Starting phenix.real_space_refine on Sun May 3 08:18:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11np_75868/05_2026/11np_75868.cif Found real_map, /net/cci-nas-00/data/ceres_data/11np_75868/05_2026/11np_75868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11np_75868/05_2026/11np_75868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11np_75868/05_2026/11np_75868.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11np_75868/05_2026/11np_75868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11np_75868/05_2026/11np_75868.map" } resolution = 2.43 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= 0.008 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 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 3141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11633 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "D" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "A" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 277 Classifications: {'water': 277} Link IDs: {None: 276} Chain: "B" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 292 Classifications: {'water': 292} Link IDs: {None: 291} Chain: "C" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 270 Classifications: {'water': 270} Link IDs: {None: 269} Chain: "D" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 322 Classifications: {'water': 322} Link IDs: {None: 321} Time building chain proxies: 3.05, per 1000 atoms: 0.26 Number of scatterers: 11633 At special positions: 0 Unit cell: (99.96, 80.115, 110.25, 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 44 16.00 O 3141 8.00 N 1860 7.00 C 6588 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: 0.72 Conformation dependent library (CDL) restraints added in 483.4 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 54.7% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 45 removed outlier: 3.819A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 removed outlier: 3.508A pdb=" N ASN A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 260 Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.535A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 319 through 338 removed outlier: 3.825A pdb=" N GLU A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 35 through 45 removed outlier: 3.736A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.926A pdb=" N TYR B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 260 removed outlier: 3.652A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 302 through 314 removed outlier: 6.437A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 338 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 35 through 45 removed outlier: 4.379A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.860A pdb=" N TYR C 84 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 179 Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 244 through 260 Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.505A pdb=" N GLN C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 338 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.805A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 79 through 85 removed outlier: 3.996A pdb=" N TYR D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 179 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 260 Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 319 through 338 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.737A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA A 32 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU A 270 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 31 removed outlier: 5.793A pdb=" N GLY B 28 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 104 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N LYS B 146 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE B 106 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ARG B 148 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 31 " --> pdb=" O TYR B 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32 removed outlier: 6.713A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA C 32 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 104 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LYS C 146 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C 106 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ARG C 148 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.778A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 104 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LYS D 146 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE D 106 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ARG D 148 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA D 145 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLU D 187 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP D 147 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU D 189 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS D 149 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU D 191 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU D 151 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 31 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 590 hydrogen bonds defined for protein. 