Starting phenix.real_space_refine on Tue Aug 4 23:45:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tig_55955/08_2026/9tig_55955.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tig_55955/08_2026/9tig_55955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tig_55955/08_2026/9tig_55955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tig_55955/08_2026/9tig_55955.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tig_55955/08_2026/9tig_55955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tig_55955/08_2026/9tig_55955.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 4685 2.51 5 N 1192 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7377 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1327 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} Chain: "B" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1327 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} Chain: "C" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1277 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 8, 'TRANS': 154} Chain breaks: 1 Chain: "D" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1319 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain: "F" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1266 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 8, 'TRANS': 152} Chain breaks: 1 Chain: "H" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 861 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Time building chain proxies: 1.96, per 1000 atoms: 0.27 Number of scatterers: 7377 At special positions: 0 Unit cell: (125.04, 116.704, 103.366, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 1488 8.00 N 1192 7.00 C 4685 6.00 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 - 3.00 Amino acid : True - 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: 0.56 Conformation dependent library (CDL) restraints added in 453.8 milliseconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1736 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 18 sheets defined 20.1% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 32 through 55 removed outlier: 4.014A pdb=" N LEU A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.765A pdb=" N LEU B 11 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASP B 12 " --> pdb=" O PRO B 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 8 through 12' Processing helix chain 'B' and resid 15 through 18 Processing helix chain 'B' and resid 32 through 53 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'C' and resid 5 through 19 removed outlier: 3.934A pdb=" N HIS C 9 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 10 " --> pdb=" O TYR C 6 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.672A pdb=" N GLU C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'D' and resid 15 through 18 Processing helix chain 'D' and resid 32 through 53 removed outlier: 3.508A pdb=" N LEU D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'F' and resid 5 through 19 removed outlier: 3.915A pdb=" N HIS F 9 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL F 10 " --> pdb=" O TYR F 6 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS F 19 " --> pdb=" O TYR F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'F' and resid 138 through 140 No H-bonds generated for 'chain 'F' and resid 138 through 140' Processing helix chain 'H' and resid 96 through 106 Processing helix chain 'H' and resid 117 through 122 removed outlier: 3.622A pdb=" N ILE H 122 " --> pdb=" O PHE H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 128 Processing helix chain 'H' and resid 157 through 166 removed outlier: 3.833A pdb=" N GLU H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE H 165 " --> pdb=" O VAL H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 181 No H-bonds generated for 'chain 'H' and resid 179 through 181' Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 25 removed outlier: 6.815A pdb=" N ARG A 20 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLU B 143 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS A 22 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 144 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU B 104 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR B 159 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B 106 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.707A pdb=" N LYS A 60 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR A 82 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A 62 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 148 Processing sheet with id=AA6, first strand: chain 'A' and resid 113 through 115 removed outlier: 4.139A pdb=" N LYS D 22 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 20 through 24 removed outlier: 6.428A pdb=" N ARG B 20 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU D 143 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS B 22 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 111 