Starting phenix.real_space_refine on Thu Jul 2 10:54:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lci_23274/07_2026/7lci_23274.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lci_23274/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lci_23274/07_2026/7lci_23274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lci_23274/07_2026/7lci_23274.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lci_23274/07_2026/7lci_23274.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lci_23274/07_2026/7lci_23274.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lci_23274/07_2026/7lci_23274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lci_23274/07_2026/7lci_23274.map" } 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): 0.00s 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: 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: 1.90, per 1000 atoms: 0.23 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: 0.76 Conformation dependent library (CDL) restraints added in 528.3 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: 0.23 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: 1.42 Time building geometry restraints manager: 1.02 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: 4551 17.95 - 35.90: 399 35.90 - 53.86: 49 53.86 - 71.81: 6 71.81 - 89.76: 9 Dihedral angle restraints: 5014 sinusoidal: 1993 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 5011 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: 2.330 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.090 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: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 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 : 13.550 89.759 3044 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/Z covalent geometry : bond 0.00463 / 0.26 ( 8492) covalent geometry : angle 0.78444 / 0.48 (11519) SS BOND : bond 0.00341 / 0.11 ( 4) SS BOND : angle 1.75125 / 1.06 ( 8) hydrogen bonds : bond 0.21884 / 14.79 ( 392) hydrogen bonds : angle 6.95354 / 4.95 ( 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 : 0.359 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: 0.5013 time to fit residues: 85.8978 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 : 0.212 ------------------------------------------------------------------------------- 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... 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 = 0.4460 r_free = 0.4460 target = 0.223097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.185868 restraints weight = 9667.697| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 1.88 r_work: 0.4009 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2182 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= 0.193 Angle : 0.664 11.064 11527 Z= 0.354 Chirality : 0.046 0.181 1269 Planarity : 0.005 0.046 1462 Dihedral : 5.050 26.808 1140 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.61 % Allowed : 10.54 % Favored : 86.85 % 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: -0.05 (0.27), residues: 1020 helix: 0.68 (0.25), residues: 441 sheet: -0.03 (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 0.037 0.003 TYR R 148 PHE 0.026 0.002 PHE B 151 TRP 0.025 0.002 TRP R 420 HIS 0.011 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 8492) covalent geometry : angle 0.66284 / 0.35 (11519) SS BOND : bond 0.00363 / 0.13 ( 4) SS BOND : angle 1.72717 / 1.08 ( 8) hydrogen bonds : bond 0.05253 / 3.49 ( 392) hydrogen bonds : angle 4.82872 / 3.41 ( 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: 0.7951 (OUTLIER) cc_final: 0.7650 (mm) REVERT: R 393 PHE cc_start: 0.7266 (m-80) cc_final: 0.7025 (m-80) REVERT: A 209 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6872 (tt0) REVERT: A 255 MET cc_start: 0.5920 (mtp) cc_final: 0.5603 (mtp) REVERT: A 309 GLU cc_start: 0.5990 (OUTLIER) cc_final: 0.5446 (mp0) REVERT: B 42 ARG cc_start: 0.5632 (mmm160) cc_final: 0.4027 (ttm-80) REVERT: B 87 THR cc_start: 0.7116 (m) cc_final: 0.6904 (m) REVERT: B 101 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7888 (mtm) outliers start: 23 outliers final: 12 residues processed: 121 average time/residue: 0.4876 time to fit residues: 63.4782 Evaluate side-chains 107 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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: 0.9990 chunk 14 optimal weight: 0.0060 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 0.0370 overall best weight: 0.4674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4493 r_free = 0.4493 target = 0.227145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.190478 restraints weight = 9505.563| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 1.84 r_work: 0.4056 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2559 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= 0.113 Angle : 0.538 8.037 11527 Z= 0.288 Chirality : 0.042 0.169 1269 Planarity : 0.004 0.043 1462 Dihedral : 4.620 24.768 1140 