Starting phenix.real_space_refine on Tue Mar 3 19:52:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lci_23274/03_2026/7lci_23274.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lci_23274/03_2026/7lci_23274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lci_23274/03_2026/7lci_23274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lci_23274/03_2026/7lci_23274.map" model { file = "/net/cci-nas-00/data/ceres_data/7lci_23274/03_2026/7lci_23274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lci_23274/03_2026/7lci_23274.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 5297 2.51 5 N 1437 2.21 5 O 1532 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8317 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3241 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2006 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 237} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2573 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" 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: "R" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 60 Unusual residues: {'UK4': 1} Classifications: {'undetermined': 1, 'water': 19} Link IDs: {None: 19} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.71, per 1000 atoms: 0.21 Number of scatterers: 8317 At special positions: 0 Unit cell: (146.91, 102.09, 112.88, 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 50 16.00 F 1 9.00 O 1532 8.00 N 1437 7.00 C 5297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.02 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 0.85 Conformation dependent library (CDL) restraints added in 279.4 milliseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 45.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.679A pdb=" N GLU R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 169 removed outlier: 3.854A pdb=" N PHE R 143 " --> pdb=" O GLU R 139 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 201 removed outlier: 3.503A pdb=" N LEU R 201 " --> pdb=" O LYS R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 209 removed outlier: 4.021A pdb=" N ALA R 208 " --> pdb=" O TYR R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 212 No H-bonds generated for 'chain 'R' and resid 210 through 212' Processing helix chain 'R' and resid 213 through 222 removed outlier: 3.708A pdb=" N GLN R 221 " --> pdb=" O LEU R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 256 Processing helix chain 'R' and resid 261 through 276 removed outlier: 3.757A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 removed outlier: 3.516A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.553A pdb=" N TYR R 291 " --> pdb=" O VAL R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 338 Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 341 through 355 removed outlier: 4.078A pdb=" N LYS R 346 " --> pdb=" O LYS R 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 361 Processing helix chain 'R' and resid 362 through 364 No H-bonds generated for 'chain 'R' and resid 362 through 364' Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 377 through 392 removed outlier: 3.533A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 403 Processing helix chain 'R' and resid 406 through 423 removed outlier: 4.337A pdb=" N TRP R 420 " --> pdb=" O SER R 416 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG R 421 " --> pdb=" O TRP R 417 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU R 423 " --> pdb=" O ARG R 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 33 removed outlier: 3.509A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 removed outlier: 3.875A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.646A pdb=" N TYR A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.968A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.507A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.612A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.742A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.804A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 4.024A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'R' and resid 80 through 84 removed outlier: 3.851A pdb=" N ARG R 102 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR R 101 " --> pdb=" O ASP R 