Starting phenix.refine on Mon May 20 17:17:37 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1m10.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1m10/1m10.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/1m10.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1m10.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1m10/1m10.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1m10/1m10.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 "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 7468 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3250 Classifications: {'peptide': 199} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "B" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 4218 Classifications: {'peptide': 267} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 246} Time building chain proxies: 2.50, per 1000 atoms: 0.33 Number of scatterers: 7468 At special positions: 0 Unit cell: (89.84, 89.84, 124.63, 90, 90, 120) Space group: P 61 (No. 169) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 682 8.00 N 628 7.00 C 2366 6.00 H 3778 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 509 " - pdb=" SG CYS A 695 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 17 " distance=2.03 Simple disulfide: pdb=" SG CYS B 209 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 211 " - pdb=" SG CYS B 264 " distance=2.04 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: 7.01 Conformation dependent library (CDL) restraints added in 880.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 886 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 5 sheets defined 21.7% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 527 through 542 removed outlier: 3.711A pdb=" N VAL A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 594 through 604 Processing helix chain 'A' and resid 628 through 644 removed outlier: 4.322A pdb=" N ARG A 632 " --> pdb=" O ARG A 629 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN A 633 " --> pdb=" O MET A 630 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL A 635 " --> pdb=" O ARG A 632 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 641 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 666 Processing helix chain 'A' and resid 680 through 695 removed outlier: 4.470A pdb=" N GLU A 684 " --> pdb=" O ASP A 681 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG A 687 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASP A 688 " --> pdb=" O GLN A 685 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 694 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 214 through 226 removed outlier: 6.240A pdb=" N GLU B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing sheet with id= A, first strand: chain 'A' and resid 646 through 650 removed outlier: 6.410A pdb=" N ARG A 616 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE A 649 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA A 618 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS A 559 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.355A pdb=" N PHE A 675 " --> pdb=" O GLY A 652 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 5 through 9 removed outlier: 6.610A pdb=" N ILE B 35 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLN B 59 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR B 81 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 104 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU B 128 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS B 152 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR B 176 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE B 199 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 45 through 47 removed outlier: 6.794A pdb=" N LYS B 69 " --> pdb=" O PHE B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 228 through 232 82 hydrogen bonds defined for protein. 