Starting phenix.real_space_refine on Wed Mar 4 15:40:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8euc_28611/03_2026/8euc_28611_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8euc_28611/03_2026/8euc_28611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8euc_28611/03_2026/8euc_28611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8euc_28611/03_2026/8euc_28611.map" model { file = "/net/cci-nas-00/data/ceres_data/8euc_28611/03_2026/8euc_28611_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8euc_28611/03_2026/8euc_28611_neut.cif" } resolution = 3.61 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= 0.006 sd= 0.077 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 P 4 5.49 5 S 66 5.16 5 C 9491 2.51 5 N 2369 2.21 5 O 2630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 163 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14560 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3634 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3623 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 444, 3623 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 bond proxies already assigned to first conformer: 3692 Chain: "B" Number of atoms: 3555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3555 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 14, 'TRANS': 419} Chain breaks: 2 Chain: "C" Number of atoms: 3681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3681 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 14, 'TRANS': 437} Chain: "D" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3556 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 12, 'TRANS': 421} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 392 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 392 " occ=0.50 Time building chain proxies: 4.33, per 1000 atoms: 0.30 Number of scatterers: 14560 At special positions: 0 Unit cell: (132.25, 108.974, 104.742, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 4 15.00 O 2630 8.00 N 2369 7.00 C 9491 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 339 " " NAG B 801 " - " ASN B 339 " " NAG C 801 " - " ASN C 339 " Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 693.9 milliseconds 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3350 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 12 sheets defined 67.8% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 166 through 192 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 200 through 222 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.776A pdb=" N VAL A 273 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 274 " --> pdb=" O PRO A 271 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.059A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 329 Processing helix chain 'A' and resid 347 through 364 Processing helix chain 'A' and resid 374 through 427 removed outlier: 3.825A pdb=" N ALA A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 448 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 461 through 473 Processing helix chain 'A' and resid 487 through 498 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 581 through 589 Processing helix chain 'A' and resid 592 through 609 Processing helix chain 'B' and resid 166 through 193 Proline residue: B 178 - end of helix removed outlier: 3.780A pdb=" N TYR B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.796A pdb=" N TYR B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 223 Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 246 through 256 removed outlier: 3.923A pdb=" N LYS B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 4.089A pdb=" N VAL B 273 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 274 " --> pdb=" O PRO B 271 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASN B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 278 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.220A pdb=" N LEU B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 329 Processing helix chain 'B' and resid 347 through 364 Processing helix chain 'B' and resid 374 through 428 removed outlier: 5.617A pdb=" N SER B 409 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG B 410 " --> pdb=" O MET B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 448 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 461 through 478 removed outlier: 3.811A pdb=" N ILE B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 Processing helix chain 'B' and resid 580 through 588 removed outlier: 3.773A pdb=" N LEU B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 610 removed outlier: 4.104A pdb=" N LYS B 595 