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.27 % Allowed : 13.72 % Favored : 84.01 % 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: 0.52 (0.27), residues: 1020 helix: 1.37 (0.26), residues: 442 sheet: 0.00 (0.37), residues: 177 loop : -0.58 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 380 TYR 0.030 0.002 TYR R 148 PHE 0.015 0.001 PHE B 241 TRP 0.016 0.002 TRP R 243 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 8492) covalent geometry : angle 0.53700 / 0.29 (11519) SS BOND : bond 0.00191 / 0.09 ( 4) SS BOND : angle 1.36786 / 0.86 ( 8) hydrogen bonds : bond 0.04193 / 2.80 ( 392) hydrogen bonds : angle 4.48496 / 3.16 ( 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 120 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 88 TYR cc_start: 0.7241 (p90) cc_final: 0.6963 (p90) REVERT: R 393 PHE cc_start: 0.7224 (m-80) cc_final: 0.6700 (m-80) REVERT: A 209 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6836 (tt0) REVERT: A 255 MET cc_start: 0.5883 (mtp) cc_final: 0.5627 (mtp) REVERT: A 283 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6710 (mtm180) REVERT: A 309 GLU cc_start: 0.5873 (mp0) cc_final: 0.5465 (mp0) REVERT: B 153 ASP cc_start: 0.6701 (t0) cc_final: 0.6405 (t70) REVERT: B 325 MET cc_start: 0.6920 (mmm) cc_final: 0.6315 (mmm) REVERT: B 339 TRP cc_start: 0.6721 (m100) cc_final: 0.5954 (m-10) outliers start: 20 outliers final: 7 residues processed: 107 average time/residue: 0.4932 time to fit residues: 56.9156 Evaluate side-chains 97 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 283 ARG Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 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: 0.0770 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 262 GLN B 75 GLN B 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.228181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.191301 restraints weight = 9597.514| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.87 r_work: 0.4066 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2892 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= 0.108 Angle : 0.511 7.619 11527 Z= 0.276 Chirality : 0.041 0.168 1269 Planarity : 0.004 0.044 1462 Dihedral : 4.462 24.782 1140 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.83 % Allowed : 14.74 % 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: 0.85 (0.27), residues: 1020 helix: 1.74 (0.26), residues: 436 sheet: 0.21 (0.38), residues: 171 loop : -0.50 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 380 TYR 0.029 0.002 TYR R 148 PHE 0.015 0.001 PHE B 241 TRP 0.016 0.001 TRP R 243 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 8492) covalent geometry : angle 0.51046 / 0.28 (11519) SS BOND : bond 0.00191 / 0.08 ( 4) SS BOND : angle 1.26622 / 0.81 ( 8) hydrogen bonds : bond 0.03791 / 2.51 ( 392) hydrogen bonds : angle 4.23989 / 3.01 ( 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 118 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 88 TYR cc_start: 0.7256 (p90) cc_final: 0.6954 (p90) REVERT: R 393 PHE cc_start: 0.7197 (m-80) cc_final: 0.6688 (m-80) REVERT: A 209 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6828 (tt0) REVERT: A 255 MET cc_start: 0.5881 (mtp) cc_final: 0.5527 (mtp) REVERT: A 271 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6332 (ptmt) REVERT: A 283 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6778 (mtm180) REVERT: A 309 GLU cc_start: 0.5961 (mp0) cc_final: 0.5696 (mp0) REVERT: B 59 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.6302 (m-80) REVERT: B 153 ASP cc_start: 0.6630 (t0) cc_final: 0.6311 (t70) REVERT: B 156 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6744 (tt0) REVERT: B 325 MET cc_start: 0.6943 (mmm) cc_final: 0.6321 (mmm) REVERT: B 339 TRP cc_start: 0.6726 (m100) cc_final: 0.5963 (m-10) outliers start: 25 outliers final: 9 residues processed: 105 average time/residue: 0.4843 time to fit residues: 54.7148 Evaluate side-chains 101 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 43 ILE 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 156 GLN Chi-restraints excluded: chain B residue 303 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: 1.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 24 optimal weight: 0.0870 chunk 51 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.224980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.187986 restraints weight = 9632.341| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 1.89 r_work: 0.4025 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8496 Z= 0.146 Angle : 0.561 8.111 11527 Z= 0.301 Chirality : 0.043 0.181 1269 Planarity : 0.004 0.046 1462 Dihedral : 4.605 26.803 1140 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.49 % Allowed : 16.78 % Favored : 80.73 % 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: 0.86 (0.27), residues: 1020 helix: 1.70 (0.26), residues: 442 sheet: 0.13 (0.37), residues: 178 loop : -0.44 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 