Starting phenix.real_space_refine on Wed Feb 4 10:01:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e4c_47505/02_2026/9e4c_47505.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e4c_47505/02_2026/9e4c_47505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e4c_47505/02_2026/9e4c_47505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e4c_47505/02_2026/9e4c_47505.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e4c_47505/02_2026/9e4c_47505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e4c_47505/02_2026/9e4c_47505.map" } resolution = 3.41 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= 0.011 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: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 6210 2.51 5 N 1605 2.21 5 O 1827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9729 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3243 Classifications: {'peptide': 404} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 385} Chain: "B" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3243 Classifications: {'peptide': 404} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 385} Chain: "C" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3243 Classifications: {'peptide': 404} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 385} Time building chain proxies: 2.30, per 1000 atoms: 0.24 Number of scatterers: 9729 At special positions: 0 Unit cell: (97.06, 97.06, 130.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 1827 8.00 N 1605 7.00 C 6210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.02 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " 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: 0.78 Conformation dependent library (CDL) restraints added in 483.6 milliseconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 39.7% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 40 through 69 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.723A pdb=" N LYS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 357 through 361 removed outlier: 4.168A pdb=" N CYS A 361 " --> pdb=" O GLN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.784A pdb=" N LYS A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 removed outlier: 3.687A pdb=" N GLY A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 443 Processing helix chain 'B' and resid 41 through 69 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.728A pdb=" N LYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.857A pdb=" N CYS B 361 " --> pdb=" O GLN B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 394 removed outlier: 4.490A pdb=" N LYS B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 403 removed outlier: 4.002A pdb=" N GLY B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 443 removed outlier: 3.838A pdb=" N LEU B 441 " --> pdb=" O GLY B 437 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 69 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.919A pdb=" N LYS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 357 Processing helix chain 'C' and resid 358 through 361 removed outlier: 3.996A pdb=" N CYS C 361 " --> pdb=" O GLN C 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 358 through 361' Processing helix chain 'C' and resid 386 through 395 Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.951A pdb=" N GLY C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 81 removed outlier: 12.851A pdb=" N ASN A 416 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N CYS A 275 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N GLU A 418 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLU A 277 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE A 420 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG A 279 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N GLN A 422 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE A 281 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N LYS A 424 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 179 removed outlier: 4.067A pdb=" N CYS A 172 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU A 169 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP A 