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 193 Proline residue: C 178 - end of helix removed outlier: 3.745A pdb=" N ASP C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 removed outlier: 3.928A pdb=" N TYR C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 222 Processing helix chain 'C' and resid 235 through 245 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.741A pdb=" N LYS C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 267 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 276 through 279 removed outlier: 3.558A pdb=" N LEU C 279 " --> pdb=" O ASN C 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 276 through 279' Processing helix chain 'C' and resid 280 through 295 Processing helix chain 'C' and resid 297 through 329 Processing helix chain 'C' and resid 347 through 364 Processing helix chain 'C' and resid 374 through 427 removed outlier: 3.503A pdb=" N ASN C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ARG C 410 " --> pdb=" O MET C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 447 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 461 through 478 removed outlier: 5.532A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 498 Processing helix chain 'C' and resid 549 through 553 removed outlier: 4.006A pdb=" N ILE C 552 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU C 553 " --> pdb=" O ILE C 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 549 through 553' Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 592 through 609 Processing helix chain 'D' and resid 215 through 242 Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 249 through 270 Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.685A pdb=" N LEU D 275 " --> pdb=" O GLN D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 297 through 307 removed outlier: 3.916A pdb=" N GLN D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 313 through 318 Processing helix chain 'D' and resid 322 through 329 removed outlier: 3.600A pdb=" N ALA D 325 " --> pdb=" O MET D 322 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN D 326 " --> pdb=" O PHE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 345 Processing helix chain 'D' and resid 347 through 379 removed outlier: 4.245A pdb=" N TYR D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'D' and resid 416 through 469 removed outlier: 3.900A pdb=" N PHE D 432 " --> pdb=" O PHE D 428 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASN D 451 " --> pdb=" O ALA D 447 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN D 452 " --> pdb=" O ALA D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 490 Processing helix chain 'D' and resid 494 through 500 removed outlier: 4.001A pdb=" N LEU D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 522 removed outlier: 5.589A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 526 removed outlier: 3.739A pdb=" N LYS D 526 " --> pdb=" O ASP D 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 523 through 526' Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 592 through 596 removed outlier: 4.126A pdb=" N LEU D 596 " --> pdb=" O ILE D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 631 through 643 Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228 removed outlier: 3.643A pdb=" N GLU A 228 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.796A pdb=" N ASP A 575 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510 removed outlier: 6.347A pdb=" N ILE A 568 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 228 removed outlier: 3.661A pdb=" N GLU B 228 " --> pdb=" O LEU B 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 503 removed outlier: 3.565A pdb=" N ARG B 499 " --> pdb=" O CYS B 578 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 540 through 541 Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'C' and resid 499 through 502 removed outlier: 3.612A pdb=" N ARG C 499 " --> pdb=" O CYS C 578 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 540 through 541 removed outlier: 3.569A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 277 through 279 removed outlier: 4.263A pdb=" N PHE D 277 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP D 282 " --> pdb=" O ARG D 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AB3, first strand: chain 'D' and resid 550 through 552 removed outlier: 6.272A pdb=" N PHE D 550 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA D 610 " --> pdb=" O PHE D 550 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS D 552 " --> pdb=" O VAL D 608 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 569 " --> pdb=" O LEU D 584 " (cutoff:3.500A) 922 hydrogen bonds defined for protein. 