177 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: 6.03 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 3777 1.15 - 1.32: 698 1.32 - 1.49: 1420 1.49 - 1.67: 1630 1.67 - 1.84: 19 Bond restraints: 7544 Sorted by residual: bond pdb=" N VAL B 256 " pdb=" H VAL B 256 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLU A 700 " pdb=" H GLU A 700 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N SER B 114 " pdb=" H SER B 114 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" ND1 HIS A 563 " pdb=" HD1 HIS A 563 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N HIS B 195 " pdb=" H HIS B 195 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 7539 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.21: 392 106.21 - 113.18: 8799 113.18 - 120.15: 2310 120.15 - 127.12: 2204 127.12 - 134.09: 31 Bond angle restraints: 13736 Sorted by residual: angle pdb=" N VAL B 78 " pdb=" CA VAL B 78 " pdb=" C VAL B 78 " ideal model delta sigma weight residual 112.43 120.71 -8.28 9.20e-01 1.18e+00 8.10e+01 angle pdb=" C LEU B 76 " pdb=" N PRO B 77 " pdb=" CA PRO B 77 " ideal model delta sigma weight residual 119.84 130.41 -10.57 1.25e+00 6.40e-01 7.15e+01 angle pdb=" C LEU B 197 " pdb=" N PRO B 198 " pdb=" CA PRO B 198 " ideal model delta sigma weight residual 119.56 127.99 -8.43 1.02e+00 9.61e-01 6.83e+01 angle pdb=" N ILE B 213 " pdb=" CA ILE B 213 " pdb=" C ILE B 213 " ideal model delta sigma weight residual 112.90 105.33 7.57 9.60e-01 1.09e+00 6.21e+01 angle pdb=" N ARG A 511 " pdb=" CA ARG A 511 " pdb=" C ARG A 511 " ideal model delta sigma weight residual 108.45 118.26 -9.81 1.26e+00 6.30e-01 6.06e+01 ... (remaining 13731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 3167 17.57 - 35.14: 236 35.14 - 52.71: 102 52.71 - 70.28: 32 70.28 - 87.84: 4 Dihedral angle restraints: 3541 sinusoidal: 1982 harmonic: 1559 Sorted by residual: dihedral pdb=" CA LYS A 585 " pdb=" CB LYS A 585 " pdb=" CG LYS A 585 " pdb=" CD LYS A 585 " ideal model delta sinusoidal sigma weight residual -60.00 -118.49 58.49 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLN B 159 " pdb=" CB GLN B 159 " pdb=" CG GLN B 159 " pdb=" CD GLN B 159 " ideal model delta sinusoidal sigma weight residual 60.00 113.33 -53.33 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" C HIS B 195 " pdb=" N HIS B 195 " pdb=" CA HIS B 195 " pdb=" CB HIS B 195 " ideal model delta harmonic sigma weight residual -122.60 -115.04 -7.56 0 2.50e+00 1.60e-01 9.15e+00 ... (remaining 3538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 349 0.080 - 0.160: 177 0.160 - 0.240: 54 0.240 - 0.320: 12 0.320 - 0.400: 4 Chirality restraints: 596 Sorted by residual: chirality pdb=" CA PRO B 2 " pdb=" N PRO B 2 " pdb=" C PRO B 2 " pdb=" CB PRO B 2 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA GLN B 21 " pdb=" N GLN B 21 " pdb=" C GLN B 21 " pdb=" CB GLN B 21 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA HIS B 195 " pdb=" N HIS B 195 " pdb=" C HIS B 195 " pdb=" CB HIS B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 593 not shown) Planarity restraints: 1091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 44 " -0.125 2.00e-02 2.50e+03 5.17e-02 8.01e+01 pdb=" CG TYR B 44 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 44 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 44 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 44 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 44 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 44 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 44 " -0.101 2.00e-02 2.50e+03 pdb=" HD1 TYR B 44 " 0.036 2.00e-02 2.50e+03 pdb=" HD2 TYR B 44 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 TYR B 44 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 TYR B 44 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 600 " 0.122 2.00e-02 2.50e+03 4.68e-02 6.58e+01 pdb=" CG TYR A 600 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 600 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 600 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 600 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 600 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 600 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 600 