223 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE A 269 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 407 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189 removed outlier: 6.899A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A 245 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 81 removed outlier: 12.947A pdb=" N ASN B 416 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N CYS B 275 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N GLU B 418 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU B 277 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE B 420 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ARG B 279 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLN B 422 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 281 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N LYS B 424 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE B 269 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 407 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASP B 223 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU B 169 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 81 removed outlier: 12.947A pdb=" N ASN B 416 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N CYS B 275 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N GLU B 418 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU B 277 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE B 420 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ARG B 279 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLN B 422 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 281 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N LYS B 424 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 189 removed outlier: 6.817A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 245 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 81 removed outlier: 7.717A pdb=" N ASN C 416 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU C 277 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 177 through 178 removed outlier: 5.906A pdb=" N LEU C 169 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP C 223 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE C 269 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL C 407 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 189 removed outlier: 6.788A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE C 245 " --> pdb=" O VAL C 265 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1320 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: 1.60 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3177 1.35 - 1.47: 2374 1.47 - 1.59: 4286 1.59 - 1.71: 0 1.71 - 1.82: 120 Bond restraints: 9957 Sorted by residual: bond pdb=" C VAL C 265 " pdb=" N ALA C 266 " ideal model delta sigma weight residual 1.333 1.307 0.026 2.74e-02 1.33e+03 8.77e-01 bond pdb=" CA ILE B 381 " pdb=" C ILE B 381 " ideal model delta sigma weight residual 1.524 1.516 0.009 1.05e-02 9.07e+03 7.15e-01 bond pdb=" C ASN C 216 " pdb=" N GLY C 217 " ideal model delta sigma weight residual 1.333 1.324 0.009 1.10e-02 8.26e+03 6.35e-01 bond pdb=" CA GLY C 234 " pdb=" C GLY C 234 " ideal model delta sigma weight residual 1.515 1.508 0.007 9.30e-03 1.16e+04 6.09e-01 bond pdb=" CA ILE A 381 " pdb=" C ILE A 381 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.05e-02 9.07e+03 5.97e-01 ... (remaining 9952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 13101 1.40 - 2.80: 283 2.80 - 4.19: 62 4.19 - 5.59: 8 5.59 - 6.99: 4 Bond angle restraints: 13458 Sorted by residual: angle pdb=" CA CYS A 172 " pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " ideal model delta sigma weight residual 114.40 120.16 -5.76 2.30e+00 1.89e-01 6.28e+00 angle pdb=" CA CYS C 172 " pdb=" CB CYS C 172 " pdb=" SG CYS C 172 " ideal model delta sigma weight residual 114.40 120.15 -5.75 2.30e+00 1.89e-01 6.25e+00 angle pdb=" CA CYS B 172 " pdb=" CB CYS B 172 " pdb=" SG CYS B 172 " ideal model delta sigma weight residual 114.40 119.94 -5.54 2.30e+00 1.89e-01 5.81e+00 angle pdb=" N TYR B 229 " pdb=" CA TYR B 229 " pdb=" C TYR B 229 " ideal model delta