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.269A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.788A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.162A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.632A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.651A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.212A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.466A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.745A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1122 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: 1.40 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1346 1.27 - 1.40: 2242 1.40 - 1.54: 4800 1.54 - 1.68: 36 1.68 - 1.81: 68 Bond restraints: 8492 Sorted by residual: bond pdb=" C27 UK4 R 501 " pdb=" C28 UK4 R 501 " ideal model delta sigma weight residual 1.535 1.421 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C38 UK4 R 501 " pdb=" C39 UK4 R 501 " ideal model delta sigma weight residual 1.427 1.526 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C28 UK4 R 501 " pdb=" C29 UK4 R 501 " ideal model delta sigma weight residual 1.529 1.448 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" N VAL A 256 " pdb=" CA VAL A 256 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.32e-02 5.74e+03 9.03e+00 bond pdb=" C06 UK4 R 501 " pdb=" O05 UK4 R 501 " ideal model delta sigma weight residual 1.345 1.405 -0.060 2.00e-02 2.50e+03 8.86e+00 ... (remaining 8487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 11442 3.66 - 7.32: 69 7.32 - 10.98: 6 10.98 - 14.65: 1 14.65 - 18.31: 1 Bond angle restraints: 11519 Sorted by residual: angle pdb=" N SER A 352 " pdb=" CA SER A 352 " pdb=" C SER A 352 " ideal model delta sigma weight residual 111.07 118.18 -7.11 1.07e+00 8.73e-01 4.41e+01 angle pdb=" C08 UK4 R 501 " pdb=" C09 UK4 R 501 " pdb=" C32 UK4 R 501 " ideal model delta sigma weight residual 110.26 91.95 18.31 3.00e+00 1.11e-01 3.72e+01 angle pdb=" N ASP R 344 " pdb=" CA ASP R 344 " pdb=" C ASP R 344 " ideal model delta sigma weight residual 111.28 105.00 6.28 1.09e+00 8.42e-01 3.32e+01 angle pdb=" CA ILE A 257 " pdb=" C ILE A 257 " pdb=" O ILE A 257 " ideal model delta sigma weight residual 122.63 117.81 4.82 8.70e-01 1.32e+00 3.07e+01 angle pdb=" N VAL R 365 " pdb=" CA VAL R 365 " pdb=" C VAL R 365 " ideal model delta sigma weight residual 111.81 107.10 4.71 8.60e-01 1.35e+00 3.00e+01 ... (remaining 11514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4559 17.95 - 35.90: 403 35.90 - 53.86: 51 53.86 - 71.81: 6 71.81 - 89.76: 9 Dihedral angle restraints: 5028 sinusoidal: 2007 harmonic: 3021 Sorted by residual: dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -120.92 34.92 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" C ASP R 344 " pdb=" N ASP R 344 " pdb=" CA ASP R 344 " pdb=" CB ASP R 344 " ideal model delta harmonic sigma weight residual -122.60 -112.30 -10.30 0 2.50e+00 1.60e-01 1.70e+01 ... (remaining 5025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1123 0.072 - 0.144: 127 0.144 - 0.216: 14 0.216 - 0.288: 4 0.288 - 0.360: 1 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CA ASP R 344 " pdb=" N ASP R 344 " pdb=" C ASP R 344 " pdb=" CB ASP R 344 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA SER A 352 " pdb=" N SER A 352 " pdb=" C SER A 352 " pdb=" CB SER A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LEU R 339 " pdb=" N LEU R 339 " pdb=" C LEU R 339 " pdb=" CB LEU R 339 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1266 not shown) Planarity restraints: 1462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO G 53 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 306 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C SER A 306 " -0.050 2.00e-02 2.50e+03 pdb=" O SER A 306 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 307 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER R 136 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO R 137 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO R 137 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 137 " -0.031 5.00e-02 4.00e+02 ... (remaining 1459 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 744 2.74 - 3.28: 8453 3.28 - 3.82: 13835 3.82 - 4.36: 17153 4.36 - 4.90: 29040 Nonbonded interactions: 69225 Sorted by model distance: nonbonded pdb=" OD1 ASN R 300 " pdb=" N SER R 301 " model vdw 2.203 3.120 nonbonded pdb=" NH2 ARG R 40 " pdb=" OD2 ASP R 222 " model vdw 2.243 3.120 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.245 3.120 nonbonded pdb=" NZ LYS R 113 " pdb=" O LEU R 118 " model vdw 2.256 3.120 nonbonded pdb=" OD2 