1701 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: 2.02 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2184 1.33 - 1.45: 2259 1.45 - 1.57: 6173 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" N ASN C 70 " pdb=" CA ASN C 70 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.65e+00 bond pdb=" N TRP B 295 " pdb=" CA TRP B 295 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.26e-02 6.30e+03 9.25e+00 bond pdb=" N PHE B 144 " pdb=" CA PHE B 144 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.29e-02 6.01e+03 9.18e+00 bond pdb=" N TRP C 295 " pdb=" CA TRP C 295 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.18e-02 7.18e+03 9.11e+00 bond pdb=" N TRP A 295 " pdb=" CA TRP A 295 " ideal model delta sigma weight residual 1.454 1.493 -0.038 1.27e-02 6.20e+03 9.06e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 13368 1.45 - 2.89: 876 2.89 - 4.34: 170 4.34 - 5.79: 36 5.79 - 7.23: 14 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA PHE B 144 " pdb=" CB PHE B 144 " pdb=" CG PHE B 144 " ideal model delta sigma weight residual 113.80 118.60 -4.80 1.00e+00 1.00e+00 2.30e+01 angle pdb=" N GLU C 277 " pdb=" CA GLU C 277 " pdb=" C GLU C 277 " ideal model delta sigma weight residual 111.07 106.03 5.04 1.07e+00 8.73e-01 2.22e+01 angle pdb=" CA PHE C 144 " pdb=" CB PHE C 144 " pdb=" CG PHE C 144 " ideal model delta sigma weight residual 113.80 118.47 -4.67 1.00e+00 1.00e+00 2.18e+01 angle pdb=" N PRO B 188 " pdb=" CA PRO B 188 " pdb=" CB PRO B 188 " ideal model delta sigma weight residual 102.36 105.79 -3.43 7.80e-01 1.64e+00 1.93e+01 angle pdb=" N ASN D 319 " pdb=" CA ASN D 319 " pdb=" C ASN D 319 " ideal model delta sigma weight residual 113.02 107.83 5.19 1.20e+00 6.94e-01 1.87e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6047 17.76 - 35.52: 334 35.52 - 53.28: 82 53.28 - 71.03: 22 71.03 - 88.79: 19 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" C PHE B 144 " pdb=" N PHE B 144 " pdb=" CA PHE B 144 " pdb=" CB PHE B 144 " ideal model delta harmonic sigma weight residual -122.60 -131.22 8.62 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" CB GLU B 53 " pdb=" CG GLU B 53 " pdb=" CD GLU B 53 " pdb=" OE1 GLU B 53 " ideal model delta sinusoidal sigma weight residual 0.00 -88.79 88.79 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU A 318 " pdb=" CG GLU A 318 " pdb=" CD GLU A 318 " pdb=" OE1 GLU A 318 " ideal model delta sinusoidal sigma weight residual 0.00 85.88 -85.88 1 3.00e+01 1.11e-03 9.90e+00 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1351 0.067 - 0.133: 230 0.133 - 0.200: 58 0.200 - 0.266: 4 0.266 - 0.333: 1 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA GLU C 277 " pdb=" N GLU C 277 " pdb=" C GLU C 277 " pdb=" CB GLU C 277 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA LYS B 329 " pdb=" N LYS B 329 " pdb=" C LYS B 329 " pdb=" CB LYS B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA LYS C 329 " pdb=" N LYS C 329 " pdb=" C LYS C 329 " pdb=" CB LYS C 329 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 144 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C PHE B 144 " -0.047 2.00e-02 2.50e+03 pdb=" O PHE B 144 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA B 145 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 329 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C LYS C 329 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS C 329 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG C 330 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 329 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C LYS B 329 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS B 329 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG B 330 " 0.011 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2815 2.79 - 3.32: 11699 3.32 - 3.85: 21985 3.85 - 4.37: 27005 4.37 - 4.90: 42320 Nonbonded interactions: 105824 Sorted by model distance: nonbonded pdb=" O GLN C 60 " pdb=" OG1 THR C 64 " model vdw 2.264 3.040 nonbonded pdb=" O GLY B 154 " pdb=" NH2 ARG B 200 " model vdw 2.293 3.120 nonbonded pdb=" O ALA C 238 " pdb=" O HOH C 401 " model vdw 2.300 3.040 nonbonded pdb=" OE1 GLU D 121 " pdb=" O HOH D 401 " model vdw 2.302 3.040 nonbonded pdb=" OD1 ASN D 168 " pdb=" O HOH D 402 " model vdw 2.304 3.040 ... (remaining 105819 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 3.930 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.460 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.005 0.039 10672 Z= 0.390 Angle : 0.817 7.234 14464 Z= 0.562 Chirality : 0.055 0.333 1644 Planarity : 0.005 0.033 1880 Dihedral : 13.253 88.792 3984 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.26 % Allowed : 2.61 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.94 (0.23), residues: 1364 helix: 1.45 (0.19), residues: 712 sheet: -0.84 (0.33), residues: 220 loop : 0.24 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 68 TYR 0.015 0.002 TYR C 327 PHE 0.025 0.003 PHE B 144 TRP 0.027 0.004 TRP A 147 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00532 (10672) covalent geometry : angle 0.81711 (14464) hydrogen bonds : bond 0.15440 ( 590) hydrogen bonds : angle 5.81270 ( 1701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.306 Fit side-chains REVERT: A 152 LYS cc_start: 0.8482 (mttt) cc_final: 