Starting phenix.real_space_refine on Wed Feb 4 09:31:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qcv_53027/02_2026/9qcv_53027.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qcv_53027/02_2026/9qcv_53027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qcv_53027/02_2026/9qcv_53027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qcv_53027/02_2026/9qcv_53027.map" model { file = "/net/cci-nas-00/data/ceres_data/9qcv_53027/02_2026/9qcv_53027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qcv_53027/02_2026/9qcv_53027.cif" } resolution = 2.5 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= 0.005 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 50 5.16 5 C 6251 2.51 5 N 1640 2.21 5 O 1810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9759 Number of models: 1 Model: "" Number of chains: 11 Chain: "K" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2346 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 18, 'TRANS': 273} Chain: "L" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2052 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 12, 'TRANS': 241} Chain breaks: 1 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2455 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 287} Chain breaks: 1 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 2.55, per 1000 atoms: 0.26 Number of scatterers: 9759 At special positions: 0 Unit cell: (85.1401, 97.1471, 129.893, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 6 15.00 Mg 2 11.99 O 1810 8.00 N 1640 7.00 C 6251 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: 0.93 Conformation dependent library (CDL) restraints added in 499.9 milliseconds 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 6 sheets defined 57.6% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'K' and resid 45 through 58 removed outlier: 3.939A pdb=" N GLU K 57 " --> pdb=" O SER K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 94 Processing helix chain 'K' and resid 100 through 121 Processing helix chain 'K' and resid 129 through 131 No H-bonds generated for 'chain 'K' and resid 129 through 131' Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'K' and resid 170 through 175 Processing helix chain 'K' and resid 182 through 199 removed outlier: 3.590A pdb=" N ILE K 186 " --> pdb=" O THR K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 220 Processing helix chain 'K' and resid 229 through 233 Processing helix chain 'K' and resid 256 through 267 Processing helix chain 'K' and resid 276 through 282 Processing helix chain 'K' and resid 283 through 287 Processing helix chain 'L' and resid 178 through 193 removed outlier: 4.107A pdb=" N VAL L 191 " --> pdb=" O ARG L 187 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS L 192 " --> pdb=" O GLU L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 226 Processing helix chain 'L' and resid 228 through 244 removed outlier: 3.592A pdb=" N LEU L 232 " --> pdb=" O GLN L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 269 Processing helix chain 'L' and resid 274 through 281 Processing helix chain 'L' and resid 287 through 303 Processing helix chain 'L' and resid 310 through 319 Processing helix chain 'L' and resid 320 through 322 No H-bonds generated for 'chain 'L' and resid 320 through 322' Processing helix chain 'L' and resid 326 through 343 removed outlier: 3.643A pdb=" N LEU L 341 " --> pdb=" O GLY L 337 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE L 342 " --> pdb=" O GLU L 338 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP L 343 " --> pdb=" O LEU L 339 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 367 Processing helix chain 'L' and resid 373 through 381 Processing helix chain 'L' and resid 383 through 400 Proline residue: L 389 - end of helix Processing helix chain 'L' and resid 407 through 414 Processing helix chain 'L' and resid 415 through 419 Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.664A pdb=" N ASN H 273 " --> pdb=" O GLY H 270 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 285 removed outlier: 3.580A pdb=" N GLY H 285 " --> pdb=" O GLN H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.827A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 removed outlier: 3.566A pdb=" N ASN I 4 " --> pdb=" O MET I 1 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1 through 4' Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 removed outlier: 3.699A pdb=" N LEU I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 70 removed outlier: 3.591A pdb=" N VAL I 70 " --> pdb=" O GLU I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 94 removed outlier: 3.864A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.696A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 removed outlier: 3.603A pdb=" N ILE I 186 " --> pdb=" O ASN I 