Starting phenix.real_space_refine on Sun May 11 09:05:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1e_35920/05_2025/8j1e_35920.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1e_35920/05_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_35920/05_2025/8j1e_35920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1e_35920/05_2025/8j1e_35920.map" model { file = "/net/cci-nas-00/data/ceres_data/8j1e_35920/05_2025/8j1e_35920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1e_35920/05_2025/8j1e_35920.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN: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: 4.74, per 1000 atoms: 0.62 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: 1.73 Conformation dependent library (CDL) restraints added in 952.5 milliseconds 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: 0.71 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: 1.84 Time building geometry restraints manager: 2.03 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: 0.05 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: 3.530 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 18.940 Find NCS groups from input model: 0.140 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (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 TRP 0.011 0.001 TRP B 182 HIS 0.008 0.001 HIS A 387 PHE 0.016 0.001 PHE B 305 TYR 0.010 0.001 TYR C 390 ARG 0.003 0.000 ARG B 432 Details of bonding type rmsd hydrogen bonds : bond 0.17918 ( 420) hydrogen bonds : angle 5.30523 ( 1224) covalent geometry : bond 0.00395 ( 7878) covalent geometry : angle 0.78704 (10836) *********************** 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 : 0.721 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: 0.1493 time to fit residues: 36.6163 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 : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.0670 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 72 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.147627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.120769 restraints weight = 11143.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.123613 restraints weight = 7776.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.125426 restraints weight = 6129.514| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7878 Z= 0.136 Angle : 0.574 6.687 10836 Z= 0.278 Chirality : 0.040 0.133 1245 Planarity : 0.005 0.045 1287 Dihedral : 8.831 48.672 1224 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.31 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.30), residues: 942 helix: 1.37 (0.22), residues: 654 sheet: None (None), residues: 0 loop : -0.94 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 315 HIS 0.002 0.001 HIS C 387 PHE 0.018 0.001 PHE C 193 TYR 0.010 0.001 TYR B 365 ARG 0.003 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.04919 ( 420) hydrogen bonds : angle 3.91248 ( 1224) covalent geometry : bond 0.00311 ( 7878) covalent geometry : angle 0.57370 (10836) *********************** 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 144 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.733 Fit side-chains REVERT: A 405 ASN cc_start: 0.9116 (t0) cc_final: 0.8628 (t0) REVERT: C 390 TYR cc_start: 0.8022 (t80) cc_final: 0.7801 (t80) REVERT: B 184 PHE cc_start: 0.8410 (t80) cc_final: 0.8035 (t80) REVERT: B 507 ASP cc_start: 0.8708 (m-30) cc_final: 0.8380 (m-30) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.1537 time to fit residues: 31.7223 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 : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 73 optimal weight: 0.0970 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.147055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.120010 restraints weight = 11372.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.122826 restraints weight = 7923.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.124788 restraints weight = 6243.467| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7878 Z= 0.123 Angle : 0.523 6.310 10836 Z= 0.253 Chirality : 0.040 0.134 1245 Planarity : 0.004 0.041 1287 Dihedral : 7.247 39.227 1224 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.64 % Allowed : 14.67 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.29), residues: 942 helix: 1.53 (0.22), residues: 636 sheet: None (None), residues: 0 loop : -1.19 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 297 HIS 0.002 0.000 HIS B 293 PHE 0.020 0.001 PHE C 480 TYR 0.010 0.001 TYR A 426 ARG 0.001 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 420) hydrogen bonds : angle 3.48100 ( 1224) covalent geometry : bond 0.00283 ( 7878) covalent geometry : angle 0.52297 (10836) *********************** 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 151 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 0.840 Fit side-chains REVERT: A 405 ASN cc_start: 0.9086 (t0) cc_final: 0.8601 (t0) REVERT: B 184 PHE cc_start: 0.8435 (t80) cc_final: 0.7981 (t80) REVERT: B 352 GLU cc_start: 0.8221 (tp30) cc_final: 0.8004 (tp30) REVERT: B 507 ASP cc_start: 0.8780 (m-30) cc_final: 0.8424 (m-30) outliers start: 5 outliers final: 5 residues processed: 148 average time/residue: 0.1591 time to fit residues: 33.8093 Evaluate side-chains 138 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 401 SER Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 495 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 5 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 72 optimal weight: 0.2980 chunk 53 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.145444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.118378 restraints weight = 11220.