2691 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2298 1.32 - 1.44: 4199 1.44 - 1.57: 8306 1.57 - 1.70: 2 1.70 - 1.82: 105 Bond restraints: 14910 Sorted by residual: bond pdb=" O5' PCG D 901 " pdb=" PA PCG D 901 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" O5' PCG B 802 " pdb=" PA PCG B 802 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" O5' PCG C 802 " pdb=" PA PCG C 802 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" O5' PCG A 802 " pdb=" PA PCG A 802 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" O3' PCG D 901 " pdb=" PA PCG D 901 " ideal model delta sigma weight residual 1.617 1.513 0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 14905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 20027 3.65 - 7.30: 152 7.30 - 10.95: 46 10.95 - 14.60: 6 14.60 - 18.26: 10 Bond angle restraints: 20241 Sorted by residual: angle pdb=" N GLY A 397 " pdb=" CA GLY A 397 " pdb=" C GLY A 397 " ideal model delta sigma weight residual 112.77 103.87 8.90 1.28e+00 6.10e-01 4.83e+01 angle pdb=" N THR B 565 " pdb=" CA THR B 565 " pdb=" C THR B 565 " ideal model delta sigma weight residual 111.37 121.98 -10.61 1.64e+00 3.72e-01 4.19e+01 angle pdb=" N ILE A 391 " pdb=" CA ILE A 391 " pdb=" C ILE A 391 " ideal model delta sigma weight residual 110.36 116.77 -6.41 1.05e+00 9.07e-01 3.72e+01 angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 109.85 128.11 -18.26 3.00e+00 1.11e-01 3.70e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 109.85 128.09 -18.24 3.00e+00 1.11e-01 3.70e+01 ... (remaining 20236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.93: 8356 25.93 - 51.86: 526 51.86 - 77.78: 32 77.78 - 103.71: 6 103.71 - 129.64: 8 Dihedral angle restraints: 8928 sinusoidal: 3718 harmonic: 5210 Sorted by residual: dihedral pdb=" N ILE A 395 " pdb=" C ILE A 395 " pdb=" CA ILE A 395 " pdb=" CB ILE A 395 " ideal model delta harmonic sigma weight residual 123.40 136.70 -13.30 0 2.50e+00 1.60e-01 2.83e+01 dihedral pdb=" C ILE A 395 " pdb=" N ILE A 395 " pdb=" CA ILE A 395 " pdb=" CB ILE A 395 " ideal model delta harmonic sigma weight residual -122.00 -134.32 12.32 0 2.50e+00 1.60e-01 2.43e+01 dihedral pdb=" CA ASP D 286 " pdb=" C ASP D 286 " pdb=" N SER D 287 " pdb=" CA SER D 287 " ideal model delta harmonic sigma weight residual -180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 8925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 2296 0.356 - 0.711: 1 0.711 - 1.067: 0 1.067 - 1.422: 0 1.422 - 1.778: 4 Chirality restraints: 2301 Sorted by residual: chirality pdb=" C4' PCG A 802 " pdb=" C3' PCG A 802 " pdb=" C5' PCG A 802 " pdb=" O4' PCG A 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.90e+01 chirality pdb=" C4' PCG B 802 " pdb=" C3' PCG B 802 " pdb=" C5' PCG B 802 " pdb=" O4' PCG B 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.90e+01 chirality pdb=" C4' PCG C 802 " pdb=" C3' PCG C 802 " pdb=" C5' PCG C 802 " pdb=" O4' PCG C 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.89e+01 ... (remaining 2298 not shown) Planarity restraints: 2490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO D 273 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 499 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO B 500 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 500 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 500 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 187 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C ILE B 187 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE B 187 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS B 188 " 0.014 2.00e-02 2.50e+03 ... (remaining 2487 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1719 2.75 - 3.29: 14094 3.29 - 3.82: 24849 3.82 - 4.36: 27258 4.36 - 4.90: 47404 Nonbonded interactions: 115324 Sorted by model distance: nonbonded pdb=" N THR D 605 " pdb=" O1A PCG D 901 " model vdw 2.211 3.120 nonbonded pdb=" O PHE D 516 " pdb=" OG SER D 520 " model vdw 2.284 3.040 nonbonded pdb=" OH TYR B 243 " pdb=" OD2 ASP B 252 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR B 565 " pdb=" N2 PCG B 802 " model vdw 2.286 3.120 nonbonded pdb=" O ARG A 603 " pdb=" CG LEU A 606 " model vdw 2.306 3.470 ... (remaining 115319 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 258 or resid 270 through 391 or resid 393 thro \ ugh 554 or resid 562 through 802)) selection = (chain 'B' and (resid 159 through 391 or resid 393 through 609 or resid 801 thro \ ugh 802)) selection = (chain 'C' and (resid 159 through 258 or resid 