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 183 through 186' Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.638A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 241 through 262 removed outlier: 3.517A pdb=" N LEU I 245 " --> pdb=" O ASN I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 281 Processing helix chain 'J' and resid 47 through 51 Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 removed outlier: 3.573A pdb=" N HIS J 131 " --> pdb=" O TYR J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.517A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 removed outlier: 3.559A pdb=" N ILE J 260 " --> pdb=" O PRO J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.780A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 removed outlier: 3.557A pdb=" N LEU J 307 " --> pdb=" O GLY J 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 12 removed outlier: 6.922A pdb=" N VAL K 7 " --> pdb=" O ARG K 22 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ARG K 22 " --> pdb=" O VAL K 7 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LYS K 9 " --> pdb=" O LYS K 20 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LYS K 20 " --> pdb=" O LYS K 9 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU K 81 " --> pdb=" O LEU K 66 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 85 through 86 removed outlier: 3.700A pdb=" N GLN K 85 " --> pdb=" O ILE K 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'J' and resid 16 through 20 removed outlier: 5.759A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA6, first strand: chain 'J' and resid 133 through 134 479 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3093 1.34 - 1.46: 1776 1.46 - 1.58: 4985 1.58 - 1.69: 6 1.69 - 1.81: 85 Bond restraints: 9945 Sorted by residual: bond pdb=" C ACE I 0 " pdb=" O ACE I 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C LYS L 388 " pdb=" N PRO L 389 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.46e+00 bond pdb=" CB GLU K 257 " pdb=" CG GLU K 257 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.10e+00 bond pdb=" CA THR K 72 " pdb=" C THR K 72 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.24e-02 6.50e+03 9.77e-01 bond pdb=" CB GLN I 152 " pdb=" CG GLN I 152 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.26e-01 ... (remaining 9940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 13246 1.77 - 3.54: 197 3.54 - 5.31: 35 5.31 - 7.08: 6 7.08 - 8.85: 2 Bond angle restraints: 13486 Sorted by residual: angle pdb=" CB ARG K 22 " pdb=" CG ARG K 22 " pdb=" CD ARG K 22 " ideal model delta sigma weight residual 111.30 117.92 -6.62 2.30e+00 1.89e-01 8.27e+00 angle pdb=" OG1 THR L 303 " pdb=" CB THR L 303 " pdb=" CG2 THR L 303 " ideal model delta sigma weight residual 109.30 103.55 5.75 2.00e+00 2.50e-01 8.27e+00 angle pdb=" C THR K 72 " pdb=" CA THR K 72 " pdb=" CB THR K 72 " ideal model delta sigma weight residual 110.24 115.06 -4.82 1.88e+00 2.83e-01 6.58e+00 angle pdb=" CA LEU K 101 " pdb=" CB LEU K 101 " pdb=" CG LEU K 101 " ideal model delta sigma weight residual 116.30 125.15 -8.85 3.50e+00 8.16e-02 6.40e+00 angle pdb=" CB LYS K 178 " pdb=" CG LYS K 178 " pdb=" CD LYS K 178 " ideal model delta sigma weight residual 111.30 116.64 -5.34 2.30e+00 1.89e-01 5.39e+00 ... (remaining 13481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.17: 5550 26.17 - 52.33: 429 52.33 - 78.50: 58 78.50 - 104.67: 6 104.67 - 130.83: 1 Dihedral angle restraints: 6044 sinusoidal: 2524 harmonic: 3520 Sorted by residual: dihedral pdb=" O1B ANP J 401 " pdb=" N3B ANP J 401 " pdb=" PB ANP J 401 " pdb=" PG ANP J 401 " ideal model delta sinusoidal sigma weight residual 35.15 -95.68 130.83 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CA ASP J 104 " pdb=" CB ASP J 104 " pdb=" CG ASP J 104 " pdb=" OD1 ASP J 104 " ideal model delta sinusoidal sigma weight residual -30.00 -87.50 57.50 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB GLU L 274 " pdb=" CG GLU L 274 " pdb=" CD GLU L 274 " pdb=" OE1 GLU L 274 " ideal model delta sinusoidal sigma weight residual 0.00 -90.84 90.84 1 3.00e+01 1.11e-03 1.08e+01 ... (remaining 6041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 896 0.029 - 0.057: 367 0.057 - 0.086: 150 0.086 - 0.115: 72 0.115 - 0.143: 16 Chirality restraints: 1501 Sorted by residual: chirality pdb=" CA ILE K 99 " pdb=" N ILE K 99 " pdb=" C ILE K 99 " pdb=" CB ILE K 99 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE K 35 " pdb=" N ILE K 35 " pdb=" C ILE K 35 " pdb=" CB ILE K 35 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CB ILE L 270 " pdb=" CA ILE L 270 " pdb=" CG1 ILE L 270 " pdb=" CG2 ILE L 270 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1498 not shown) Planarity restraints: 1702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 110 