380 TYR 0.029 0.002 TYR R 148 PHE 0.020 0.002 PHE B 151 TRP 0.019 0.002 TRP R 243 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 8492) covalent geometry : angle 0.55921 / 0.30 (11519) SS BOND : bond 0.00402 / 0.17 ( 4) SS BOND : angle 1.74679 / 1.14 ( 8) hydrogen bonds : bond 0.04118 / 2.70 ( 392) hydrogen bonds : angle 4.27614 / 3.03 ( 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 112 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 393 PHE cc_start: 0.7314 (m-80) cc_final: 0.7089 (m-80) REVERT: A 209 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6882 (tt0) REVERT: A 255 MET cc_start: 0.5820 (mtp) cc_final: 0.5462 (mtp) REVERT: A 271 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6432 (ptmt) REVERT: A 283 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6866 (mtm180) REVERT: A 309 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5688 (mp0) REVERT: A 372 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.8024 (mp) REVERT: B 59 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.6430 (m-80) REVERT: B 153 ASP cc_start: 0.6592 (t0) cc_final: 0.6316 (t70) REVERT: B 325 MET cc_start: 0.6977 (mmm) cc_final: 0.6529 (mmm) REVERT: B 339 TRP cc_start: 0.6670 (m100) cc_final: 0.6300 (m-10) outliers start: 22 outliers final: 8 residues processed: 101 average time/residue: 0.4432 time to fit residues: 48.3191 Evaluate side-chains 96 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 309 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 234 GLN B 91 HIS B 156 GLN ** B 340 ASN ** 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 = 0.4429 r_free = 0.4429 target = 0.220006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.183313 restraints weight = 9536.510| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.84 r_work: 0.3985 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8496 Z= 0.201 Angle : 0.651 9.101 11527 Z= 0.349 Chirality : 0.046 0.196 1269 Planarity : 0.005 0.047 1462 Dihedral : 4.994 29.392 1140 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.95 % Allowed : 17.80 % Favored : 79.25 % 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: 0.58 (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 0.009 0.001 ARG R 380 TYR 0.032 0.003 TYR R 148 PHE 0.028 0.002 PHE B 151 TRP 0.025 0.002 TRP R 243 HIS 0.008 0.002 HIS R 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 ( 8492) covalent geometry : angle 0.64827 / 0.35 (11519) SS BOND : bond 0.00379 / 0.13 ( 4) SS BOND : angle 2.20515 / 1.43 ( 8) hydrogen bonds : bond 0.04666 / 3.03 ( 392) hydrogen bonds : angle 4.54876 / 3.21 ( 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 116 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 170 ARG cc_start: 0.6500 (ttm-80) cc_final: 0.5491 (tpt90) REVERT: R 286 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7668 (mm) REVERT: R 393 PHE cc_start: 0.7296 (m-80) cc_final: 0.7074 (m-80) REVERT: A 255 MET cc_start: 0.5867 (mtp) cc_final: 0.5595 (mtp) REVERT: A 271 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6421 (ptmt) REVERT: A 283 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6859 (mtm180) REVERT: A 311 TYR cc_start: 0.5901 (m-80) cc_final: 0.4865 (t80) REVERT: B 59 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.6506 (m-80) REVERT: B 325 MET cc_start: 0.7109 (mmm) cc_final: 0.6601 (mmm) REVERT: B 339 TRP cc_start: 0.6593 (m100) cc_final: 0.6220 (m-10) outliers start: 26 outliers final: 14 residues processed: 104 average time/residue: 0.4388 time to fit residues: 49.0045 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 : 0.302 ------------------------------------------------------------------------------- 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 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 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 135 VAL 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 Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 40 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4475 r_free = 0.4475 target = 0.224976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.188335 restraints weight = 9596.855| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 1.84 r_work: 0.4039 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8496 Z= 0.122 Angle : 0.550 8.497 11527 Z= 0.298 Chirality : 0.042 0.180 1269 Planarity : 0.004 0.043 1462 Dihedral : 4.672 27.574 1140 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.61 % Allowed : 18.71 % Favored : 78.68 % 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 (0.28), residues: 1020 helix: 1.76 (0.26), residues: 442 sheet: 0.14 (0.38), residues: 178 loop : -0.41 (0.33), residues: 400 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 0.022 0.001 PHE B 241 TRP 0.021 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8492) covalent geometry : angle 0.54819 / 0.30 (11519) SS BOND : bond 0.00660 / 0.34 ( 4) SS BOND : angle 1.69233 / 1.10 ( 8) hydrogen bonds : bond 0.03907 / 2.56 ( 392) hydrogen