sigma weight residual 110.35 113.61 -3.26 1.36e+00 5.41e-01 5.73e+00 angle pdb=" N PHE A 257 " pdb=" CA PHE A 257 " pdb=" C PHE A 257 " ideal model delta sigma weight residual 110.44 107.60 2.84 1.20e+00 6.94e-01 5.62e+00 ... (remaining 13453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 5458 16.65 - 33.29: 462 33.29 - 49.94: 78 49.94 - 66.59: 31 66.59 - 83.23: 13 Dihedral angle restraints: 6042 sinusoidal: 2499 harmonic: 3543 Sorted by residual: dihedral pdb=" CB CYS C 290 " pdb=" SG CYS C 290 " pdb=" SG CYS C 367 " pdb=" CB CYS C 367 " ideal model delta sinusoidal sigma weight residual -86.00 -147.03 61.03 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS B 290 " pdb=" SG CYS B 290 " pdb=" SG CYS B 367 " pdb=" CB CYS B 367 " ideal model delta sinusoidal sigma weight residual -86.00 -143.46 57.46 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS A 290 " pdb=" SG CYS A 290 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual -86.00 -142.27 56.27 1 1.00e+01 1.00e-02 4.27e+01 ... (remaining 6039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 985 0.034 - 0.069: 340 0.069 - 0.103: 84 0.103 - 0.137: 21 0.137 - 0.172: 7 Chirality restraints: 1437 Sorted by residual: chirality pdb=" CB THR B 289 " pdb=" CA THR B 289 " pdb=" OG1 THR B 289 " pdb=" CG2 THR B 289 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CB ILE B 220 " pdb=" CA ILE B 220 " pdb=" CG1 ILE B 220 " pdb=" CG2 ILE B 220 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA ILE B 124 " pdb=" N ILE B 124 " pdb=" C ILE B 124 " pdb=" CB ILE B 124 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 1434 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 229 " -0.017 2.00e-02 2.50e+03 9.48e-03 1.80e+00 pdb=" CG TYR B 229 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 229 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 229 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 229 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 229 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 229 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 229 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 179 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.29e+00 pdb=" C CYS B 179 " 0.020 2.00e-02 2.50e+03 pdb=" O CYS B 179 " -0.007 2.00e-02 2.50e+03 pdb=" N SER B 180 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 148 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO A 149 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " 0.015 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 879 2.75 - 3.28: 10008 3.28 - 3.82: 15871 3.82 - 4.36: 19069 4.36 - 4.90: 32929 Nonbonded interactions: 78756 Sorted by model distance: nonbonded pdb=" OE1 GLU B 235 " pdb=" OH TYR C 389 " model vdw 2.208 3.040 nonbonded pdb=" NE2 GLN A 422 " pdb=" OD1 ASP B 78 " model vdw 2.246 3.120 nonbonded pdb=" OE1 GLU A 235 " pdb=" OH TYR B 389 " model vdw 2.249 3.040 nonbonded pdb=" O HIS B 163 " pdb=" OH TYR B 195 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR A 426 " pdb=" OD2 ASP A 434 " model vdw 2.274 3.040 ... (remaining 78751 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.360 Find NCS groups from input model: 0.130 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 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 : 0.002 0.034 9978 Z= 0.119 Angle : 0.548 6.989 13500 Z= 0.303 Chirality : 0.039 0.172 1437 Planarity : 0.003 0.028 1758 Dihedral : 13.152 83.232 3705 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.87 (0.25), residues: 1206 helix: 2.27 (0.28), residues: 333 sheet: -1.25 (0.27), residues: 318 loop : 0.89 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.020 0.001 TYR B 229 PHE 0.011 0.001 PHE A 257 TRP 0.008 0.001 TRP B 233 HIS 0.002 0.001 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9957) covalent geometry : angle 0.54236 (13458) SS BOND : bond 0.00261 ( 21) SS BOND : angle 1.53888 ( 42) hydrogen bonds : bond 0.21759 ( 465) hydrogen bonds : angle 9.12580 ( 1320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.6302 (m-10) cc_final: 0.5963 (m-10) REVERT: A 210 MET cc_start: 0.8569 (mpp) cc_final: 0.7987 (mmm) REVERT: A 431 LEU cc_start: 