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO J 111 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO J 111 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 111 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 271 " -0.008 2.00e-02 2.50e+03 1.23e-02 3.04e+00 pdb=" CG TYR L 271 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR L 271 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR L 271 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR L 271 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR L 271 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR L 271 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 271 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 257 " 0.008 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" CD GLU K 257 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU K 257 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU K 257 " 0.011 2.00e-02 2.50e+03 ... (remaining 1699 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 83 2.59 - 3.17: 8018 3.17 - 3.74: 16067 3.74 - 4.32: 22425 4.32 - 4.90: 36458 Nonbonded interactions: 83051 Sorted by model distance: nonbonded pdb=" O1B ANP K 301 " pdb="MG MG K 302 " model vdw 2.010 2.170 nonbonded pdb=" OD1 ASP K 145 " pdb="MG MG K 302 " model vdw 2.082 2.170 nonbonded pdb=" OD2 ASP J 155 " pdb="MG MG J 402 " model vdw 2.115 2.170 nonbonded pdb=" O GLY L 251 " pdb=" OH TYR L 286 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR K 14 " pdb=" O3G ANP K 301 " model vdw 2.220 3.040 ... (remaining 83046 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:8.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 : 0.003 0.035 9945 Z= 0.125 Angle : 0.565 8.853 13486 Z= 0.295 Chirality : 0.041 0.143 1501 Planarity : 0.004 0.045 1702 Dihedral : 17.628 130.832 3766 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.13 % Allowed : 21.74 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.32 (0.25), residues: 1181 helix: 1.88 (0.22), residues: 601 sheet: -0.05 (0.75), residues: 51 loop : -0.14 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 22 TYR 0.030 0.001 TYR L 271 PHE 0.013 0.001 PHE K 152 TRP 0.012 0.001 TRP L 372 HIS 0.016 0.001 HIS L 361 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9945) covalent geometry : angle 0.56544 (13486) hydrogen bonds : bond 0.13224 ( 479) hydrogen bonds : angle 5.58250 ( 1365) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: K 3 ASN cc_start: 0.7294 (t0) cc_final: 0.7034 (t160) REVERT: K 28 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6558 (mm-30) REVERT: K 36 ARG cc_start: 0.7515 (mtt-85) cc_final: 0.6758 (mtp-110) REVERT: K 101 LEU cc_start: 0.7452 (tm) cc_final: 0.6787 (tp) REVERT: L 361 HIS cc_start: 0.6964 (t-90) cc_final: 0.6650 (t70) REVERT: L 365 TYR cc_start: 0.6854 (t80) cc_final: 0.6638 (t80) REVERT: L 391 LEU cc_start: 0.7866 (tm) cc_final: 0.7628 (tt) REVERT: I 138 LYS cc_start: 0.7622 (tttm) cc_final: 0.7381 (ttpp) REVERT: I 250 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6880 (m-30) REVERT: J 50 GLU cc_start: 0.6655 (mt-10) cc_final: 0.6305 (pt0) REVERT: J 94 MET cc_start: 0.7994 (mmm) cc_final: 0.7724 (mmp) REVERT: J 118 MET cc_start: 0.8571 (mmm) cc_final: 0.8366 (mmp) REVERT: J 160 LYS cc_start: 0.8906 (ptmm) cc_final: 0.8462 (pttp) REVERT: J 172 GLN cc_start: 0.5827 (mm-40) cc_final: 0.4859 (mt0) REVERT: J 213 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8433 (mt) REVERT: J 234 GLU cc_start: 0.7398 (tp30) cc_final: 0.7024 (mm-30) outliers start: 12 outliers final: 5 residues processed: 159 average time/residue: 0.5383 time to fit residues: 91.1352 Evaluate side-chains 158 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 213 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 117 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 296 HIS L 317 GLN L 322 GLN L 419 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.160546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.132751 restraints weight = 11780.562| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.55 r_work: 0.3385 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9945 Z= 0.165 Angle : 0.576 6.888 13486 Z= 0.296 Chirality : 0.044 0.145 1501 Planarity : 0.005 0.046 1702 Dihedral : 9.116 136.685 1383 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.40 % Allowed : 18.53 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.43 (0.25), residues: 1181 helix: 2.08 (0.22), residues: 597 sheet: -0.42 (0.72), residues: 49 loop : -0.18 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 22 TYR 0.016 0.002 TYR I 91 PHE 0.015 0.002 PHE K 152 TRP 0.009 0.002 TRP L 372 HIS 0.005 0.001 HIS L 179 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9945) covalent geometry : angle 0.57563 (13486) hydrogen bonds : bond 0.04659 ( 479) hydrogen bonds : angle 4.56379 ( 1365) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: K 1 MET cc_start: 0.4883 (tpt) cc_final: 0.4546 (tpt) REVERT: L 365 TYR cc_start: 0.6946 (t80) cc_final: 0.6510 (t80) REVERT: L 391 LEU cc_start: 0.7870 (tm) cc_final: 0.7646 (tt) REVERT: H 295 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8000 (ttt-90) REVERT: I 33 LYS cc_start: 0.6875 (ttmt) cc_final: 0.6201 (mptm) REVERT: I 138 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7379 (ttpp) REVERT: I 230 SER cc_start: 0.7646 (p) cc_final: 0.7337 (p) REVERT: J 13 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6431 (tp30) REVERT: J 94 MET cc_start: 0.8037 (mmm) cc_final: 0.7790 (mmp) REVERT: J 118 MET cc_start: 0.8581 (mmm) cc_final: 0.8349 (mmp) REVERT: J 160 LYS cc_start: 0.8918 (ptmm) cc_final: 0.8522 (pttp) REVERT: J 172 GLN cc_start: 0.5981 (mm-40) cc_final: 0.5053 (mt0) REVERT: J 234 GLU cc_start: 0.7454 (tp30) cc_final: 0.7142 (mm-30) REVERT: J 235 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: J 257 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7665 (mp) outliers start: 36 outliers final: 15 residues processed: 173 average time/residue: 0.6322 time to fit residues: 116.0867 Evaluate side-chains 167 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 78 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 0.0010 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 3 ASN K 71 HIS L 361 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.160953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132792 restraints weight = 11689.660| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.64 r_work: 0.3384 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9945 Z= 0.145 Angle : 0.544 7.173 13486 Z= 0.279 Chirality : 0.043 0.147 1501 Planarity : 0.004 0.047 1702 Dihedral : 8.612 133.769 1379 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.50 % Allowed : 19.09 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.46 (0.25), residues: 1181 helix: 2.12 (0.21), residues: 599 sheet: -0.49 (0.72), residues: 49 loop : -0.20 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 22 TYR 0.014 0.002 TYR I 91 PHE 0.014 0.001 PHE K 152 TRP 0.007 0.001 TRP L 217 HIS 0.005 0.001 HIS L 179 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9945) covalent geometry : angle 0.54433 (13486) hydrogen bonds : bond 0.04335 ( 479) hydrogen bonds : angle 4.40708 ( 1365) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: K 1 MET cc_start: 0.4933 (tpt) cc_final: 0.4587 (tpt) REVERT: K 3 ASN cc_start: 0.7205 (t0) cc_final: 0.6745 (m-40) REVERT: K 28 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6490 (mm-30) REVERT: K 247 ASP cc_start: 0.6753 (t70) cc_final: 0.6493 (t70) REVERT: L 274 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5983 (mt-10) REVERT: L 300 LYS cc_start: 0.7596 (ttpt) cc_final: 0.7298 (ttmm) REVERT: L 361 HIS cc_start: 0.7058 (t-90) cc_final: 0.6779 (t-170) REVERT: L 365 TYR cc_start: 0.6902 (t80) cc_final: 0.6397 (t80) REVERT: H 295 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7998 (ttt-90) REVERT: I 138 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7378 (ttpp) REVERT: I 230 SER cc_start: 0.7501 (p) cc_final: 0.7182 (p) REVERT: I 269 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: J 13 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6397 (tp30) REVERT: J 94 MET cc_start: 0.8024 (mmm) cc_final: 0.7743 (mmp) REVERT: J 118 MET cc_start: 0.8580 (mmm) cc_final: 0.8332 (mmp) REVERT: J 160 LYS cc_start: 0.8951 (ptmm) cc_final: 0.8561 (pttp) REVERT: J 172 GLN cc_start: 0.5850 (mm-40) cc_final: 0.4956 (mt0) REVERT: J 234 GLU cc_start: 0.7371 (tp30) cc_final: 0.7119 (mm-30) REVERT: J 235 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: J 257 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7670 (mp) outliers start: 37 outliers final: 18 residues processed: 179 average time/residue: 0.6587 time to fit residues: 125.2890 Evaluate side-chains 174 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 68 ASP Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 213 ILE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 274 GLU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.162459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133893 restraints weight = 11682.836| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.58 r_work: 0.3411 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9945 Z= 0.111 Angle : 0.505 7.647 13486 Z= 0.258 Chirality : 0.041 0.146 1501 Planarity : 0.004 0.049 1702 Dihedral : 8.115 131.332 1376 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.40 % Allowed : 19.28 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.62 (0.25), residues: 1181 helix: 2.22 (0.21), residues: 609 sheet: -0.42 (0.75), residues: 49 loop : -0.12 