Starting phenix.real_space_refine on Fri Aug 22 20:45:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1e_35920/08_2025/8j1e_35920.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1e_35920/08_2025/8j1e_35920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j1e_35920/08_2025/8j1e_35920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1e_35920/08_2025/8j1e_35920.map" model { file = "/net/cci-nas-00/data/ceres_data/8j1e_35920/08_2025/8j1e_35920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1e_35920/08_2025/8j1e_35920.cif" } resolution = 3.84 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= 0.001 sd= 0.019 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 39 5.16 5 Cl 6 4.86 5 C 5184 2.51 5 N 1152 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7590 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2493 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 20, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' CL': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: C, B Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" CAA Y01 A 901 " occ=0.00 ... (33 atoms not shown) pdb=" OAW Y01 A 901 " occ=0.00 residue: pdb=" CAA Y01 C 901 " occ=0.00 ... (33 atoms not shown) pdb=" OAW Y01 C 901 " occ=0.00 residue: pdb=" CAA Y01 B 901 " occ=0.00 ... (33 atoms not shown) pdb=" OAW Y01 B 901 " occ=0.00 Time building chain proxies: 1.56, per 1000 atoms: 0.21 Number of scatterers: 7590 At special positions: 0 Unit cell: (105.84, 100.8, 66.36, 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) Cl 6 17.00 S 39 16.00 O 1209 8.00 N 1152 7.00 C 5184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.48 Conformation dependent library (CDL) restraints added in 332.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 73.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 191 through 209 removed outlier: 3.840A pdb=" N ILE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 250 removed outlier: 3.670A pdb=" N LEU A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.690A pdb=" N VAL A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.656A pdb=" N ASN A 265 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 266 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 280 removed outlier: 3.514A pdb=" N SER A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 317 removed outlier: 3.671A pdb=" N CYS A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 335 through 349 removed outlier: 4.121A pdb=" N PHE A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 373 removed outlier: 3.569A pdb=" N ALA A 354 " --> pdb=" O TRP A 350 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 368 " --> pdb=" O HIS A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.990A pdb=" N SER A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 409 removed outlier: 3.781A pdb=" N SER A 401 " --> pdb=" O PRO A 397 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 433 Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 448 through 463 removed outlier: 4.601A pdb=" N MET A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 456 " --> pdb=" O MET A 452 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 496 Processing helix chain 'C' and resid 191 through 209 removed outlier: 3.840A pdb=" N ILE C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS C 196 " --> pdb=" O CYS C 192 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN C 202 " --> pdb=" O GLY C 198 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 250 removed outlier: 3.670A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 removed outlier: 3.690A pdb=" N VAL C 254 " --> pdb=" O TYR C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 267 removed outlier: 3.656A pdb=" N ASN C 265 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE C 266 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 280 removed outlier: 3.514A pdb=" N SER C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 317 removed outlier: 3.671A pdb=" N CYS C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 335 through 349 removed outlier: 4.121A pdb=" N PHE C 339 " --> pdb=" O VAL C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 373 removed outlier: 3.570A pdb=" N ALA C 354 " --> pdb=" O TRP C 350 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS C 355 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 357 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL C 367 " --> pdb=" O ALA C 363 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 368 " --> pdb=" O HIS C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 386 through 391 removed outlier: 3.991A pdb=" N SER C 391 " --> pdb=" O HIS C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 409 removed outlier: 3.780A pdb=" N SER C 401 " --> pdb=" O PRO C 397 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN C 405 " --> pdb=" O SER C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 433 Processing helix chain 'C' and resid 442 through 447 Processing helix chain 'C' and resid 448 through 463 removed outlier: 4.601A pdb=" N MET C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER C 456 " --> pdb=" O MET C 452 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL C 457 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 