Starting phenix.real_space_refine on Wed Mar 12 23:58:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lci_23274/03_2025/7lci_23274.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lci_23274/03_2025/7lci_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_2025/7lci_23274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lci_23274/03_2025/7lci_23274.map" model { file = "/net/cci-nas-00/data/ceres_data/7lci_23274/03_2025/7lci_23274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lci_23274/03_2025/7lci_23274.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 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: {'GLU:plan': 1, 'ARG:plan': 2, '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: 5.50, per 1000 atoms: 0.66 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: 2.27 Conformation dependent library (CDL) restraints added in 884.2 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: 0.84 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: 2.27 Time building geometry restraints manager: 2.61 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: 0.010 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.210 ------------------------------------------------------------------------------- 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 8492 Z= 0.302 Angle : 0.784 18.306 11519 Z= 0.475 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 : 10.74 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.002 TRP R 243 HIS 0.005 0.001 HIS R 180 PHE 0.016 0.002 PHE R 280 TYR 0.017 0.002 TYR B 59 ARG 0.009 0.001 ARG B 8 *********************** 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 : 0.940 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: 1.0606 time to fit residues: 181.9534 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 : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN R 234 GLN A 31 GLN A 35 GLN A 218 ASN A 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.226634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.189984 restraints weight = 9583.892| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.86 r_work: 0.4048 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8492 Z= 0.218 Angle : 0.604 10.212 11519 Z= 0.324 Chirality : 0.044 0.175 1269 Planarity : 0.005 0.044 1462 Dihedral : 5.060 24.682 1154 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.38 % Allowed : 10.20 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.27), residues: 1020 helix: 0.91 (0.25), residues: 439 sheet: 0.01 (0.37), residues: 175 loop : -0.74 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 420 HIS 0.008 0.001 HIS A 357 PHE 0.017 0.002 PHE B 151 TYR 0.034 0.002 TYR R 148 ARG 0.008 0.001 ARG A 380 *********************** 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 129 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: R 286 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7621 (mm) REVERT: R 393 PHE cc_start: 0.7155 (m-80) cc_final: 0.6709 (m-80) REVERT: A 209 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6779 (tt0) REVERT: A 255 MET cc_start: 0.5939 (mtp) cc_final: 0.5643 (mtp) REVERT: A 309 GLU cc_start: 0.6003 (OUTLIER) cc_final: 0.5432 (mp0) REVERT: B 42 ARG cc_start: 0.5634 (mmm160) cc_final: 0.3953 (ttm-80) REVERT: B 101 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7870 (mtm) outliers start: 21 outliers final: 11 residues processed: 119 average time/residue: 1.0439 time to fit residues: 133.8729 Evaluate side-chains 102 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 386 MET 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 17 optimal weight: 0.3980 chunk 97 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.226100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.189153 restraints weight = 9686.941| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 1.86 r_work: 0.4041 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8492 Z= 0.193 Angle : 0.562 8.965 11519 Z= 0.299 Chirality : 0.042 0.175 1269 Planarity : 0.004 0.044 1462 Dihedral : 4.882 25.442 1154 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.27 % Allowed : 13.38 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 1020 helix: 1.32 (0.26), residues: 442 sheet: -0.02 (0.37), residues: 177 loop : -0.58 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 243 HIS 0.007 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.031 0.002 TYR R 148 ARG 0.007 0.001 ARG R 380 *********************** 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 116 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: R 393 PHE cc_start: 0.7240 (m-80) cc_final: 0.6706 (m-80) REVERT: A 209 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6806 (tt0) REVERT: A 213 GLN cc_start: 0.6588 (mm-40) cc_final: 0.6358 (mm-40) REVERT: A 255 MET cc_start: 0.5911 (mtp) cc_final: 0.5652 (mtp) REVERT: A 283 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6727 (mtm180) REVERT: A 372 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7461 (pt) REVERT: B 217 MET cc_start: 0.7188 (ptm) cc_final: 0.6162 (pmm) REVERT: B 325 MET cc_start: 0.6966 (mmm) cc_final: 0.6291 (mmm) REVERT: B 339 TRP cc_start: 0.6758 (m100) cc_final: 0.6035 (m-10) REVERT: G 21 MET cc_start: 0.2951 (mpp) cc_final: 0.1996 (ttm) outliers start: 20 outliers final: 11 residues processed: 104 average time/residue: 0.9829 time to fit residues: 110.6896 Evaluate side-chains 103 