270 through 391 or resid 393 thro \ ugh 554 or resid 562 through 802)) } 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=0.50 max=1.00 mean=1.00 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: 2.550 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.650 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.007 0.117 14913 Z= 0.329 Angle : 1.044 18.256 20250 Z= 0.535 Chirality : 0.095 1.778 2301 Planarity : 0.007 0.078 2487 Dihedral : 15.994 129.641 5578 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.32 % Allowed : 8.25 % Favored : 91.43 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.15), residues: 1751 helix: -2.41 (0.10), residues: 1160 sheet: -2.80 (0.45), residues: 94 loop : -2.74 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 603 TYR 0.017 0.002 TYR A 352 PHE 0.023 0.002 PHE A 483 TRP 0.023 0.002 TRP A 171 HIS 0.005 0.001 HIS D 293 Details of bonding type rmsd covalent geometry : bond 0.00691 (14910) covalent geometry : angle 1.04349 (20241) hydrogen bonds : bond 0.12584 ( 922) hydrogen bonds : angle 5.94078 ( 2691) link_NAG-ASN : bond 0.00427 ( 3) link_NAG-ASN : angle 2.13071 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 281 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.6758 (mmm) cc_final: 0.6291 (mpp) REVERT: A 297 TYR cc_start: 0.6889 (m-80) cc_final: 0.6669 (m-80) REVERT: A 389 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8113 (p) REVERT: A 498 LEU cc_start: 0.8704 (mt) cc_final: 0.8485 (mt) REVERT: B 201 MET cc_start: 0.6987 (ppp) cc_final: 0.6664 (ppp) REVERT: B 425 GLN cc_start: 0.7710 (mt0) cc_final: 0.7471 (mt0) REVERT: B 434 GLU cc_start: 0.7235 (tp30) cc_final: 0.6430 (tp30) REVERT: B 524 GLU cc_start: 0.7415 (tt0) cc_final: 0.7209 (tt0) REVERT: B 547 PHE cc_start: 0.8751 (p90) cc_final: 0.8404 (p90) REVERT: C 353 ILE cc_start: 0.8968 (mm) cc_final: 0.8676 (mt) REVERT: D 316 PHE cc_start: 0.8225 (m-80) cc_final: 0.7779 (m-10) REVERT: D 619 LEU cc_start: 0.7295 (tp) cc_final: 0.7089 (tp) outliers start: 4 outliers final: 1 residues processed: 285 average time/residue: 0.1259 time to fit residues: 52.1917 Evaluate side-chains 187 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain C residue 563 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.0040 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 299 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 471 ASN B 196 GLN B 407 ASN B 414 GLN C 242 HIS C 317 ASN C 414 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN D 340 HIS D 365 HIS D 367 ASN D 426 ASN D 531 GLN D 566 HIS D 570 GLN D 607 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.152272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121820 restraints weight = 37956.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125360 restraints weight = 44118.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.126189 restraints weight = 26097.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127729 restraints weight = 16242.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.128807 restraints weight = 12973.045| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14913 Z= 0.129 Angle : 0.584 9.674 20250 Z= 0.306 Chirality : 0.040 0.159 2301 Planarity : 0.005 0.063 2487 Dihedral : 10.383 152.477 2144 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.39 % Allowed : 14.49 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.19), residues: 1751 helix: -0.12 (0.14), residues: 1155 sheet: -1.71 (0.57), residues: 73 loop : -2.21 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 564 TYR 0.019 0.001 TYR A 443 PHE 0.014 0.001 PHE D 590 TRP 0.027 0.002 TRP C 440 HIS 0.003 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00277 (14910) covalent geometry : angle 0.58053 (20241) hydrogen bonds : bond 0.04299 ( 922) hydrogen bonds : angle 4.50353 ( 2691) link_NAG-ASN : bond 0.01940 ( 3) link_NAG-ASN : angle 3.17969 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 TYR cc_start: 0.7432 (m-80) cc_final: 0.7153 (m-80) REVERT: C 217 ASP cc_start: 0.7169 (t70) cc_final: 0.6619 (t70) REVERT: C 311 LEU cc_start: 0.8648 (tp) cc_final: 0.8358 (tt) REVERT: D 398 TYR cc_start: 0.8518 (t80) cc_final: 0.8302 (t80) REVERT: D 561 MET cc_start: 0.7441 (tpp) cc_final: 0.6960 (tpp) outliers start: 21 outliers final: 9 residues processed: 226 average time/residue: 0.1063 time to fit residues: 37.2062 Evaluate side-chains 186 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 553 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 120 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 122 optimal weight: 0.0170 chunk 158 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS B 248 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.152464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122154 restraints weight = 37402.