0.9224 (tp) cc_final: 0.8955 (pp) REVERT: B 70 HIS cc_start: 0.8610 (m-70) cc_final: 0.8338 (m90) REVERT: B 330 MET cc_start: 0.9156 (mtt) cc_final: 0.8942 (mtp) REVERT: C 327 MET cc_start: 0.8797 (mtm) cc_final: 0.8422 (mtp) REVERT: C 330 MET cc_start: 0.8991 (mtt) cc_final: 0.8546 (mtt) REVERT: C 352 PHE cc_start: 0.9510 (t80) cc_final: 0.9230 (t80) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1156 time to fit residues: 19.8766 Evaluate side-chains 75 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 117 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS B 70 HIS ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.095104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.069350 restraints weight = 31246.653| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 4.05 r_work: 0.3213 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9978 Z= 0.216 Angle : 0.649 11.314 13500 Z= 0.331 Chirality : 0.045 0.182 1437 Planarity : 0.004 0.037 1758 Dihedral : 4.605 18.152 1323 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.04 % Allowed : 5.56 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.53 (0.24), residues: 1206 helix: 1.61 (0.26), residues: 381 sheet: -1.23 (0.26), residues: 312 loop : 0.67 (0.30), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 204 TYR 0.015 0.001 TYR B 389 PHE 0.020 0.001 PHE C 50 TRP 0.015 0.001 TRP B 287 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 9957) covalent geometry : angle 0.64603 (13458) SS BOND : bond 0.00399 ( 21) SS BOND : angle 1.21522 ( 42) hydrogen bonds : bond 0.04750 ( 465) hydrogen bonds : angle 6.62575 ( 1320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8716 (mpp) cc_final: 0.8090 (mmm) REVERT: A 330 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8821 (mtp) REVERT: A 426 TYR cc_start: 0.7758 (t80) cc_final: 0.7205 (t80) REVERT: B 330 MET cc_start: 0.9345 (mtt) cc_final: 0.9104 (mtp) REVERT: B 378 MET cc_start: 0.8604 (ptp) cc_final: 0.8175 (ptp) REVERT: C 70 HIS cc_start: 0.8767 (m90) cc_final: 0.8487 (m90) REVERT: C 129 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7681 (mmm) REVERT: C 327 MET cc_start: 0.8913 (mtm) cc_final: 0.8483 (mtp) REVERT: C 330 MET cc_start: 0.9196 (mtt) cc_final: 0.8570 (mtt) REVERT: C 352 PHE cc_start: 0.9613 (t80) cc_final: 0.9317 (t80) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 0.0985 time to fit residues: 11.9093 Evaluate side-chains 75 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 442 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 64 optimal weight: 0.3980 chunk 24 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 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 = 0.3882 r_free = 0.3882 target = 0.096401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.069076 restraints weight = 31224.528| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 4.16 r_work: 0.3169 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9978 Z= 0.115 Angle : 0.578 12.202 13500 Z= 0.287 Chirality : 0.042 0.158 1437 Planarity : 0.003 0.026 1758 Dihedral : 4.357 18.012 1323 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.94 % Allowed : 8.57 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.69 (0.24), residues: 1206 helix: 1.64 (0.26), residues: 390 sheet: -1.09 (0.26), residues: 309 loop : 0.79 (0.30), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 145 TYR 0.010 0.001 TYR B 417 PHE 0.020 0.001 PHE C 50 TRP 0.008 0.001 TRP B 287 HIS 0.002 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9957) covalent geometry : angle 0.57655 (13458) SS BOND : bond 0.00279 ( 21) SS BOND : angle 0.83663 ( 42) hydrogen bonds : bond 0.04047 ( 465) hydrogen bonds : angle 6.13398 ( 1320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.8164 (mmp80) cc_final: 0.7602 (ptp-110) REVERT: A 210 MET cc_start: 0.8715 (mpp) cc_final: 0.8059 (mmm) REVERT: A 330 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8602 (mtp) REVERT: A 409 ASP cc_start: 0.8581 (t0) cc_final: 0.8328 (t0) REVERT: B 330 MET cc_start: 0.9348 (mtt) cc_final: 0.9100 (mtp) REVERT: C 70 HIS cc_start: 0.8833 (m90) cc_final: 0.8522 (m90) REVERT: C 129 