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 235 ILE 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 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 66 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.226658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.189622 restraints weight = 9534.529| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 1.85 r_work: 0.4042 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3922 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8492 Z= 0.183 Angle : 0.539 8.055 11519 Z= 0.290 Chirality : 0.042 0.174 1269 Planarity : 0.004 0.044 1462 Dihedral : 4.749 25.775 1154 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.61 % Allowed : 14.63 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 1020 helix: 1.61 (0.26), residues: 442 sheet: 0.07 (0.37), residues: 177 loop : -0.49 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 243 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.029 0.002 TYR R 148 ARG 0.004 0.000 ARG R 64 *********************** 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 121 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: R 64 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6855 (ptp-170) REVERT: R 215 ASP cc_start: 0.7984 (t0) cc_final: 0.7735 (t70) REVERT: R 286 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7638 (mm) REVERT: R 393 PHE cc_start: 0.7275 (m-80) cc_final: 0.7052 (m-80) REVERT: A 209 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6803 (tt0) REVERT: A 213 GLN cc_start: 0.6666 (mm-40) cc_final: 0.6394 (mm-40) REVERT: A 255 MET cc_start: 0.5776 (mtp) cc_final: 0.5520 (mtp) REVERT: A 283 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6801 (mtm180) REVERT: A 309 GLU cc_start: 0.5735 (mp0) cc_final: 0.5434 (mp0) REVERT: B 217 MET cc_start: 0.7373 (ptm) cc_final: 0.6304 (pmm) REVERT: B 325 MET cc_start: 0.6936 (mmm) cc_final: 0.6346 (mmm) REVERT: B 339 TRP cc_start: 0.6691 (m100) cc_final: 0.6085 (m-10) REVERT: G 21 MET cc_start: 0.2630 (OUTLIER) cc_final: 0.1929 (ttm) outliers start: 23 outliers final: 11 residues processed: 109 average time/residue: 1.0253 time to fit residues: 120.5503 Evaluate side-chains 102 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 283 ARG Chi-restraints excluded: chain A residue 386 MET 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 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.226455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.190161 restraints weight = 9385.025| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.85 r_work: 0.4050 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8492 Z= 0.172 Angle : 0.521 7.580 11519 Z= 0.281 Chirality : 0.041 0.174 1269 Planarity : 0.004 0.045 1462 Dihedral : 4.684 25.830 1154 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.15 % Allowed : 15.99 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.27), residues: 1020 helix: 1.75 (0.26), residues: 443 sheet: 0.09 (0.37), residues: 179 loop : -0.45 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 243 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.001 PHE B 241 TYR 0.028 0.002 TYR R 148 ARG 0.005 0.000 ARG R 64 *********************** 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 105 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: R 393 PHE cc_start: 0.7271 (m-80) cc_final: 0.6704 (m-80) REVERT: A 209 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6831 (tt0) REVERT: A 220 HIS cc_start: 0.7825 (t-170) cc_final: 0.7420 (t-170) REVERT: A 255 MET cc_start: 0.5880 (mtp) cc_final: 0.5661 (mtp) REVERT: A 262 GLN cc_start: 0.6572 (tt0) cc_final: 0.6317 (mt0) REVERT: A 271 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6371 (ptmt) REVERT: A 283 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6771 (mtm180) REVERT: A 309 GLU cc_start: 0.5805 (mp0) cc_final: 0.5490 (mp0) REVERT: B 87 THR cc_start: 0.6898 (OUTLIER) cc_final: 0.6617 (m) REVERT: B 325 MET cc_start: 0.6960 (mmm) cc_final: 0.6568 (mmm) REVERT: B 339 TRP cc_start: 0.6561 (m100) cc_final: 0.6291 (m-10) outliers start: 19 outliers final: 8 residues processed: 97 average time/residue: 1.0267 time to fit residues: 107.5396 Evaluate side-chains 90 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 30 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 48 optimal weight: 0.0370 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.2980 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 75 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 = 0.4510 r_free = 0.4510 target = 0.228812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.192964 restraints weight = 9474.094| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 1.83 r_work: 0.4075 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8492 Z= 0.143 Angle : 0.505 7.800 11519 Z= 0.272 Chirality : 0.041 0.195 1269 Planarity : 0.003 0.044 1462 Dihedral : 4.515 24.661 1154 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.15 % Allowed : 16.67 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1020 helix: 1.98 (0.26), residues: 438 sheet: 0.37 (0.38), residues: 171 loop : -0.44 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 306 HIS 0.003 0.001 HIS A 357 PHE 0.018 0.001 PHE B 241 TYR 0.027 0.002 TYR R 148 ARG 0.004 0.000 ARG R 64 *********************** 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 106 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 