Starting phenix.real_space_refine on Thu Jul 2 13:14:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vie_32006/07_2026/7vie_32006.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vie_32006/07_2026/7vie_32006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vie_32006/07_2026/7vie_32006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vie_32006/07_2026/7vie_32006.map" model { file = "/net/cci-nas-00/data/ceres_data/7vie_32006/07_2026/7vie_32006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vie_32006/07_2026/7vie_32006.cif" } resolution = 2.86 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= -0.002 sd= 0.049 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 65 5.16 5 C 5680 2.51 5 N 1505 2.21 5 O 1654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8905 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1808 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "F" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2229 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 6, 'TRANS': 271} Chain breaks: 2 Chain: "D" Number of atoms: 1806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1800 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 225, 1800 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 1822 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'S1P': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS D 305 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 305 " occ=0.50 Time building chain proxies: 2.11, per 1000 atoms: 0.24 Number of scatterers: 8905 At special positions: 0 Unit cell: (91.3, 119.52, 129.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 P 1 15.00 O 1654 8.00 N 1505 7.00 C 5680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 282 " - pdb=" SG CYS F 287 " distance=2.03 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: 0.66 Conformation dependent library (CDL) restraints added in 425.1 milliseconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 39.2% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 24 Processing helix chain 'A' and resid 28 through 33 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.942A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.988A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.706A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 33 Processing helix chain 'F' and resid 49 through 73 Processing helix chain 'F' and resid 74 through 77 Processing helix chain 'F' and resid 78 through 105 Processing helix chain 'F' and resid 106 through 109 removed outlier: 3.639A pdb=" N THR F 109 " --> pdb=" O GLY F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 109' Processing helix chain 'F' and resid 113 through 148 Processing helix chain 'F' and resid 156 through 177 removed outlier: 3.693A pdb=" N LEU F 160 " --> pdb=" O ASN F 156 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP F 168 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER F 171 " --> pdb=" O CYS F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 199 through 234 Processing helix chain 'F' and resid 250 through 282 Proline residue: F 271 - end of helix removed outlier: 4.437A pdb=" N VAL F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 292 Processing helix chain 'F' and resid 293 through 314 removed outlier: 3.547A pdb=" N LEU F 297 " --> pdb=" O ALA F 293 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER F 304 " --> pdb=" O ALA F 300 " (cutoff:3.500A) Proline residue: F 308 - end of helix Processing helix chain 'F' and resid 315 through 324 removed outlier: 3.761A pdb=" N ARG F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 32 removed outlier: 3.696A pdb=" N ARG D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 56 Processing helix chain 'D' and resid 207 through 216 removed outlier: 4.741A pdb=" N ILE D 212 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N HIS D 213 " --> pdb=" O LYS D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 231 removed outlier: 4.128A pdb=" N ASP D 231 " --> pdb=" O SER D 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 228 through 231' Processing helix chain 'D' and resid 241 through 255 removed outlier: 3.556A pdb=" N GLU D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 282 through 286 Processing helix chain 'D' and resid 295 through 309 Processing helix chain 'D' and resid 330 through 351 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 