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7684 (mmm) REVERT: C 327 MET cc_start: 0.8884 (mtm) cc_final: 0.8506 (mtp) REVERT: C 330 MET cc_start: 0.9159 (mtt) cc_final: 0.8590 (mtt) REVERT: C 352 PHE cc_start: 0.9614 (t80) cc_final: 0.9346 (t80) outliers start: 10 outliers final: 4 residues processed: 81 average time/residue: 0.1010 time to fit residues: 11.9245 Evaluate side-chains 74 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 442 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 108 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.092834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.068851 restraints weight = 30052.247| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.88 r_work: 0.3139 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 9978 Z= 0.214 Angle : 0.597 10.738 13500 Z= 0.299 Chirality : 0.042 0.155 1437 Planarity : 0.003 0.025 1758 Dihedral : 4.414 17.592 1323 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.79 % Allowed : 9.79 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.74 (0.25), residues: 1206 helix: 1.74 (0.26), residues: 390 sheet: -1.08 (0.26), residues: 309 loop : 0.77 (0.30), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 145 TYR 0.011 0.001 TYR B 417 PHE 0.016 0.001 PHE B 301 TRP 0.007 0.001 TRP A 233 HIS 0.003 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 9957) covalent geometry : angle 0.59589 (13458) SS BOND : bond 0.00391 ( 21) SS BOND : angle 0.88827 ( 42) hydrogen bonds : bond 0.03853 ( 465) hydrogen bonds : angle 5.88911 ( 1320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8701 (mpp) cc_final: 0.8089 (mmm) REVERT: A 330 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8790 (mtp) REVERT: B 70 HIS cc_start: 0.9090 (m90) cc_final: 0.8847 (m90) REVERT: B 330 MET cc_start: 0.9341 (mtt) cc_final: 0.9111 (mtp) REVERT: C 70 HIS cc_start: 0.8837 (m90) cc_final: 0.8503 (m90) REVERT: C 129 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7645 (mmm) REVERT: C 327 MET cc_start: 0.8777 (mtm) cc_final: 0.8438 (mtp) REVERT: C 330 MET cc_start: 0.9201 (mtt) cc_final: 0.8535 (mtt) REVERT: C 352 PHE cc_start: 0.9596 (t80) cc_final: 0.9342 (t80) outliers start: 19 outliers final: 10 residues processed: 82 average time/residue: 0.0925 time to fit residues: 11.4268 Evaluate side-chains 77 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 442 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 24 optimal weight: 0.0370 chunk 9 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.097221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069566 restraints weight = 31339.084| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.19 r_work: 0.3147 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9978 Z= 0.137 Angle : 0.565 11.371 13500 Z= 0.280 Chirality : 0.041 0.152 1437 Planarity : 0.003 0.026 1758 Dihedral : 4.389 20.255 1323 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.69 % Allowed : 10.92 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.76 (0.25), residues: 1206 helix: 1.58 (0.26), residues: 408 sheet: -1.00 (0.27), residues: 291 loop : 0.79 (0.30), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.010 0.001 TYR B 417 PHE 0.017 0.001 PHE C 50 TRP 0.006 0.001 TRP A 233 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9957) covalent geometry : angle 0.56232 (13458) SS BOND : bond 0.00285 ( 21) SS BOND : angle 1.13945 ( 42) hydrogen bonds : bond 0.03597 ( 465) hydrogen bonds : angle 5.77981 ( 1320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8699 (mpp) cc_final: 0.8054 (mmm) REVERT: A 330 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8869 (mtp) REVERT: A 409 ASP cc_start: 0.8567 (t0) cc_final: 0.8297 (t0) REVERT: B 70 HIS cc_start: 0.9083 (m90) cc_final: 0.8768 (m90) REVERT: B 330 MET cc_start: 0.9356 (mtt) cc_final: 0.9103 (mtp) REVERT: C 58 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9390 (pp) REVERT: C 70 HIS cc_start: 0.8847 (m90) cc_final: 0.8490 (m90) REVERT: C 129 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7622 (mmm) REVERT: C 327 MET cc_start: 0.8724 (mtm) cc_final: 0.8452 (mtp) REVERT: C 330 MET cc_start: 0.9197 (mtt) cc_final: 0.8576 (mtt) REVERT: C 352 PHE cc_start: 0.9599 (t80) cc_final: 0.9362 (t80) REVERT: C 439 MET cc_start: 0.9350 (tmm) cc_final: 0.9083 (tmm) outliers start: 18 outliers final: 9 residues processed: 81 average time/residue: 0.0859 time to fit residues: 10.4864 Evaluate side-chains 78 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 442 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 98 optimal weight: 0.0870 chunk 70 optimal weight: 5.