64 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6765 (ptp-170) REVERT: R 69 TYR cc_start: 0.7700 (t80) cc_final: 0.7308 (t80) REVERT: R 71 CYS cc_start: 0.4039 (p) cc_final: 0.3812 (t) REVERT: R 88 TYR cc_start: 0.7175 (p90) cc_final: 0.6898 (p90) REVERT: R 222 ASP cc_start: 0.7786 (p0) cc_final: 0.7448 (p0) REVERT: R 393 PHE cc_start: 0.7210 (m-80) cc_final: 0.6681 (m-80) REVERT: A 255 MET cc_start: 0.5840 (mtp) cc_final: 0.5624 (mtp) REVERT: A 262 GLN cc_start: 0.6564 (tt0) cc_final: 0.6346 (mt0) REVERT: A 271 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6406 (ptmt) REVERT: A 283 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6739 (mtm180) REVERT: A 339 TYR cc_start: 0.7225 (m-80) cc_final: 0.6914 (m-80) REVERT: A 372 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7369 (pt) REVERT: B 325 MET cc_start: 0.7105 (mmm) cc_final: 0.6217 (mmm) REVERT: B 339 TRP cc_start: 0.6465 (m100) cc_final: 0.6233 (m-10) outliers start: 19 outliers final: 9 residues processed: 98 average time/residue: 1.0743 time to fit residues: 113.5596 Evaluate side-chains 94 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 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 43 ILE 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 67 optimal weight: 6.9990 chunk 23 optimal weight: 0.0970 chunk 92 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 96 optimal weight: 0.0570 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 75 GLN 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 = 0.4509 r_free = 0.4509 target = 0.228968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.192847 restraints weight = 9410.945| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 1.86 r_work: 0.4078 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8492 Z= 0.144 Angle : 0.503 8.395 11519 Z= 0.273 Chirality : 0.041 0.169 1269 Planarity : 0.003 0.047 1462 Dihedral : 4.468 24.580 1154 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.93 % Allowed : 17.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.27), residues: 1020 helix: 2.02 (0.26), residues: 438 sheet: 0.55 (0.38), residues: 176 loop : -0.45 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 306 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.001 PHE B 241 TYR 0.027 0.002 TYR R 148 ARG 0.006 0.000 ARG R 380 *********************** 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 104 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 222 ASP cc_start: 0.7778 (p0) cc_final: 0.7542 (p0) REVERT: R 393 PHE cc_start: 0.7199 (m-80) cc_final: 0.6664 (m-80) REVERT: A 255 MET cc_start: 0.5764 (mtp) cc_final: 0.5434 (mtp) REVERT: A 262 GLN cc_start: 0.6618 (tt0) cc_final: 0.6415 (mt0) REVERT: A 271 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6390 (ptmt) REVERT: A 283 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6754 (mtm180) REVERT: A 339 TYR cc_start: 0.7193 (m-80) cc_final: 0.6922 (m-80) REVERT: A 372 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7422 (pt) REVERT: B 156 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6913 (tt0) REVERT: B 325 MET cc_start: 0.6918 (mmm) cc_final: 0.6320 (mmm) REVERT: B 339 TRP cc_start: 0.6435 (m100) cc_final: 0.6166 (m-10) outliers start: 17 outliers final: 9 residues processed: 97 average time/residue: 1.2259 time to fit residues: 128.1928 Evaluate side-chains 95 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 A residue 372 ILE 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 156 GLN Chi-restraints excluded: chain B residue 303 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 50 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 64 optimal weight: 0.0970 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4481 r_free = 0.4481 target = 0.225652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.189007 restraints weight = 9555.559| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.88 r_work: 0.4038 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8492 Z= 0.203 Angle : 0.550 8.014 11519 Z= 0.296 Chirality : 0.043 0.174 1269 Planarity : 0.004 0.048 1462 Dihedral : 4.655 26.172 1154 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.15 % Allowed : 18.25 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 1020 helix: 1.93 (0.26), residues: 442 sheet: 0.54 (0.38), residues: 178 loop : -0.37 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 306 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.002 PHE B 241 TYR 0.028 0.002 TYR R 148 ARG 0.005 0.000 ARG A 38 *********************** 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 108 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 393 PHE cc_start: 0.7263 (m-80) cc_final: 0.7045 (m-80) REVERT: A 255 MET cc_start: 0.5883 (mtp) cc_final: 0.5658 (mtp) REVERT: A 262 GLN cc_start: 0.6802 (tt0) cc_final: 0.6550 (mt0) REVERT: A 271 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6412 (ptmt) REVERT: A 283 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6829 (mtm180) REVERT: A 311 TYR cc_start: 0.5883 (m-80) cc_final: 0.4866 (t80) REVERT: B 87 THR cc_start: 0.6610 (m) cc_final: 0.6407 (m) REVERT: B 325 MET cc_start: 0.6970 (mmm) cc_final: 0.6443 (mmm) REVERT: B 339 TRP cc_start: 0.6442 (m100) cc_final: 0.6189 (m-10) outliers start: 19 outliers final: 11 residues processed: 103 average time/residue: 1.0692 time to fit residues: 118.4797 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 : 0.850 ------------------------------------------------------------------------------- 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 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 303 ASP 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 0 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.0000 chunk 47 optimal weight: 0.