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE D 108 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N THR D 156 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N THR D 159 " --> pdb=" O TYR D 166 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR D 166 " --> pdb=" O THR D 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.340A pdb=" N LYS B 60 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR B 82 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 62 " --> pdb=" O TYR B 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 4 removed outlier: 5.984A pdb=" N LEU F 148 " --> pdb=" O MET F 124 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N MET F 124 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE F 150 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ARG F 118 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY F 28 " --> pdb=" O ARG F 118 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL F 120 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR F 26 " --> pdb=" O VAL F 120 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE F 122 " --> pdb=" O TYR F 24 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR F 24 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE F 27 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY F 54 " --> pdb=" O ILE F 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.867A pdb=" N GLY C 54 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE C 27 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N THR C 116 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N PHE C 156 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ARG C 118 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 150 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET C 124 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU C 148 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 78 through 80 removed outlier: 7.851A pdb=" N SER C 84 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER C 67 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL C 101 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL C 171 " --> pdb=" O VAL C 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 127 through 128 Processing sheet with id=AB5, first strand: chain 'D' and resid 59 through 63 removed outlier: 3.957A pdb=" N ASP D 59 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR D 82 " --> pdb=" O ASP D 59 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR D 80 " --> pdb=" O GLN D 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 73 through 75 Processing sheet with id=AB7, first strand: chain 'F' and resid 77 through 80 removed outlier: 3.918A pdb=" N LEU F 63 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS F 60 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU F 104 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP F 100 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR F 164 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP H 177 " --> pdb=" O ILE H 150 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER H 114 " --> pdb=" O SER H 149 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 77 through 80 removed outlier: 3.918A pdb=" N LEU F 63 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS F 60 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU F 104 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP F 100 " --> pdb=" O VAL F 64 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 127 through 128 254 hydrogen bonds defined for protein. 651 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: 1.07 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2400 1.34 - 1.46: 1485 1.46 - 1.57: 3614 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 7523 Sorted by residual: bond pdb=" N ILE B 87 " pdb=" CA ILE B 87 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.21e+00 bond pdb=" CA VAL D 73 " pdb=" CB VAL D 73 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 9.79e-01 bond pdb=" N GLY H 138 " pdb=" CA GLY H 138 " ideal model delta sigma weight residual 1.458 1.449 0.009 9.20e-03 1.18e+04 8.88e-01 bond pdb=" N PRO F 39 " pdb=" CA PRO F 39 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 7.18e-01 bond pdb=" N PRO C 39 " pdb=" CA PRO C 39 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 6.58e-01 ... (remaining 7518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.77: 9391 0.77 - 1.53: 683 1.53 - 2.30: 78 2.30 - 3.06: 32 3.06 - 3.83: 22 Bond angle restraints: 10206 Sorted by residual: angle pdb=" N ILE A 157 " pdb=" CA ILE A 157 " pdb=" C ILE A 157 " ideal model delta sigma weight residual 111.90 109.09 2.81 8.10e-01 1.52e+00 1.20e+01 angle pdb=" N ILE D 157 " pdb=" CA ILE D 157 " pdb=" C ILE D 157 " ideal model delta sigma weight residual 111.90 109.44 2.46 8.10e-01 1.52e+00 9.25e+00 angle pdb=" N GLU D 119 " pdb=" CA GLU D 119 " pdb=" C GLU D 119 " ideal model delta sigma weight residual 113.88 110.61 3.27 1.23e+00 6.61e-01 7.05e+00 angle pdb=" N TYR A 10 " pdb=" CA TYR A 10 " pdb=" C