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 TYR A 600 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 TYR A 600 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR A 600 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 600 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 54 " 0.112 2.00e-02 2.50e+03 4.13e-02 5.13e+01 pdb=" CG TYR B 54 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 54 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 54 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 54 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 54 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 54 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR B 54 " 0.042 2.00e-02 2.50e+03 pdb=" HD1 TYR B 54 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 TYR B 54 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR B 54 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 54 " 0.006 2.00e-02 2.50e+03 ... (remaining 1088 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.73: 110 1.73 - 2.45: 4470 2.45 - 3.17: 24469 3.17 - 3.88: 32738 3.88 - 4.60: 50864 Nonbonded interactions: 112651 Sorted by model distance: nonbonded pdb=" HA HIS A 559 " pdb=" HA ALA A 592 " model vdw 1.014 2.440 nonbonded pdb="HH22 ARG A 545 " pdb=" HG3 PRO A 703 " model vdw 1.092 2.270 nonbonded pdb=" HA ARG A 636 " pdb="HH11 ARG A 636 " model vdw 1.130 2.270 nonbonded pdb="HD22 LEU A 512 " pdb="HH21 ARG A 611 " model vdw 1.155 2.270 nonbonded pdb=" OE1 GLU A 613 " pdb=" H GLU A 613 " model vdw 1.278 1.850 ... (remaining 112646 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 14 15.96 2 O 682 7.97 1 N 628 6.97 1 C 2366 5.97 2 H 3778 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: 3778 of 7468 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 7468 n_use_u_iso = 7468 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 = 7468 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (7468 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 7468 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 527 through 542 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 574 through 583 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 594 through 604 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 628 through 644 helix_type = alpha pi *3_10 unknown } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 659 through 666 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 680 through 695 helix_type = alpha pi *3_10 unknown } helix { serial_number = "7" helix_identifier = "7" selection = chain 'B' and resid 48 through 51 helix_type = alpha pi *3_10 unknown } helix { serial_number = "8" helix_identifier = "8" selection = chain 'B' and resid 214 through 226 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'B' and resid 243 through 245 helix_type = alpha pi *3_10 unknown } helix { serial_number = "10" helix_identifier = "10" selection = chain 'B' and resid 256 through 258 helix_type = alpha pi *3_10 unknown } sheet { first_strand = chain 'A' and resid 646 through 650 sheet_id = " A" strand { selection = chain 'A' and resid 615 through 621 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 616 and name N bond_start_previous = chain 'A' and resid 647 and name O } strand { selection = chain 'A' and resid 513 through 520 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 514 and name N bond_start_previous = chain 'A' and resid 615 and name O } strand { selection = chain 'A' and resid 551 through 559 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 552 and name N bond_start_previous = chain 'A' and resid 513 and name O } strand { selection = chain 'A' and resid 561 through 564 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 563 and name N bond_start_previous = chain 'A' and resid 557 and name O } } sheet { first_strand = chain 'A' and resid 651 through 653 sheet_id = " B" strand { selection = chain 'A' and resid 675 through 677 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 675 and name N bond_start_previous = chain 'A' and resid 652 and