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125465 restraints weight = 40392.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126287 restraints weight = 26181.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127714 restraints weight = 16038.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128775 restraints weight = 12993.479| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14913 Z= 0.123 Angle : 0.562 9.689 20250 Z= 0.291 Chirality : 0.040 0.157 2301 Planarity : 0.004 0.055 2487 Dihedral : 10.107 153.131 2139 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.14 % Allowed : 16.13 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1751 helix: 0.74 (0.15), residues: 1155 sheet: -1.38 (0.58), residues: 73 loop : -1.90 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG B 221 TYR 0.021 0.001 TYR A 423 PHE 0.017 0.001 PHE B 413 TRP 0.029 0.001 TRP C 440 HIS 0.005 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00268 (14910) covalent geometry : angle 0.55862 (20241) hydrogen bonds : bond 0.04027 ( 922) hydrogen bonds : angle 4.25744 ( 2691) link_NAG-ASN : bond 0.00622 ( 3) link_NAG-ASN : angle 3.08077 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 524 GLU cc_start: 0.7144 (tt0) cc_final: 0.6868 (tt0) REVERT: C 217 ASP cc_start: 0.7124 (t70) cc_final: 0.6627 (t70) REVERT: C 311 LEU cc_start: 0.8706 (tp) cc_final: 0.8424 (tt) REVERT: D 210 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8454 (mt) REVERT: D 561 MET cc_start: 0.7301 (tpp) cc_final: 0.7032 (tpp) outliers start: 33 outliers final: 19 residues processed: 219 average time/residue: 0.0985 time to fit residues: 34.2786 Evaluate side-chains 197 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 13 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 GLN D 426 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.149853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.118826 restraints weight = 34196.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121992 restraints weight = 39629.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122747 restraints weight = 27164.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123836 restraints weight = 16919.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125795 restraints weight = 13748.468| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14913 Z= 0.154 Angle : 0.562 8.160 20250 Z= 0.292 Chirality : 0.041 0.157 2301 Planarity : 0.004 0.051 2487 Dihedral : 9.987 155.340 2139 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.02 % Allowed : 17.45 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.20), residues: 1751 helix: 1.02 (0.15), residues: 1154 sheet: -1.32 (0.60), residues: 68 loop : -1.80 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 283 TYR 0.018 0.001 TYR B 423 PHE 0.019 0.001 PHE B 413 TRP 0.020 0.001 TRP C 440 HIS 0.005 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00352 (14910) covalent geometry : angle 0.55846 (20241) hydrogen bonds : bond 0.04109 ( 922) hydrogen bonds : angle 4.15385 ( 2691) link_NAG-ASN : bond 0.00473 ( 3) link_NAG-ASN : angle 3.04321 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8071 (m) REVERT: A 590 GLU cc_start: 0.7817 (mp0) cc_final: 0.7593 (mp0) REVERT: B 524 GLU cc_start: 0.7225 (tt0) cc_final: 0.6951 (tt0) REVERT: C 217 ASP cc_start: 0.7187 (t70) cc_final: 0.6740 (t70) REVERT: C 311 LEU cc_start: 0.8738 (tp) cc_final: 0.8443 (tt) REVERT: C 519 MET cc_start: 0.7445 (tpt) cc_final: 0.7202 (tpt) REVERT: C 608 LYS cc_start: 0.4793 (pttp) cc_final: 0.4435 (mmtm) REVERT: D 210 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8519 (mt) outliers start: 31 outliers final: 20 residues processed: 204 average time/residue: 0.1028 time to fit residues: 33.0094 Evaluate side-chains 191 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 66 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.151023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119838 restraints weight = 28349.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118823 restraints weight = 27789.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120233 restraints weight = 22910.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.120649 restraints weight = 17221.