TYR A 10 " ideal model delta sigma weight residual 114.04 111.53 2.51 1.24e+00 6.50e-01 4.10e+00 angle pdb=" CA THR A 170 " pdb=" C THR A 170 " pdb=" N ASN A 171 " ideal model delta sigma weight residual 114.90 117.64 -2.74 1.37e+00 5.33e-01 3.99e+00 ... (remaining 10201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4442 17.53 - 35.05: 67 35.05 - 52.58: 10 52.58 - 70.10: 2 70.10 - 87.63: 1 Dihedral angle restraints: 4522 sinusoidal: 1806 harmonic: 2716 Sorted by residual: dihedral pdb=" N LEU A 64 " pdb=" CA LEU A 64 " pdb=" CB LEU A 64 " pdb=" CG LEU A 64 " ideal model delta sinusoidal sigma weight residual -60.00 -116.39 56.39 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA ARG B 29 " pdb=" CB ARG B 29 " pdb=" CG ARG B 29 " pdb=" CD ARG B 29 " ideal model delta sinusoidal sigma weight residual -180.00 -124.22 -55.78 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" N GLN D 40 " pdb=" CA GLN D 40 " pdb=" CB GLN D 40 " pdb=" CG GLN D 40 " ideal model delta sinusoidal sigma weight residual 180.00 -133.58 -46.42 3 1.50e+01 4.44e-03 8.33e+00 ... (remaining 4519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 668 0.026 - 0.052: 314 0.052 - 0.078: 41 0.078 - 0.104: 67 0.104 - 0.130: 54 Chirality restraints: 1144 Sorted by residual: chirality pdb=" CA ILE F 107 " pdb=" N ILE F 107 " pdb=" C ILE F 107 " pdb=" CB ILE F 107 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL C 120 " pdb=" N VAL C 120 " pdb=" C VAL C 120 " pdb=" CB VAL C 120 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA VAL C 48 " pdb=" N VAL C 48 " pdb=" C VAL C 48 " pdb=" CB VAL C 48 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1141 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 154 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO H 155 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO H 155 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 155 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 8 " -0.014 5.00e-02 4.00e+02 2.13e-02 7.27e-01 pdb=" N PRO D 9 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO D 9 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO D 9 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 31 " 0.014 5.00e-02 4.00e+02 2.12e-02 7.18e-01 pdb=" N PRO C 32 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO C 32 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 32 " 0.012 5.00e-02 4.00e+02 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 99 2.60 - 3.18: 6516 3.18 - 3.75: 10426 3.75 - 4.33: 15115 4.33 - 4.90: 25477 Nonbonded interactions: 57633 Sorted by model distance: nonbonded pdb=" OG1 THR D 99 " pdb=" OE2 GLU D 104 " model vdw 2.026 3.040 nonbonded pdb=" OH TYR H 116 " pdb=" OD1 ASN H 121 " model vdw 2.065 3.040 nonbonded pdb=" OG SER B 69 " pdb=" OD1 ASP B 71 " model vdw 2.104 3.040 nonbonded pdb=" O GLY H 151 " pdb=" OG1 THR H 181 " model vdw 2.187 3.040 nonbonded pdb=" O SER F 30 " pdb=" NH1 ARG F 118 " model vdw 2.208 3.120 ... (remaining 57628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 171) selection = (chain 'B' and resid 5 through 171) selection = chain 'D' } ncs_group { reference = (chain 'C' and (resid 4 through 66 or resid 77 through 173)) selection = (chain 'F' and (resid 4 through 66 or resid 77 through 173)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.040 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7523 Z= 0.108 Angle : 0.465 3.826 10206 Z= 0.290 Chirality : 0.042 0.130 1144 Planarity : 0.003 0.029 1325 Dihedral : 6.979 87.628 2786 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.24 % Allowed : 1.94 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.29), residues: 918 helix: 2.72 (0.52), residues: 114 sheet: 0.97 (0.37), residues: 194 loop : 0.54 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 140 TYR 0.007 0.000 TYR F 102 PHE 0.005 0.000 PHE H 119 TRP 0.004 0.000 TRP C 33 HIS 0.000 0.000 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.11 ( 7523) covalent geometry : angle 0.46470 / 0.29 (10206) hydrogen bonds : bond 0.26958 / 17.78 ( 244) hydrogen bonds : angle 9.09176 / 6.67 ( 651) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8230 (ttpt) cc_final: 0.7600 (ttpt) REVERT: A 60 LYS cc_start: 0.7317 (mtmt) cc_final: 0.7032 (mtmm) REVERT: A 156 THR cc_start: 0.9005 (m) cc_final: 0.8683 (p) REVERT: A 165 LEU cc_start: 0.7949 (tp) cc_final: 0.7745 (tp) REVERT: B 32 GLN cc_start: 0.8766 (mt0) cc_final: 0.8168 (mt0) REVERT: B 37 ASN cc_start: 0.8351 (m-40) cc_final: 0.7598 (m-40) REVERT: B 40 GLN cc_start: 0.7373 (mm-40) cc_final: 0.7144 (mm110) REVERT: B 75 THR cc_start: 0.8981 (m) cc_final: 0.8762 (p) REVERT: B 90 TYR cc_start: 0.8887 (t80) cc_final: 0.8302 (t80) REVERT: B 106 ILE cc_start: 0.9126 (mm) cc_final: 0.8833 (mt) REVERT: B 158 TYR cc_start: 0.8198 (m-80) cc_final: 0.7713 (m-80) REVERT: B 164 ASP cc_start: 0.7113 (m-30) cc_final: 0.6880 (m-30) REVERT: C 92 ASN cc_start: 0.7967 (m-40) cc_final: 0.7682 (p0) REVERT: C 169 PHE cc_start: 0.6200 (m-10) cc_final: 