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** 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 = 0.4489 r_free = 0.4489 target = 0.226524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.190012 restraints weight = 9635.152| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 1.86 r_work: 0.4049 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8492 Z= 0.181 Angle : 0.547 8.979 11519 Z= 0.295 Chirality : 0.042 0.177 1269 Planarity : 0.004 0.047 1462 Dihedral : 4.659 26.032 1154 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.47 % Allowed : 19.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.27), residues: 1020 helix: 1.96 (0.26), residues: 441 sheet: 0.53 (0.38), residues: 178 loop : -0.43 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 306 HIS 0.005 0.001 HIS A 357 PHE 0.022 0.001 PHE B 241 TYR 0.028 0.002 TYR R 148 ARG 0.006 0.000 ARG B 49 *********************** 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: 13 poor density : 84 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 64 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6751 (ptp-170) REVERT: R 393 PHE cc_start: 0.7295 (m-80) cc_final: 0.7082 (m-80) REVERT: A 255 MET cc_start: 0.5898 (mtp) cc_final: 0.5667 (mtp) REVERT: A 283 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6767 (mtm180) REVERT: A 311 TYR cc_start: 0.5911 (m-80) cc_final: 0.4897 (t80) REVERT: B 75 GLN cc_start: 0.6581 (mm-40) cc_final: 0.6377 (mt0) REVERT: B 87 THR cc_start: 0.6622 (m) cc_final: 0.6380 (m) REVERT: B 325 MET cc_start: 0.6916 (mmm) cc_final: 0.6380 (mmm) REVERT: B 339 TRP cc_start: 0.6444 (m100) cc_final: 0.6189 (m-10) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 1.1418 time to fit residues: 113.7041 Evaluate side-chains 91 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 ARG 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 386 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 97 optimal weight: 0.0020 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- 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 ** 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 = 0.4492 r_free = 0.4492 target = 0.227012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.190754 restraints weight = 9523.033| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 1.84 r_work: 0.4058 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3937 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8492 Z= 0.166 Angle : 0.543 8.731 11519 Z= 0.293 Chirality : 0.042 0.178 1269 Planarity : 0.004 0.047 1462 Dihedral : 4.602 25.834 1154 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.13 % Allowed : 20.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.27), residues: 1020 helix: 1.99 (0.26), residues: 441 sheet: 0.64 (0.39), residues: 176 loop : -0.42 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 306 HIS 0.005 0.001 HIS A 357 PHE 0.022 0.001 PHE B 241 TYR 0.027 0.002 TYR R 148 ARG 0.010 0.000 ARG R 380 ********************** 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 98 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 393 PHE cc_start: 0.7282 (m-80) cc_final: 0.7071 (m-80) REVERT: A 255 MET cc_start: 0.5897 (mtp) cc_final: 0.5661 (mtp) REVERT: A 283 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6767 (mtm180) REVERT: A 311 TYR cc_start: 0.5948 (m-80) cc_final: 0.4944 (t80) REVERT: A 339 TYR cc_start: 0.7267 (m-80) cc_final: 0.7054 (m-80) REVERT: B 87 THR cc_start: 0.6515 (m) cc_final: 0.6254 (m) REVERT: B 325 MET cc_start: 0.6906 (mmm) cc_final: 0.6392 (mmm) REVERT: B 339 TRP cc_start: 0.6437 (m100) cc_final: 0.6223 (m-10) outliers start: 10 outliers final: 9 residues processed: 93 average time/residue: 1.1203 time to fit residues: 112.6284 Evaluate side-chains 93 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 386 MET 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 303 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 16 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** 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 = 0.4468 r_free = 0.4468 target = 0.224181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.187630 restraints weight = 9614.583| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 1.84 r_work: 0.4039 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3921 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8492 Z= 0.230 Angle : 0.595 8.422 11519 Z= 0.321 Chirality : 0.044 0.180 1269 Planarity : 0.004 0.049 1462 Dihedral : 4.850 27.191 1154 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.59 % Allowed : 20.18 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.27), residues: 1020 helix: 1.78 (0.26), residues: 443 sheet: 0.34 (0.39), residues: 182 loop : -0.44 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP R 306 HIS 0.007 0.001 HIS A 357 PHE 0.025 0.002 PHE B 241 TYR 0.029 0.002 TYR R 148 ARG 0.014 0.001 ARG R 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7190.70 seconds wall clock time: 125 minutes 14.28 seconds (7514.28 seconds total)