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121928 restraints weight = 16038.110| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14913 Z= 0.129 Angle : 0.541 8.621 20250 Z= 0.281 Chirality : 0.040 0.156 2301 Planarity : 0.004 0.080 2487 Dihedral : 9.906 154.552 2139 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.58 % Allowed : 17.64 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.20), residues: 1751 helix: 1.19 (0.15), residues: 1154 sheet: -1.19 (0.60), residues: 68 loop : -1.71 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 427 TYR 0.015 0.001 TYR C 573 PHE 0.018 0.001 PHE B 413 TRP 0.036 0.001 TRP C 440 HIS 0.004 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00288 (14910) covalent geometry : angle 0.53813 (20241) hydrogen bonds : bond 0.03950 ( 922) hydrogen bonds : angle 4.08310 ( 2691) link_NAG-ASN : bond 0.00432 ( 3) link_NAG-ASN : angle 2.87916 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8190 (m) REVERT: B 241 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6723 (mt0) REVERT: B 413 PHE cc_start: 0.7821 (t80) cc_final: 0.7608 (t80) REVERT: C 217 ASP cc_start: 0.7003 (t70) cc_final: 0.6499 (t70) REVERT: C 311 LEU cc_start: 0.8848 (tp) cc_final: 0.8581 (tt) REVERT: C 608 LYS cc_start: 0.4844 (pttp) cc_final: 0.4545 (mmtm) REVERT: D 210 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8442 (mt) REVERT: D 639 MET cc_start: 0.5991 (tmm) cc_final: 0.5790 (tmm) outliers start: 40 outliers final: 23 residues processed: 216 average time/residue: 0.0945 time to fit residues: 32.5206 Evaluate side-chains 194 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 616 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 0.0060 chunk 95 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 GLN C 299 ASN C 317 ASN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN D 426 ASN D 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.144827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113384 restraints weight = 33880.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114936 restraints weight = 33945.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.115745 restraints weight = 27687.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117084 restraints weight = 15982.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118055 restraints weight = 13168.670| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 14913 Z= 0.262 Angle : 0.670 9.270 20250 Z= 0.343 Chirality : 0.044 0.171 2301 Planarity : 0.005 0.077 2487 Dihedral : 9.973 156.557 2139 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.15 % Allowed : 18.40 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.20), residues: 1751 helix: 0.91 (0.15), residues: 1159 sheet: -1.09 (0.61), residues: 66 loop : -1.79 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 221 TYR 0.020 0.002 TYR B 354 PHE 0.022 0.002 PHE C 301 TRP 0.027 0.002 TRP C 440 HIS 0.005 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00615 (14910) covalent geometry : angle 0.66651 (20241) hydrogen bonds : bond 0.04700 ( 922) hydrogen bonds : angle 4.32427 ( 2691) link_NAG-ASN : bond 0.00609 ( 3) link_NAG-ASN : angle 3.13271 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 ASP cc_start: 0.7117 (m-30) cc_final: 0.6740 (m-30) REVERT: B 241 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6836 (mt0) REVERT: B 424 MET cc_start: 0.7780 (mmm) cc_final: 0.7573 (mmm) REVERT: C 217 ASP cc_start: 0.7394 (t70) cc_final: 0.7012 (t70) REVERT: C 309 TYR cc_start: 0.8306 (m-10) cc_final: 0.8095 (m-80) REVERT: C 311 LEU cc_start: 0.8718 (tp) cc_final: 0.8432 (tt) REVERT: D 530 THR cc_start: 0.7611 (p) cc_final: 0.7210 (t) REVERT: D 532 MET cc_start: 0.7380 (mmp) cc_final: 0.7147 (tpt) outliers start: 49 outliers final: 35 residues processed: 213 average time/residue: 0.1048 time to fit residues: 34.8320 Evaluate side-chains 197 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 616 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 150 optimal weight: 0.5980 chunk 127 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 159 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 ASN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.149931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.111968 restraints weight = 44919.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114031 restraints weight = 35811.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115576 restraints weight = 21600.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115778 restraints weight = 15078.