removed outlier: 5.435A pdb=" N THR A 46 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN A 339 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 48 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 61 removed outlier: 3.636A pdb=" N SER A 73 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU A 78 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA A 91 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 80 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 104 removed outlier: 5.970A pdb=" N ASN A 124 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL A 134 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 150 removed outlier: 4.269A pdb=" N THR A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP A 169 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLN A 175 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.366A pdb=" N ASP A 211 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N CYS A 217 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 233 removed outlier: 6.544A pdb=" N CYS A 249 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR A 262 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 251 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 277 removed outlier: 3.604A pdb=" N SER A 274 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N CYS A 293 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A 306 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A 295 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.669A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.602A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR E 213 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.583A pdb=" N VAL E 147 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 185 through 191 removed outlier: 6.208A pdb=" N VAL D 34 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE D 199 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU D 36 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE D 221 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N PHE D 267 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE D 223 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASN D 269 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D 225 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE D 264 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N HIS D 322 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU D 266 " --> pdb=" O HIS D 322 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1288 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: 1.62 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1428 1.30 - 1.43: 2384 1.43 - 1.56: 5174 1.56 - 1.68: 2 1.68 - 1.81: 92 Bond restraints: 9080 Sorted by residual: bond pdb=" C MET F 124 " pdb=" O MET F 124 " ideal model delta sigma weight residual 1.236 1.172 0.065 1.15e-02 7.56e+03 3.16e+01 bond pdb=" O1 S1P F 401 " pdb=" P22 S1P F 401 " ideal model delta sigma weight residual 1.677 1.592 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" CA SER F 123 " pdb=" CB SER F 123 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.57e-02 4.06e+03 7.76e+00 bond pdb=" N LEU D 353 " pdb=" CA LEU D 353 " ideal model delta sigma weight residual 1.456 1.421 0.035 1.32e-02 5.74e+03 6.87e+00 bond pdb=" N VAL F 126 " pdb=" CA VAL F 126 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 6.75e+00 ... (remaining 9075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 12113 2.09 - 4.18: 132 4.18 - 6.27: 29 6.27 - 8.37: 5 8.37 - 10.46: 3 Bond angle restraints: 12282 Sorted by residual: angle pdb=" CA MET F 124 " pdb=" C MET F 124 " pdb=" O MET F 124 " ideal model delta sigma weight residual 120.82 116.51 4.31 1.05e+00 9.07e-01 1.69e+01 angle pdb=" CA PHE F 125 " pdb=" C PHE F 125 " pdb=" O PHE F 125 " ideal model delta sigma weight residual 120.55 116.34 4.21 1.06e+00 8.90e-01 1.58e+01 angle pdb=" CA GLY F 122 " pdb=" C GLY F 122 " pdb=" N SER F 123 " ideal model delta sigma weight residual 117.80 113.43 4.37 1.11e+00 8.12e-01 1.55e+01 angle pdb=" C MET F 124 " pdb=" CA MET F 124 " pdb=" CB MET F 124 " ideal model delta sigma weight residual 110.88 105.60 5.28 1.57e+00 4.06e-01 1.13e+01 angle pdb=" N SER F 123 " pdb=" CA SER F 123 " pdb=" C SER F 123 " ideal model delta sigma weight residual 111.03 107.37 3.66 1.11e+00 8.12e-01 1.09e+01 ... (remaining 12277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.37: 