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.121099 restraints weight = 7959.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.123030 restraints weight = 6341.436| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7878 Z= 0.129 Angle : 0.528 5.549 10836 Z= 0.255 Chirality : 0.040 0.132 1245 Planarity : 0.004 0.038 1287 Dihedral : 6.728 40.616 1224 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.90 % Allowed : 17.50 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.30), residues: 942 helix: 1.61 (0.22), residues: 636 sheet: None (None), residues: 0 loop : -1.19 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 404 HIS 0.003 0.001 HIS C 387 PHE 0.008 0.001 PHE A 480 TYR 0.011 0.001 TYR C 426 ARG 0.002 0.000 ARG C 432 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 420) hydrogen bonds : angle 3.36807 ( 1224) covalent geometry : bond 0.00307 ( 7878) covalent geometry : angle 0.52756 (10836) *********************** 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 150 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.787 Fit side-chains REVERT: A 405 ASN cc_start: 0.9075 (t0) cc_final: 0.8581 (t0) REVERT: C 305 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: B 507 ASP cc_start: 0.8811 (m-30) cc_final: 0.8457 (m-30) outliers start: 7 outliers final: 6 residues processed: 147 average time/residue: 0.1575 time to fit residues: 33.0647 Evaluate side-chains 140 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 B residue 239 VAL 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 84 optimal weight: 0.3980 chunk 92 optimal weight: 0.0370 chunk 82 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 79 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 overall best weight: 0.2456 ------------------------------------------------------------------------------- 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 = 0.149854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.125029 restraints weight = 11185.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.127104 restraints weight = 8488.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.128540 restraints weight = 6568.416| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1912 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= 0.102 Angle : 0.504 5.922 10836 Z= 0.242 Chirality : 0.039 0.133 1245 Planarity : 0.004 0.034 1287 Dihedral : 6.094 41.467 1224 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.77 % Allowed : 18.66 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.30), residues: 942 helix: 1.74 (0.22), residues: 636 sheet: None (None), residues: 0 loop : -1.27 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 404 HIS 0.002 0.000 HIS C 387 PHE 0.008 0.001 PHE C 480 TYR 0.008 0.001 TYR A 426 ARG 0.001 0.000 ARG B 472 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 420) hydrogen bonds : angle 3.16979 ( 1224) covalent geometry : bond 0.00224 ( 7878) covalent geometry : angle 0.50362 (10836) *********************** 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 158 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 0.734 Fit side-chains REVERT: A 405 ASN cc_start: 0.9046 (t0) cc_final: 0.8548 (t0) REVERT: C 305 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: B 305 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.6365 (m-80) REVERT: B 507 ASP cc_start: 0.8825 (m-30) cc_final: 0.8478 (m-30) outliers start: 6 outliers final: 3 residues processed: 157 average time/residue: 0.1704 time to fit residues: 38.5430 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 : 0.876 ------------------------------------------------------------------------------- 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 C residue 401 SER 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 14 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.143213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.115926 restraints weight = 11357.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.118548 restraints weight = 8144.