0.5932 (m-10) REVERT: D 39 MET cc_start: 0.7269 (ttp) cc_final: 0.6444 (ttp) REVERT: F 22 SER cc_start: 0.8254 (m) cc_final: 0.7359 (p) REVERT: F 23 VAL cc_start: 0.8729 (t) cc_final: 0.8254 (t) REVERT: F 77 LEU cc_start: 0.7694 (mt) cc_final: 0.7477 (mm) REVERT: F 85 TRP cc_start: 0.6936 (m100) cc_final: 0.6653 (m100) REVERT: F 103 LEU cc_start: 0.7723 (mt) cc_final: 0.7479 (mt) REVERT: H 127 LYS cc_start: 0.8420 (tttt) cc_final: 0.7720 (tmmt) REVERT: H 148 VAL cc_start: 0.8883 (t) cc_final: 0.8639 (m) outliers start: 2 outliers final: 1 residues processed: 326 average time/residue: 0.1003 time to fit residues: 42.4418 Evaluate side-chains 200 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 150 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN A 168 GLN B 44 GLN C 157 GLN D 32 GLN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.144559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125544 restraints weight = 12435.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125230 restraints weight = 10837.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126701 restraints weight = 9011.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127057 restraints weight = 5940.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127663 restraints weight = 5027.796| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7523 Z= 0.136 Angle : 0.595 9.781 10206 Z= 0.310 Chirality : 0.046 0.228 1144 Planarity : 0.004 0.035 1325 Dihedral : 3.490 35.112 1011 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.42 % Allowed : 12.71 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.28), residues: 918 helix: 1.59 (0.48), residues: 119 sheet: 0.50 (0.37), residues: 197 loop : 0.48 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 168 TYR 0.018 0.001 TYR H 116 PHE 0.012 0.001 PHE C 150 TRP 0.012 0.002 TRP C 100 HIS 0.003 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 7523) covalent geometry : angle 0.59505 / 0.31 (10206) hydrogen bonds : bond 0.05724 / 3.81 ( 244) hydrogen bonds : angle 6.53177 / 4.68 ( 651) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.6696 (m-30) REVERT: B 32 GLN cc_start: 0.8876 (mt0) cc_final: 0.8598 (mt0) REVERT: B 90 TYR cc_start: 0.8851 (t80) cc_final: 0.8422 (t80) REVERT: B 106 ILE cc_start: 0.9181 (mm) cc_final: 0.8891 (mt) REVERT: B 133 TYR cc_start: 0.7459 (t80) cc_final: 0.7090 (t80) REVERT: B 158 TYR cc_start: 0.8314 (m-80) cc_final: 0.7834 (m-80) REVERT: B 164 ASP cc_start: 0.7182 (m-30) cc_final: 0.6889 (m-30) REVERT: C 29 LYS cc_start: 0.5039 (tptp) cc_final: 0.4527 (tppt) REVERT: C 92 ASN cc_start: 0.8291 (m-40) cc_final: 0.7680 (p0) REVERT: D 39 MET cc_start: 0.6743 (ttp) cc_final: 0.6041 (ttp) REVERT: D 106 ILE cc_start: 0.9112 (mm) cc_final: 0.8736 (mt) REVERT: F 22 SER cc_start: 0.8163 (m) cc_final: 0.7382 (p) REVERT: F 23 VAL cc_start: 0.8521 (t) cc_final: 0.8168 (t) REVERT: F 33 TRP cc_start: 0.8652 (m100) cc_final: 0.8250 (m100) REVERT: F 65 ARG cc_start: 0.8328 (ptt-90) cc_final: 0.7263 (ttp80) REVERT: F 77 LEU cc_start: 0.7424 (mt) cc_final: 0.7214 (mm) REVERT: F 119 GLN cc_start: 0.8872 (mt0) cc_final: 0.8570 (tt0) REVERT: H 100 ASP cc_start: 0.8435 (t0) cc_final: 0.7988 (m-30) REVERT: H 127 LYS cc_start: 0.8616 (tttt) cc_final: 0.7845 (ttpt) REVERT: H 198 GLU cc_start: 0.5224 (tt0) cc_final: 0.4886 (tt0) outliers start: 20 outliers final: 14 residues processed: 225 average time/residue: 0.0728 time to fit residues: 23.1269 Evaluate side-chains 189 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain H residue 114 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 82 optimal weight: 0.0870 chunk 58 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 168 GLN B 40 GLN B 44 GLN B 49 ASN D 26 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.133850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114054 restraints weight = 12770.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114230 restraints weight = 12653.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114601 restraints weight = 11068.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.115039 restraints weight = 9126.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115381 restraints weight = 7488.054| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 7523 Z= 0.234 Angle : 0.686 6.841 10206 Z= 0.357 Chirality : 0.050 0.191 1144 Planarity : 0.005 0.046 1325 Dihedral : 4.617 39.389 1011 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.51 % Allowed : 14.41 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.27), residues: 918 helix: 1.06 (0.46), residues: 118 sheet: 0.27 (0.37), residues: 196 loop : -0.03 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 20 TYR 0.020 0.002 TYR B 45 PHE 0.021 0.002 PHE H 119 TRP 0.015 0.002 TRP F 85 HIS 0.004 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 ( 7523) covalent geometry : angle 0.68576 / 0.36 (10206) hydrogen bonds : bond 0.05607 / 3.71 ( 244) hydrogen bonds : angle 6.08299 / 4.33 ( 651) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 TYR cc_start: 0.8042 (t80) cc_final: 0.7625 (t80) REVERT: C 29 LYS cc_start: 0.5113 (tptp) cc_final: 0.4712 (tppp) REVERT: C 92 ASN cc_start: 0.8337 (m-40) cc_final: 0.7889 (p0) REVERT: D 39 MET cc_start: 0.7382 (ttp) cc_final: 0.6664 (ttp) REVERT: D 55 PHE cc_start: 0.8225 (m-80) cc_final: 0.7995 (m-80) REVERT: F 22 SER cc_start: 0.8227 (m) cc_final: 0.7453 (p) REVERT: F 23 VAL cc_start: 0.8665 (t) cc_final: 0.8269 (t) REVERT: F 65 ARG cc_start: 0.7606 (ptt-90) cc_final: 0.7284 (ttp80) REVERT: F 166 LYS cc_start: 0.6765 (ttpt) cc_final: 0.6339 (tttt) REVERT: H 127 LYS cc_start: 0.8341 (tttt) cc_final: 0.7682 (ttpp) REVERT: H 198 GLU cc_start: 0.4780 (tt0) cc_final: 0.4449 (tt0) outliers start: 29 outliers final: 22 residues processed: 207 average time/residue: 0.0706 time to fit residues: 20.4218 Evaluate side-chains 181 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain H residue 114 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 71 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 35 optimal weight: 0.0370 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 126 GLN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116457 restraints weight = 12979.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.115951 restraints weight = 12051.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116869 restraints weight = 10471.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117178 restraints weight = 8029.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.117346 restraints weight = 7317.407| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7523 Z= 0.144 Angle : 0.591 6.875 10206 Z= 0.307 Chirality : 0.047 0.162 1144 Planarity : 0.005 0.060 1325 Dihedral : 4.433 42.351 1011 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.87 % Allowed : 16.22 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.27), residues: 918 helix: 1.07 (0.46), residues: 118 sheet: 0.05 (0.36), residues: 212 loop : 0.10 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 140 TYR 0.015 0.002 TYR F 102 PHE 0.025 0.002 PHE H 119 TRP 0.007 0.001 TRP F 100 HIS 0.004 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 7523) covalent geometry : angle 0.59057 / 0.31 (10206) hydrogen bonds : bond 0.04722 / 3.11 ( 244) hydrogen bonds : angle 5.72305 / 4.01 ( 651) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ILE cc_start: 0.9310 (mt) cc_final: 0.8854 (pt) REVERT: B 106 ILE cc_start: 0.9333 (mm) cc_final: 0.8958 (mt) REVERT: B 126 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7189 (mt0) REVERT: B 133 TYR cc_start: 0.8074 (t80) cc_final: 0.7795 (t80) REVERT: C 92 ASN cc_start: 0.8374 (m-40) cc_final: 0.7877 (p0) REVERT: C 153 ASN cc_start: 0.5522 (m-40) cc_final: 0.4994 (p0) REVERT: D 39 MET cc_start: 0.7448 (ttp) cc_final: 0.6876 (ttp) REVERT: F 5 THR cc_start: 0.7917 (p) cc_final: 0.7660 (p) REVERT: F 22 SER cc_start: 0.7758 (m) cc_final: 0.6744 (t) REVERT: F 23 VAL cc_start: 0.8377 (t) cc_final: 0.8153 (t) REVERT: F 33 TRP cc_start: 0.8776 (m100) cc_final: 0.8477 (m100) REVERT: F 119 GLN cc_start: 0.9019 (mt0) cc_final: 0.8771 (tt0) REVERT: F 127 VAL cc_start: 0.8331 (p) cc_final: 0.7951 (m) REVERT: H 127 LYS cc_start: 0.8348 (tttt) cc_final: 0.7741 (ttpt) outliers start: 32 outliers final: 24 residues processed: 185 average time/residue: 0.0681 time to fit residues: 17.9500 Evaluate side-chains 181 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain H residue 114 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 168 GLN B 126 GLN C 136 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115861 restraints weight = 12836.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115010 restraints weight = 13089.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.116152 restraints weight = 10790.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.116976 restraints weight = 7509.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117193 restraints weight = 5967.705| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7523 Z= 0.135 Angle : 0.580 7.789 10206 Z= 0.300 Chirality : 0.046 0.155 1144 Planarity : 0.004 0.058 1325 Dihedral : 4.402 44.030 1011 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.12 % Allowed : 16.71 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.28), residues: 918 helix: 1.16 (0.47), residues: 118 sheet: 0.11 (0.36), residues: 211 loop : 0.05 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 140 TYR 0.016 0.001 TYR F 102 PHE 0.026 0.001 PHE H 119 TRP 0.008 0.001 TRP F 85 HIS 0.003 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 7523) covalent geometry : angle 0.58004 / 0.30 (10206) hydrogen bonds : bond 0.04436 / 2.92 ( 244) hydrogen bonds : angle 5.59349 / 3.91 ( 651) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ILE cc_start: 0.9326 (mm) cc_final: 0.8970 (mt) REVERT: B 133 TYR cc_start: 0.8200 (t80) cc_final: 0.7907 (t80) REVERT: C 29 LYS cc_start: 0.5072 (tptp) cc_final: 0.4661 (tppp) REVERT: C 92 ASN cc_start: 