name O } } sheet { first_strand = chain 'B' and resid 5 through 9 sheet_id = " C" strand { selection = chain 'B' and resid 12 through 16 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 16 and name N bond_start_previous = chain 'B' and resid 5 and name O } strand { selection = chain 'B' and resid 35 through 37 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 35 and name N bond_start_previous = chain 'B' and resid 15 and name O } strand { selection = chain 'B' and resid 59 through 61 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 59 and name N bond_start_previous = chain 'B' and resid 36 and name O } strand { selection = chain 'B' and resid 81 through 83 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 81 and name N bond_start_previous = chain 'B' and resid 60 and name O } strand { selection = chain 'B' and resid 104 through 106 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 104 and name N bond_start_previous = chain 'B' and resid 82 and name O } strand { selection = chain 'B' and resid 128 through 130 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 128 and name N bond_start_previous = chain 'B' and resid 105 and name O } strand { selection = chain 'B' and resid 152 through 154 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 152 and name N bond_start_previous = chain 'B' and resid 129 and name O } strand { selection = chain 'B' and resid 176 through 178 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 176 and name N bond_start_previous = chain 'B' and resid 153 and name O } strand { selection = chain 'B' and resid 199 through 201 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 199 and name N bond_start_previous = chain 'B' and resid 177 and name O } } sheet { first_strand = chain 'B' and resid 45 through 47 sheet_id = " D" strand { selection = chain 'B' and resid 69 through 71 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 69 and name N bond_start_previous = chain 'B' and resid 46 and name O } } sheet { first_strand = chain 'B' and resid 228 through 232 sheet_id = " E" strand { selection = chain 'B' and resid 237 through 241 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 240 and name N bond_start_previous = chain 'B' and resid 229 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1m10_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3778 occupancy sum: 3778.00 (% of total atoms 50.59) Rotatable: count: 1103 occupancy sum: 1103.00 (% of total atoms 14.77) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.09 - 30.50 A, n_refl.=10454 (all), 5.11 % free)------------| | | | r_work= 0.3804 r_free= 0.4305 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.437560 | | target function (ml) not normalized (work): 53940.591815 | | target function (ml) not normalized (free): 2943.016547 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 30.50 - 4.90 1.00 2530 123 0.3660 0.4501 6.0037 5.8545| | 2: 4.90 - 3.90 1.00 2453 134 0.3747 0.3971 5.604 5.8298| | 3: 3.89 - 3.40 1.00 2476 150 0.4079 0.4323 5.2694 5.4009| | 4: 3.40 - 3.09 1.00 2461 127 0.3903 0.4710 4.8588 4.973| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 30.50 - 4.90 2530 123 0.59 44.84 0.82 0.19 23753.52| | 2: 4.90 - 3.90 2453 134 0.66 39.62 1.40 0.30 15554.07| | 3: 3.89 - 3.40 2476 150 0.61 43.67 1.52 0.32 9054.65| | 4: 3.40 - 3.09 2461 127 0.53 49.92 1.29 0.25 4255.28| |alpha: min = 0.19 max = 0.32 mean = 0.27| |beta: min = 4255.28 max = 23753.52 mean = 13219.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.60| |phase err.(work): min = 0.00 max = 89.91 mean = 44.52| |phase err.