ASP R 67 " pdb=" NH1 ARG R 121 " model vdw 2.276 3.120 ... (remaining 69220 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=0.00 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.500 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 8496 Z= 0.263 Angle : 0.786 18.306 11527 Z= 0.476 Chirality : 0.050 0.360 1269 Planarity : 0.004 0.084 1462 Dihedral : 13.609 89.759 3058 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: -0.99 (0.26), residues: 1020 helix: -0.13 (0.25), residues: 437 sheet: -0.56 (0.37), residues: 183 loop : -1.13 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 8 TYR 0.017 0.002 TYR B 59 PHE 0.016 0.002 PHE R 280 TRP 0.022 0.002 TRP R 243 HIS 0.005 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 8492) covalent geometry : angle 0.78444 (11519) SS BOND : bond 0.00341 ( 4) SS BOND : angle 1.75125 ( 8) hydrogen bonds : bond 0.21884 ( 392) hydrogen bonds : angle 6.95354 ( 1122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: R 88 TYR cc_start: 0.7010 (p90) cc_final: 0.6511 (p90) REVERT: R 393 PHE cc_start: 0.6826 (m-80) cc_final: 0.6497 (m-80) REVERT: A 208 PHE cc_start: 0.7260 (t80) cc_final: 0.6795 (m-80) REVERT: A 255 MET cc_start: 0.5990 (mtp) cc_final: 0.5764 (mtp) REVERT: A 372 ILE cc_start: 0.7550 (mt) cc_final: 0.7217 (pt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.4989 time to fit residues: 85.2719 Evaluate side-chains 96 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN A 31 GLN A 35 GLN A 218 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.223067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.186441 restraints weight = 9646.724| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 1.83 r_work: 0.4011 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3891 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8496 Z= 0.192 Angle : 0.664 11.057 11527 Z= 0.354 Chirality : 0.046 0.183 1269 Planarity : 0.005 0.045 1462 Dihedral : 5.211 26.732 1154 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.61 % Allowed : 10.43 % Favored : 86.96 % 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: -0.03 (0.27), residues: 1020 helix: 0.70 (0.25), residues: 441 sheet: -0.02 (0.38), residues: 177 loop : -0.72 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 380 TYR 0.036 0.003 TYR R 148 PHE 0.025 0.002 PHE B 151 TRP 0.026 0.002 TRP R 420 HIS 0.011 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8492) covalent geometry : angle 0.66232 (11519) SS BOND : bond 0.00367 ( 4) SS BOND : angle 1.78210 ( 8) hydrogen bonds : bond 0.05174 ( 392) hydrogen bonds : angle 4.82590 ( 1122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.285 Fit side-chains REVERT: R 286 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7655 (mm) REVERT: R 393 PHE cc_start: 0.7268 (m-80) cc_final: 0.7026 (m-80) REVERT: A 209 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6865 (tt0) REVERT: A 255 MET cc_start: 0.5905 (mtp) cc_final: 0.5607 (mtp) REVERT: A 309 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5458 (mp0) REVERT: B 42 ARG cc_start: 0.5639 (mmm160) cc_final: 0.4033 (ttm-80) REVERT: B 87 THR cc_start: 0.7094 (m) cc_final: 0.6892 (m) REVERT: B 101 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7888 (mtm) outliers start: 23 outliers final: 12 residues processed: 121 average time/residue: 0.4623 time to fit residues: 60.0829 Evaluate side-chains 108 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 410 GLN A 35 GLN A 239 ASN B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.226388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.189330 restraints weight = 9430.554| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 1.86 r_work: 0.4044 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8496 Z= 0.127 Angle : 0.558 8.727 11527 Z= 0.298 Chirality : 0.042 0.171 1269 Planarity : 0.004 0.043 1462 Dihedral : 4.904 25.775 1154 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.38 % Allowed : 13.95 % Favored : 83.67 % 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: 0.48 (0.27), residues: 1020 helix: 1.29 (0.26), residues: 442 sheet: -0.00 (0.37), residues: 177 loop : -0.55 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 380 TYR 0.030 0.002 TYR R 148 PHE 0.014 0.001 PHE B 241 TRP 0.018 0.002 TRP R 243 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8492) covalent geometry : angle 0.55671 (11519) SS BOND : bond 0.00203 ( 4) SS BOND : angle 1.40546 ( 