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 169 TYR 0.013 0.001 TYR I 91 PHE 0.015 0.001 PHE K 152 TRP 0.008 0.001 TRP L 217 HIS 0.005 0.001 HIS J 47 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9945) covalent geometry : angle 0.50529 (13486) hydrogen bonds : bond 0.03810 ( 479) hydrogen bonds : angle 4.25598 ( 1365) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: K 3 ASN cc_start: 0.7133 (t0) cc_final: 0.6746 (m-40) REVERT: K 28 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6423 (mm-30) REVERT: K 247 ASP cc_start: 0.6725 (t70) cc_final: 0.6498 (t70) REVERT: L 300 LYS cc_start: 0.7531 (ttpt) cc_final: 0.7236 (ttmm) REVERT: L 365 TYR cc_start: 0.6909 (t80) cc_final: 0.6355 (t80) REVERT: L 391 LEU cc_start: 0.7932 (tm) cc_final: 0.7652 (tp) REVERT: H 295 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.7971 (ttt-90) REVERT: I 63 ARG cc_start: 0.7658 (mmm-85) cc_final: 0.7403 (mmm160) REVERT: I 138 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7474 (ttpp) REVERT: I 230 SER cc_start: 0.7470 (p) cc_final: 0.7146 (p) REVERT: J 13 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6386 (tp30) REVERT: J 118 MET cc_start: 0.8564 (mmm) cc_final: 0.8321 (mmp) REVERT: J 160 LYS cc_start: 0.8879 (ptmm) cc_final: 0.8514 (pttp) REVERT: J 172 GLN cc_start: 0.5938 (mm-40) cc_final: 0.5097 (mt0) REVERT: J 234 GLU cc_start: 0.7292 (tp30) cc_final: 0.7072 (mm-30) REVERT: J 257 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7657 (mp) outliers start: 36 outliers final: 13 residues processed: 172 average time/residue: 0.6188 time to fit residues: 113.0309 Evaluate side-chains 163 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 68 ASP Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 103 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 0.0170 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 0.0670 chunk 117 optimal weight: 0.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 322 GLN L 361 HIS I 100 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.163859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.135658 restraints weight = 11618.596| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.62 r_work: 0.3431 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9945 Z= 0.096 Angle : 0.480 7.817 13486 Z= 0.245 Chirality : 0.040 0.161 1501 Planarity : 0.004 0.049 1702 Dihedral : 7.569 129.569 1371 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.55 % Allowed : 20.51 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.80 (0.25), residues: 1181 helix: 2.38 (0.21), residues: 609 sheet: -0.37 (0.77), residues: 49 loop : -0.04 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 102 TYR 0.011 0.001 TYR I 91 PHE 0.014 0.001 PHE K 152 TRP 0.008 0.001 TRP L 217 HIS 0.009 0.001 HIS I 100 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 9945) covalent geometry : angle 0.48035 (13486) hydrogen bonds : bond 0.03424 ( 479) hydrogen bonds : angle 4.13540 ( 1365) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: K 3 ASN cc_start: 0.7101 (t0) cc_final: 0.6777 (t160) REVERT: K 36 ARG cc_start: 0.7557 (mtt-85) cc_final: 0.7141 (mmm160) REVERT: L 300 LYS cc_start: 0.7554 (ttpt) cc_final: 0.7236 (ttmm) REVERT: L 365 TYR cc_start: 0.6927 (t80) cc_final: 0.6430 (t80) REVERT: L 391 LEU cc_start: 0.7926 (tm) cc_final: 0.7625 (tp) REVERT: H 295 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8066 (ttt-90) REVERT: I 63 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.7408 (mmm160) REVERT: I 194 PHE cc_start: 0.8300 (t80) cc_final: 0.7943 (t80) REVERT: I 230 SER cc_start: 0.7402 (p) cc_final: 0.7067 (p) REVERT: I 234 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7079 (mm-30) REVERT: I 269 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: J 13 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6360 (tp30) REVERT: J 94 MET cc_start: 0.8141 (mmm) cc_final: 0.7829 (mmp) REVERT: J 118 MET cc_start: 0.8546 (mmm) cc_final: 0.8312 (mmp) REVERT: J 160 LYS cc_start: 0.8815 (ptmm) cc_final: 0.8450 (pttp) REVERT: J 172 GLN cc_start: 0.5947 (mm-40) cc_final: 0.5092 (mt0) REVERT: J 234 GLU cc_start: 0.7159 (tp30) cc_final: 0.6958 (mm-30) REVERT: J 235 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: J 257 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7640 (mp) REVERT: J 291 LYS cc_start: 0.8573 (mttt) cc_final: 0.8340 (mttm) outliers start: 27 outliers final: 14 residues processed: 172 average time/residue: 0.6494 time to fit residues: 118.3817 Evaluate side-chains 163 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 68 ASP Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 71 HIS L 317 GLN L 322 GLN I 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.161790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132943 restraints weight = 