(test): min = 0.00 max = 89.08 mean = 44.81| |-----------------------------------------------------------------------------| ----------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 : 0.010 0.119 3766 Z= 0.613 Angle : 1.710 10.944 5117 Z= 1.081 Chirality : 0.104 0.400 596 Planarity : 0.010 0.086 656 Dihedral : 15.487 87.844 1425 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 35.50 Ramachandran Plot: Outliers : 4.98 % Allowed : 12.77 % Favored : 82.25 % Rotamer: Outliers : 5.28 % Allowed : 6.24 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.24 (0.31), residues: 462 helix: -4.51 (0.29), residues: 98 sheet: -2.23 (0.51), residues: 89 loop : -3.68 (0.30), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG A 545 TYR 0.104 0.022 TYR B 44 PHE 0.051 0.010 PHE B 201 TRP 0.058 0.016 TRP B 219 HIS 0.003 0.001 HIS B 86 Individual atomic B min max mean iso aniso Overall: 15.65 95.55 52.24 1.37 3690 0 Protein: 15.65 95.55 52.24 1.37 3690 0 Chain A: 21.62 95.55 60.64 N/A 1602 0 Chain B: 15.65 77.97 45.80 N/A 2088 0 Histogram: Values Number of atoms 15.65 - 23.64 14 23.64 - 31.63 190 31.63 - 39.62 520 39.62 - 47.61 817 47.61 - 55.60 852 55.60 - 63.59 530 63.59 - 71.58 302 71.58 - 79.57 236 79.57 - 87.56 164 87.56 - 95.55 65 |-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 3 ************************* |--(resolution: 3.09 - 30.50 A, n_refl.=10454 (all), 5.11 % free)------------| | | | r_work= 0.3804 r_free= 0.4305 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.437560 | | target function (ml) not normalized (work): 53940.591815 | | target function (ml) not normalized (free): 2943.016547 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3828 0.3804 0.4305 n_refl.: 10454 re-set all scales: r(all,work,free)=0.3828 0.3804 0.4305 n_refl.: 10454 remove outliers: r(all,work,free)=0.3829 0.3805 0.4299 n_refl.: 10449 overall B=16.31 to atoms: r(all,work,free)=0.4448 0.4429 0.4826 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2288 0.2260 0.2819 n_refl.: 10449 remove outliers: r(all,work,free)=0.2288 0.2260 0.2819 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2311 1395.912 1343.970 1.051 1.212 0.395 14.512-11.594 100.00 95 5 0.1560 1328.531 1301.200 0.918 1.199 0.369 11.568-9.227 100.00 193 11 0.1404 1283.724 1248.849 0.929 1.180 0.359 9.162-7.352 100.00 368 15 0.2071 850.463 820.636 0.919 1.149 0.348 7.349-5.862 100.00 740 33 0.2226 628.811 611.546 0.853 1.103 0.326 5.858-4.671 100.00 1425 79 0.1948 673.689 650.894 0.916 1.028 0.283 4.669-3.723 99.86 2790 156 0.2269 618.917 593.677 1.202 0.910 0.181 3.723-3.092 99.93 4210 230 0.2720 337.947 316.886 1.511 0.750 0.063 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-5.7724 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.762419 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.201646 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2381 0.2739 0.0358 0.003 0.6 5.0 3.0 3.1 0 0.125 0.2350 0.2722 0.0372 0.003 0.6 4.6 2.8 3.4 0 0.250 0.2304 0.2698 0.0395 0.003 0.6 4.4 2.8 3.4 0 0.500 0.2247 0.2697 0.0450 0.004 0.7 6.2 2.4 3.6 0 1.000 0.2178 0.2677 0.0499 0.005 0.8 8.6 2.2 3.8 0 2.000 0.2137 0.2686 0.0549 0.007 0.9 11.0 3.0 4.1 0 3.000 0.2110 0.2716 0.0606 0.008 1.0 12.3 3.7 4.8 0 4.000 0.2085 0.2719 0.0634 0.010 1.1 13.5 3.9 5.0 0 5.000 0.2066 0.2726 0.0659 0.011 1.2 15.7 3.9 5.5 0 6.000 0.2051 0.2726 0.0675 0.013 1.3 17.4 4.3 5.8 0 7.000 0.2040 0.2730 0.0690 0.014 1.4 19.7 4.1 5.8 0 8.000 0.2027 0.2734 0.0706 0.015 1.5 20.0 4.3 6.2 0 9.000 0.2015 0.2738 0.0723 0.017 1.6 21.0 4.1 6.5 0 10.000 0.2040 0.2730 0.0690 0.014 1.4 18.8 4.1 5.8 0 7.881 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2304 0.2698 0.0395 0.003 0.6 4.4 2.8 3.4 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.04 26.98 3.95 0.970 68.287 0.202 0.058 23.23 26.91 3.68 1.902 68.384 0.006 0.059 22.85 26.83 3.98 1.936 68.431 0.025 0.057 22.08 26.73 4.65 2.889 68.571 0.101 0.053 21.08 26.63 5.55 6.073 69.140 0.202 0.049 20.79 26.64 5.85 7.202 69.421 0.302 0.047 20.49 26.70 6.21 8.523 69.844 0.403 0.046 20.36 26.73 6.37 9.255 70.046 0.504 0.045 20.25 26.77 6.52 9.846 70.213 0.605 0.045 20.17 26.79 6.62 10.332 70.352 0.706 0.045 20.08 26.81 6.73 10.926 70.533 0.807 0.044 20.01 26.84 6.82 11.391 70.672 0.907 0.044 19.97 26.86 6.89 11.722 70.768 1.008 0.044 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.202 Accepted refinement result: 21.08 26.63 5.55 6.073 69.140 0.202 0.049 Individual atomic B min max mean iso aniso Overall: 34.77 120.65 70.28 6.03 3690 0 Protein: 34.77 120.65 70.28 6.03 3690 0 Chain A: 35.52 120.65 78.03 N/A 1602 0 Chain B: 34.77 116.72 64.33 N/A 2088 0 Histogram: Values Number of atoms 34.77 - 43.36 46 43.36 - 51.95 311 51.95 - 60.53 681 60.53 - 69.12 927 69.12 - 77.71 684 77.71 - 86.30 429 86.30 - 94.89 306 94.89 - 103.47 223 103.47 - 112.06 70 112.06 - 120.65 13 =========================== Idealize ADP of riding H ========================== r_work=0.2108 r_free=0.2663 r_work=0.2087 r_free=0.2646 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2087 r_free= 0.2646 coordinate error (max.