981 0.306 9.605-7.558 100.00 374 15 0.2156 774.203 744.900 1.304 0.980 0.291 7.551-5.945 99.50 761 39 0.2794 423.788 394.929 1.054 0.980 0.244 5.945-4.677 99.31 1515 77 0.2405 371.634 346.345 0.956 0.977 0.166 4.676-3.603 95.60 3309 171 0.2429 261.483 250.751 1.032 0.977 0.094 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.9576 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2444 r_free=0.2834 After: r_work=0.2445 r_free=0.2833 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.118722 wxc_scale = 0.029 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.043486 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 0.2449 0.2836 0.0387 0.003 0.5 4.1 0.0 4.3 0 0.012 0.2447 0.2832 0.0386 0.003 0.5 3.9 0.0 4.3 0 0.036 0.2445 0.2832 0.0387 0.003 0.5 3.9 0.0 4.3 0 0.072 0.2444 0.2829 0.0385 0.003 0.5 3.9 0.0 4.3 0 0.107 0.2441 0.2832 0.0391 0.003 0.5 3.9 0.0 4.3 0 0.143 0.2439 0.2830 0.0391 0.003 0.5 4.1 0.0 4.3 0 0.179 0.2435 0.2830 0.0396 0.003 0.5 4.1 0.0 4.3 0 0.215 0.2431 0.2827 0.0396 0.003 0.5 3.9 0.0 4.3 0 0.250 0.2443 0.2829 0.0386 0.003 0.5 3.7 0.0 4.3 0 0.119 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2443 0.2829 0.0386 0.003 0.5 3.7 0.0 4.3 0 0.119 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.43 28.29 3.86 22.379 116.131 0.043 6.137 28.85 29.07 0.22 17.967 124.599 0.001 6.222 28.08 28.65 0.56 17.444 123.559 0.005 6.207 26.30 27.58 1.28 17.774 120.542 0.022 6.172 25.52 27.31 1.79 18.699 119.462 0.043 6.151 24.91 27.35 2.44 19.320 118.627 0.065 6.136 24.65 27.35 2.70 19.761 118.846 0.087 6.129 24.23 27.32 3.09 20.174 118.443 0.109 6.119 24.01 27.37 3.36 20.696 118.147 0.130 6.115 23.89 27.43 3.54 21.157 117.964 0.152 6.112 23.80 27.48 3.68 21.509 118.125 0.174 6.110 23.73 27.52 3.78 21.850 118.265 0.196 6.108 23.68 27.57 3.89 22.168 118.401 0.217 6.106 max suggested for this run: 23.23 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.043 Accepted refinement result: 25.52 27.31 1.79 18.699 119.462 0.043 6.151 Individual atomic B min max mean iso aniso Overall: 50.62 265.74 112.89 13.59 2438 0 Protein: 50.62 265.74 112.89 13.59 2438 0 Chain A: 53.70 264.07 112.97 N/A 1219 0 Chain C: 50.62 265.74 112.81 N/A 1219 0 Histogram: Values Number of atoms 50.62 - 72.14 34 72.14 - 93.65 491 93.65 - 115.16 1011 115.16 - 136.67 475 136.67 - 158.18 247 158.18 - 179.69 143 179.69 - 201.20 33 201.20 - 222.71 2 222.71 - 244.23 0 244.23 - 265.74 2 =========================== Idealize ADP of riding H ========================== r_work=0.2552 r_free=0.2731 r_work=0.2576 r_free=0.2741 ----------X-ray data---------- |--(resolution: 3.60 - 36.79 A, n_refl.=6654 (all), 4.72 % free)-------------| | | | r_work= 0.2576 r_free= 0.2741 coordinate error (max.-lik. estimate): 0.22 A | | | | normalized target function (ml) (work): 6.159077 | | target function (ml) not normalized (work): 39048.546754 | | target function (ml) not normalized (free): 1946.068822 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2524 0.2653 6.5159 6.5123| | 2: 4.54 - 3.60 0.95 3036 156 0.2691 0.2914 5.7708 5.8791| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 30.39 0.99 1.02 66790.16| | 2: 4.54 - 3.60 3036 156 0.78 28.42 1.05 1.00 18595.29| |alpha: min = 1.00 max = 1.02 mean = 1.01| |beta: min = 18595.29 max = 66790.16 mean = 43711.