0.8406 (m-40) cc_final: 0.7866 (p0) REVERT: C 153 ASN cc_start: 0.5711 (m-40) cc_final: 0.5379 (p0) REVERT: D 39 MET cc_start: 0.7413 (ttp) cc_final: 0.6868 (ttp) REVERT: F 5 THR cc_start: 0.7908 (p) cc_final: 0.7622 (p) REVERT: F 22 SER cc_start: 0.7698 (m) cc_final: 0.6717 (t) REVERT: F 23 VAL cc_start: 0.8368 (t) cc_final: 0.8161 (t) REVERT: F 104 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7444 (tm-30) REVERT: F 119 GLN cc_start: 0.9033 (mt0) cc_final: 0.8747 (tt0) REVERT: F 127 VAL cc_start: 0.8337 (p) cc_final: 0.8004 (m) REVERT: H 127 LYS cc_start: 0.8267 (tttt) cc_final: 0.7711 (ttpt) outliers start: 34 outliers final: 24 residues processed: 181 average time/residue: 0.0590 time to fit residues: 15.2740 Evaluate side-chains 177 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain H residue 114 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 41 optimal weight: 7.9990 chunk 35 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 74 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 ASN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.136038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116726 restraints weight = 12851.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.116892 restraints weight = 12056.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117931 restraints weight = 10685.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118467 restraints weight = 7414.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118559 restraints weight = 6063.725| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7523 Z= 0.127 Angle : 0.567 7.612 10206 Z= 0.294 Chirality : 0.045 0.150 1144 Planarity : 0.004 0.056 1325 Dihedral : 4.375 44.244 1011 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.87 % Allowed : 18.16 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.28), residues: 918 helix: 1.28 (0.47), residues: 118 sheet: 0.14 (0.36), residues: 211 loop : 0.07 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 140 TYR 0.030 0.001 TYR C 55 PHE 0.028 0.001 PHE H 119 TRP 0.007 0.001 TRP F 85 HIS 0.002 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7523) covalent geometry : angle 0.56689 / 0.29 (10206) hydrogen bonds : bond 0.04288 / 2.82 ( 244) hydrogen bonds : angle 5.49558 / 3.82 ( 651) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8094 (tpp80) cc_final: 0.7842 (tpp-160) REVERT: B 106 ILE cc_start: 0.9316 (mm) cc_final: 0.8966 (mt) REVERT: B 133 TYR cc_start: 0.8222 (t80) cc_final: 0.7947 (t80) REVERT: C 29 LYS cc_start: 0.5182 (tptp) cc_final: 0.4832 (tppp) REVERT: C 92 ASN cc_start: 0.8365 (m-40) cc_final: 0.7881 (p0) REVERT: C 153 ASN cc_start: 0.5310 (m-40) cc_final: 0.5009 (p0) REVERT: D 39 MET cc_start: 0.7396 (ttp) cc_final: 0.6856 (ttp) REVERT: F 5 THR cc_start: 0.7850 (p) cc_final: 0.7557 (p) REVERT: F 22 SER cc_start: 0.7988 (m) cc_final: 0.7016 (t) REVERT: F 23 VAL cc_start: 0.8492 (t) cc_final: 0.8279 (t) REVERT: F 119 GLN cc_start: 0.9021 (mt0) cc_final: 0.8736 (tt0) REVERT: F 127 VAL cc_start: 0.8377 (p) cc_final: 0.8043 (m) REVERT: H 127 LYS cc_start: 0.8251 (tttt) cc_final: 0.7710 (ttpt) outliers start: 32 outliers final: 29 residues processed: 179 average time/residue: 0.0678 time to fit residues: 17.2598 Evaluate side-chains 182 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain H residue 114 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 0.0070 chunk 38 optimal weight: 0.8980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115072 restraints weight = 12856.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115398 restraints weight = 11463.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.115776 restraints weight = 10574.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116298 restraints weight = 7965.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116517 restraints weight = 6417.552| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7523 Z= 0.158 Angle : 0.589 7.500 10206 Z= 0.305 Chirality : 0.047 0.163 1144 Planarity : 0.004 0.057 1325 Dihedral : 4.491 44.841 1011 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.36 % Allowed : 18.16 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.28), residues: 918 helix: 1.28 (0.47), residues: 118 sheet: 0.07 (0.35), residues: 211 loop : 0.01 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 140 TYR 0.018 0.002 TYR F 24 PHE 0.028 0.002 PHE H 119 TRP 0.008 0.001 TRP F 85 HIS 0.003 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 7523) covalent geometry : angle 0.58926 / 0.30 (10206) hydrogen bonds : bond 0.04347 / 2.85 ( 244) hydrogen bonds : angle 5.44311 / 3.79 ( 651) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8105 (tpp80) cc_final: 0.7788 (tpp80) REVERT: A 45 TYR cc_start: 0.7908 (t80) cc_final: 0.7658 (t80) REVERT: A 74 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8782 (tp) REVERT: B 84 ASN cc_start: 0.9312 (OUTLIER) cc_final: 0.8866 (t0) REVERT: B 106 ILE cc_start: 0.9315 (mm) cc_final: 0.8960 (mt) REVERT: B 133 TYR