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116089 restraints weight = 16070.200| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14913 Z= 0.125 Angle : 0.554 9.826 20250 Z= 0.286 Chirality : 0.040 0.154 2301 Planarity : 0.004 0.067 2487 Dihedral : 9.812 153.398 2139 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.21 % Allowed : 20.16 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1751 helix: 1.17 (0.15), residues: 1163 sheet: -1.03 (0.65), residues: 61 loop : -1.58 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 439 TYR 0.015 0.001 TYR C 573 PHE 0.025 0.001 PHE B 413 TRP 0.025 0.001 TRP C 440 HIS 0.004 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00276 (14910) covalent geometry : angle 0.55062 (20241) hydrogen bonds : bond 0.03985 ( 922) hydrogen bonds : angle 4.13010 ( 2691) link_NAG-ASN : bond 0.00361 ( 3) link_NAG-ASN : angle 2.77676 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6748 (mt0) REVERT: B 424 MET cc_start: 0.7363 (mmm) cc_final: 0.7075 (mmm) REVERT: B 603 ARG cc_start: 0.6218 (tpp80) cc_final: 0.5460 (mmt180) REVERT: C 217 ASP cc_start: 0.6984 (t70) cc_final: 0.6577 (t70) REVERT: C 309 TYR cc_start: 0.8236 (m-10) cc_final: 0.7940 (m-10) REVERT: C 311 LEU cc_start: 0.8819 (tp) cc_final: 0.8604 (tt) REVERT: C 519 MET cc_start: 0.7628 (tpt) cc_final: 0.6942 (tpt) REVERT: C 608 LYS cc_start: 0.5004 (pttp) cc_final: 0.4719 (mmtm) REVERT: D 307 ILE cc_start: 0.8115 (tp) cc_final: 0.7780 (tp) REVERT: D 530 THR cc_start: 0.7554 (p) cc_final: 0.7169 (t) outliers start: 34 outliers final: 25 residues processed: 212 average time/residue: 0.0942 time to fit residues: 31.7943 Evaluate side-chains 206 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 0.0770 chunk 85 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.150659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120882 restraints weight = 40482.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124474 restraints weight = 53271.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.126675 restraints weight = 21894.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.128062 restraints weight = 14346.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.128735 restraints weight = 11592.931| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14913 Z= 0.123 Angle : 0.561 10.429 20250 Z= 0.289 Chirality : 0.040 0.156 2301 Planarity : 0.004 0.065 2487 Dihedral : 9.725 154.033 2139 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.21 % Allowed : 21.24 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1751 helix: 1.31 (0.15), residues: 1164 sheet: -1.00 (0.63), residues: 61 loop : -1.49 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 439 TYR 0.013 0.001 TYR C 573 PHE 0.013 0.001 PHE A 483 TRP 0.045 0.001 TRP C 440 HIS 0.004 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00273 (14910) covalent geometry : angle 0.55831 (20241) hydrogen bonds : bond 0.03883 ( 922) hydrogen bonds : angle 4.05880 ( 2691) link_NAG-ASN : bond 0.00357 ( 3) link_NAG-ASN : angle 2.75383 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6754 (mt0) REVERT: B 603 ARG cc_start: 0.6245 (tpp80) cc_final: 0.5499 (mmt180) REVERT: C 217 ASP cc_start: 0.7018 (t70) cc_final: 0.6565 (t70) REVERT: C 311 LEU cc_start: 0.8691 (tp) cc_final: 0.8432 (tt) REVERT: C 519 MET cc_start: 0.7565 (tpt) cc_final: 0.6896 (tpt) REVERT: C 608 LYS cc_start: 0.5038 (pttp) cc_final: 0.4624 (ttpt) REVERT: D 530 THR cc_start: 0.7506 (p) cc_final: 0.7074 (t) outliers start: 34 outliers final: 31 residues processed: 212 average time/residue: 0.1005 time to fit residues: 33.3912 Evaluate side-chains 204 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 618 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 117 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 152 optimal weight: 0.6980 chunk 166 optimal weight: 0.0170 chunk 79 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.148318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111045 restraints weight = 49330.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113295 restraints weight = 42434.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.115313 restraints weight = 24849.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115180 restraints weight = 17996.