-lik. estimate): 0.50 A | | | | normalized target function (ls_wunit_k1) (work): 0.047592 | | target function (ls_wunit_k1) not normalized (work): 471.920065 | | target function (ls_wunit_k1) not normalized (free): 43.145708 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2115 0.2087 0.2646 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4383 0.4366 0.4709 n_refl.: 10449 remove outliers: r(all,work,free)=0.4383 0.4366 0.4709 n_refl.: 10449 overall B=-5.93 to atoms: r(all,work,free)=0.4141 0.4124 0.4490 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2127 0.2097 0.2679 n_refl.: 10449 remove outliers: r(all,work,free)=0.2127 0.2097 0.2679 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2210 771.651 751.318 1.347 1.128 0.406 14.512-11.594 100.00 95 5 0.1432 734.403 726.361 1.119 1.119 0.370 11.568-9.227 100.00 193 11 0.1370 709.634 696.897 1.115 1.107 0.365 9.162-7.352 100.00 368 15 0.1785 470.130 461.276 1.094 1.087 0.368 7.349-5.862 100.00 740 33 0.1989 347.602 342.836 0.966 1.058 0.342 5.858-4.671 100.00 1425 79 0.1828 372.411 362.870 0.976 1.011 0.296 4.669-3.723 99.93 2790 156 0.2015 342.133 333.836 1.178 0.937 0.197 3.723-3.092 100.00 4210 230 0.2661 186.815 177.698 1.329 0.836 0.057 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=-0.4558 ============================ 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 = 3.471570 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.043592 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2094 0.2662 0.0568 0.003 0.6 4.7 1.9 2.4 0 0.125 0.2044 0.2647 0.0603 0.003 0.6 5.8 1.9 3.1 0 0.250 0.2005 0.2658 0.0653 0.005 0.8 7.9 1.9 4.3 0 0.500 0.1958 0.2679 0.0721 0.009 1.0 11.3 2.8 4.8 0 1.000 0.1913 0.2729 0.0816 0.015 1.4 16.6 3.5 5.8 0 2.000 0.1887 0.2743 0.0856 0.020 1.8 18.6 3.5 5.8 0 3.000 0.1867 0.2753 0.0886 0.024 2.0 19.6 3.5 5.5 0 4.000 0.1848 0.2734 0.0886 0.027 2.2 26.7 4.8 11.5 0 5.000 0.1835 0.2736 0.0901 0.031 2.4 29.1 5.2 12.2 0 6.000 0.1827 0.2736 0.0909 0.034 2.7 32.8 5.4 13.7 0 7.000 0.1820 0.2750 0.0929 0.037 2.8 34.3 5.6 15.3 0 8.000 0.1815 0.2771 0.0956 0.040 3.0 36.4 6.1 15.8 0 9.000 0.1802 0.2768 0.0965 0.043 3.2 37.8 6.1 14.6 0 10.000 0.1921 0.2708 0.0787 0.013 1.3 14.3 3.0 5.5 0 1.736 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2094 0.2662 0.0568 0.003 0.6 4.7 1.9 2.4 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.94 26.62 5.68 11.041 71.529 0.044 5.744 23.93 28.09 4.16 8.944 75.582 0.001 5.810 23.19 27.26 4.07 10.663 73.602 0.005 5.794 21.02 26.53 5.50 11.221 71.299 0.022 5.738 20.80 26.55 5.75 11.429 71.250 0.044 5.733 20.61 26.54 5.92 11.859 71.086 0.065 5.726 20.04 26.57 6.53 13.502 71.698 0.087 5.706 20.13 26.50 6.38 13.042 71.244 0.109 5.709 20.05 26.53 6.47 13.169 71.346 0.131 5.708 20.00 26.55 6.55 13.280 71.430 0.153 5.706 19.96 26.57 6.61 13.376 71.498 0.174 5.706 19.93 26.58 6.66 13.463 71.557 0.196 5.705 19.90 26.60 6.70 13.539 71.606 0.218 5.704 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.022 Accepted refinement result: 21.02 26.53 5.50 11.221 71.299 0.022 5.738 Individual atomic B min max mean iso aniso Overall: 28.70 114.10 63.89 5.50 3690 0 Protein: 28.70 114.10 63.89 5.50 3690 0 Chain A: 33.22 114.10 71.64 N/A 1602 0 Chain B: 28.70 111.23 57.94 N/A 2088 0 Histogram: Values Number of atoms 28.70 - 37.24 48 37.24 - 45.78 322 45.78 - 54.32 685 54.32 - 62.86 942 62.86 - 71.40 660 71.40 - 79.94 422 79.94 - 88.48 288 88.48 - 97.02 237 97.02 - 105.56 72 105.56 - 114.10 14 =========================== Idealize ADP of riding H ========================== r_work=0.2102 r_free=0.2653 r_work=0.2104 r_free=0.2655 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2104 r_free= 0.2655 coordinate error (max.