11690.761| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.60 r_work: 0.3404 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9945 Z= 0.137 Angle : 0.527 8.128 13486 Z= 0.269 Chirality : 0.042 0.146 1501 Planarity : 0.004 0.048 1702 Dihedral : 7.656 129.353 1371 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.31 % Allowed : 19.57 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.65 (0.25), residues: 1181 helix: 2.25 (0.21), residues: 608 sheet: -0.51 (0.75), residues: 49 loop : -0.09 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 217 TYR 0.014 0.001 TYR I 91 PHE 0.015 0.001 PHE J 91 TRP 0.005 0.001 TRP J 237 HIS 0.004 0.001 HIS L 179 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9945) covalent geometry : angle 0.52688 (13486) hydrogen bonds : bond 0.03998 ( 479) hydrogen bonds : angle 4.23772 ( 1365) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.403 Fit side-chains REVERT: K 3 ASN cc_start: 0.7103 (t0) cc_final: 0.6790 (t160) REVERT: K 36 ARG cc_start: 0.7556 (mtt-85) cc_final: 0.7144 (mmm160) REVERT: L 300 LYS cc_start: 0.7576 (ttpt) cc_final: 0.7272 (ttmm) REVERT: L 365 TYR cc_start: 0.6940 (t80) cc_final: 0.6455 (t80) REVERT: H 295 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8069 (ttt-90) REVERT: I 63 ARG cc_start: 0.7668 (mmm-85) cc_final: 0.7421 (mmm160) REVERT: I 138 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7505 (ttpp) REVERT: I 230 SER cc_start: 0.7401 (p) cc_final: 0.7061 (p) REVERT: I 234 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7561 (mt-10) REVERT: J 13 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6399 (tp30) REVERT: J 50 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6092 (pt0) REVERT: J 118 MET cc_start: 0.8551 (mmm) cc_final: 0.8299 (mmp) REVERT: J 160 LYS cc_start: 0.8824 (ptmm) cc_final: 0.8492 (pttp) REVERT: J 172 GLN cc_start: 0.6015 (mm-40) cc_final: 0.5190 (mt0) REVERT: J 235 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: J 257 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7663 (mp) outliers start: 35 outliers final: 18 residues processed: 176 average time/residue: 0.6747 time to fit residues: 125.9395 Evaluate side-chains 171 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 68 ASP Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 101 optimal weight: 0.0770 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 322 GLN L 361 HIS I 100 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.160545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132060 restraints weight = 11662.195| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.64 r_work: 0.3382 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9945 Z= 0.176 Angle : 0.579 8.334 13486 Z= 0.295 Chirality : 0.044 0.147 1501 Planarity : 0.005 0.048 1702 Dihedral : 7.869 128.380 1371 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.69 % Allowed : 19.19 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.45 (0.25), residues: 1181 helix: 2.11 (0.21), residues: 599 sheet: -0.55 (0.74), residues: 49 loop : -0.19 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 217 TYR 0.016 0.002 TYR I 91 PHE 0.016 0.002 PHE J 91 TRP 0.008 0.002 TRP J 237 HIS 0.005 0.001 HIS K 161 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9945) covalent geometry : angle 0.57931 (13486) hydrogen bonds : bond 0.04443 ( 479) hydrogen bonds : angle 4.38625 ( 1365) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.410 Fit side-chains REVERT: K 3 ASN cc_start: 0.7202 (t0) cc_final: 0.6879 (t160) REVERT: L 300 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7312 (ttmm) REVERT: L 361 HIS cc_start: 0.7186 (t-90) cc_final: 0.6903 (t-170) REVERT: L 365 TYR cc_start: 0.6965 (t80) cc_final: 0.6535 (t80) REVERT: L 391 LEU cc_start: 0.8008 (tm) cc_final: 0.7704 (tp) REVERT: H 295 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8079 (ttt-90) REVERT: I 63 ARG cc_start: 0.7709 (mmm-85) cc_final: 0.7451 (mmm160) REVERT: I 138 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7484 (ttpp) REVERT: I 230 SER cc_start: 0.7444 (p) cc_final: 0.7109 (p) REVERT: I 234 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7577 (mt-10) REVERT: J 13 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6475 (tp30) REVERT: J 118 MET cc_start: 0.8570 (mmm) cc_final: 0.8297 (mmp) REVERT: J 160 LYS cc_start: 0.8844 (ptmm) cc_final: 0.8517 (pttp) REVERT: J 172 GLN cc_start: 0.6242 (mm-40) cc_final: 0.5196 (mt0) REVERT: J 235 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: J 239 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: J 257 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7708 (mp) outliers start: 39 outliers final: 20 residues processed: 179 average time/residue: 0.6988 time to fit residues: 132.7833 Evaluate side-chains 176 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 