0.8150 (mmmt) REVERT: A 199 LYS cc_start: 0.8518 (mtpt) cc_final: 0.7967 (mmpt) REVERT: A 303 ARG cc_start: 0.7967 (mtp180) cc_final: 0.6877 (mtm110) REVERT: B 95 GLN cc_start: 0.7873 (tt0) cc_final: 0.7421 (tp-100) REVERT: B 241 GLN cc_start: 0.7508 (tt0) cc_final: 0.7233 (tt0) REVERT: B 303 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.6513 (ttt180) REVERT: B 317 LYS cc_start: 0.7562 (mmtt) cc_final: 0.7296 (mptt) REVERT: C 13 LYS cc_start: 0.8521 (tttp) cc_final: 0.8195 (ttpt) REVERT: C 42 ARG cc_start: 0.6956 (mtp180) cc_final: 0.6560 (tpp-160) REVERT: C 292 LEU cc_start: 0.8396 (tt) cc_final: 0.8101 (tm) REVERT: C 311 LYS cc_start: 0.8051 (tttm) cc_final: 0.7624 (ttmt) REVERT: D 41 LYS cc_start: 0.7903 (mmtm) cc_final: 0.7602 (mtmt) REVERT: D 42 ARG cc_start: 0.6789 (mtp180) cc_final: 0.6530 (mmp80) REVERT: D 44 GLN cc_start: 0.6754 (mm110) cc_final: 0.6340 (mt0) REVERT: D 52 GLU cc_start: 0.7578 (tt0) cc_final: 0.7255 (tm-30) REVERT: D 152 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8050 (tptp) REVERT: D 207 LYS cc_start: 0.8210 (tttp) cc_final: 0.7889 (mmtm) REVERT: D 242 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7588 (tttt) REVERT: D 278 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7773 (tp30) REVERT: D 303 ARG cc_start: 0.7744 (mtp85) cc_final: 0.7199 (mtm180) REVERT: D 311 LYS cc_start: 0.8117 (tttm) cc_final: 0.7492 (mppt) outliers start: 14 outliers final: 4 residues processed: 197 average time/residue: 0.9128 time to fit residues: 189.1581 Evaluate side-chains 94 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN A 156 HIS A 168 ASN A 284 ASN A 306 GLN A 319 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS B 168 ASN C 44 GLN C 168 ASN C 241 GLN D 4 HIS D 80 HIS D 119 ASN D 339 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106019 restraints weight = 11893.113| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.30 r_work: 0.3097 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10672 Z= 0.122 Angle : 0.523 6.383 14464 Z= 0.273 Chirality : 0.040 0.140 1644 Planarity : 0.004 0.034 1880 Dihedral : 5.062 56.469 1480 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.98 % Allowed : 8.00 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.76 (0.23), residues: 1364 helix: 2.38 (0.19), residues: 712 sheet: -0.89 (0.32), residues: 232 loop : 0.41 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.012 0.002 TYR C 213 PHE 0.013 0.002 PHE A 144 TRP 0.015 0.002 TRP A 147 HIS 0.005 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00272 (10672) covalent geometry : angle 0.52277 (14464) hydrogen bonds : bond 0.04854 ( 590) hydrogen bonds : angle 4.32405 ( 1701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.456 Fit side-chains REVERT: A 67 ASP cc_start: 0.6971 (m-30) cc_final: 0.6748 (m-30) REVERT: A 152 LYS cc_start: 0.8373 (mttt) cc_final: 0.7514 (mmmt) REVERT: A 199 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7481 (mmtt) REVERT: A 317 LYS cc_start: 0.7813 (tttm) cc_final: 0.7492 (ttmt) REVERT: A 325 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7304 (tp30) REVERT: B 10 GLU cc_start: 0.8008 (mp0) cc_final: 0.7751 (mp0) REVERT: B 49 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: B 66 ASP cc_start: 0.7709 (t70) cc_final: 0.7476 (t70) REVERT: B 95 GLN cc_start: 0.7581 (tt0) cc_final: 0.6821 (tp-100) REVERT: B 241 GLN cc_start: 0.7266 (tt0) cc_final: 0.6902 (tt0) REVERT: B 303 ARG cc_start: 0.7574 (ttm-80) cc_final: 0.6132 (tmt170) REVERT: B 311 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8078 (tmtt) REVERT: B 317 LYS cc_start: 0.7507 (mmtt) cc_final: 0.7106 (mptt) REVERT: C 13 LYS cc_start: 0.8329 (tttp) cc_final: 0.7770 (ttpt) REVERT: C 42 ARG cc_start: 0.6901 (mtp180) cc_final: 0.6403 (tpp-160) REVERT: C 292 LEU cc_start: 0.8244 (tt) cc_final: 0.7910 (tm) REVERT: C 311 LYS cc_start: 0.7913 (tttm) cc_final: 0.7433 (ttmt) REVERT: D 41 LYS cc_start: 0.7571 (mmtm) cc_final: 0.7018 (mtmt) REVERT: D 42 ARG cc_start: 0.6591 (mtp180) cc_final: 0.6082 (mmp80) REVERT: D 44 GLN cc_start: 0.6597 (mm110) cc_final: 0.5990 (mt0) REVERT: D 52 GLU cc_start: 0.7351 (tt0) cc_final: 0.6831 (tm-30) REVERT: D 152 LYS cc_start: 0.8278 (ttmm) cc_final: 0.7668 (tptp) REVERT: D 207 LYS cc_start: 0.8193 (tttp) cc_final: 0.7389 (mmtm) REVERT: D 242 LYS cc_start: 0.7880 (mmtm) cc_final: 0.7258 (tttt) REVERT: D 278 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7258 (tp30) REVERT: D 303 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7316 (mtm180) REVERT: D 311 LYS cc_start: 0.7894 (tttm) cc_final: 0.7092 (mppt) outliers start: 22 outliers final: 14 residues processed: 116 average time/residue: 0.9128 time to fit residues: 111.7844 Evaluate side-chains 104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS B 166 ASN C 44 GLN C 241 GLN D 166 ASN D 168 ASN D 319 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104118 restraints weight = 12063.838| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.30 r_work: 0.3076 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10672 Z= 0.115 Angle : 0.492 5.382 14464 Z= 0.257 Chirality : 0.040 0.139 1644 Planarity : 0.004 0.034 1880 Dihedral : 5.080 57.260 1480 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.80 % Allowed : 8.90 