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.120064 restraints weight = 6538.526| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2116 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= 0.139 Angle : 0.547 6.184 10836 Z= 0.263 Chirality : 0.040 0.131 1245 Planarity : 0.004 0.034 1287 Dihedral : 6.265 47.628 1224 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.29 % Allowed : 20.21 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.30), residues: 942 helix: 1.62 (0.22), residues: 645 sheet: None (None), residues: 0 loop : -1.28 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 297 HIS 0.002 0.001 HIS B 293 PHE 0.009 0.001 PHE A 305 TYR 0.011 0.001 TYR B 426 ARG 0.001 0.000 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.04670 ( 420) hydrogen bonds : angle 3.31592 ( 1224) covalent geometry : bond 0.00337 ( 7878) covalent geometry : angle 0.54661 (10836) *********************** 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 150 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.812 Fit side-chains REVERT: C 305 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.6964 (m-80) REVERT: C 445 TRP cc_start: 0.7778 (m100) cc_final: 0.7153 (m100) REVERT: B 305 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6453 (m-80) REVERT: B 507 ASP cc_start: 0.8878 (m-30) cc_final: 0.8521 (m-30) outliers start: 10 outliers final: 5 residues processed: 148 average time/residue: 0.1603 time to fit residues: 33.9243 Evaluate side-chains 144 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 305 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 88 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 70 optimal weight: 0.0570 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.144350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.117056 restraints weight = 11218.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.119430 restraints weight = 8064.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.121307 restraints weight = 6523.000| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7878 Z= 0.130 Angle : 0.535 6.304 10836 Z= 0.257 Chirality : 0.040 0.133 1245 Planarity : 0.004 0.034 1287 Dihedral : 6.137 48.705 1224 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.90 % Allowed : 21.11 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.30), residues: 942 helix: 1.72 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -1.20 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 315 HIS 0.002 0.001 HIS A 387 PHE 0.008 0.001 PHE A 305 TYR 0.011 0.001 TYR B 426 ARG 0.001 0.000 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 420) hydrogen bonds : angle 3.24947 ( 1224) covalent geometry : bond 0.00315 ( 7878) covalent geometry : angle 0.53545 (10836) *********************** 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 154 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.878 Fit side-chains REVERT: A 405 ASN cc_start: 0.9059 (t0) cc_final: 0.8526 (t0) REVERT: C 305 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: C 445 TRP cc_start: 0.7787 (m100) cc_final: 0.7136 (m100) REVERT: B 305 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.6422 (m-80) REVERT: B 507 ASP cc_start: 0.8882 (m-30) cc_final: 0.8506 (m-30) outliers start: 7 outliers final: 5 residues processed: 150 average time/residue: 0.1663 time to fit residues: 35.5227 Evaluate side-chains 148 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 C residue 401 SER Chi-restraints excluded: chain B residue 239 VAL 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 83 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 92 optimal weight: 0.0370 chunk 50 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 40 optimal weight: 0.0030 chunk 85 optimal weight: 0.9980 overall best weight: 0.4668 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.145388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.118121 restraints weight = 11346.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.120765 restraints weight = 8064.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.122385 restraints weight = 6496.068| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2272 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= 0.118 Angle : 0.537 6.840 10836 Z= 0.256 Chirality : 0.040 0.132 1245 Planarity : 0.004 0.034 1287 Dihedral : 6.169 50.180 1224 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.90 % Allowed : 21.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.30), residues: 942 helix: 1.74 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -1.26 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 404 HIS 0.002 0.001 HIS B 293 PHE 0.008 0.001 PHE A 305 TYR 0.010 0.001 TYR B 426 ARG 0.000 0.000 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 420) hydrogen bonds : angle 3.19347 ( 1224) covalent geometry : bond 0.00280 ( 7878) covalent geometry : angle 0.53698 (10836) *********************** 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 152 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.787 Fit side-chains REVERT: A 405 ASN cc_start: 0.9041 (t0) cc_final: 0.8504 (t0) REVERT: C 305 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: C 445 TRP cc_start: 0.7783 (m100) cc_final: 0.7067 (m100) REVERT: B 305 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.6383 (m-80) REVERT: B 507 ASP cc_start: 0.8916 (m-30) cc_final: 0.8535 (m-30) outliers start: 7 outliers final: 4 residues processed: 150 average time/residue: 0.1577 time to fit residues: 33.4869 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 : 0.821 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 70 optimal weight: 0.0070 chunk 45 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.144430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.116895 restraints weight = 11415.