496 Processing helix chain 'B' and resid 191 through 209 removed outlier: 3.840A pdb=" N ILE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 250 removed outlier: 3.670A pdb=" N LEU B 226 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE B 231 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 removed outlier: 3.689A pdb=" N VAL B 254 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 267 removed outlier: 3.655A pdb=" N ASN B 265 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 266 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 280 removed outlier: 3.513A pdb=" N SER B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 317 removed outlier: 3.670A pdb=" N CYS B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 335 through 349 removed outlier: 4.122A pdb=" N PHE B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 373 removed outlier: 3.569A pdb=" N ALA B 354 " --> pdb=" O TRP B 350 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 368 " --> pdb=" O HIS B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 386 through 391 removed outlier: 3.990A pdb=" N SER B 391 " --> pdb=" O HIS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 409 removed outlier: 3.782A pdb=" N SER B 401 " --> pdb=" O PRO B 397 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 433 Processing helix chain 'B' and resid 442 through 447 Processing helix chain 'B' and resid 448 through 463 removed outlier: 4.601A pdb=" N MET B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 456 " --> pdb=" O MET B 452 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B 457 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 496 420 hydrogen bonds defined for protein. 1224 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: 0.87 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1344 1.33 - 1.45: 2228 1.45 - 1.57: 4252 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 7878 Sorted by residual: bond pdb=" CAK Y01 A 901 " pdb=" CBD Y01 A 901 " ideal model delta sigma weight residual 1.525 1.452 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" CAK Y01 C 901 " pdb=" CBD Y01 C 901 " ideal model delta sigma weight residual 1.525 1.453 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" CAK Y01 B 901 " pdb=" CBD Y01 B 901 " ideal model delta sigma weight residual 1.525 1.453 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CBD Y01 C 901 " pdb=" CBF Y01 C 901 " ideal model delta sigma weight residual 1.536 1.473 0.063 2.00e-02 2.50e+03 9.91e+00 bond pdb=" CBD Y01 B 901 " pdb=" CBF Y01 B 901 " ideal model delta sigma weight residual 1.536 1.474 0.062 2.00e-02 2.50e+03 9.65e+00 ... (remaining 7873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 10651 2.39 - 4.79: 134 4.79 - 7.18: 21 7.18 - 9.58: 18 9.58 - 11.97: 12 Bond angle restraints: 10836 Sorted by residual: angle pdb=" CAK Y01 A 901 " pdb=" CAI Y01 A 901 " pdb=" CAZ Y01 A 901 " ideal model delta sigma weight residual 124.96 112.99 11.97 3.00e+00 1.11e-01 1.59e+01 angle pdb=" CAK Y01 B 901 " pdb=" CAI Y01 B 901 " pdb=" CAZ Y01 B 901 " ideal model delta sigma weight residual 124.96 113.00 11.96 3.00e+00 1.11e-01 1.59e+01 angle pdb=" CAK Y01 C 901 " pdb=" CAI Y01 C 901 " pdb=" CAZ Y01 C 901 " ideal model delta sigma weight residual 124.96 113.04 11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CAZ Y01 A 901 " pdb=" CAV Y01 A 901 " pdb=" CBC Y01 A 901 " ideal model delta sigma weight residual 111.19 99.91 11.28 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CAZ Y01 B 901 " pdb=" CAV Y01 B 901 " pdb=" CBC Y01 B 901 " ideal model delta sigma weight residual 111.19 99.92 11.27 3.00e+00 1.11e-01 1.41e+01 ... (remaining 10831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.09: 3854 13.09 - 26.19: 462 26.19 - 39.28: 166 39.28 - 52.38: 51 52.38 - 65.47: 15 Dihedral angle restraints: 4548 sinusoidal: 1728 harmonic: 2820 Sorted by residual: dihedral pdb=" CA PHE C 305 " pdb=" CB PHE C 305 " pdb=" CG PHE C 305 " pdb=" CD1 PHE C 305 " ideal model delta sinusoidal sigma weight residual -20.00 33.33 -53.33 2 2.00e+01 2.50e-03 7.72e+00 dihedral pdb=" CA PHE B 305 " pdb=" CB PHE B 305 " pdb=" CG PHE B 305 " pdb=" CD1 PHE B 305 " ideal model delta sinusoidal sigma weight residual -20.00 33.30 -53.30 2 2.00e+01 2.50e-03 7.71e+00 dihedral pdb=" CA PHE A 305 " pdb=" CB PHE A 305 " pdb=" CG PHE A 305 " pdb=" CD1 PHE A 305 " ideal model delta sinusoidal sigma weight residual -20.00 33.29 -53.29 2 2.00e+01 2.50e-03 7.71e+00 ... (remaining 4545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1222 0.107 - 0.214: 14 0.214 - 0.322: 6 0.322 - 0.429: 0 0.429 - 0.536: 3 Chirality restraints: 1245 Sorted by residual: chirality pdb=" CBH Y01 B 901 " pdb=" CAT Y01 B 901 " pdb=" CAZ Y01 B 901 " pdb=" CBF Y01 B 901 " both_signs ideal model delta sigma weight residual False -2.85 -2.32 -0.54 2.00e-01 2.50e+01 7.19e+00 chirality pdb=" CBH Y01 A 901 " pdb=" CAT Y01 A 901 " pdb=" CAZ Y01 A 901 " pdb=" CBF Y01 A 901 " both_signs ideal model delta sigma weight residual False -2.85 -2.32 -0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" CBH Y01 C 901 " pdb=" CAT Y01 C 901 " pdb=" CAZ Y01 C 901 " pdb=" CBF Y01 C 901 " both_signs ideal model delta sigma weight residual False -2.85 -2.32 -0.53 2.00e-01 2.50e+01 7.10e+00 ... (remaining 1242 not shown) Planarity restraints: 1287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 387 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO B 388 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 388 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 388 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 387 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO A 388 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 387 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO C 388 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 388 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 388 " -0.025 5.00e-02 4.00e+02 ... (remaining 1284 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2374 2.83 - 3.35: 7398 3.35 - 3.86: 12202 3.86 - 4.38: 12751 4.38 - 4.90: 22469 Nonbonded interactions: 57194 Sorted by model distance: nonbonded pdb=" OE1 GLU C 308 " pdb=" OG SER C 334 " model vdw 2.310 3.040 nonbonded pdb=" OE1 GLU B 308 " pdb=" OG SER B 334 " model vdw 2.310 3.040 nonbonded pdb=" OE1 GLU A 308 " pdb=" OG SER A 334 " model vdw 2.310 3.040 nonbonded pdb=" N ALA A 214 " pdb=" OE2 GLU A 464 " model vdw 2.390 3.120 nonbonded pdb=" N ALA C 214 " pdb=" OE2 GLU C 464 " model vdw 2.390 3.120 ... (remaining 57189 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.340 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.800 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 7878 Z= 0.192 Angle : 0.787 11.972 10836 Z= 0.328 Chirality : 0.051 0.536 1245 Planarity : 0.005 0.046 1287 Dihedral : 14.025 65.471 2718 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.29), residues: 942 helix: 1.14 (0.22), residues: 654 sheet: None (None), residues: 0 loop : -0.54 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 432 TYR 0.010 0.001 TYR C 390 PHE 0.016 0.001 PHE B 305 TRP 0.011 0.001 TRP B 182 HIS 0.008 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7878) covalent geometry : angle 0.78704 (10836) hydrogen bonds : bond 0.17918 ( 420) hydrogen bonds : angle 5.30523 ( 1224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.262 Fit side-chains REVERT: A 405 ASN cc_start: 0.9086 (t0) cc_final: 0.8668 (t0) REVERT: C 390 TYR cc_start: 0.7581 (t80) cc_final: 0.7226 (t80) REVERT: B 184 PHE cc_start: 0.8138 (t80) cc_final: 0.7826 (t80) REVERT: B 507 ASP cc_start: 0.8308 (m-30) cc_final: 0.8010 (m-30) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.0572 time to fit residues: 14.5762 Evaluate side-chains 132 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.0570 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0050 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 0.4312 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.147696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.120874 restraints weight = 11164.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.123613 restraints weight = 7796.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.125685 restraints weight = 6141.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.126902 restraints weight = 5235.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.127803 restraints weight = 4683.384| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7878 Z= 0.139 Angle : 0.574 6.951 10836 Z= 0.278 Chirality : 0.040 0.136 1245 Planarity : 0.005 0.045 1287 Dihedral : 8.794 48.875 1224 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.13 % Allowed : 11.07 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.30), residues: 942 helix: 1.37 (0.22), residues: 654 sheet: None (None), residues: 0 loop : -0.93 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 432 TYR 0.010 0.001 TYR B 365 PHE 0.021 0.001 PHE C 193 TRP 0.007 0.001 TRP A 315 HIS 0.002 0.001 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7878) covalent geometry : angle 0.57440 (10836) hydrogen bonds : bond 0.04977 ( 420) hydrogen bonds : angle 3.92353 ( 1224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.173 Fit side-chains REVERT: A 405 ASN cc_start: 0.9119 (t0) cc_final: 0.8625 (t0) REVERT: C 390 TYR cc_start: 0.7988 (t80) cc_final: 0.7772 (t80) REVERT: B 184 PHE cc_start: 0.8362 (t80) cc_final: 0.7998 (t80) REVERT: B 507 ASP cc_start: 0.8660 (m-30) cc_final: 0.8351 (m-30) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.0542 time to fit residues: 11.2363 Evaluate side-chains 133 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 19 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 0.0570 chunk 9 optimal weight: 0.0980 chunk 86 optimal weight: 4.9990 overall best weight: 0.2476 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.151309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.125848 restraints weight = 11276.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.128590 restraints weight = 8768.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.129731 restraints weight = 6503.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.130992 restraints weight = 5815.