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.95 (0.23), residues: 1364 helix: 2.64 (0.19), residues: 712 sheet: -1.05 (0.31), residues: 252 loop : 0.54 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 68 TYR 0.014 0.002 TYR C 213 PHE 0.015 0.001 PHE A 144 TRP 0.016 0.002 TRP C 147 HIS 0.005 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00261 (10672) covalent geometry : angle 0.49176 (14464) hydrogen bonds : bond 0.04722 ( 590) hydrogen bonds : angle 4.10366 ( 1701) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.466 Fit side-chains REVERT: A 152 LYS cc_start: 0.8427 (mttt) cc_final: 0.7531 (mmmt) REVERT: A 199 LYS cc_start: 0.8351 (mtpt) cc_final: 0.7526 (mmtt) REVERT: A 303 ARG cc_start: 0.7741 (mtp180) cc_final: 0.7523 (mtp180) REVERT: A 317 LYS cc_start: 0.7781 (tttm) cc_final: 0.7455 (ttmt) REVERT: A 325 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7187 (tp30) REVERT: B 10 GLU cc_start: 0.8041 (mp0) cc_final: 0.7769 (mp0) REVERT: B 49 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7421 (pt0) REVERT: B 66 ASP cc_start: 0.7670 (t70) cc_final: 0.7335 (t70) REVERT: B 95 GLN cc_start: 0.7595 (tt0) cc_final: 0.6845 (tp-100) REVERT: B 241 GLN cc_start: 0.7285 (tt0) cc_final: 0.6935 (tt0) REVERT: B 303 ARG cc_start: 0.7593 (ttm-80) cc_final: 0.6087 (tmt170) REVERT: B 317 LYS cc_start: 0.7604 (mmtt) cc_final: 0.7177 (mptt) REVERT: C 13 LYS cc_start: 0.8336 (tttp) cc_final: 0.7767 (ttpt) REVERT: C 42 ARG cc_start: 0.6889 (mtp180) cc_final: 0.6402 (tpp-160) REVERT: C 292 LEU cc_start: 0.8261 (tt) cc_final: 0.7911 (tm) REVERT: C 311 LYS cc_start: 0.7868 (tttm) cc_final: 0.7379 (ttmt) REVERT: D 41 LYS cc_start: 0.7482 (mmtm) cc_final: 0.7041 (mtmt) REVERT: D 42 ARG cc_start: 0.6597 (mtp180) cc_final: 0.6077 (mmp80) REVERT: D 44 GLN cc_start: 0.6583 (mm110) cc_final: 0.6055 (mt0) REVERT: D 52 GLU cc_start: 0.7340 (tt0) cc_final: 0.6785 (tm-30) REVERT: D 152 LYS cc_start: 0.8327 (ttmm) cc_final: 0.7670 (tptp) REVERT: D 207 LYS cc_start: 0.8242 (tttp) cc_final: 0.7406 (mmtt) REVERT: D 242 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7275 (tttt) REVERT: D 278 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7254 (tp30) REVERT: D 303 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7145 (mtm180) REVERT: D 311 LYS cc_start: 0.7941 (tttm) cc_final: 0.7096 (mppt) outliers start: 20 outliers final: 14 residues processed: 111 average time/residue: 0.9146 time to fit residues: 107.3895 Evaluate side-chains 99 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 87 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 119 ASN C 44 GLN C 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.105321 restraints weight = 12079.622| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.27 r_work: 0.3091 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10672 Z= 0.106 Angle : 0.469 5.243 14464 Z= 0.244 Chirality : 0.039 0.134 1644 Planarity : 0.004 0.034 1880 Dihedral : 5.005 58.183 1480 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.07 % Allowed : 8.90 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.05 (0.23), residues: 1364 helix: 2.75 (0.19), residues: 712 sheet: -1.06 (0.31), residues: 252 loop : 0.58 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 68 TYR 0.015 0.001 TYR D 213 PHE 0.014 0.001 PHE A 144 TRP 0.014 0.002 TRP A 147 HIS 0.004 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00241 (10672) covalent geometry : angle 0.46851 (14464) hydrogen bonds : bond 0.04344 ( 590) hydrogen bonds : angle 4.00468 ( 1701) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.452 Fit side-chains REVERT: A 152 LYS cc_start: 0.8440 (mttt) cc_final: 0.7551 (mmmt) REVERT: A 199 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7538 (mmpt) REVERT: A 317 LYS cc_start: 0.7775 (tttm) cc_final: 0.7434 (tttp) REVERT: A 325 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7187 (tp30) REVERT: B 10 GLU cc_start: 0.8023 (mp0) cc_final: 0.7730 (mp0) REVERT: B 66 ASP cc_start: 0.7594 (t70) cc_final: 0.7169 (t70) REVERT: B 95 GLN cc_start: 0.7611 (tt0) cc_final: 0.6894 (tp-100) REVERT: B 241 GLN cc_start: 0.7293 (tt0) cc_final: 0.6951 (tt0) REVERT: B 303 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.6047 (tmt90) REVERT: B 317 LYS cc_start: 0.7605 (mmtt) cc_final: 0.7134 (mptt) REVERT: C 13 LYS cc_start: 0.8301 (tttp) cc_final: 0.7724 (ttpt) REVERT: C 42 ARG cc_start: 0.6878 (mtp180) cc_final: 0.6426 (tpp-160) REVERT: C 292 LEU cc_start: 0.8241 (tt) cc_final: 0.7894 (tm) REVERT: C 295 TRP cc_start: 0.9046 (OUTLIER) cc_final: 0.6537 (m-90) REVERT: C 311 LYS cc_start: 0.7812 (tttm) cc_final: 0.7321 (ttmt) REVERT: D 41 LYS cc_start: 0.7454 (mmtm) cc_final: 0.7059 (mtmt) REVERT: D 42 ARG cc_start: 0.6643 (mtp180) cc_final: 0.6092 (mmp80) REVERT: D 44 GLN cc_start: 0.6489 (mm110) cc_final: 0.6111 (mt0) REVERT: D 52 GLU cc_start: 0.7369 (tt0) cc_final: 0.6817 (tm-30) REVERT: D 107 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8608 (ttmm) REVERT: D 152 LYS cc_start: 0.8344 (ttmm) cc_final: 0.7697 (tptp) REVERT: D 207 LYS cc_start: 0.8248 (tttp) cc_final: 0.7418 (mmtt) REVERT: D 278 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7259 (tp30) REVERT: D 303 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7108 (mtm180) REVERT: D 