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.76| |phase err.(work): min = 0.00 max = 89.82 mean = 29.45| |phase err.(test): min = 0.00 max = 89.54 mean = 28.49| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2583 0.2576 0.2741 n_refl.: 6654 re-set all scales: r(all,work,free)=0.5698 0.5701 0.5454 n_refl.: 6654 remove outliers: r(all,work,free)=0.5698 0.5701 0.5454 n_refl.: 6654 overall B=-6.52 to atoms: r(all,work,free)=0.5493 0.5496 0.5257 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2572 0.2562 0.2775 n_refl.: 6654 remove outliers: r(all,work,free)=0.2572 0.2562 0.2775 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 0.4543 1147.286 1071.911 1.491 0.979 0.354 15.485-12.238 97.00 96 1 0.2206 1149.981 1100.283 1.286 0.984 0.333 12.212-9.617 100.00 192 10 0.1624 1231.706 1197.898 1.362 0.986 0.314 9.605-7.558 100.00 374 15 0.2254 774.203 745.538 1.309 0.983 0.297 7.551-5.945 99.50 761 39 0.2825 423.788 393.898 1.062 0.981 0.249 5.945-4.677 99.31 1515 77 0.2433 371.634 345.523 0.970 0.975 0.170 4.676-3.603 95.60 3309 171 0.2705 261.483 249.243 1.060 0.969 0.099 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.9470 ================= 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: 0.2658 0.2994 0.015 1.235 66.6 168.2 104.9 0 0.292 1_adp: 0.2410 0.2882 0.015 1.235 61.6 254.0 109.8 0 0.292 1_regHadp: 0.2397 0.2858 0.015 1.235 61.6 254.0 109.8 0 0.292 2_bss: 0.2361 0.2869 0.015 1.235 61.6 254.0 109.8 0 0.292 2_settarget: 0.2361 0.2869 0.015 1.235 61.6 254.0 109.8 0 0.292 2_updatecdl: 0.2361 0.2869 0.015 1.282 61.6 254.0 109.8 0 0.292 2_weight: 0.2361 0.2869 0.015 1.282 61.6 254.0 109.8 0 0.292 2_xyzrec: 0.2538 0.2890 0.003 0.528 61.6 254.0 109.8 0 0.272 2_adp: 0.2421 0.2773 0.003 0.528 56.6 281.3 116.8 0 0.272 2_regHadp: 0.2420 0.2765 0.003 0.528 56.6 281.3 116.8 0 0.272 3_bss: 0.2444 0.2834 0.003 0.528 46.0 270.7 106.3 0 0.272 3_settarget: 0.2444 0.2834 0.003 0.528 46.0 270.7 106.3 0 0.272 3_updatecdl: 0.2444 0.2834 0.003 0.581 46.0 270.7 106.3 0 0.272 3_setrh: 0.2445 0.2833 0.003 0.581 46.0 270.7 106.3 0 0.272 3_weight: 0.2445 0.2833 0.003 0.581 46.0 270.7 106.3 0 0.272 3_xyzrec: 0.2443 0.2829 0.003 0.532 46.0 270.7 106.3 0 0.272 3_adp: 0.2552 0.2731 0.003 0.532 50.6 265.7 112.9 0 0.272 3_regHadp: 0.2576 0.2741 0.003 0.532 50.6 265.7 112.9 0 0.272 end: 0.2562 0.2775 0.003 0.532 44.1 259.2 106.4 0 0.272 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/4iy2_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/4iy2_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.2000 Refinement macro-cycles (run) : 183.7500 Write final files (write_after_run_outputs) : 19.5000 Total : 210.4500 Total CPU time: 4.06 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:30:57 PDT -0700 (1716251457.46 s) Start R-work = 0.2929, R-free = 0.2829 Final R-work = 0.2562, R-free = 0.2775 =============================================================================== Job complete usr+sys time: 260.32 seconds wall clock time: 13 minutes 55.29 seconds (835.29 seconds total)