5249 30.37 - 60.75: 144 60.75 - 91.12: 11 91.12 - 121.50: 1 121.50 - 151.87: 6 Dihedral angle restraints: 5411 sinusoidal: 2121 harmonic: 3290 Sorted by residual: dihedral pdb=" C2 S1P F 401 " pdb=" C1 S1P F 401 " pdb=" O1 S1P F 401 " pdb=" P22 S1P F 401 " ideal model delta sinusoidal sigma weight residual -97.87 54.00 -151.87 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C12 S1P F 401 " pdb=" C13 S1P F 401 " pdb=" C14 S1P F 401 " pdb=" C15 S1P F 401 " ideal model delta sinusoidal sigma weight residual 300.92 151.35 149.57 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" C3 S1P F 401 " pdb=" C1 S1P F 401 " pdb=" C2 S1P F 401 " pdb=" O1 S1P F 401 " ideal model delta sinusoidal sigma weight residual 52.36 -85.42 137.78 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 5408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1191 0.057 - 0.114: 194 0.114 - 0.171: 22 0.171 - 0.228: 2 0.228 - 0.285: 1 Chirality restraints: 1410 Sorted by residual: chirality pdb=" C3 S1P F 401 " pdb=" C2 S1P F 401 " pdb=" C4 S1P F 401 " pdb=" O3 S1P F 401 " both_signs ideal model delta sigma weight residual False -2.52 -2.23 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA MET F 124 " pdb=" N MET F 124 " pdb=" C MET F 124 " pdb=" CB MET F 124 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CG LEU F 177 " pdb=" CB LEU F 177 " pdb=" CD1 LEU F 177 " pdb=" CD2 LEU F 177 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.94e-01 ... (remaining 1407 not shown) Planarity restraints: 1535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 122 " 0.022 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C GLY F 122 " -0.080 2.00e-02 2.50e+03 pdb=" O GLY F 122 " 0.031 2.00e-02 2.50e+03 pdb=" N SER F 123 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 281 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO D 282 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 282 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 282 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO E 236 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.033 5.00e-02 4.00e+02 ... (remaining 1532 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 611 2.74 - 3.28: 8910 3.28 - 3.82: 15021 3.82 - 4.36: 18275 4.36 - 4.90: 32197 Nonbonded interactions: 75014 Sorted by model distance: nonbonded pdb=" O LEU D 234 " pdb=" NH1 ARG D 242 " model vdw 2.198 3.120 nonbonded pdb=" O LEU F 174 " pdb=" OH TYR F 202 " model vdw 2.216 3.040 nonbonded pdb=" OD2 ASP E 73 " pdb=" NZ LYS E 76 " model vdw 2.253 3.120 nonbonded pdb=" O ILE A 57 " pdb=" OG SER A 315 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR E 175 " pdb=" OE2 GLU D 8 " model vdw 2.280 3.040 ... (remaining 75009 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=0.50 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.350 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.004 0.085 9084 Z= 0.183 Angle : 0.606 10.458 12290 Z= 0.326 Chirality : 0.042 0.285 1410 Planarity : 0.005 0.062 1535 Dihedral : 14.791 151.871 3277 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.51 % Allowed : 0.31 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.25), residues: 1117 helix: 2.28 (0.26), residues: 394 sheet: 0.15 (0.29), residues: 286 loop : -0.64 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 231 TYR 0.029 0.001 TYR E 235 PHE 0.018 0.001 PHE F 125 TRP 0.015 0.001 TRP A 81 HIS 0.004 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 ( 9080) covalent geometry : angle 0.60577 / 0.33 (12282) SS BOND : bond 0.00169 / 0.09 ( 4) SS BOND : angle 0.66913 / 0.36 ( 8) hydrogen bonds : bond 0.14458 / 9.69 ( 463) hydrogen bonds : angle 5.58582 / 3.89 ( 1288) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 0.225 Fit side-chains REVERT: D 17 LYS cc_start: 0.8314 (mmtp) cc_final: 0.8094 (mtmt) outliers start: 5 outliers final: 2 residues processed: 153 average time/residue: 0.5052 time to fit residues: 82.2950 Evaluate side-chains 112 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain D residue 354 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 186 GLN F 86 ASN D 188 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.150914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118001 restraints weight = 20321.039| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.57 r_work: 0.3162 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9084 