311 LYS cc_start: 0.7950 (tttm) cc_final: 0.7118 (mppt) outliers start: 23 outliers final: 11 residues processed: 105 average time/residue: 0.8255 time to fit residues: 91.7637 Evaluate side-chains 97 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 80 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 11 optimal weight: 0.0060 chunk 86 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN C 44 GLN C 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107794 restraints weight = 12045.958| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.28 r_work: 0.3125 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10672 Z= 0.092 Angle : 0.439 4.902 14464 Z= 0.228 Chirality : 0.038 0.132 1644 Planarity : 0.003 0.033 1880 Dihedral : 4.835 58.664 1480 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.80 % Allowed : 9.62 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.22 (0.24), residues: 1364 helix: 2.90 (0.19), residues: 712 sheet: -1.03 (0.31), residues: 252 loop : 0.67 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 55 TYR 0.016 0.001 TYR C 203 PHE 0.014 0.001 PHE A 144 TRP 0.011 0.001 TRP A 147 HIS 0.003 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00203 (10672) covalent geometry : angle 0.43879 (14464) hydrogen bonds : bond 0.03805 ( 590) hydrogen bonds : angle 3.86171 ( 1701) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.427 Fit side-chains REVERT: A 152 LYS cc_start: 0.8427 (mttt) cc_final: 0.7537 (mmmt) REVERT: A 173 TYR cc_start: 0.8870 (OUTLIER) cc_final: 0.7522 (t80) REVERT: A 199 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7529 (mmpt) REVERT: A 317 LYS cc_start: 0.7723 (tttm) cc_final: 0.7424 (ttmm) REVERT: A 325 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7134 (tp30) REVERT: B 10 GLU cc_start: 0.7978 (mp0) cc_final: 0.7673 (mp0) REVERT: B 66 ASP cc_start: 0.7549 (t70) cc_final: 0.7093 (t70) REVERT: B 95 GLN cc_start: 0.7569 (tt0) cc_final: 0.6839 (tp-100) REVERT: B 241 GLN cc_start: 0.7270 (tt0) cc_final: 0.6930 (tt0) REVERT: B 303 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.6030 (tmt90) REVERT: B 317 LYS cc_start: 0.7534 (mmtt) cc_final: 0.7072 (mptt) REVERT: B 341 LYS cc_start: 0.8417 (mttt) cc_final: 0.8158 (mtpt) REVERT: C 2 HIS cc_start: 0.4087 (OUTLIER) cc_final: 0.3868 (m170) REVERT: C 13 LYS cc_start: 0.8238 (tttp) cc_final: 0.7659 (ttpt) REVERT: C 42 ARG cc_start: 0.6856 (mtp180) cc_final: 0.6485 (tpp-160) REVERT: C 292 LEU cc_start: 0.8221 (tt) cc_final: 0.7884 (tm) REVERT: C 295 TRP cc_start: 0.9011 (OUTLIER) cc_final: 0.6546 (m-90) REVERT: C 311 LYS cc_start: 0.7806 (tttm) cc_final: 0.7320 (ttmt) REVERT: D 41 LYS cc_start: 0.7429 (mmtm) cc_final: 0.7036 (mtmt) REVERT: D 42 ARG cc_start: 0.6608 (mtp180) cc_final: 0.6052 (mmp80) REVERT: D 44 GLN cc_start: 0.6539 (mm110) cc_final: 0.6180 (mt0) REVERT: D 52 GLU cc_start: 0.7361 (tt0) cc_final: 0.6814 (tm-30) REVERT: D 152 LYS cc_start: 0.8340 (ttmm) cc_final: 0.7690 (tptp) REVERT: D 207 LYS cc_start: 0.8192 (tttp) cc_final: 0.7380 (mmtt) REVERT: D 242 LYS cc_start: 0.7922 (mmtm) cc_final: 0.7608 (mmtm) REVERT: D 278 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7251 (tp30) REVERT: D 303 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7185 (mtm180) REVERT: D 311 LYS cc_start: 0.7868 (tttm) cc_final: 0.7034 (mppt) outliers start: 20 outliers final: 9 residues processed: 113 average time/residue: 0.8340 time to fit residues: 100.0564 Evaluate side-chains 101 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 102 optimal weight: 0.0670 chunk 62 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 61 optimal weight: 0.0870 chunk 82 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 119 ASN A 166 ASN C 44 GLN C 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107433 restraints weight = 12064.020| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.28 r_work: 0.3122 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10672 Z= 0.094 Angle : 0.440 4.927 14464 Z= 0.228 Chirality : 0.038 0.124 1644 Planarity : 0.003 0.033 1880 Dihedral : 4.813 58.804 1480 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.71 % Allowed : 10.16 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.25 (0.24), residues: 1364 helix: 2.94 (0.19), residues: 712 sheet: -1.02 (0.31), residues: 252 loop : 0.65 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.018 0.001 TYR C 203 PHE 0.014 0.001 PHE A 144 TRP 0.012 0.001 TRP A 147 HIS 0.003 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00209 (10672) covalent geometry : angle 0.43990 (14464) hydrogen bonds : bond 0.03833 ( 590) hydrogen bonds : angle 3.81176 ( 1701) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.462 Fit side-chains REVERT: A 152 LYS cc_start: 0.8432 (mttt) cc_final: 0.7541 (mmmt) REVERT: A 173 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.7609 (t80) REVERT: A 199 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7518 (mmtt) REVERT: A 317 LYS cc_start: 0.7700 (tttm) cc_final: 0.7422 (tttm) REVERT: A 325 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7130 (tp30) REVERT: B 10 GLU cc_start: 0.7971 (mp0) cc_final: 0.7659 (mp0) REVERT: B 66 ASP cc_start: 0.7505 (t70) cc_final: 0.7015 (t70) REVERT: B 95 GLN cc_start: 0.7553 (tt0) cc_final: 0.6839 (tp-100) REVERT: B 241 GLN cc_start: 0.7276 (tt0) cc_final: 0.6944 (tt0) REVERT: B 303 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.6008 (tmt90) REVERT: B 317 LYS cc_start: 0.7514 (mmtt) cc_final: 0.7036 (mptt) REVERT: B 341 LYS cc_start: 0.8398 (mttt) cc_final: 0.8141 (mtpt) REVERT: C 2 HIS cc_start: 0.4173 (OUTLIER) cc_final: 0.3954 (m170) REVERT: C 13 LYS cc_start: 0.8253 (tttp) cc_final: 0.7679 (ttpt) REVERT: C 42 ARG cc_start: 0.6829 (mtp180) cc_final: 0.6480 (tpp-160) REVERT: C 292 LEU cc_start: 0.8227 (tt) cc_final: 0.7878 (tm) REVERT: C 295 TRP cc_start: 0.9010 (OUTLIER) cc_final: 0.6527 (m-90) REVERT: C 311 LYS cc_start: 0.7824 (tttm) cc_final: 0.7325 (ttmt) REVERT: D 41 LYS cc_start: 0.7441 (mmtm) cc_final: 0.7035 (mtmt) REVERT: D 42 ARG cc_start: 0.6569 (mtp180) cc_final: 0.6010 (mmp80) REVERT: D 44 GLN cc_start: 0.6539 (mm110) cc_final: 0.6177 (mt0) REVERT: D 52 GLU cc_start: 0.7375 (tt0) cc_final: 0.6815 (tm-30) REVERT: D 152 LYS cc_start: 0.8354 (ttmm) cc_final: 0.7698 (tptp) REVERT: D 207 LYS cc_start: 0.8203 (tttp) cc_final: 0.7391 (mmtt) REVERT: D 242 LYS cc_start: 0.7940 (mmtm) cc_final: 0.7681 (mmtm) REVERT: D 278 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7257 (tp30) REVERT: D 303 ARG cc_start: 0.7808 (mtp85) cc_final: 0.7229 (mtm180) REVERT: D 311 LYS cc_start: 0.7833 (tttm) cc_final: 0.7014 (mppt) outliers start: 19 outliers final: 11 residues processed: 105 average time/residue: 0.8668 time to fit residues: 96.4998 Evaluate side-chains 103 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 16 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 65 optimal weight: 0.0030 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 119 ASN C 44 GLN C 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.128392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.104412 restraints weight = 12039.663| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.28 r_work: 0.3079 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10672 Z= 0.114 Angle : 0.473 5.187 14464 Z= 0.246 Chirality : 0.039 0.136 1644 Planarity : 0.004 0.033 1880 Dihedral : 4.962 58.442 1480 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.71 % Allowed : 10.34 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.15 (0.24), residues: 1364 helix: 2.87 (0.19), residues: 712 sheet: -1.06 (0.31), residues: 252 loop : 0.56 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.020 0.002 TYR C 203 PHE 0.014 0.001 PHE A 144 TRP 0.015 0.002 TRP A 147 HIS 0.004 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00261 (10672) covalent geometry : angle 0.47346 (14464) hydrogen bonds : bond 0.04496 ( 590) hydrogen bonds : angle 3.90499 ( 1701) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.383 Fit side-chains REVERT: A 152 LYS cc_start: 0.8440 (mttt) cc_final: 0.7559 (mmmt) REVERT: A 173 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.7840 (t80) REVERT: A 199 LYS cc_start: 0.8370 (mtpt) cc_final: 0.7561 (mmpt) REVERT: A 317 LYS cc_start: 0.7792 (tttm) cc_final: 0.7465 (ttmm) REVERT: A 325 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7159 (tp30) REVERT: B 10 GLU cc_start: 0.8042 (mp0) cc_final: 0.7730 (mp0) REVERT: B 66 ASP cc_start: 0.7511 (t70) cc_final: 0.7006 (t70) REVERT: B 95 GLN cc_start: 0.7633 (tt0) cc_final: 0.6941 (tp-100) REVERT: B 165 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: B 241 GLN cc_start: 0.7270 (tt0) cc_final: 0.6932 (tt0) REVERT: B 303 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.5991 (tmt90) REVERT: B 317 LYS cc_start: 0.7586 (mmtt) cc_final: 0.7103 (mptt) REVERT: B 341 LYS cc_start: 0.8434 (mttt) cc_final: 0.8148 (mtpt) REVERT: C 13 LYS cc_start: 0.8309 (tttp) cc_final: 0.7721 (ttpt) REVERT: C 42 ARG cc_start: 0.6825 (mtp180) cc_final: 0.6454 (tpp-160) REVERT: C 155 GLU cc_start: 0.6612 (tp30) cc_final: 0.5971 (tp30) REVERT: C 292 LEU cc_start: 0.8218 (tt) cc_final: 0.7853 (tm) REVERT: C 295 TRP cc_start: 0.9057 (OUTLIER) cc_final: 0.6450 (m-90) REVERT: C 311 LYS cc_start: 0.7871 (tttm) cc_final: 0.7414 (ttmt) REVERT: D 41 LYS cc_start: 0.7451 (mmtm) cc_final: 0.7064 (mtmt) REVERT: D 42 ARG cc_start: 0.6601 (mtp180) cc_final: 0.6002 (mmp80) REVERT: D 44 GLN cc_start: 0.6515 (mm110) cc_final: 0.6198 (mt0) REVERT: D 52 GLU cc_start: 0.7411 (tt0) cc_final: 0.6837 (tm-30) REVERT: D 152 LYS cc_start: 0.8366 (ttmm) cc_final: 0.7701 (tptp) REVERT: D 207 LYS cc_start: 0.8291 (tttp) cc_final: 0.7446 (mmtt) REVERT: D 242 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7718 (mmtm) REVERT: D 278 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7321 (tp30) REVERT: D 303 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7215 (mtm180) REVERT: D 311 LYS cc_start: 0.7902 (tttm) cc_final: 0.7102 (mppt) outliers start: 19 outliers final: 11 residues processed: 102 average time/residue: 0.9070 time to fit residues: 97.8063 Evaluate side-chains 100 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 101 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN C 44 GLN C 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.104076 restraints weight = 12008.034| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.28 r_work: 0.3075 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10672 Z= 0.114 Angle : 0.476 5.832 14464 Z= 0.247 Chirality : 0.039 0.135 1644 Planarity : 0.004 0.033 1880 Dihedral : 4.979 58.442 1480 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.80 % Allowed : 10.16 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.14 (0.23), residues: 1364 helix: 2.85 (0.19), residues: 712 sheet: -1.07 (0.31), residues: 252 loop : 0.59 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.020 0.002 TYR C 203 PHE 0.015 0.001 PHE A 144 TRP 0.014 0.002 TRP A 147 HIS 0.004 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00261 (10672) covalent geometry : angle 0.47572 (14464) hydrogen bonds : bond 0.04496 ( 590) hydrogen bonds : angle 3.93600 ( 1701) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.408 Fit side-chains REVERT: A 152 LYS cc_start: 0.8455 (mttt) cc_final: 0.7563 (mmmt) REVERT: A 173 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.7762 (t80) REVERT: A 199 LYS cc_start: 0.8392 (mtpt) cc_final: 0.7575 (mmpt) REVERT: A 242 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7523 (mtpt) REVERT: A 317 LYS cc_start: 0.7812 (tttm) cc_final: 0.7475 (ttmm) REVERT: A 325 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7166 (tp30) REVERT: B 10 GLU cc_start: 0.8053 (mp0) cc_final: 0.7743 (mp0) REVERT: B 66 ASP cc_start: 0.7507 (t70) cc_final: 0.6991 (t70) REVERT: B 95 GLN cc_start: 0.7624 (tt0) cc_final: 0.6946 (tp-100) REVERT: B 165 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: B 241 GLN cc_start: 0.7275 (tt0) cc_final: 0.6951 (tt0) REVERT: B 303 ARG cc_start: 0.7574 (ttm-80) cc_final: 0.6026 (tmt90) REVERT: B 317 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7126 (mptt) REVERT: B 341 LYS cc_start: 0.8419 (mttt) cc_final: 0.8115 (mtmp) REVERT: C 13 LYS cc_start: 0.8309 (tttp) cc_final: 0.7713 (ttpt) REVERT: C 42 ARG cc_start: 0.6847 (mtp180) cc_final: 0.6434 (tpp-160) REVERT: C 155 GLU cc_start: 0.6624 (tp30) cc_final: 0.5984 (tp30) REVERT: C 292 LEU cc_start: 0.8231 (tt) cc_final: 0.7881 (tm) REVERT: C 295 TRP cc_start: 0.9065 (OUTLIER) cc_final: 0.6524 (m-90) REVERT: C 311 LYS cc_start: 0.7897 (tttm) cc_final: 0.7395 (ttmt) REVERT: D 41 LYS cc_start: 0.7511 (mmtm) cc_final: 0.7094 (mtmt) REVERT: D 42 ARG cc_start: 0.6610 (mtp180) cc_final: 0.5990 (mmp80) REVERT: D 44 GLN cc_start: 0.6466 (mm110) cc_final: 0.6164 (mt0) REVERT: D 52 GLU cc_start: 0.7401 (tt0) cc_final: 0.6830 (tm-30) REVERT: D 152 LYS cc_start: 0.8337 (ttmm) cc_final: 0.7679 (tptp) REVERT: D 207 LYS cc_start: 0.8282 (tttp) cc_final: 0.7459 (mmtm) REVERT: D 242 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7729 (mmtm) REVERT: D 278 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7336 (tp30) REVERT: D 311 LYS cc_start: 0.7907 (tttm) cc_final: 0.7101 (mppt) outliers start: 20 outliers final: 11 residues processed: 106 average time/residue: 0.8864 time to fit residues: 99.5743 Evaluate side-chains 103 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 119 ASN C 44 GLN C 241 GLN D 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.104309 restraints weight = 11890.371| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.27 r_work: 0.3079 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10672 Z= 0.112 Angle : 0.476 6.468 14464 Z= 0.248 Chirality : 0.039 0.129 1644 Planarity : 0.004 0.033 1880 Dihedral : 4.963 58.484 1480 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.53 % Allowed : 10.88 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.12 (0.23), residues: 1364 helix: 2.83 (0.19), residues: 712 sheet: -1.08 (0.31), residues: 252 loop : 0.58 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 303 TYR 0.019 0.002 TYR C 203 PHE 0.015 0.001 PHE A 144 TRP 0.014 0.002 TRP A 147 HIS 0.004 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00256 (10672) covalent geometry : angle 0.47571 (14464) hydrogen bonds : bond 0.04441 ( 590) hydrogen bonds : angle 3.92392 ( 1701) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.481 Fit side-chains REVERT: A 152 LYS cc_start: 0.8455 (mttt) cc_final: 0.7570 (mmmt) REVERT: A 173 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.7760 (t80) REVERT: A 199 LYS cc_start: 0.8390 (mtpt) cc_final: 0.7577 (mmpt) REVERT: A 242 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7536 (mtpt) REVERT: A 303 ARG cc_start: 0.7677 (mtp180) cc_final: 0.6580 (mtm110) REVERT: A 317 LYS cc_start: 0.7837 (tttm) cc_final: 0.7484 (ttmm) REVERT: A 325 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: B 10 GLU cc_start: 0.8052 (mp0) cc_final: 0.7740 (mp0) REVERT: B 66 ASP cc_start: 0.7476 (t70) cc_final: 0.6918 (t70) REVERT: B 95 GLN cc_start: 0.7626 (tt0) cc_final: 0.6953 (tp-100) REVERT: B 165 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: B 241 GLN cc_start: 0.7267 (tt0) cc_final: 0.6943 (tt0) REVERT: B 303 ARG cc_start: 0.7572 (ttm-80) cc_final: 0.6025 (tmt90) REVERT: B 317 LYS cc_start: 0.7583 (mmtt) cc_final: 0.7118 (mptt) REVERT: B 341 LYS cc_start: 0.8401 (mttt) cc_final: 0.8101 (mtmp) REVERT: C 13 LYS cc_start: 0.8317 (tttp) cc_final: 0.7731 (ttpt) REVERT: C 42 ARG cc_start: 0.6851 (mtp180) cc_final: 0.6447 (tpp-160) REVERT: C 155 GLU cc_start: 0.6635 (tp30) cc_final: 0.5754 (tp30) REVERT: C 292 LEU cc_start: 0.8235 (tt) cc_final: 0.7883 (tm) REVERT: C 295 TRP cc_start: 0.9058 (OUTLIER) cc_final: 0.6510 (m-90) REVERT: C 311 LYS