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.131147 restraints weight = 5318.899| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7878 Z= 0.107 Angle : 0.512 6.520 10836 Z= 0.246 Chirality : 0.039 0.133 1245 Planarity : 0.004 0.040 1287 Dihedral : 7.275 39.279 1224 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.51 % Allowed : 14.29 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.29), residues: 942 helix: 1.55 (0.22), residues: 636 sheet: None (None), residues: 0 loop : -1.23 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 432 TYR 0.008 0.001 TYR C 426 PHE 0.019 0.001 PHE C 480 TRP 0.006 0.001 TRP A 404 HIS 0.002 0.000 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 7878) covalent geometry : angle 0.51156 (10836) hydrogen bonds : bond 0.03923 ( 420) hydrogen bonds : angle 3.42309 ( 1224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 0.202 Fit side-chains REVERT: A 211 LYS cc_start: 0.8364 (tppt) cc_final: 0.8086 (mptt) REVERT: A 405 ASN cc_start: 0.9099 (t0) cc_final: 0.8625 (t0) REVERT: B 184 PHE cc_start: 0.8371 (t80) cc_final: 0.7981 (t80) REVERT: B 507 ASP cc_start: 0.8699 (m-30) cc_final: 0.8383 (m-30) outliers start: 4 outliers final: 4 residues processed: 156 average time/residue: 0.0573 time to fit residues: 12.9526 Evaluate side-chains 144 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 401 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 5 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.142018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.114821 restraints weight = 11487.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.117454 restraints weight = 8149.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.118941 restraints weight = 6526.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.120199 restraints weight = 5643.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.120245 restraints weight = 5057.720| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7878 Z= 0.166 Angle : 0.563 5.691 10836 Z= 0.276 Chirality : 0.042 0.136 1245 Planarity : 0.005 0.040 1287 Dihedral : 7.109 40.965 1224 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.29 % Allowed : 17.63 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.30), residues: 942 helix: 1.45 (0.22), residues: 648 sheet: None (None), residues: 0 loop : -1.08 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 432 TYR 0.013 0.001 TYR C 426 PHE 0.010 0.001 PHE C 480 TRP 0.008 0.001 TRP B 297 HIS 0.002 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7878) covalent geometry : angle 0.56253 (10836) hydrogen bonds : bond 0.05250 ( 420) hydrogen bonds : angle 3.56535 ( 1224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.230 Fit side-chains REVERT: C 305 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.6897 (m-80) REVERT: B 507 ASP cc_start: 0.8818 (m-30) cc_final: 0.8463 (m-30) outliers start: 10 outliers final: 8 residues processed: 139 average time/residue: 0.0540 time to fit residues: 10.7671 Evaluate side-chains 137 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 495 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.0670 chunk 59 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.149807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.124936 restraints weight = 11450.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.127217 restraints weight = 9083.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.128150 restraints weight = 6887.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.129762 restraints weight = 6191.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.129923 restraints weight = 5515.166| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7878 Z= 0.117 Angle : 0.516 5.694 10836 Z= 0.251 Chirality : 0.040 0.132 1245 Planarity : 0.004 0.036 1287 Dihedral : 6.381 41.745 1224 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.51 % Allowed : 19.95 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.30), residues: 942 helix: 1.68 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -1.14 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 472 TYR 0.010 0.001 TYR A 426 PHE 0.009 0.001 PHE C 480 TRP 0.007 0.001 TRP A 404 HIS 0.003 0.001 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7878) covalent geometry : angle 0.51626 (10836) hydrogen bonds : bond 0.04285 ( 420) hydrogen bonds : angle 3.30106 ( 1224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 145 time to evaluate : 0.175 Fit side-chains REVERT: A 405 ASN cc_start: 0.9097 (t0) cc_final: 0.8584 (t0) REVERT: C 305 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6806 (m-80) REVERT: B 305 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.6429 (m-80) REVERT: B 507 ASP cc_start: 0.8834 (m-30) cc_final: 0.8484 (m-30) outliers start: 4 outliers final: 2 residues processed: 148 average time/residue: 0.0604 time to fit residues: 12.9914 Evaluate side-chains 143 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain B residue 305 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 0.0010 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.144124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.116778 restraints weight = 11429.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.119415 restraints weight = 8121.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.121037 restraints weight = 6514.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.122442 restraints weight = 5636.