cc_start: 0.8525 (t80) cc_final: 0.8252 (t80) REVERT: C 29 LYS cc_start: 0.5333 (tptp) cc_final: 0.4941 (tppp) REVERT: C 92 ASN cc_start: 0.8368 (m-40) cc_final: 0.7895 (p0) REVERT: C 153 ASN cc_start: 0.5669 (m-40) cc_final: 0.5445 (p0) REVERT: D 39 MET cc_start: 0.7475 (ttp) cc_final: 0.6897 (ttp) REVERT: F 5 THR cc_start: 0.7876 (p) cc_final: 0.7545 (p) REVERT: F 22 SER cc_start: 0.8104 (m) cc_final: 0.7060 (t) REVERT: F 23 VAL cc_start: 0.8344 (t) cc_final: 0.8083 (t) REVERT: F 127 VAL cc_start: 0.8372 (p) cc_final: 0.8038 (m) REVERT: F 136 ASN cc_start: 0.7366 (p0) cc_final: 0.6795 (p0) REVERT: H 127 LYS cc_start: 0.8361 (tttt) cc_final: 0.7734 (ttpt) REVERT: H 128 SER cc_start: 0.9079 (m) cc_final: 0.8638 (m) outliers start: 36 outliers final: 32 residues processed: 180 average time/residue: 0.0749 time to fit residues: 18.8885 Evaluate side-chains 187 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 187 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.114154 restraints weight = 12945.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.113997 restraints weight = 10936.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.114700 restraints weight = 9344.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115067 restraints weight = 7808.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115367 restraints weight = 6464.812| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7523 Z= 0.171 Angle : 0.617 11.082 10206 Z= 0.315 Chirality : 0.047 0.181 1144 Planarity : 0.005 0.058 1325 Dihedral : 4.663 46.252 1011 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.84 % Allowed : 17.92 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.27), residues: 918 helix: 1.24 (0.47), residues: 118 sheet: -0.08 (0.36), residues: 198 loop : -0.08 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 65 TYR 0.023 0.002 TYR F 24 PHE 0.028 0.002 PHE H 119 TRP 0.010 0.001 TRP F 85 HIS 0.003 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 7523) covalent geometry : angle 0.61737 / 0.31 (10206) hydrogen bonds : bond 0.04409 / 2.90 ( 244) hydrogen bonds : angle 5.38554 / 3.76 ( 651) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8117 (tpp80) cc_final: 0.7810 (tpp80) REVERT: B 84 ASN cc_start: 0.9335 (OUTLIER) cc_final: 0.8916 (t0) REVERT: B 106 ILE cc_start: 0.9306 (mm) cc_final: 0.8966 (mt) REVERT: B 133 TYR cc_start: 0.8664 (t80) cc_final: 0.8173 (t80) REVERT: B 159 THR cc_start: 0.8426 (m) cc_final: 0.8004 (t) REVERT: C 153 ASN cc_start: 0.5681 (m-40) cc_final: 0.5461 (p0) REVERT: D 39 MET cc_start: 0.7544 (ttp) cc_final: 0.6959 (ttp) REVERT: F 5 THR cc_start: 0.7861 (p) cc_final: 0.7528 (p) REVERT: F 22 SER cc_start: 0.8155 (m) cc_final: 0.7099 (t) REVERT: F 23 VAL cc_start: 0.8254 (t) cc_final: 0.8016 (t) REVERT: F 127 VAL cc_start: 0.8236 (p) cc_final: 0.7923 (m) REVERT: F 136 ASN cc_start: 0.7439 (p0) cc_final: 0.6851 (p0) REVERT: H 124 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.6634 (t80) REVERT: H 127 LYS cc_start: 0.8214 (tttt) cc_final: 0.7524 (ttpt) REVERT: H 128 SER cc_start: 0.9183 (m) cc_final: 0.8791 (m) outliers start: 40 outliers final: 33 residues processed: 183 average time/residue: 0.0754 time to fit residues: 19.2607 Evaluate side-chains 188 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 124 TYR Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 187 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 60 optimal weight: 0.0970 chunk 68 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115241 restraints weight = 12755.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.114783 restraints weight = 14761.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116145 restraints weight = 11886.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116516 restraints weight = 7972.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.116987 restraints weight = 6570.239| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7523 Z= 0.136 Angle : 0.596 9.378 10206 Z= 0.306 Chirality : 0.046 0.179 1144 Planarity : 0.004 0.061 1325 Dihedral : 4.580 46.529 1011 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.00 % Allowed : 19.25 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.28), residues: 918 helix: 1.35 (0.47), residues: 118 sheet: 0.14 (0.36), residues: 194 loop : -0.10 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 20 TYR 0.021 0.002 TYR F 24 PHE 0.030 0.001 PHE H 119 TRP 0.007 0.001 TRP F 85 HIS 0.002 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 7523) covalent geometry : angle 0.59577 / 0.31 (10206) hydrogen bonds : bond 0.04182 / 2.75 ( 244) hydrogen bonds : angle 5.33020 / 3.70 ( 651) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8026 (tpp80) cc_final: 0.7767 (tpp-160) REVERT: A 74 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8721 (tp) REVERT: B 84 ASN cc_start: 0.9328 (OUTLIER) cc_final: 0.8915 (t0) REVERT: B 106 ILE cc_start: 0.9315 (mm) cc_final: 0.8970 (mt) REVERT: B 133 TYR cc_start: 0.8655 (t80) cc_final: 0.8353 (t80) REVERT: B 159 THR cc_start: 0.8389 (m) cc_final: 0.7999 (t) REVERT: D 39 MET cc_start: 0.7406 (ttp) cc_final: 0.6856 (ttp) REVERT: F 5 THR cc_start: 0.7824 (p) cc_final: 0.7474 (p) REVERT: F 22 SER cc_start: 0.8113 (m) cc_final: 0.7374 (p) REVERT: F 23 VAL cc_start: 0.7997 (t) cc_final: 0.7762 (t) REVERT: F 127 VAL cc_start: 0.8310 (p) cc_final: 0.8040 (m) REVERT: F 136 ASN cc_start: 0.7412 (p0) cc_final: 0.6838 (p0) REVERT: H 124 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.6631 (t80) REVERT: H 127 LYS cc_start: 0.8387 (tttt) cc_final: 0.7709 (ttpt) REVERT: H 128 SER cc_start: 0.9088 (m) cc_final: 0.8696 (m) outliers start: 33 outliers final: 26 residues processed: 180 average time/residue: 0.0661 time to fit residues: 17.0396 Evaluate side-chains 183 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 124 TYR Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 187 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.0570 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 78 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116177 restraints weight = 12788.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115689 restraints weight = 12616.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116483 restraints weight = 10159.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116886 restraints weight = 7906.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.116945 restraints weight = 7035.912| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7523 Z= 0.129 Angle : 0.603 9.256 10206 Z= 0.310 Chirality : 0.046 0.186 1144 Planarity : 0.004 0.062 1325 Dihedral : 4.536 47.201 1011 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.00 % Allowed : 19.13 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.28), residues: 918 helix: 1.42 (0.47), residues: 118 sheet: 0.15 (0.36), residues: 200 loop : -0.07 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 20 TYR 0.021 0.002 TYR A 45 PHE 0.030 0.001 PHE H 119 TRP 0.007 0.001 TRP C 33 HIS 0.002 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7523) covalent geometry : angle 0.60291 / 0.31 (10206) hydrogen bonds : bond 0.04019 / 2.64 ( 244) hydrogen bonds : angle 5.27245 / 3.66 ( 651) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8038 (tpp80) cc_final: 0.7706 (tpp80) REVERT: B 84 ASN cc_start: 0.9308 (OUTLIER) cc_final: 0.8881 (t0) REVERT: B 106 ILE cc_start: 0.9265 (mm) cc_final: 0.8913 (mt) REVERT: B 133 TYR cc_start: 0.8597 (t80) cc_final: 0.8309 (t80) REVERT: B 159 THR cc_start: 0.8400 (m) cc_final: 0.8012 (t) REVERT: D 39 MET cc_start: 0.7403 (ttp) cc_final: 0.6843 (ttp) REVERT: F 5 THR cc_start: 0.7792 (p) cc_final: 0.7453 (p) REVERT: F 22 SER cc_start: 0.8146 (m) cc_final: 0.7089 (t) REVERT: F 119 GLN cc_start: 0.8977 (mt0) cc_final: 0.8714 (tt0) REVERT: F 127 VAL cc_start: 0.8339 (p) cc_final: 0.8086 (m) REVERT: F 136 ASN cc_start: 0.7389 (p0) cc_final: 0.6741 (p0) REVERT: F 166 LYS cc_start: 0.6577 (ttmt) cc_final: 0.6099 (ttmm) REVERT: H 124 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.6587 (t80) REVERT: H 127 LYS cc_start: 0.8374 (tttt) cc_final: 0.7697 (ttpt) REVERT: H 128 SER cc_start: 0.9113 (m) cc_final: 0.8708 (m) outliers start: 33 outliers final: 29 residues processed: 183 average time/residue: 0.0634 time to fit residues: 16.6828 Evaluate side-chains 185 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 124 TYR Chi-restraints excluded: chain H residue 187 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 67 optimal weight: 0.0060 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.0060 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 126 GLN C 136 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.116039 restraints weight = 12757.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.115314 restraints weight = 14057.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.117290 restraints weight = 11028.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117466 restraints weight = 6802.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117669 restraints weight = 5902.939| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.155 7523 Z= 0.303 Angle : 1.306 59.197 10206 Z= 0.800 Chirality : 0.051 0.717 1144 Planarity : 0.005 0.070 1325 Dihedral : 4.847 47.194 1011 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.87 % Allowed : 19.73 % Favored : 76.39 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.28), residues: 918 helix: 1.42 (0.47), residues: 118 sheet: 0.14 (0.36), residues: 200 loop : -0.09 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 140 TYR 0.019 0.001 TYR A 45 PHE 0.029 0.002 PHE H 119 TRP 0.006 0.001 TRP C 33 HIS 0.002 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.30 ( 7523) covalent geometry : angle 1.30604 / 0.80 (10206) hydrogen bonds : bond 0.04016 / 2.64 ( 244) hydrogen bonds : angle 5.27223 / 3.65 ( 651) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1290.29 seconds wall clock time: 23 minutes 2.22 seconds (1382.22 seconds total)