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.119109 restraints weight = 8146.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.121224 restraints weight = 6579.284| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7878 Z= 0.127 Angle : 0.547 9.445 10836 Z= 0.261 Chirality : 0.040 0.143 1245 Planarity : 0.004 0.033 1287 Dihedral : 6.167 52.249 1224 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.16 % Allowed : 21.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.29), residues: 942 helix: 1.99 (0.22), residues: 612 sheet: None (None), residues: 0 loop : -0.71 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 297 HIS 0.002 0.001 HIS A 387 PHE 0.008 0.001 PHE A 305 TYR 0.010 0.001 TYR A 426 ARG 0.001 0.000 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 420) hydrogen bonds : angle 3.21404 ( 1224) covalent geometry : bond 0.00305 ( 7878) covalent geometry : angle 0.54708 (10836) *********************** 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 152 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.720 Fit side-chains REVERT: A 405 ASN cc_start: 0.9048 (t0) cc_final: 0.8513 (t0) REVERT: C 305 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.6891 (m-80) REVERT: C 445 TRP cc_start: 0.7778 (m100) cc_final: 0.7088 (m100) REVERT: B 305 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.6386 (m-80) REVERT: B 507 ASP cc_start: 0.8892 (m-30) cc_final: 0.8525 (m-30) outliers start: 9 outliers final: 5 residues processed: 150 average time/residue: 0.1562 time to fit residues: 33.0968 Evaluate side-chains 148 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 C residue 335 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 19 optimal weight: 0.0170 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.0010 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.4024 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.145757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.118189 restraints weight = 11408.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.120640 restraints weight = 8077.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.122631 restraints weight = 6478.272| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2362 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= 0.116 Angle : 0.548 10.018 10836 Z= 0.262 Chirality : 0.040 0.144 1245 Planarity : 0.004 0.037 1287 Dihedral : 6.091 52.425 1224 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.90 % Allowed : 22.14 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.29), residues: 942 helix: 2.02 (0.22), residues: 612 sheet: None (None), residues: 0 loop : -0.73 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 297 HIS 0.002 0.001 HIS A 387 PHE 0.007 0.001 PHE A 305 TYR 0.010 0.001 TYR A 426 ARG 0.001 0.000 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 420) hydrogen bonds : angle 3.16168 ( 1224) covalent geometry : bond 0.00272 ( 7878) covalent geometry : angle 0.54781 (10836) ********************** 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 154 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.889 Fit side-chains REVERT: A 405 ASN cc_start: 0.9031 (t0) cc_final: 0.8501 (t0) REVERT: C 305 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.6841 (m-80) REVERT: B 305 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.6378 (m-80) REVERT: B 507 ASP cc_start: 0.8909 (m-30) cc_final: 0.8522 (m-30) outliers start: 7 outliers final: 3 residues processed: 152 average time/residue: 0.1737 time to fit residues: 37.4684 Evaluate side-chains 150 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 503 LEU 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 70 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.0050 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 54 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 overall best weight: 0.4010 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.146117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.118676 restraints weight = 11297.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.121133 restraints weight = 8008.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.123080 restraints weight = 6456.349| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2388 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= 0.116 Angle : 0.547 7.532 10836 Z= 0.262 Chirality : 0.040 0.133 1245 Planarity : 0.004 0.033 1287 Dihedral : 6.118 52.944 1224 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.51 % Allowed : 22.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.30), residues: 942 helix: 2.00 (0.22), residues: 615 sheet: None (None), residues: 0 loop : -0.65 (0.38), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 445 HIS 0.002 0.001 HIS A 387 PHE 0.008 0.001 PHE A 305 TYR 0.010 0.001 TYR A 426 ARG 0.000 0.000 ARG A 289 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 420) hydrogen bonds : angle 3.14393 ( 1224) covalent geometry : bond 0.00273 ( 7878) covalent geometry : angle 0.54698 (10836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2329.57 seconds wall clock time: 41 minutes 45.67 seconds (2505.67 seconds total)