68 ASP Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 239 ASP Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 296 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 0.0270 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 312 ASN I 100 HIS J 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.161060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132665 restraints weight = 11630.794| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.64 r_work: 0.3390 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9945 Z= 0.149 Angle : 0.557 8.693 13486 Z= 0.284 Chirality : 0.043 0.146 1501 Planarity : 0.004 0.050 1702 Dihedral : 7.777 127.125 1371 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.84 % Allowed : 20.79 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.45 (0.25), residues: 1181 helix: 2.13 (0.21), residues: 600 sheet: -0.59 (0.75), residues: 49 loop : -0.21 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 279 TYR 0.015 0.002 TYR I 91 PHE 0.015 0.001 PHE K 152 TRP 0.007 0.002 TRP L 372 HIS 0.004 0.001 HIS L 179 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9945) covalent geometry : angle 0.55690 (13486) hydrogen bonds : bond 0.04158 ( 479) hydrogen bonds : angle 4.33179 ( 1365) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.414 Fit side-chains REVERT: K 3 ASN cc_start: 0.7216 (t0) cc_final: 0.6877 (t160) REVERT: K 162 GLU cc_start: 0.7645 (pt0) cc_final: 0.7302 (pt0) REVERT: K 247 ASP cc_start: 0.6733 (t0) cc_final: 0.6477 (t70) REVERT: L 300 LYS cc_start: 0.7569 (ttpt) cc_final: 0.7261 (ttmm) REVERT: L 361 HIS cc_start: 0.7191 (t-90) cc_final: 0.6943 (t-170) REVERT: L 365 TYR cc_start: 0.6985 (t80) cc_final: 0.6605 (t80) REVERT: L 391 LEU cc_start: 0.7995 (tm) cc_final: 0.7688 (tp) REVERT: H 295 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8080 (ttt-90) REVERT: I 138 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7488 (ttpp) REVERT: I 230 SER cc_start: 0.7403 (p) cc_final: 0.7053 (p) REVERT: I 234 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7573 (mt-10) REVERT: J 13 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6451 (tp30) REVERT: J 50 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6012 (pt0) REVERT: J 118 MET cc_start: 0.8570 (mmm) cc_final: 0.8304 (mmp) REVERT: J 160 LYS cc_start: 0.8859 (ptmm) cc_final: 0.8524 (pttp) REVERT: J 172 GLN cc_start: 0.6230 (mm-40) cc_final: 0.5189 (mt0) REVERT: J 235 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: J 239 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: J 257 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7721 (mp) outliers start: 30 outliers final: 20 residues processed: 172 average time/residue: 0.6407 time to fit residues: 117.1496 Evaluate side-chains 170 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 68 ASP Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 239 ASP Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 257 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 9.9990 chunk 94 optimal weight: 0.0470 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.160860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132760 restraints weight = 11617.307| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.61 r_work: 0.3392 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9945 Z= 0.158 Angle : 0.569 8.922 13486 Z= 0.290 Chirality : 0.043 0.151 1501 Planarity : 0.005 0.050 1702 Dihedral : 7.784 127.154 1371 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.21 % Allowed : 20.51 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.39 (0.25), residues: 1181 helix: 2.08 (0.21), residues: 600 sheet: -0.64 (0.74), residues: 49 loop : -0.24 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 102 TYR 0.015 0.002 TYR I 91 PHE 0.015 0.002 PHE K 152 TRP 0.007 0.002 TRP L 372 HIS 0.005 0.001 HIS L 179 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9945) covalent geometry : angle 0.56889 (13486) hydrogen bonds : bond 0.04249 ( 479) hydrogen bonds : angle 4.35261 ( 1365) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.414 Fit side-chains REVERT: K 3 ASN cc_start: 0.7217 (t0) cc_final: 0.6883 (t160) REVERT: K 162 GLU cc_start: 0.7508 (pt0) cc_final: 0.7238 (pt0) REVERT: K 247 ASP cc_start: 0.6771 (t0) cc_final: 0.6529 (t70) REVERT: L 300 LYS cc_start: 0.7573 (ttpt) cc_final: 0.7267 (ttmm) REVERT: L 361 HIS cc_start: 0.7236 (t-90) cc_final: 0.6993 (t-170) REVERT: L 365 TYR cc_start: 0.7031 (t80) cc_final: 0.6662 (t80) REVERT: L 391 LEU cc_start: 0.7977 (tm) cc_final: 0.7679 (tp) REVERT: H 295 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8077 (ttt-90) REVERT: I 138 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7484 (ttpp) REVERT: I 230 SER cc_start: 0.7385 (p) cc_final: 0.7028 (p) REVERT: J 13 