cc_start: 0.7895 (tttm) cc_final: 0.7393 (ttmt) REVERT: D 41 LYS cc_start: 0.7475 (mmtm) cc_final: 0.7065 (mtmt) REVERT: D 42 ARG cc_start: 0.6591 (mtp180) cc_final: 0.5978 (mmp80) REVERT: D 44 GLN cc_start: 0.6459 (mm110) cc_final: 0.6163 (mt0) REVERT: D 52 GLU cc_start: 0.7401 (tt0) cc_final: 0.6836 (tm-30) REVERT: D 152 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7679 (tptp) REVERT: D 207 LYS cc_start: 0.8279 (tttp) cc_final: 0.7458 (mmtm) REVERT: D 242 LYS cc_start: 0.7981 (mmtm) cc_final: 0.7732 (mmtm) REVERT: D 278 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7306 (tp30) REVERT: D 311 LYS cc_start: 0.7904 (tttm) cc_final: 0.7104 (mppt) outliers start: 17 outliers final: 11 residues processed: 103 average time/residue: 0.9490 time to fit residues: 103.3070 Evaluate side-chains 102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 121 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN C 44 GLN C 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.104746 restraints weight = 12071.009| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.28 r_work: 0.3086 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10672 Z= 0.107 Angle : 0.469 6.610 14464 Z= 0.244 Chirality : 0.039 0.128 1644 Planarity : 0.004 0.033 1880 Dihedral : 4.927 58.718 1480 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.53 % Allowed : 10.88 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.15 (0.23), residues: 1364 helix: 2.86 (0.19), residues: 712 sheet: -1.08 (0.31), residues: 252 loop : 0.59 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 303 TYR 0.019 0.001 TYR C 203 PHE 0.015 0.001 PHE A 144 TRP 0.013 0.002 TRP A 147 HIS 0.003 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00244 (10672) covalent geometry : angle 0.46939 (14464) hydrogen bonds : bond 0.04288 ( 590) hydrogen bonds : angle 3.91234 ( 1701) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.497 Fit side-chains REVERT: A 152 LYS cc_start: 0.8449 (mttt) cc_final: 0.7567 (mmmt) REVERT: A 173 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.7749 (t80) REVERT: A 199 LYS cc_start: 0.8407 (mtpt) cc_final: 0.7594 (mmpt) REVERT: A 242 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7533 (mtpt) REVERT: A 303 ARG cc_start: 0.7637 (mtp180) cc_final: 0.6550 (mtm110) REVERT: A 317 LYS cc_start: 0.7822 (tttm) cc_final: 0.7479 (ttmm) REVERT: A 325 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: B 10 GLU cc_start: 0.8020 (mp0) cc_final: 0.7712 (mp0) REVERT: B 66 ASP cc_start: 0.7477 (t70) cc_final: 0.6916 (t70) REVERT: B 95 GLN cc_start: 0.7632 (tt0) cc_final: 0.6959 (tp-100) REVERT: B 165 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: B 241 GLN cc_start: 0.7260 (tt0) cc_final: 0.6937 (tt0) REVERT: B 303 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.6027 (tmt90) REVERT: B 317 LYS cc_start: 0.7575 (mmtt) cc_final: 0.7110 (mptt) REVERT: B 341 LYS cc_start: 0.8395 (mttt) cc_final: 0.8096 (mtmp) REVERT: C 13 LYS cc_start: 0.8324 (tttp) cc_final: 0.7745 (ttpt) REVERT: C 42 ARG cc_start: 0.6857 (mtp180) cc_final: 0.6467 (tpp-160) REVERT: C 155 GLU cc_start: 0.6654 (tp30) cc_final: 0.5796 (tp30) REVERT: C 292 LEU cc_start: 0.8232 (tt) cc_final: 0.7884 (tm) REVERT: C 295 TRP cc_start: 0.9050 (OUTLIER) cc_final: 0.6497 (m-90) REVERT: C 311 LYS cc_start: 0.7903 (tttm) cc_final: 0.7402 (ttmt) REVERT: D 41 LYS cc_start: 0.7536 (mmtm) cc_final: 0.7128 (mtmt) REVERT: D 42 ARG cc_start: 0.6606 (mtp180) cc_final: 0.5992 (mmp80) REVERT: D 44 GLN cc_start: 0.6460 (mm110) cc_final: 0.6169 (mt0) REVERT: D 52 GLU cc_start: 0.7407 (tt0) cc_final: 0.6835 (tm-30) REVERT: D 152 LYS cc_start: 0.8310 (ttmm) cc_final: 0.7667 (tptp) REVERT: D 207 LYS cc_start: 0.8281 (tttp) cc_final: 0.7457 (mmtm) REVERT: D 242 LYS cc_start: 0.7989 (mmtm) cc_final: 0.7737 (mmtm) REVERT: D 278 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7339 (tp30) REVERT: D 311 LYS cc_start: 0.7862 (tttm) cc_final: 0.7063 (mppt) outliers start: 17 outliers final: 11 residues processed: 101 average time/residue: 0.9325 time to fit residues: 99.7185 Evaluate side-chains 100 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN A 156 HIS B 319 ASN C 44 GLN C 54 ASN C 166 ASN C 241 GLN D 166 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.097954 restraints weight = 12141.709| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.22 r_work: 0.2988 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10672 Z= 0.245 Angle : 0.649 7.643 14464 Z= 0.339 Chirality : 0.048 0.146 1644 Planarity : 0.005 0.036 1880 Dihedral : 5.589 57.111 1480 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.71 % Allowed : 10.88 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.56 (0.23), residues: 1364 helix: 2.47 (0.19), residues: 688 sheet: -1.14 (0.31), residues: 252 loop : 0.13 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 303 TYR 0.026 0.003 TYR D 213 PHE 0.018 0.002 PHE A 144 TRP 0.025 0.003 TRP B 147 HIS 0.009 0.002 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00598 (10672) covalent geometry : angle 0.64904 (14464) hydrogen bonds : bond 0.06939 ( 590) hydrogen bonds : angle 4.41930 ( 1701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4018.94 seconds wall clock time: 69 minutes 28.50 seconds (4168.50 seconds total)