8) hydrogen bonds : bond 0.04387 ( 392) hydrogen bonds : angle 4.52210 ( 1122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: R 88 TYR cc_start: 0.7332 (p90) cc_final: 0.7051 (p90) REVERT: R 122 ASP cc_start: 0.6454 (t70) cc_final: 0.6080 (t0) REVERT: R 393 PHE cc_start: 0.7261 (m-80) cc_final: 0.6692 (m-80) REVERT: A 209 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6825 (tt0) REVERT: A 255 MET cc_start: 0.5871 (mtp) cc_final: 0.5605 (mtp) REVERT: A 283 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6762 (mtm180) REVERT: A 309 GLU cc_start: 0.6026 (mp0) cc_final: 0.5572 (mp0) REVERT: B 325 MET cc_start: 0.6941 (mmm) cc_final: 0.6331 (mmm) REVERT: B 339 TRP cc_start: 0.6740 (m100) cc_final: 0.5954 (m-10) outliers start: 21 outliers final: 11 residues processed: 106 average time/residue: 0.4860 time to fit residues: 55.1176 Evaluate side-chains 101 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 239 ASN A 262 GLN B 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.227302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.190554 restraints weight = 9604.545| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.88 r_work: 0.4050 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8496 Z= 0.114 Angle : 0.517 7.627 11527 Z= 0.279 Chirality : 0.042 0.172 1269 Planarity : 0.004 0.044 1462 Dihedral : 4.725 25.444 1154 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.38 % Allowed : 15.19 % Favored : 82.43 % 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: 0.80 (0.27), residues: 1020 helix: 1.64 (0.26), residues: 442 sheet: 0.18 (0.38), residues: 176 loop : -0.50 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 64 TYR 0.029 0.002 TYR R 148 PHE 0.016 0.001 PHE B 241 TRP 0.018 0.001 TRP R 243 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8492) covalent geometry : angle 0.51570 (11519) SS BOND : bond 0.00189 ( 4) SS BOND : angle 1.25617 ( 8) hydrogen bonds : bond 0.03861 ( 392) hydrogen bonds : angle 4.28016 ( 1122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 88 TYR cc_start: 0.7304 (p90) cc_final: 0.6992 (p90) REVERT: R 393 PHE cc_start: 0.7260 (m-80) cc_final: 0.6704 (m-80) REVERT: A 209 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6765 (tt0) REVERT: A 220 HIS cc_start: 0.7842 (t-170) cc_final: 0.7361 (t-170) REVERT: A 255 MET cc_start: 0.5855 (mtp) cc_final: 0.5614 (mtp) REVERT: A 271 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6310 (ptmt) REVERT: A 283 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6800 (mtm180) REVERT: A 309 GLU cc_start: 0.5963 (mp0) cc_final: 0.5679 (mp0) REVERT: B 59 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.6359 (m-80) REVERT: B 153 ASP cc_start: 0.6610 (t0) cc_final: 0.6310 (t70) REVERT: B 325 MET cc_start: 0.6899 (mmm) cc_final: 0.6304 (mmm) REVERT: B 339 TRP cc_start: 0.6724 (m100) cc_final: 0.6072 (m-10) outliers start: 21 outliers final: 9 residues processed: 104 average time/residue: 0.4567 time to fit residues: 51.3920 Evaluate side-chains 92 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 53 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 24 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 234 GLN A 239 ASN B 91 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.221510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.184445 restraints weight = 9655.503| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 1.86 r_work: 0.3991 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8496 Z= 0.189 Angle : 0.625 8.939 11527 Z= 0.334 Chirality : 0.045 0.192 1269 Planarity : 0.005 0.046 1462 Dihedral : 5.135 29.146 1154 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.95 % Allowed : 16.44 % Favored : 80.61 % 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: 0.57 (0.27), residues: 1020 helix: 1.41 (0.26), residues: 443 sheet: -0.01 (0.38), residues: 178 loop : -0.54 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 380 TYR 0.032 0.003 TYR R 148 PHE 0.027 0.002 PHE B 151 TRP 0.023 0.002 TRP R 243 HIS 0.008 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8492) covalent geometry : angle 0.62336 (11519) SS BOND : bond 0.00451 ( 4) SS BOND : angle 1.83445 ( 8) hydrogen bonds : bond 0.04605 ( 392) hydrogen bonds : angle 4.51548 ( 1122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 64 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.7051 (ptp-170) REVERT: R 170 ARG cc_start: 0.6565 (ttm-80) cc_final: 0.5536 (tpt90) REVERT: R 286 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7674 (mm) REVERT: R 393 PHE cc_start: 0.7288 (m-80) cc_final: 0.7061 (m-80) REVERT: A 209 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6976 (tt0) REVERT: A 212 PHE cc_start: 0.6333 (p90) cc_final: 0.5973 (p90) REVERT: A 220 HIS cc_start: 0.7860 (t-170) cc_final: 0.7328 (t-170) REVERT: A 255 MET cc_start: 0.5842 (mtp) cc_final: 0.5572 (mtp) REVERT: A 262 GLN cc_start: 0.6457 (tt0) cc_final: 0.6125 (mt0) REVERT: A 271 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6486 (ptmt) REVERT: A 283 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6896 (mtm180) REVERT: A 309 GLU cc_start: 0.5985 (mp0) cc_final: 0.5760 (mp0) REVERT: A 311 TYR cc_start: 0.5872 (m-80) cc_final: 0.4839 (t80) REVERT: A 372 ILE cc_start: 0.8167 (mp) cc_final: 0.7946 (mp) REVERT: B 59 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6537 (m-80) REVERT: B 156 GLN cc_start: 0.7218 (mt0) cc_final: 0.6916 (tt0) REVERT: B 325 MET cc_start: 0.7110 (mmm) cc_final: 0.6697 (mmm) REVERT: B 339 TRP cc_start: 0.6623 (m100) cc_final: 0.6256 (m-10) outliers start: 26 outliers final: 13 residues processed: 108 average time/residue: 0.4851 time to fit residues: 56.1400 Evaluate side-chains 104 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 ARG Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 71 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.225557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.189312 restraints weight = 9478.947| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.84 r_work: 0.4048 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3927 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8496 Z= 0.115 Angle : 0.542 7.888 11527 Z= 0.293 Chirality : 0.042 0.179 1269 Planarity : 0.003 0.044 1462 Dihedral : 4.758 26.675 1154 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.95 % Allowed : 17.69 % Favored : 79.37 % 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: 0.94 (0.28), residues: 1020 helix: 1.76 (0.26), residues: 442 sheet: 0.14 (0.39), residues: 173 loop : -0.37 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.027 0.002 TYR R 148 PHE 0.020 0.001 PHE B 241 TRP 0.018 0.002 TRP R 243 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8492) covalent geometry : angle 0.53919 (11519) SS BOND : bond 0.00358 ( 4) SS BOND : angle 1.98240 ( 8) hydrogen bonds : bond 0.03827 ( 392) hydrogen bonds : angle 4.32802 ( 1122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 64 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6758 (ptp-170) REVERT: R 393 PHE cc_start: 0.7262 (m-80) cc_final: 0.7046 (m-80) REVERT: A 220 HIS cc_start: 0.7856 (t-170) cc_final: 0.7380 (t-170) REVERT: A 271 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6433 (ptmt) REVERT: A 283 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6812 (mtm180) REVERT: A 372 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7920 (mp) REVERT: B 59 TYR cc_start: 0.6781 (OUTLIER) cc_final: 0.6377 (m-80) REVERT: B 153 ASP cc_start: 0.6553 (t0) cc_final: 0.6251 (t70) REVERT: B 325 MET cc_start: 0.7148 (mmm) cc_final: 0.6671 (mmm) REVERT: B 339 TRP cc_start: 0.6558 (m100) cc_final: 0.6219 (m-10) outliers start: 26 outliers final: 12 residues processed: 102 average time/residue: 0.4917 time to fit residues: 53.7845 Evaluate side-chains 100 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 ARG Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 40 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 156 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.226552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.190164 restraints weight = 9589.717| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.85 r_work: 0.4057 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3936 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8496 Z= 0.110 Angle : 0.524 7.607 11527 Z= 0.284 Chirality : 0.041 0.173 1269 Planarity : 0.004 0.046 1462 Dihedral : 4.675 26.133 1154 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.61 % Allowed : 19.27 % Favored : 78.12 % 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: 1.00 (0.27), residues: 1020 helix: 1.86 (0.26), residues: 437 sheet: 0.23 (0.39), residues: 173 loop : -0.39 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 49 TYR 0.027 0.002 TYR R 148 PHE 0.021 0.001 PHE B 241 TRP 0.021 0.002 TRP R 306 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8492) covalent