-lik. estimate): 0.53 A | | | | normalized target function (ml) (work): 5.738379 | | target function (ml) not normalized (work): 56901.769195 | | target function (ml) not normalized (free): 3151.164634 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2131 0.2104 0.2655 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4119 0.4103 0.4436 n_refl.: 10449 remove outliers: r(all,work,free)=0.4119 0.4103 0.4436 n_refl.: 10449 overall B=-0.24 to atoms: r(all,work,free)=0.4109 0.4093 0.4427 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2139 0.2111 0.2668 n_refl.: 10449 remove outliers: r(all,work,free)=0.2139 0.2111 0.2668 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2036 870.932 853.757 1.428 1.074 0.405 14.512-11.594 100.00 95 5 0.1346 828.892 827.941 1.194 1.068 0.376 11.568-9.227 100.00 193 11 0.1288 800.936 790.533 1.172 1.062 0.370 9.162-7.352 100.00 368 15 0.1715 530.617 522.422 1.134 1.049 0.370 7.349-5.862 100.00 740 33 0.2016 392.325 386.062 1.002 1.032 0.351 5.858-4.671 100.00 1425 79 0.1856 420.325 407.848 0.976 1.003 0.291 4.669-3.723 99.86 2790 156 0.2045 386.152 375.502 1.142 0.958 0.191 3.723-3.092 99.93 4210 230 0.2705 210.850 199.283 1.211 0.897 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=0.0607 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2111 r_free=0.2668 After: r_work=0.2111 r_free=0.2669 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.452888 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.044866 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2111 0.2669 0.0558 0.003 0.6 4.7 1.9 2.4 0 0.125 0.2107 0.2672 0.0566 0.003 0.6 4.7 1.9 2.4 0 0.250 0.2079 0.2669 0.0590 0.006 0.7 5.4 1.9 2.4 0 0.500 0.1987 0.2687 0.0700 0.012 1.4 12.1 1.9 2.6 0 1.000 0.1949 0.2716 0.0767 0.016 2.0 19.4 1.7 4.3 0 2.000 0.1919 0.2723 0.0804 0.020 2.2 19.7 1.9 5.0 0 3.000 0.1904 0.2737 0.0833 0.023 2.6 22.5 1.9 7.0 0 4.000 0.1896 0.2753 0.0857 0.027 2.6 28.5 3.2 9.1 0 5.000 0.1877 0.2768 0.0891 0.028 3.1 30.0 3.5 10.6 0 6.000 0.1873 0.2786 0.0913 0.034 3.2 31.7 4.1 10.8 0 7.000 0.1862 0.2783 0.0922 0.037 3.5 35.1 4.8 12.7 1 8.000 0.1852 0.2800 0.0948 0.041 3.8 37.8 5.2 13.9 1 9.000 0.1841 0.2807 0.0966 0.045 4.1 40.7 6.1 15.3 2 10.000 0.1954 0.2704 0.0750 0.016 1.8 16.1 1.7 4.1 0 1.726 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2111 0.2669 0.0558 0.003 0.6 4.7 1.9 2.4 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.11 26.69 5.58 10.084 70.192 0.045 5.866 24.20 28.25 4.05 8.593 74.294 0.001 5.940 22.23 26.63 4.40 10.291 70.041 0.006 5.890 21.11 26.69 5.58 10.084 70.192 0.022 5.866 21.10 26.69 5.58 10.103 70.179 0.045 5.865 20.84 26.69 5.85 10.712 69.857 0.067 5.854 20.10 26.62 6.52 12.994 70.351 0.090 5.830 19.98 26.62 6.64 13.220 70.468 0.112 5.826 19.99 26.64 6.65 13.078 70.389 0.135 5.826 19.96 26.68 6.72 13.154 70.433 0.157 5.826 19.91 26.70 6.79 13.383 70.559 0.179 5.825 20.01 26.70 6.69 12.900 70.281 0.202 5.828 19.99 26.72 6.73 12.998 70.340 0.224 5.828 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 22.23 26.63 4.40 10.291 70.041 0.006 5.890 Individual atomic B min max mean iso aniso Overall: 33.48 108.86 63.34 2.88 3690 0 Protein: 33.48 108.86 63.34 2.88 3690 0 Chain A: 36.94 108.86 70.96 N/A 1602 0 Chain B: 33.48 105.99 57.50 N/A 2088 0 Histogram: Values Number of atoms 33.48 - 41.02 65 41.02 - 48.56 440 48.56 - 56.09 701 56.09 - 63.63 979 63.63 - 71.17 553 71.17 - 78.71 350 78.71 - 86.25 276 86.25 - 93.79 229 93.79 - 101.32 75 101.32 - 108.86 22 =========================== Idealize ADP of riding H ========================== r_work=0.2223 r_free=0.2663 r_work=0.2236 r_free=0.2664 ----------X-ray data---------- |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2236 r_free= 0.2664 coordinate error (max.