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6452 (tp30) REVERT: J 36 GLN cc_start: 0.6622 (tm-30) cc_final: 0.6219 (tm-30) REVERT: J 50 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6008 (pt0) REVERT: J 118 MET cc_start: 0.8575 (mmm) cc_final: 0.8307 (mmp) REVERT: J 160 LYS cc_start: 0.8863 (ptmm) cc_final: 0.8529 (pttp) REVERT: J 172 GLN cc_start: 0.6241 (mm-40) cc_final: 0.5190 (mt0) REVERT: J 235 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: J 239 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7071 (m-30) REVERT: J 257 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7728 (mp) outliers start: 34 outliers final: 21 residues processed: 166 average time/residue: 0.6743 time to fit residues: 119.0288 Evaluate side-chains 171 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 68 ASP Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 239 ASP Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 296 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 7 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 15 optimal weight: 0.0070 chunk 75 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.161984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.133548 restraints weight = 11490.440| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.56 r_work: 0.3410 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9945 Z= 0.126 Angle : 0.539 9.036 13486 Z= 0.275 Chirality : 0.042 0.146 1501 Planarity : 0.004 0.051 1702 Dihedral : 7.593 126.189 1371 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.46 % Allowed : 21.46 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.51 (0.25), residues: 1181 helix: 2.16 (0.21), residues: 608 sheet: -0.60 (0.75), residues: 49 loop : -0.20 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 298 TYR 0.013 0.001 TYR I 91 PHE 0.014 0.001 PHE K 152 TRP 0.008 0.001 TRP L 372 HIS 0.004 0.001 HIS L 179 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9945) covalent geometry : angle 0.53893 (13486) hydrogen bonds : bond 0.03854 ( 479) hydrogen bonds : angle 4.25817 ( 1365) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.434 Fit side-chains REVERT: K 3 ASN cc_start: 0.7214 (t0) cc_final: 0.6884 (t160) REVERT: K 36 ARG cc_start: 0.7556 (mtt-85) cc_final: 0.7149 (mmm160) REVERT: K 162 GLU cc_start: 0.7560 (pt0) cc_final: 0.7292 (pt0) REVERT: K 247 ASP cc_start: 0.6711 (t0) cc_final: 0.6434 (t70) REVERT: L 300 LYS cc_start: 0.7525 (ttpt) cc_final: 0.7234 (ttmm) REVERT: L 361 HIS cc_start: 0.7212 (t-90) cc_final: 0.6958 (t-170) REVERT: L 365 TYR cc_start: 0.7169 (t80) cc_final: 0.6825 (t80) REVERT: L 391 LEU cc_start: 0.7933 (tm) cc_final: 0.7638 (tp) REVERT: H 295 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8047 (ttt-90) REVERT: I 138 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7493 (ttpp) REVERT: I 230 SER cc_start: 0.7390 (p) cc_final: 0.7032 (p) REVERT: J 13 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6420 (tp30) REVERT: J 118 MET cc_start: 0.8555 (mmm) cc_final: 0.8289 (mmp) REVERT: J 160 LYS cc_start: 0.8899 (ptmm) cc_final: 0.8572 (pttp) REVERT: J 172 GLN cc_start: 0.6247 (mm-40) cc_final: 0.5212 (mt0) REVERT: J 235 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: J 239 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6966 (m-30) REVERT: J 257 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7706 (mp) outliers start: 26 outliers final: 17 residues processed: 162 average time/residue: 0.6745 time to fit residues: 116.3804 Evaluate side-chains 166 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 68 ASP Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 239 ASP Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 296 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 86 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134393 restraints weight = 11678.310| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.55 r_work: 0.3432 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9945 Z= 0.105 Angle : 0.515 8.981 13486 Z= 0.262 Chirality : 0.041 0.145 1501 Planarity : 0.004 0.052 1702 Dihedral : 7.289 124.980 1371 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.08 % Allowed : 22.12 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.66 (0.25), residues: 1181 helix: 2.31 (0.21), residues: 609 sheet: -0.46 (0.70), residues: 54 loop : -0.18 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 298 TYR 0.012 0.001 TYR K 159 PHE 0.014 0.001 PHE K 152 TRP 0.009 0.001 TRP L 217 HIS 0.004 0.001 HIS L 179 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9945) covalent geometry : angle 0.51491 (13486) hydrogen bonds : bond 0.03434 ( 479) hydrogen bonds : angle 4.14471 ( 1365) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4173.13 seconds wall clock time: 71 minutes 46.70 seconds (4306.70 seconds total)