geometry : angle 0.52281 (11519) SS BOND : bond 0.00382 ( 4) SS BOND : angle 1.46684 ( 8) hydrogen bonds : bond 0.03654 ( 392) hydrogen bonds : angle 4.23110 ( 1122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 393 PHE cc_start: 0.7269 (m-80) cc_final: 0.7046 (m-80) REVERT: A 271 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6309 (ptmt) REVERT: A 283 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.6804 (mtm180) REVERT: A 311 TYR cc_start: 0.5844 (m-80) cc_final: 0.4853 (t80) REVERT: A 339 TYR cc_start: 0.7242 (m-80) cc_final: 0.6951 (m-80) REVERT: A 372 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7974 (mp) REVERT: B 59 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.6385 (m-80) REVERT: B 153 ASP cc_start: 0.6600 (t0) cc_final: 0.6274 (t70) REVERT: B 156 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6891 (tt0) REVERT: B 325 MET cc_start: 0.7118 (mmm) cc_final: 0.6573 (mmm) REVERT: B 339 TRP cc_start: 0.6477 (m100) cc_final: 0.6200 (m-10) outliers start: 23 outliers final: 12 residues processed: 94 average time/residue: 0.5053 time to fit residues: 50.9155 Evaluate side-chains 96 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 56 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 64 optimal weight: 0.0050 chunk 55 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.226480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.190604 restraints weight = 9535.587| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.86 r_work: 0.4054 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8496 Z= 0.115 Angle : 0.533 8.458 11527 Z= 0.287 Chirality : 0.042 0.171 1269 Planarity : 0.004 0.046 1462 Dihedral : 4.662 26.118 1154 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.04 % Allowed : 20.07 % Favored : 77.89 % 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: 1.06 (0.27), residues: 1020 helix: 1.89 (0.26), residues: 437 sheet: 0.31 (0.39), residues: 173 loop : -0.38 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 380 TYR 0.027 0.002 TYR R 148 PHE 0.022 0.001 PHE B 241 TRP 0.027 0.002 TRP R 306 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8492) covalent geometry : angle 0.53199 (11519) SS BOND : bond 0.00358 ( 4) SS BOND : angle 1.51639 ( 8) hydrogen bonds : bond 0.03660 ( 392) hydrogen bonds : angle 4.20937 ( 1122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 71 CYS cc_start: 0.4121 (p) cc_final: 0.3846 (t) REVERT: R 393 PHE cc_start: 0.7260 (m-80) cc_final: 0.7042 (m-80) REVERT: A 271 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6312 (ptmt) REVERT: A 283 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6809 (mtm180) REVERT: A 309 GLU cc_start: 0.5603 (mp0) cc_final: 0.3882 (mm-30) REVERT: A 311 TYR cc_start: 0.5900 (m-80) cc_final: 0.4888 (t80) REVERT: A 372 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7966 (mp) REVERT: B 59 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.6372 (m-80) REVERT: B 153 ASP cc_start: 0.6490 (t0) cc_final: 0.6194 (t70) REVERT: B 325 MET cc_start: 0.7117 (mmm) cc_final: 0.6585 (mmm) REVERT: B 339 TRP cc_start: 0.6435 (m100) cc_final: 0.6127 (m-10) outliers start: 18 outliers final: 10 residues processed: 93 average time/residue: 0.5071 time to fit residues: 50.6668 Evaluate side-chains 93 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 76 optimal weight: 6.9990 chunk 79 optimal weight: 0.0000 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.227276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.191238 restraints weight = 9501.555| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 1.83 r_work: 0.4062 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8496 Z= 0.107 Angle : 0.526 9.381 11527 Z= 0.284 Chirality : 0.041 0.168 1269 Planarity : 0.004 0.047 1462 Dihedral : 4.619 25.543 1154 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.70 % Allowed : 20.63 % Favored : 77.66 % 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: 1.14 (0.27), residues: 1020 helix: 1.98 (0.26), residues: 438 sheet: 0.44 (0.39), residues: 178 loop : -0.43 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 380 TYR 0.027 0.002 TYR R 148 PHE 0.023 0.001 PHE B 241 TRP 0.026 0.002 TRP R 306 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8492) covalent geometry : angle 0.52474 (11519) SS BOND : bond 0.00347 ( 4) SS BOND : angle 1.34295 ( 8) hydrogen bonds : bond 0.03542 ( 392) hydrogen bonds : angle 