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.123032 restraints weight = 5109.586| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7878 Z= 0.129 Angle : 0.529 6.252 10836 Z= 0.256 Chirality : 0.040 0.132 1245 Planarity : 0.004 0.035 1287 Dihedral : 6.235 46.086 1224 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.29 % Allowed : 20.33 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.30), residues: 942 helix: 1.67 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -1.17 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 432 TYR 0.010 0.001 TYR B 426 PHE 0.008 0.001 PHE A 305 TRP 0.006 0.001 TRP A 404 HIS 0.002 0.001 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7878) covalent geometry : angle 0.52859 (10836) hydrogen bonds : bond 0.04454 ( 420) hydrogen bonds : angle 3.30847 ( 1224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.275 Fit side-chains REVERT: C 305 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.6774 (m-80) REVERT: C 352 GLU cc_start: 0.8253 (tp30) cc_final: 0.8035 (tp30) REVERT: C 445 TRP cc_start: 0.7733 (m100) cc_final: 0.7131 (m100) REVERT: B 305 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.6408 (m-80) REVERT: B 507 ASP cc_start: 0.8815 (m-30) cc_final: 0.8456 (m-30) outliers start: 10 outliers final: 8 residues processed: 149 average time/residue: 0.0630 time to fit residues: 13.6051 Evaluate side-chains 145 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 305 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 52 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.143774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.116381 restraints weight = 11418.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.118698 restraints weight = 8123.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.120787 restraints weight = 6553.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.121575 restraints weight = 5663.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.122558 restraints weight = 5223.634| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7878 Z= 0.131 Angle : 0.533 6.158 10836 Z= 0.257 Chirality : 0.040 0.134 1245 Planarity : 0.004 0.035 1287 Dihedral : 6.189 49.255 1224 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.42 % Allowed : 20.72 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.30), residues: 942 helix: 1.68 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -1.16 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 289 TYR 0.018 0.001 TYR A 462 PHE 0.008 0.001 PHE A 305 TRP 0.007 0.001 TRP B 297 HIS 0.003 0.001 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7878) covalent geometry : angle 0.53271 (10836) hydrogen bonds : bond 0.04479 ( 420) hydrogen bonds : angle 3.28892 ( 1224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.268 Fit side-chains REVERT: C 305 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.6847 (m-80) REVERT: C 352 GLU cc_start: 0.8243 (tp30) cc_final: 0.8034 (tp30) REVERT: C 445 TRP cc_start: 0.7793 (m100) cc_final: 0.7199 (m100) REVERT: B 305 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: B 507 ASP cc_start: 0.8868 (m-30) cc_final: 0.8502 (m-30) outliers start: 11 outliers final: 6 residues processed: 153 average time/residue: 0.0657 time to fit residues: 14.3289 Evaluate side-chains 146 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 495 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 71 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 48 optimal weight: 0.0980 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.146824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.119636 restraints weight = 11369.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.122255 restraints weight = 7981.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.124276 restraints weight = 6343.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.125252 restraints weight = 5453.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.126362 restraints weight = 4953.843| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7878 Z= 0.104 Angle : 0.520 6.697 10836 Z= 0.249 Chirality : 0.039 0.132 1245 Planarity : 0.004 0.033 1287 Dihedral : 6.021 49.190 1224 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.90 % Allowed : 22.01 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.30), residues: 942 helix: 1.77 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -1.22 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 472 TYR 0.014 0.001 TYR A 462 PHE 0.006 0.001 PHE A 305 TRP 0.008 0.001 TRP B 404 HIS 0.002 0.001 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 7878) covalent geometry : angle 0.52015 (10836) hydrogen bonds : bond 0.03755 ( 420) hydrogen bonds : angle 3.12562 ( 1224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.265 Fit side-chains REVERT: A 405 ASN cc_start: 0.9037 (t0) cc_final: 0.8512 (t0) REVERT: C 305 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.6756 (m-80) REVERT: C 352 GLU cc_start: 0.8205 (tp30) cc_final: 0.7986 (tp30) REVERT: B 305 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.6343 (m-80) REVERT: B 507 ASP cc_start: 0.8840 (m-30) cc_final: 0.8487 (m-30) outliers start: 7 outliers final: 3 residues processed: 157 average time/residue: 0.0618 time to fit residues: 14.0568 Evaluate side-chains 152 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 147 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 495 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 41 optimal weight: 0.0570 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.145143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.117718 restraints weight = 11378.