bonds : angle 4.33914 / 3.06 ( 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 109 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 393 PHE cc_start: 0.7295 (m-80) cc_final: 0.7076 (m-80) REVERT: A 271 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6380 (ptmt) REVERT: A 283 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6795 (mtm180) REVERT: A 311 TYR cc_start: 0.5932 (m-80) cc_final: 0.4865 (t80) REVERT: B 59 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.6393 (m-80) REVERT: B 153 ASP cc_start: 0.6579 (t0) cc_final: 0.6288 (t70) REVERT: B 325 MET cc_start: 0.7160 (mmm) cc_final: 0.6634 (mmm) REVERT: B 339 TRP cc_start: 0.6521 (m100) cc_final: 0.6186 (m-10) outliers start: 23 outliers final: 11 residues processed: 99 average time/residue: 0.4875 time to fit residues: 51.7648 Evaluate side-chains 96 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 204 MET 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 50 THR Chi-restraints excluded: chain B residue 59 TYR 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 317 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 56 optimal weight: 0.0020 chunk 42 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.223702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.187103 restraints weight = 9513.543| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 1.83 r_work: 0.4032 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3915 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8496 Z= 0.141 Angle : 0.572 7.945 11527 Z= 0.307 Chirality : 0.043 0.186 1269 Planarity : 0.004 0.045 1462 Dihedral : 4.692 28.420 1140 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.27 % Allowed : 19.73 % Favored : 78.00 % 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 (0.28), residues: 1020 helix: 1.69 (0.26), residues: 442 sheet: 0.21 (0.38), residues: 178 loop : -0.42 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 380 TYR 0.028 0.002 TYR R 148 PHE 0.022 0.002 PHE B 241 TRP 0.028 0.002 TRP R 306 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8492) covalent geometry : angle 0.57099 / 0.31 (11519) SS BOND : bond 0.00340 / 0.15 ( 4) SS BOND : angle 1.53749 / 1.00 ( 8) hydrogen bonds : bond 0.03995 / 2.61 ( 392) hydrogen bonds : angle 4.36826 / 3.09 ( 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: 20 poor density : 81 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 233 MET cc_start: 0.8147 (ttp) cc_final: 0.7931 (ttt) REVERT: R 393 PHE cc_start: 0.7323 (m-80) cc_final: 0.7109 (m-80) REVERT: A 54 ASN cc_start: 0.7591 (m-40) cc_final: 0.7314 (m110) REVERT: A 60 MET cc_start: 0.7414 (mtt) cc_final: 0.6923 (mtt) REVERT: A 208 PHE cc_start: 0.7722 (t80) cc_final: 0.6485 (m-80) REVERT: A 271 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6385 (ptmt) REVERT: A 283 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6860 (mtm180) REVERT: A 311 TYR cc_start: 0.5852 (m-80) cc_final: 0.4882 (t80) REVERT: A 372 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7947 (mp) REVERT: B 59 TYR cc_start: 0.6819 (OUTLIER) cc_final: 0.6423 (m-80) REVERT: B 153 ASP cc_start: 0.6673 (t0) cc_final: 0.6375 (t70) REVERT: B 325 MET cc_start: 0.7250 (mmm) cc_final: 0.6678 (mmm) REVERT: B 339 TRP cc_start: 0.6437 (m100) cc_final: 0.6125 (m-10) outliers start: 20 outliers final: 11 residues processed: 91 average time/residue: 0.4432 time to fit residues: 43.3431 Evaluate side-chains 94 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 50 THR 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: 7.9990 chunk 79 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 0.2980 chunk 18 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4491 r_free = 0.4491 target = 0.226761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.190825 restraints weight = 9492.660| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 1.81 r_work: 0.4055 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3912 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= 0.107 Angle : 0.538 9.002 11527 Z= 0.290 Chirality : 0.042 0.172 1269 Planarity : 0.004 0.043 1462 Dihedral : 4.481 26.480 1140 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.36 % Allowed : 20.63 % Favored : 78.00 % 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 (0.28), residues: 1020 helix: 1.95 (0.26), residues: 438 sheet: 0.31 (0.40), residues: 173 loop : -0.38 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 49 TYR 0.027 0.002 TYR R 148 PHE 0.025 0.001 PHE B 241 TRP 0.033 0.002 TRP R 306 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 8492) covalent geometry : angle 0.53720 / 0.29 (11519) SS BOND : bond 0.00415 / 0.21 ( 4) SS BOND : angle 1.44002 / 0.93 ( 8) hydrogen bonds : bond 0.03595 / 2.36 ( 392) hydrogen bonds : angle 4.22948 / 3.00 ( 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 97 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 393 PHE cc_start: 0.7263 (m-80) cc_final: 0.7038 (m-80) REVERT: A 54 ASN cc_start: 0.7598 (m-40) cc_final: 0.7318 (m110) REVERT: A 60 MET cc_start: 0.7514 (mtt) cc_final: 0.7029 (mtt) REVERT: A 283 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.6780 (mtm180) REVERT: A 309 GLU cc_start: 0.5654 (mp0) cc_final: 0.4310 (mm-30) REVERT: A 311 TYR cc_start: 0.5885 (m-80) cc_final: 0.4950 (t80) REVERT: A 339 TYR cc_start: 0.7248 (m-80) cc_final: 0.6965 (m-80) REVERT: B 59 TYR cc_start: 0.6776 (OUTLIER) cc_final: 0.6386 (m-80) REVERT: B 153 ASP cc_start: 0.6544 (t0) cc_final: 0.6235 (t70) REVERT: B 325 MET cc_start: 0.7236 (mmm) cc_final: 0.6641 (mmm) REVERT: B 339 TRP cc_start: 0.6404 (m100) cc_final: 0.6101 (m-10) outliers start: 12 outliers final: 8 residues processed: 91 average time/residue: 0.5276 time to fit residues: 51.4450 Evaluate side-chains 90 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 67 optimal weight: 0.0470 chunk 23 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN B 88 ASN B 156 GLN ** B 340 ASN ** 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 = 0.4482 r_free = 0.4482 target = 0.225652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.189522 restraints weight = 9488.621| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.82 r_work: 0.4049 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8496 Z= 0.122 Angle : 0.556 8.490 11527 Z= 0.299 Chirality : 0.042 0.174 1269 Planarity : 0.004 0.046 1462 Dihedral : 4.501 26.990 1140 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.59 % Allowed : 20.63 % Favored : 77.78 % 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: 1.09 (0.27), residues: 1020 helix: 1.93 (0.26), residues: 441 sheet: 0.37 (0.39), residues: 178 loop : -0.43 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 380 TYR 0.027 0.002 TYR R 148 PHE 0.026 0.002 PHE B 241 TRP 0.037 0.002 TRP R 306 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8492) covalent geometry : angle 0.55483 / 0.30 (11519) SS BOND : bond 0.00369 / 0.17 ( 4) SS BOND : angle 1.39210 / 0.90 ( 8) hydrogen bonds : bond 0.03716 / 2.44 ( 392) hydrogen bonds : angle 4.21267 / 2.99 ( 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 97 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 393 PHE cc_start: 0.7302 (m-80) cc_final: 0.7076 (m-80) REVERT: A 54 ASN cc_start: 0.7587 (m-40) cc_final: 0.7305 (m110) REVERT: A 60 MET cc_start: 0.7485 (mtt) cc_final: 0.7115 (mtt) REVERT: A 283 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6784 (mtm180) REVERT: A 309 GLU cc_start: 0.5604 (mp0) cc_final: 0.5286 (mm-30) REVERT: A 311 TYR cc_start: 0.5925 (m-80) cc_final: 0.4978 (t80) REVERT: A 339 TYR cc_start: 0.7265 (m-80) cc_final: 0.7030 (m-80) REVERT: A 344 GLU cc_start: 0.7112 (pp20) cc_final: 0.4833 (pp20) REVERT: A 372 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7923 (mp) REVERT: B 59 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.6408 (m-80) REVERT: B 153 ASP cc_start: 0.6563 (t0) cc_final: 0.6249 (t70) REVERT: B 325 MET cc_start: 0.7231 (mmm) cc_final: 0.6657 (mmm) REVERT: B 339 TRP cc_start: 0.6367 (m100) cc_final: 0.6115 (m-10) outliers start: 14 outliers final: 7 residues processed: 91 average time/residue: 0.5161 time to fit residues: 50.5118 Evaluate side-chains 92 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 283 ARG Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR 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: 1.9990 chunk 97 optimal weight: 0.0470 chunk 39 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 chunk 60 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 chunk 94 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN B 88 ASN B 156 GLN ** B 340 ASN ** 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 = 0.4505 r_free = 0.4505 target = 0.228322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.192779 restraints weight = 9447.523| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 1.81 r_work: 0.4084 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3963 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.4093 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= 0.101 Angle : 0.527 8.800 11527 Z= 0.285 Chirality : 0.041 0.165 1269 Planarity : 0.004 0.045 1462 Dihedral : 4.356 25.221 1140 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.36 % Allowed : 20.86 % Favored : 77.78 % 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: 1.23 (0.27), residues: 1020 helix: 2.09 (0.26), residues: 437 sheet: 0.58 (0.39), residues: 174 loop : -0.46 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 380 TYR 0.027 0.002 TYR R 148 PHE 0.024 0.001 PHE B 241 TRP 0.033 0.002 TRP R 306 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 8492) covalent geometry : angle 0.52568 / 0.28 (11519) SS BOND : bond 0.00313 / 0.16 ( 4) SS BOND : angle 1.24980 / 0.80 ( 8) hydrogen bonds : bond 0.03404 / 2.24 ( 392) hydrogen bonds : angle 4.09776 / 2.91 ( 1122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3336.04 seconds wall clock time: 57 minutes 30.47 seconds (3450.47 seconds total)