4.15491 ( 1122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 393 PHE cc_start: 0.7251 (m-80) cc_final: 0.7035 (m-80) REVERT: A 271 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6301 (ptmt) REVERT: A 283 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6804 (mtm180) REVERT: A 309 GLU cc_start: 0.5604 (mp0) cc_final: 0.5277 (mm-30) REVERT: A 311 TYR cc_start: 0.5947 (m-80) cc_final: 0.4963 (t80) REVERT: A 339 TYR cc_start: 0.7264 (m-80) cc_final: 0.7036 (m-80) REVERT: B 59 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.6373 (m-80) REVERT: B 153 ASP cc_start: 0.6561 (t0) cc_final: 0.6224 (t70) REVERT: B 325 MET cc_start: 0.7148 (mmm) cc_final: 0.6584 (mmm) outliers start: 15 outliers final: 11 residues processed: 92 average time/residue: 0.4985 time to fit residues: 49.1279 Evaluate side-chains 94 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.0470 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 23 optimal weight: 0.0030 chunk 68 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 88 ASN B 156 GLN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.228715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.192970 restraints weight = 9494.264| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 1.84 r_work: 0.4076 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3955 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8496 Z= 0.103 Angle : 0.527 8.605 11527 Z= 0.285 Chirality : 0.041 0.168 1269 Planarity : 0.004 0.046 1462 Dihedral : 4.556 25.068 1154 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.81 % Allowed : 20.29 % Favored : 77.89 % 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: 1.21 (0.27), residues: 1020 helix: 2.07 (0.26), residues: 438 sheet: 0.47 (0.38), residues: 178 loop : -0.43 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 380 TYR 0.027 0.002 TYR R 148 PHE 0.024 0.001 PHE B 241 TRP 0.038 0.002 TRP B 339 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8492) covalent geometry : angle 0.52566 (11519) SS BOND : bond 0.00502 ( 4) SS BOND : angle 1.59439 ( 8) hydrogen bonds : bond 0.03491 ( 392) hydrogen bonds : angle 4.17125 ( 1122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 74 ASP cc_start: 0.7386 (m-30) cc_final: 0.6962 (m-30) REVERT: R 393 PHE cc_start: 0.7241 (m-80) cc_final: 0.7022 (m-80) REVERT: A 271 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6337 (ptmt) REVERT: A 283 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6760 (mtm180) REVERT: A 309 GLU cc_start: 0.5539 (mp0) cc_final: 0.5173 (mm-30) REVERT: A 311 TYR cc_start: 0.5955 (m-80) cc_final: 0.4975 (t80) REVERT: A 339 TYR cc_start: 0.7184 (m-80) cc_final: 0.6926 (m-80) REVERT: B 59 TYR cc_start: 0.6759 (OUTLIER) cc_final: 0.6398 (m-80) REVERT: B 153 ASP cc_start: 0.6519 (t0) cc_final: 0.6190 (t70) REVERT: B 175 GLN cc_start: 0.6888 (tp-100) cc_final: 0.6640 (tp40) REVERT: B 239 ASN cc_start: 0.6142 (m-40) cc_final: 0.5571 (t0) REVERT: B 325 MET cc_start: 0.7115 (mmm) cc_final: 0.6552 (mmm) outliers start: 16 outliers final: 9 residues processed: 94 average time/residue: 0.4679 time to fit residues: 47.4000 Evaluate side-chains 95 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 94 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.228388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.192842 restraints weight = 9479.718| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 1.83 r_work: 0.4071 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3950 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8496 Z= 0.114 Angle : 0.544 8.603 11527 Z= 0.293 Chirality : 0.042 0.191 1269 Planarity : 0.004 0.051 1462 Dihedral : 4.562 25.430 1154 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.47 % Allowed : 20.86 % Favored : 77.66 % 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: 1.22 (0.27), residues: 1020 helix: 2.06 (0.26), residues: 438 sheet: 0.48 (0.39), residues: 178 loop : -0.40 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG R 380 TYR 0.027 0.002 TYR R 148 PHE 0.025 0.001 PHE B 241 TRP 0.082 0.003 TRP B 339 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8492) covalent geometry : angle 0.54294 (11519) SS BOND : bond 0.00396 ( 4) SS BOND : angle 1.56268 ( 8) hydrogen bonds : bond 0.03594 ( 392) hydrogen bonds : angle 4.22464 ( 1122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3308.62 seconds wall clock time: 56 minutes 57.35 seconds (3417.35 seconds total)