-lik. estimate): 0.51 A | | | | normalized target function (ml) (work): 5.893694 | | target function (ml) not normalized (work): 58441.871046 | | target function (ml) not normalized (free): 3216.934571 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 30.50 - 4.90 1.00 2530 123 0.1841 0.2142 6.1395 6.1715| | 2: 4.90 - 3.90 1.00 2451 133 0.2102 0.2468 6.0687 6.337| | 3: 3.89 - 3.40 1.00 2475 150 0.2604 0.3071 5.8695 6.031| | 4: 3.40 - 3.09 1.00 2460 127 0.3095 0.3732 5.4908 5.5935| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 30.50 - 4.90 2530 123 0.86 21.28 1.00 0.92 32963.11| | 2: 4.90 - 3.90 2451 133 0.84 23.13 1.01 0.96 30804.56| | 3: 3.89 - 3.40 2475 150 0.74 32.13 1.03 0.91 24534.61| | 4: 3.40 - 3.09 2460 127 0.67 39.11 0.91 0.77 14153.27| |alpha: min = 0.77 max = 0.96 mean = 0.89| |beta: min = 14153.27 max = 32963.11 mean = 25659.42| |figures of merit: min = 0.00 max = 1.00 mean = 0.78| |phase err.(work): min = 0.00 max = 89.82 mean = 28.87| |phase err.(test): min = 0.00 max = 87.63 mean = 29.80| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2257 0.2236 0.2664 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4159 0.4144 0.4455 n_refl.: 10449 remove outliers: r(all,work,free)=0.4159 0.4144 0.4455 n_refl.: 10449 overall B=-0.09 to atoms: r(all,work,free)=0.4155 0.4140 0.4451 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2265 0.2243 0.2675 n_refl.: 10449 remove outliers: r(all,work,free)=0.2265 0.2243 0.2675 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2028 870.932 855.451 1.476 1.041 0.405 14.512-11.594 100.00 95 5 0.1345 828.892 829.819 1.234 1.038 0.376 11.568-9.227 100.00 193 11 0.1299 800.936 791.388 1.206 1.034 0.370 9.162-7.352 100.00 368 15 0.1761 530.617 522.408 1.162 1.026 0.370 7.349-5.862 100.00 740 33 0.2087 392.325 385.629 1.031 1.016 0.360 5.858-4.671 100.00 1425 79 0.1952 420.325 406.507 0.982 0.999 0.290 4.669-3.723 99.86 2790 156 0.2216 386.152 373.336 1.124 0.971 0.200 3.723-3.092 99.93 4210 230 0.2898 210.850 197.193 1.161 0.934 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=0.0424 ================= 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 : 0.3804 0.4305 0.010 1.710 15.7 95.5 52.2 0 0.000 1_bss: 0.2260 0.2819 0.010 1.710 32.0 111.9 68.6 0 0.000 1_settarget: 0.2260 0.2819 0.010 1.710 32.0 111.9 68.6 0 0.000 1_weight: 0.2260 0.2819 0.010 1.710 32.0 111.9 68.6 0 0.000 1_xyzrec: 0.2304 0.2698 0.003 0.617 32.0 111.9 68.6 0 0.187 1_adp: 0.2108 0.2663 0.003 0.617 34.8 120.6 70.3 0 0.187 1_regHadp: 0.2087 0.2646 0.003 0.617 34.8 120.6 70.3 0 0.187 2_bss: 0.2097 0.2679 0.003 0.617 28.8 114.7 64.4 0 0.187 2_settarget: 0.2097 0.2679 0.003 0.617 28.8 114.7 64.4 0 0.187 2_updatecdl: 0.2097 0.2679 0.003 0.673 28.8 114.7 64.4 0 0.187 2_weight: 0.2097 0.2679 0.003 0.673 28.8 114.7 64.4 0 0.187 2_xyzrec: 0.2094 0.2662 0.003 0.567 28.8 114.7 64.4 0 0.233 2_adp: 0.2102 0.2653 0.003 0.567 28.7 114.1 63.9 0 0.233 2_regHadp: 0.2104 0.2655 0.003 0.567 28.7 114.1 63.9 0 0.233 3_bss: 0.2111 0.2668 0.003 0.567 28.5 113.9 63.6 0 0.233 3_settarget: 0.2111 0.2668 0.003 0.567 28.5 113.9 63.6 0 0.233 3_updatecdl: 0.2111 0.2668 0.003 0.612 28.5 113.9 63.6 0 0.233 3_setrh: 0.2111 0.2669 0.003 0.612 28.5 113.9 63.6 0 0.233 3_weight: 0.2111 0.2669 0.003 0.612 28.5 113.9 63.6 0 0.233 3_xyzrec: 0.2111 0.2669 0.003 0.583 28.5 113.9 63.6 0 0.233 3_adp: 0.2223 0.2663 0.003 0.583 33.5 108.9 63.3 0 0.233 3_regHadp: 0.2236 0.2664 0.003 0.583 33.5 108.9 63.3 0 0.233 end: 0.2243 0.2675 0.003 0.583 33.4 108.8 63.2 0 0.233 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1m10_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1m10_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 10.9200 Refinement macro-cycles (run) : 263.5700 Write final files (write_after_run_outputs) : 18.9300 Total : 293.4200 Total CPU time: 5.64 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:14 PDT -0700 (1716251714.86 s) Start R-work = 0.2260, R-free = 0.2819 Final R-work = 0.2243, R-free = 0.2675 =============================================================================== Job complete usr+sys time: 354.45 seconds wall clock time: 17 minutes 58.14 seconds (1078.14 seconds total)