Z= 0.160 Angle : 0.543 10.359 12290 Z= 0.285 Chirality : 0.042 0.223 1410 Planarity : 0.004 0.058 1535 Dihedral : 11.267 165.604 1255 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.16 % Allowed : 9.56 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.25), residues: 1117 helix: 2.39 (0.25), residues: 398 sheet: 0.20 (0.29), residues: 280 loop : -0.79 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 208 TYR 0.036 0.001 TYR E 235 PHE 0.011 0.001 PHE A 198 TRP 0.010 0.001 TRP A 168 HIS 0.003 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 9080) covalent geometry : angle 0.54243 / 0.29 (12282) SS BOND : bond 0.00312 / 0.16 ( 4) SS BOND : angle 0.80733 / 0.36 ( 8) hydrogen bonds : bond 0.04012 / 2.72 ( 463) hydrogen bonds : angle 4.41282 / 3.12 ( 1288) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.299 Fit side-chains REVERT: F 124 MET cc_start: 0.6910 (tpp) cc_final: 0.6671 (mtp) REVERT: D 247 MET cc_start: 0.8949 (mtp) cc_final: 0.8502 (mtt) outliers start: 21 outliers final: 9 residues processed: 131 average time/residue: 0.4805 time to fit residues: 67.3708 Evaluate side-chains 115 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 77 ASN E 186 GLN F 63 ASN F 86 ASN D 188 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.152602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120733 restraints weight = 27643.535| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.65 r_work: 0.3148 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9084 Z= 0.114 Angle : 0.491 11.508 12290 Z= 0.258 Chirality : 0.040 0.214 1410 Planarity : 0.004 0.052 1535 Dihedral : 10.628 172.812 1253 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.06 % Allowed : 11.51 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.25), residues: 1117 helix: 2.56 (0.25), residues: 401 sheet: 0.36 (0.30), residues: 277 loop : -0.76 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 242 TYR 0.034 0.001 TYR E 235 PHE 0.010 0.001 PHE A 198 TRP 0.011 0.001 TRP A 210 HIS 0.003 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 9080) covalent geometry : angle 0.49099 / 0.26 (12282) SS BOND : bond 0.00168 / 0.08 ( 4) SS BOND : angle 0.61219 / 0.29 ( 8) hydrogen bonds : bond 0.03573 / 2.42 ( 463) hydrogen bonds : angle 4.15114 / 2.96 ( 1288) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.346 Fit side-chains REVERT: A 157 VAL cc_start: 0.8903 (t) cc_final: 0.8682 (p) REVERT: C 37 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7170 (mp) REVERT: E 235 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6448 (t80) REVERT: E 244 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8160 (tttt) REVERT: F 297 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5924 (tp) outliers start: 20 outliers final: 8 residues processed: 130 average time/residue: 0.5341 time to fit residues: 74.2622 Evaluate side-chains 119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain D residue 18 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 3 optimal weight: 0.0040 chunk 1 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 186 GLN F 63 ASN F 86 ASN F 303 ASN D 188 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.151053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118086 restraints weight = 24772.611| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.16 r_work: 0.3145 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9084 Z= 0.139 Angle : 0.506 12.046 12290 Z= 0.267 Chirality : 0.041 0.225 1410 Planarity : 0.004 0.054 1535 Dihedral : 9.910 179.566 1253 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.19 % Allowed : 11.92 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.25), residues: 1117 helix: 2.51 (0.25), residues: 401 sheet: 0.23 (0.30), residues: 276 loop : -0.77 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 202 TYR 0.036 0.001 TYR E 235 PHE 0.010 0.001 PHE A 198 TRP 0.010 0.001 TRP A 168 HIS 0.004 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 9080) covalent geometry : angle 0.50606 / 0.27 (12282) SS BOND : bond 0.00210 / 0.11 ( 4) SS BOND : angle 0.72799 / 0.33 ( 8) hydrogen bonds : bond 0.03631 / 2.46 ( 463) hydrogen bonds : angle 4.14281 / 2.95 ( 1288) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.341 Fit side-chains REVERT: A 157 VAL cc_start: 0.8921 (t) cc_final: 0.8684 (p) REVERT: A 303 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7473 (tmm-80) REVERT: C 37 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7343 (mp) REVERT: E 235 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6439 (t80) REVERT: E 244 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8166 (tttt) REVERT: F 297 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5841 (tp) REVERT: D 240 MET cc_start: 0.6375 (pmm) cc_final: 0.5354 (ppp) REVERT: D 309 ASP cc_start: 0.7714 (m-30) cc_final: 0.7374 (m-30) outliers start: 31 outliers final: 13 residues processed: 131 average time/residue: 0.5207 time to fit residues: 73.2187 Evaluate side-chains 127 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.148839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115749 restraints weight = 19272.108| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.48 r_work: 0.3127 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9084 Z= 0.177 Angle : 0.539 12.424 12290 Z= 0.285 Chirality : 0.042 0.247 1410 Planarity : 0.004 0.050 1535 Dihedral : 9.210 174.077 1253 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.98 % Allowed : 13.77 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.25), residues: 1117 helix: 2.31 (0.25), residues: 400 sheet: 0.16 (0.30), residues: 276 loop : -0.83 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 242 TYR 0.040 0.002 TYR E 235 PHE 0.010 0.001 PHE A 150 TRP 0.012 0.001 TRP A 98 HIS 0.003 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 9080) covalent geometry : angle 0.53841 / 0.28 (12282) SS BOND : bond 0.00246 / 0.12 ( 4) SS BOND : angle 0.96520 / 0.44 ( 8) hydrogen bonds : bond 0.03895 / 2.64 ( 463) hydrogen bonds : angle 4.24652 / 3.03 ( 1288) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.342 Fit side-chains REVERT: A 303 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7722 (tmm-80) REVERT: C 37 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7564 (mp) REVERT: E 235 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.6765 (t80) REVERT: E 244 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8171 (tttt) REVERT: D 51 LYS cc_start: 0.7777 (mttp) cc_final: 0.7575 (mttp) REVERT: D 247 MET cc_start: 0.8924 (mtp) cc_final: 0.8711 (mtt) outliers start: 29 outliers final: 13 residues processed: 132 average time/residue: 0.5369 time to fit residues: 75.5793 Evaluate side-chains 126 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN F 63 ASN F 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.148932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115673 restraints weight = 20656.173| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.64 r_work: 0.3128 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9084 Z= 0.169 Angle : 0.541 12.619 12290 Z= 0.284 Chirality : 0.042 0.241 1410 Planarity : 0.004 0.050 1535 Dihedral : 8.601 167.171 1251 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.29 % Allowed : 14.49 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1117 helix: 2.28 (0.25), residues: 400 sheet: 0.11 (0.30), residues: 266 loop : -0.81 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 160 TYR 0.039 0.002 TYR E 235 PHE 0.011 0.001 PHE A 198 TRP 0.011 0.001 TRP A 168 HIS 0.002 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 9080) covalent geometry : angle 0.54109 / 0.28 (12282) SS BOND : bond 0.00244 / 0.12 ( 4) SS BOND : angle 0.96941 / 0.46 ( 8) hydrogen bonds : bond 0.03810 / 2.58 ( 463) hydrogen bonds : angle 4.24273 / 3.03 ( 1288) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.307 Fit side-chains REVERT: A 194 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7592 (p0) REVERT: A 303 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7481 (tmm-80) REVERT: C 37 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7456 (mp) REVERT: E 160 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7048 (mtm-85) REVERT: E 235 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.6583 (t80) REVERT: E 244 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8174 (tttt) REVERT: D 17 LYS cc_start: 0.8376 (mmtp) cc_final: 0.7636 (mtmt) REVERT: D 35 LYS cc_start: 0.8017 (mmtm) cc_final: 0.7684 (mmmm) REVERT: D 51 LYS cc_start: 0.7885 (mttp) cc_final: 0.7663 (mttp) REVERT: D 247 MET cc_start: 0.8922 (mtp) cc_final: 0.8638 (mtt) outliers start: 32 outliers final: 19 residues processed: 133 average time/residue: 0.4865 time to fit residues: 69.1122 Evaluate side-chains 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 