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115910 restraints weight = 17347.962| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14913 Z= 0.154 Angle : 0.589 10.812 20250 Z= 0.300 Chirality : 0.041 0.155 2301 Planarity : 0.005 0.158 2487 Dihedral : 9.720 154.744 2139 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.46 % Allowed : 21.30 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.21), residues: 1751 helix: 1.29 (0.15), residues: 1162 sheet: -1.07 (0.62), residues: 62 loop : -1.48 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 439 TYR 0.015 0.001 TYR C 573 PHE 0.035 0.001 PHE B 413 TRP 0.040 0.001 TRP C 440 HIS 0.004 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00356 (14910) covalent geometry : angle 0.58602 (20241) hydrogen bonds : bond 0.04001 ( 922) hydrogen bonds : angle 4.08801 ( 2691) link_NAG-ASN : bond 0.00392 ( 3) link_NAG-ASN : angle 2.77701 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6754 (mt0) REVERT: B 603 ARG cc_start: 0.6235 (tpp80) cc_final: 0.5409 (mmt180) REVERT: C 217 ASP cc_start: 0.7102 (t70) cc_final: 0.6646 (t70) REVERT: C 311 LEU cc_start: 0.8863 (tp) cc_final: 0.8638 (tt) REVERT: C 519 MET cc_start: 0.7614 (tpt) cc_final: 0.6941 (tpt) REVERT: C 607 MET cc_start: 0.6536 (ttm) cc_final: 0.6315 (mtt) REVERT: C 608 LYS cc_start: 0.5077 (pttp) cc_final: 0.4675 (ttpt) outliers start: 38 outliers final: 35 residues processed: 201 average time/residue: 0.0994 time to fit residues: 31.6313 Evaluate side-chains 210 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 618 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.150739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.113905 restraints weight = 44065.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116075 restraints weight = 41292.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117944 restraints weight = 25229.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118026 restraints weight = 16626.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118692 restraints weight = 16210.342| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14913 Z= 0.119 Angle : 0.556 11.607 20250 Z= 0.285 Chirality : 0.040 0.154 2301 Planarity : 0.005 0.124 2487 Dihedral : 9.657 153.984 2139 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.27 % Allowed : 21.36 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1751 helix: 1.43 (0.15), residues: 1159 sheet: -1.09 (0.60), residues: 61 loop : -1.36 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 439 TYR 0.014 0.001 TYR C 573 PHE 0.047 0.001 PHE B 413 TRP 0.041 0.001 TRP C 440 HIS 0.005 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00264 (14910) covalent geometry : angle 0.55344 (20241) hydrogen bonds : bond 0.03758 ( 922) hydrogen bonds : angle 4.01835 ( 2691) link_NAG-ASN : bond 0.00334 ( 3) link_NAG-ASN : angle 2.68614 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6754 (mt0) REVERT: B 603 ARG cc_start: 0.6167 (tpp80) cc_final: 0.5465 (mmt180) REVERT: B 607 MET cc_start: 0.8215 (ppp) cc_final: 0.8015 (ppp) REVERT: C 217 ASP cc_start: 0.7093 (t70) cc_final: 0.6611 (t70) REVERT: C 442 ASP cc_start: 0.7432 (t70) cc_final: 0.7098 (t0) REVERT: C 519 MET cc_start: 0.7555 (tpt) cc_final: 0.6932 (tpt) REVERT: C 607 MET cc_start: 0.6576 (ttm) cc_final: 0.6369 (mtt) REVERT: C 608 LYS cc_start: 0.5018 (pttp) cc_final: 0.4708 (ttpt) outliers start: 35 outliers final: 31 residues processed: 211 average time/residue: 0.1034 time to fit residues: 34.2527 Evaluate side-chains 212 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 618 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 171 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 159 optimal weight: 0.0870 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.149598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112092 restraints weight = 50235.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114105 restraints weight = 43147.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115953 restraints weight = 25037.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115967 restraints weight = 16943.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116555 restraints weight = 16472.745| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14913 Z= 0.135 Angle : 0.576 12.414 20250 Z= 0.292 Chirality : 0.040 0.209 2301 Planarity : 0.004 0.109 2487 Dihedral : 9.642 154.738 2139 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.14 % Allowed : 21.49 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.21), residues: 1751 helix: 1.45 (0.15), residues: 1159 sheet: -1.06 (0.59), residues: 61 loop : -1.36 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 439 TYR 0.015 0.001 TYR C 573 PHE 0.046 0.001 PHE B 413 TRP 0.038 0.001 TRP C 440 HIS 0.004 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00307 (14910) covalent geometry : angle 0.57305 (20241) hydrogen bonds : bond 0.03836 ( 922) hydrogen bonds : angle 4.00980 ( 2691) link_NAG-ASN : bond 0.00374 ( 3) link_NAG-ASN : angle 2.71163 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2344.86 seconds wall clock time: 41 minutes 23.38 seconds (2483.38 seconds total)