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.097304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.069859 restraints weight = 31545.016| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 4.20 r_work: 0.3167 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9978 Z= 0.114 Angle : 0.544 11.407 13500 Z= 0.270 Chirality : 0.041 0.168 1437 Planarity : 0.003 0.026 1758 Dihedral : 4.242 17.258 1323 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.51 % Allowed : 11.11 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.84 (0.25), residues: 1206 helix: 1.76 (0.26), residues: 405 sheet: -1.00 (0.27), residues: 291 loop : 0.76 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 64 TYR 0.010 0.001 TYR B 417 PHE 0.011 0.001 PHE C 50 TRP 0.006 0.001 TRP B 287 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9957) covalent geometry : angle 0.54151 (13458) SS BOND : bond 0.00286 ( 21) SS BOND : angle 1.12766 ( 42) hydrogen bonds : bond 0.03395 ( 465) hydrogen bonds : angle 5.63662 ( 1320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8736 (mpp) cc_final: 0.8074 (mmm) REVERT: A 330 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8873 (mtp) REVERT: A 409 ASP cc_start: 0.8544 (t0) cc_final: 0.8278 (t0) REVERT: B 204 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7705 (mtm180) REVERT: B 330 MET cc_start: 0.9337 (mtt) cc_final: 0.9087 (mtp) REVERT: C 46 TRP cc_start: 0.7584 (t60) cc_final: 0.6314 (t60) REVERT: C 70 HIS cc_start: 0.8834 (m90) cc_final: 0.8523 (m90) REVERT: C 129 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7548 (mmm) REVERT: C 327 MET cc_start: 0.8725 (mtm) cc_final: 0.8367 (mtp) REVERT: C 330 MET cc_start: 0.9165 (mtt) cc_final: 0.8562 (mtt) REVERT: C 352 PHE cc_start: 0.9583 (t80) cc_final: 0.9362 (t80) REVERT: C 439 MET cc_start: 0.9347 (tmm) cc_final: 0.9132 (tmm) outliers start: 16 outliers final: 10 residues processed: 83 average time/residue: 0.0782 time to fit residues: 9.5900 Evaluate side-chains 81 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 442 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.095016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.070449 restraints weight = 29488.208| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.95 r_work: 0.3165 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9978 Z= 0.148 Angle : 0.570 13.194 13500 Z= 0.277 Chirality : 0.041 0.178 1437 Planarity : 0.003 0.033 1758 Dihedral : 4.208 16.531 1323 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.41 % Allowed : 11.58 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.25), residues: 1206 helix: 1.79 (0.26), residues: 405 sheet: -0.98 (0.28), residues: 291 loop : 0.73 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 64 TYR 0.010 0.001 TYR A 195 PHE 0.008 0.001 PHE C 157 TRP 0.009 0.001 TRP C 46 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9957) covalent geometry : angle 0.56759 (13458) SS BOND : bond 0.00310 ( 21) SS BOND : angle 1.04917 ( 42) hydrogen bonds : bond 0.03325 ( 465) hydrogen bonds : angle 5.57629 ( 1320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8702 (mpp) cc_final: 0.8054 (mmm) REVERT: A 330 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8895 (mtp) REVERT: A 409 ASP cc_start: 0.8577 (t0) cc_final: 0.8375 (t0) REVERT: B 70 HIS cc_start: 0.9070 (m90) cc_final: 0.8787 (m90) REVERT: B 204 ARG cc_start: 0.8099 (mtm110) cc_final: 0.7662 (mtm180) REVERT: B 330 MET cc_start: 0.9329 (mtt) cc_final: 0.9081 (mtp) REVERT: C 129 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7504 (mmm) REVERT: C 327 MET cc_start: 0.8708 (mtm) cc_final: 0.8352 (mtp) REVERT: C 330 MET cc_start: 0.9174 (mtt) cc_final: 0.8553 (mtt) REVERT: C 352 PHE