68 optimal weight: 0.0470 chunk 43 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN F 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.151124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119861 restraints weight = 23087.624| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.96 r_work: 0.3163 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9084 Z= 0.111 Angle : 0.497 12.878 12290 Z= 0.260 Chirality : 0.040 0.204 1410 Planarity : 0.004 0.050 1535 Dihedral : 7.585 149.341 1251 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.47 % Allowed : 16.55 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.25), residues: 1117 helix: 2.39 (0.25), residues: 400 sheet: 0.23 (0.30), residues: 271 loop : -0.70 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 160 TYR 0.036 0.001 TYR E 235 PHE 0.010 0.001 PHE F 296 TRP 0.013 0.001 TRP A 168 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9080) covalent geometry : angle 0.49641 / 0.26 (12282) SS BOND : bond 0.00140 / 0.07 ( 4) SS BOND : angle 0.62542 / 0.29 ( 8) hydrogen bonds : bond 0.03397 / 2.30 ( 463) hydrogen bonds : angle 4.09244 / 2.92 ( 1288) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8843 (t) cc_final: 0.8611 (p) REVERT: C 20 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7104 (mtpp) REVERT: E 235 TYR cc_start: 0.6918 (OUTLIER) cc_final: 0.6277 (t80) REVERT: E 244 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8162 (tttt) REVERT: D 17 LYS cc_start: 0.8337 (mmtp) cc_final: 0.7636 (mtmt) outliers start: 24 outliers final: 14 residues processed: 140 average time/residue: 0.4485 time to fit residues: 67.2223 Evaluate side-chains 129 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 77 ASN E 186 GLN F 63 ASN F 156 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.150277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118164 restraints weight = 17897.386| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.32 r_work: 0.3186 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9084 Z= 0.132 Angle : 0.519 13.021 12290 Z= 0.271 Chirality : 0.041 0.211 1410 Planarity : 0.004 0.052 1535 Dihedral : 7.186 136.073 1251 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.67 % Allowed : 17.57 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1117 helix: 2.34 (0.25), residues: 400 sheet: 0.21 (0.30), residues: 271 loop : -0.69 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 62 TYR 0.037 0.001 TYR E 235 PHE 0.012 0.001 PHE D 189 TRP 0.011 0.001 TRP A 168 HIS 0.002 0.001 HIS D 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9080) covalent geometry : angle 0.51854 / 0.27 (12282) SS BOND : bond 0.00209 / 0.10 ( 4) SS BOND : angle 0.77111 / 0.37 ( 8) hydrogen bonds : bond 0.03546 / 2.39 ( 463) hydrogen bonds : angle 4.11923 / 2.94 ( 1288) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.403 Fit side-chains REVERT: A 157 VAL cc_start: 0.8914 (t) cc_final: 0.8681 (p) REVERT: A 194 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7627 (p0) REVERT: A 303 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7664 (tmm-80) REVERT: C 20 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7167 (mtpp) REVERT: E 43 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7119 (mptt) REVERT: E 235 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.6426 (t80) REVERT: E 244 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8187 (tttt) REVERT: D 17 LYS cc_start: 0.8460 (mmtp) cc_final: 0.7745 (mtmt) REVERT: D 35 LYS cc_start: 0.8015 (mmtm) cc_final: 0.7780 (mmtp) outliers start: 26 outliers final: 16 residues processed: 131 average time/residue: 0.5388 time to fit residues: 75.5487 Evaluate side-chains 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 0.0170 chunk 82 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN F 63 ASN F 183 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.148945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116498 restraints weight = 23784.149| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.07 r_work: 0.3107 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9084 Z= 0.179 Angle : 0.557 13.508 12290 Z= 0.292 Chirality : 0.043 0.243 1410 Planarity : 0.004 0.055 1535 Dihedral : 7.236 128.595 1251 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.88 % Allowed : 17.27 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.25), residues: 1117 