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.120067 restraints weight = 8094.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.122178 restraints weight = 6513.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.123110 restraints weight = 5619.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.123110 restraints weight = 5139.663| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7878 Z= 0.126 Angle : 0.544 9.103 10836 Z= 0.261 Chirality : 0.040 0.142 1245 Planarity : 0.004 0.034 1287 Dihedral : 6.125 51.918 1224 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.77 % Allowed : 21.62 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.30), residues: 942 helix: 1.96 (0.22), residues: 624 sheet: None (None), residues: 0 loop : -0.72 (0.39), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 289 TYR 0.016 0.001 TYR B 291 PHE 0.008 0.001 PHE A 305 TRP 0.008 0.001 TRP C 445 HIS 0.002 0.001 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7878) covalent geometry : angle 0.54360 (10836) hydrogen bonds : bond 0.04210 ( 420) hydrogen bonds : angle 3.19272 ( 1224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 0.278 Fit side-chains REVERT: A 405 ASN cc_start: 0.9047 (t0) cc_final: 0.8522 (t0) REVERT: C 305 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.6822 (m-80) REVERT: C 352 GLU cc_start: 0.8225 (tp30) cc_final: 0.7999 (tp30) REVERT: B 305 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.6381 (m-80) REVERT: B 507 ASP cc_start: 0.8896 (m-30) cc_final: 0.8524 (m-30) outliers start: 6 outliers final: 3 residues processed: 149 average time/residue: 0.0704 time to fit residues: 14.9234 Evaluate side-chains 148 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 495 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.142768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.115099 restraints weight = 11472.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.117585 restraints weight = 8240.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.119457 restraints weight = 6650.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.120442 restraints weight = 5786.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.121393 restraints weight = 5272.735| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7878 Z= 0.153 Angle : 0.574 9.547 10836 Z= 0.280 Chirality : 0.041 0.142 1245 Planarity : 0.005 0.034 1287 Dihedral : 6.312 54.032 1224 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.51 % Allowed : 22.27 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.30), residues: 942 helix: 1.89 (0.22), residues: 624 sheet: None (None), residues: 0 loop : -0.72 (0.39), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 289 TYR 0.016 0.001 TYR A 462 PHE 0.010 0.001 PHE A 305 TRP 0.009 0.001 TRP B 297 HIS 0.003 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 7878) covalent geometry : angle 0.57370 (10836) hydrogen bonds : bond 0.04804 ( 420) hydrogen bonds : angle 3.33673 ( 1224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.165 Fit side-chains REVERT: C 305 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.6869 (m-80) REVERT: C 352 GLU cc_start: 0.8292 (tp30) cc_final: 0.8055 (tp30) REVERT: B 305 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: B 507 ASP cc_start: 0.8905 (m-30) cc_final: 0.8553 (m-30) outliers start: 4 outliers final: 2 residues processed: 145 average time/residue: 0.0663 time to fit residues: 13.5587 Evaluate side-chains 140 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain B residue 305 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.142570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.114808 restraints weight = 11455.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.117307 restraints weight = 8283.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.119156 restraints weight = 6709.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.120063 restraints weight = 5826.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.120698 restraints weight = 5353.153| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7878 Z= 0.169 Angle : 0.595 7.739 10836 Z= 0.290 Chirality : 0.042 0.134 1245 Planarity : 0.005 0.037 1287 Dihedral : 6.534 54.188 1224 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.77 % Allowed : 22.52 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.30), residues: 942 helix: 1.78 (0.22), residues: 630 sheet: None (None), residues: 0 loop : -0.64 (0.40), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 289 TYR 0.017 0.002 TYR C 291 PHE 0.011 0.001 PHE A 305 TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 7878) covalent geometry : angle 0.59454 (10836) hydrogen bonds : bond 0.05154 ( 420) hydrogen bonds : angle 3.43120 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1049.77 seconds wall clock time: 18 minutes 53.33 seconds (1133.33 seconds total)