cc_start: 0.9571 (t80) cc_final: 0.9350 (t80) REVERT: C 439 MET cc_start: 0.9347 (tmm) cc_final: 0.9097 (tmm) outliers start: 15 outliers final: 11 residues processed: 82 average time/residue: 0.0781 time to fit residues: 9.4902 Evaluate side-chains 78 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 442 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 25 optimal weight: 0.3980 chunk 46 optimal weight: 0.0870 chunk 66 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.096817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.069078 restraints weight = 31498.157| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 4.20 r_work: 0.3163 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9978 Z= 0.124 Angle : 0.569 13.044 13500 Z= 0.273 Chirality : 0.041 0.181 1437 Planarity : 0.003 0.034 1758 Dihedral : 4.126 16.455 1323 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.32 % Allowed : 11.96 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.25), residues: 1206 helix: 1.79 (0.26), residues: 405 sheet: -1.00 (0.28), residues: 291 loop : 0.71 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 145 TYR 0.009 0.001 TYR A 195 PHE 0.006 0.001 PHE C 394 TRP 0.005 0.001 TRP B 287 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9957) covalent geometry : angle 0.56710 (13458) SS BOND : bond 0.00279 ( 21) SS BOND : angle 0.96102 ( 42) hydrogen bonds : bond 0.03259 ( 465) hydrogen bonds : angle 5.53266 ( 1320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8719 (mpp) cc_final: 0.8157 (mmt) REVERT: A 330 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8907 (mtp) REVERT: A 409 ASP cc_start: 0.8535 (t0) cc_final: 0.8214 (t0) REVERT: B 70 HIS cc_start: 0.9110 (m90) cc_final: 0.8812 (m90) REVERT: B 204 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7631 (mtm180) REVERT: B 330 MET cc_start: 0.9336 (mtt) cc_final: 0.9081 (mtp) REVERT: C 70 HIS cc_start: 0.8814 (m90) cc_final: 0.8581 (m90) REVERT: C 129 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7331 (mmm) REVERT: C 327 MET cc_start: 0.8732 (mtm) cc_final: 0.8381 (mtp) REVERT: C 330 MET cc_start: 0.9168 (mtt) cc_final: 0.8579 (mtt) REVERT: C 352 PHE cc_start: 0.9573 (t80) cc_final: 0.9362 (t80) REVERT: C 439 MET cc_start: 0.9322 (tmm) cc_final: 0.9048 (tmm) outliers start: 14 outliers final: 12 residues processed: 79 average time/residue: 0.0969 time to fit residues: 11.1309 Evaluate side-chains 82 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 442 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 73 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 38 optimal weight: 0.0370 chunk 70 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 31 optimal weight: 5.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.098525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.071085 restraints weight = 31131.175| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 4.19 r_work: 0.3195 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9978 Z= 0.099 Angle : 0.554 12.966 13500 Z= 0.266 Chirality : 0.041 0.229 1437 Planarity : 0.003 0.033 1758 Dihedral : 4.008 16.244 1323 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.41 % Allowed : 12.05 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.87 (0.25), residues: 1206 helix: 1.87 (0.27), residues: 405 sheet: -0.98 (0.28), residues: 291 loop : 0.70 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.010 0.001 TYR B 417 PHE 0.005 0.001 PHE B 152 TRP 0.005 0.001 TRP B 287 HIS 0.003 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9957) covalent geometry : angle 0.55273 (13458) SS BOND : bond 0.00226 ( 21) SS BOND : angle 0.87379 ( 42) hydrogen bonds : bond 0.03100 ( 465) hydrogen bonds : angle 5.41202 ( 1320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.8666 (mpp) cc_final: 0.8003 (mmm) REVERT: A 330 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8884 (mtp) REVERT: A 409 ASP cc_start: 0.8510 (t0) cc_final: 0.8230 (t0) REVERT: B 70 HIS cc_start: 0.9122 (m90) cc_final: 0.8820 (m90) REVERT: B 204 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7662 (mtm180) REVERT: B 235 GLU cc_start: 0.7845 (tp30) cc_final: 0.7555 (tp30) REVERT: B 330 MET cc_start: 0.9341 (mtt) cc_final: 0.9107 (mtp) REVERT: B 439 MET cc_start: 0.9056 (ptt) cc_final: 0.8307 (tmm) REVERT: C 70 HIS cc_start: 0.8820 (m90) cc_final: 0.8572 (m90) REVERT: C 129 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7291 (mmm) REVERT: C 327 MET cc_start: 0.8695 (mtm) cc_final: 0.8304 (mtp) REVERT: C 330 MET cc_start: 0.9137 (mtt) cc_final: 0.8495 (mtt) REVERT: C 352 PHE cc_start: 0.9581 (t80) cc_final: 0.9375 (t80) REVERT: C 439 MET cc_start: 0.9338 (tmm) cc_final: 0.9068 (tmm) outliers start: 15 outliers final: 11 residues processed: 81 average time/residue: 0.0749 time to fit residues: 8.9206 Evaluate side-chains 78 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 442 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.0060 chunk 14 optimal weight: 4.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.098414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.071114 restraints weight = 31231.823| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 4.19 r_work: 0.3179 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9978 Z= 0.116 Angle : 0.572 13.203 13500 Z= 0.273 Chirality : 0.042 0.198 1437 Planarity : 0.003 0.035 1758 Dihedral : 4.000 15.922 1323 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.51 % Allowed : 12.05 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.90 (0.25), residues: 1206 helix: 1.88 (0.27), residues: 405 sheet: -0.98 (0.28), residues: 291 loop : 0.73 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 145 TYR 0.011 0.001 TYR B 158 PHE 0.007 0.001 PHE C 144 TRP 0.013 0.001 TRP B 233 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9957) covalent geometry : angle 0.57061 (13458) SS BOND : bond 0.00271 ( 21) SS BOND : angle 0.87049 ( 42) hydrogen bonds : bond 0.03075 ( 465) hydrogen bonds : angle 5.40778 ( 1320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8680 (mpp) cc_final: 0.8017 (mmm) REVERT: A 330 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8937 (mtp) REVERT: A 409 ASP cc_start: 0.8507 (t0) cc_final: 0.8185 (t0) REVERT: B 70 HIS cc_start: 0.9114 (m90) cc_final: 0.8808 (m90) REVERT: B 204 ARG cc_start: 0.8074 (mtm110) cc_final: 0.7659 (mtm180) REVERT: B 235 GLU cc_start: 0.7841 (tp30) cc_final: 0.7552 (tp30) REVERT: B 330 MET cc_start: 0.9342 (mtt) cc_final: 0.9092 (mtp) REVERT: C 70 HIS cc_start: 0.8823 (m90) cc_final: 0.8574 (m90) REVERT: C 129 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7282 (mmm) REVERT: C 327 MET cc_start: 0.8719 (mtm) cc_final: 0.8357 (mtp) REVERT: C 330 MET cc_start: 0.9141 (mtt) cc_final: 0.8587 (mtt) REVERT: C 439 MET cc_start: 0.9342 (tmm) cc_final: 0.9045 (tmm) outliers start: 16 outliers final: 13 residues processed: 77 average time/residue: 0.0922 time to fit residues: 10.1641 Evaluate side-chains 79 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 442 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.0670 chunk 96 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 61 optimal weight: 0.0970 chunk 41 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.098820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.071606 restraints weight = 31372.551| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 4.22 r_work: 0.3191 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9978 Z= 0.102 Angle : 0.559 13.226 13500 Z= 0.267 Chirality : 0.041 0.185 1437 Planarity : 0.003 0.029 1758 Dihedral : 3.956 15.892 1323 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.60 % Allowed : 12.05 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.25), residues: 1206 helix: 2.22 (0.27), residues: 387 sheet: -0.95 (0.27), residues: 309 loop : 0.73 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.012 0.001 TYR B 158 PHE 0.037 0.001 PHE C 352 TRP 0.009 0.001 TRP B 233 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9957) covalent geometry : angle 0.55796 (13458) SS BOND : bond 0.00231 ( 21) SS BOND : angle 0.83896 ( 42) hydrogen bonds : bond 0.02991 ( 465) hydrogen bonds : angle 5.35467 ( 1320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2097.21 seconds wall clock time: 36 minutes 41.67 seconds (2201.67 seconds total)