helix: 2.17 (0.25), residues: 400 sheet: 0.08 (0.30), residues: 273 loop : -0.73 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 242 TYR 0.040 0.002 TYR E 235 PHE 0.012 0.001 PHE F 58 TRP 0.011 0.001 TRP A 98 HIS 0.003 0.001 HIS D 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 9080) covalent geometry : angle 0.55699 / 0.29 (12282) SS BOND : bond 0.00294 / 0.15 ( 4) SS BOND : angle 0.99770 / 0.49 ( 8) hydrogen bonds : bond 0.03867 / 2.62 ( 463) hydrogen bonds : angle 4.25374 / 3.04 ( 1288) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.260 Fit side-chains REVERT: A 194 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7582 (p0) REVERT: A 303 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7531 (tmm-80) REVERT: C 20 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7109 (mtpp) REVERT: E 43 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7213 (mptt) REVERT: E 234 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7515 (mm-30) REVERT: E 235 TYR cc_start: 0.7167 (OUTLIER) cc_final: 0.6531 (t80) REVERT: D 17 LYS cc_start: 0.8354 (mmtp) cc_final: 0.7615 (mtmt) REVERT: D 35 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7647 (mmmm) outliers start: 28 outliers final: 17 residues processed: 122 average time/residue: 0.5080 time to fit residues: 66.3040 Evaluate side-chains 126 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN F 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.113412 restraints weight = 20671.929| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.61 r_work: 0.3083 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9084 Z= 0.251 Angle : 0.627 13.696 12290 Z= 0.327 Chirality : 0.045 0.275 1410 Planarity : 0.005 0.064 1535 Dihedral : 7.418 129.046 1251 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.88 % Allowed : 17.16 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1117 helix: 1.87 (0.25), residues: 399 sheet: 0.12 (0.30), residues: 264 loop : -0.89 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 242 TYR 0.042 0.002 TYR E 235 PHE 0.013 0.002 PHE D 189 TRP 0.015 0.002 TRP A 98 HIS 0.003 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.25 ( 9080) covalent geometry : angle 0.62593 / 0.33 (12282) SS BOND : bond 0.00384 / 0.19 ( 4) SS BOND : angle 1.36690 / 0.66 ( 8) hydrogen bonds : bond 0.04335 / 2.94 ( 463) hydrogen bonds : angle 4.46626 / 3.20 ( 1288) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.297 Fit side-chains REVERT: A 194 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7565 (p0) REVERT: A 303 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7769 (tmm-80) REVERT: C 20 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7141 (mtpp) REVERT: E 160 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7155 (mtm-85) REVERT: E 235 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.7076 (t80) REVERT: F 124 MET cc_start: 0.7122 (tpp) cc_final: 0.6803 (mtp) REVERT: D 17 LYS cc_start: 0.8491 (mmtp) cc_final: 0.7791 (mtmt) REVERT: D 35 LYS cc_start: 0.8199 (mmtm) cc_final: 0.7881 (mmmm) outliers start: 28 outliers final: 14 residues processed: 117 average time/residue: 0.5306 time to fit residues: 66.0413 Evaluate side-chains 115 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN E 186 GLN F 63 ASN D 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114852 restraints weight = 14750.260| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.04 r_work: 0.3179 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9084 Z= 0.133 Angle : 0.542 13.576 12290 Z= 0.283 Chirality : 0.042 0.280 1410 Planarity : 0.004 0.064 1535 Dihedral : 6.844 119.347 1251 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.06 % Allowed : 18.29 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.25), residues: 1117 helix: 2.06 (0.25), residues: 400 sheet: 0.13 (0.30), residues: 271 loop : -0.77 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 242 TYR 0.039 0.002 TYR E 235 PHE 0.013 0.001 PHE F 58 TRP 0.012 0.001 TRP A 168 HIS 0.003 0.001 HIS D 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9080) covalent geometry : angle 0.54197 / 0.28 (12282) SS BOND : bond 0.00223 / 0.11 ( 4) SS BOND : angle 0.82998 / 0.40 ( 8) hydrogen bonds : bond 0.03726 / 2.52 ( 463) hydrogen bonds : angle 4.29196 / 3.07 ( 1288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3102.50 seconds wall clock time: 53 minutes 36.59 seconds (3216.59 seconds total)