Starting phenix.real_space_refine on Wed Mar 4 15:48:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ev9_28623/03_2026/8ev9_28623_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ev9_28623/03_2026/8ev9_28623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ev9_28623/03_2026/8ev9_28623_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ev9_28623/03_2026/8ev9_28623_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ev9_28623/03_2026/8ev9_28623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ev9_28623/03_2026/8ev9_28623.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 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 9556 2.51 5 N 2387 2.21 5 O 2648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 190 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: 14661 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3631 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: 3695 Chain: "B" Number of atoms: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3624 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 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: 3591 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 438, 3583 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 438, 3583 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 1 bond proxies already assigned to first conformer: 3663 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} Time building chain proxies: 4.29, per 1000 atoms: 0.29 Number of scatterers: 14661 At special positions: 0 Unit cell: (109.56, 109.56, 126.99, 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 2648 8.00 N 2387 7.00 C 9556 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: 1.30 Conformation dependent library (CDL) restraints added in 904.5 milliseconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 12 sheets defined 66.3% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 166 through 193 Proline residue: A 178 - end of helix removed outlier: 4.049A pdb=" N ASP A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.832A pdb=" N TYR A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 222 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.942A pdb=" N LYS A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.680A pdb=" N LEU A 278 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 279 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.148A 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 405 removed outlier: 3.576A pdb=" N LEU A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 428 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 478 removed outlier: 3.693A pdb=" N LEU A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASP A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N THR A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 498 Processing helix chain 'A' and resid 548 through 554 Processing helix chain 'A' and resid 581 through 589 Processing helix chain 'A' and resid 591 through 608 removed outlier: 3.728A pdb=" N LYS A 595 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 193 Proline residue: B 178 - end of helix removed outlier: 4.060A pdb=" N ASP B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 199 through 223 Processing helix chain 'B' and resid 235 through 246 removed outlier: 3.642A pdb=" N THR B 246 " --> pdb=" O HIS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.887A pdb=" N LEU B 278 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.149A 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 407 removed outlier: 3.649A pdb=" N ASN B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 427 Processing helix chain 'B' and resid 430 through 447 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 461 through 478 removed outlier: 5.559A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 480 No H-bonds generated for 'chain 'B' and resid 479 through 480' Processing helix chain 'B' and resid 481 through 485 removed outlier: 4.063A pdb=" N ASP B 485 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 498 Processing helix chain 'B' and resid 581 through 589 removed outlier: 4.237A pdb=" N ALA B 587 " --> pdb=" O ASP B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 610 Processing helix chain 'C' and resid 166 through 193 Proline residue: C 178 - end of helix removed outlier: 4.142A pdb=" N ASP C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 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 255 removed outlier: 4.123A pdb=" N LYS C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 266 Processing helix chain 'C' and resid 270 through 279 removed outlier: 4.140A pdb=" N VAL C 273 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASN C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 278 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.830A pdb=" N LEU C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) 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 407 removed outlier: 3.760A pdb=" N ASN C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 427 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: 5.628A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 497 Processing helix chain 'C' and resid 581 through 586 Processing helix chain 'C' and resid 591 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 271 removed outlier: 3.896A pdb=" N ILE D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 275 removed outlier: 4.231A pdb=" N LEU D 275 " --> pdb=" O GLN D 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 275' Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 298 through 307 removed outlier: 4.062A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 removed outlier: 3.594A pdb=" N ILE D 312 " --> pdb=" O PRO D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 309 through 312' Processing helix chain 'D' and resid 313 through 318 removed outlier: 3.904A pdb=" N PHE D 317 " --> pdb=" O CYS D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 329 Processing helix chain 'D' and resid 330 through 345 removed outlier: 4.058A pdb=" N PHE D 334 " --> pdb=" O LYS D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 379 removed outlier: 4.042A 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 447 Processing helix chain 'D' and resid 449 through 469 Processing helix chain 'D' and resid 472 through 491 Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.598A pdb=" N LEU D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 521 removed outlier: 3.654A pdb=" N VAL D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 631 through 646 Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228 removed outlier: 3.630A pdb=" N LEU A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 502 Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510 removed outlier: 6.723A pdb=" N ILE A 568 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 228 removed outlier: 3.565A 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 Processing sheet with id=AA6, first strand: chain 'B' and resid 540 through 541 removed outlier: 3.621A pdb=" N ALA B 528 " --> pdb=" O ARG B 569 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 228 removed outlier: 3.510A pdb=" N GLU C 228 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 231 " --> pdb=" O GLU C 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 499 through 502 Processing sheet with id=AA9, first strand: chain 'C' and resid 508 through 510 removed outlier: 6.934A pdb=" N ILE C 568 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 278 through 279 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: 6.713A pdb=" N PHE D 550 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA D 610 " --> pdb=" O PHE D 550 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS D 552 " --> pdb=" O VAL D 608 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL D 569 " --> pdb=" O THR D 583 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N THR D 583 " --> pdb=" O VAL D 569 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL D 571 " --> pdb=" O LEU D 581 " (cutoff:3.500A) 901 hydrogen bonds defined for protein. 2644 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: 2.19 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3951 1.34 - 1.46: 3340 1.46 - 1.58: 7615 1.58 - 1.70: 2 1.70 - 1.82: 105 Bond restraints: 15013 Sorted by residual: 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 3.42e+01 bond pdb=" O5' PCG C 802 " pdb=" PA PCG C 802 " ideal model delta sigma weight residual 1.606 1.490 0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" O5' PCG D 901 " pdb=" PA PCG D 901 " ideal model delta sigma weight residual 1.606 1.490 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" O5' PCG B 802 " pdb=" PA PCG B 802 " ideal model delta sigma weight residual 1.606 1.490 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" O3' PCG B 802 " pdb=" PA PCG B 802 " ideal model delta sigma weight residual 1.617 1.513 0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 15008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 20074 3.66 - 7.31: 240 7.31 - 10.97: 49 10.97 - 14.63: 6 14.63 - 18.28: 12 Bond angle restraints: 20381 Sorted by residual: angle pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " pdb=" C5' PCG A 802 " ideal model delta sigma weight residual 109.85 128.13 -18.28 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 109.85 128.12 -18.27 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 109.85 128.08 -18.23 3.00e+00 1.11e-01 3.69e+01 angle pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " pdb=" C5' PCG B 802 " ideal model delta sigma weight residual 109.85 128.05 -18.20 3.00e+00 1.11e-01 3.68e+01 angle pdb=" N ALA C 566 " pdb=" CA ALA C 566 " pdb=" C ALA C 566 " ideal model delta sigma weight residual 108.99 118.23 -9.24 1.57e+00 4.06e-01 3.46e+01 ... (remaining 20376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 8360 25.94 - 51.87: 559 51.87 - 77.81: 51 77.81 - 103.74: 10 103.74 - 129.68: 16 Dihedral angle restraints: 8996 sinusoidal: 3745 harmonic: 5251 Sorted by residual: dihedral pdb=" CA GLY D 389 " pdb=" C GLY D 389 " pdb=" N GLU D 390 " pdb=" CA GLU D 390 " ideal model delta harmonic sigma weight residual -180.00 -154.48 -25.52 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA APHE A 392 " pdb=" C PHE A 392 " pdb=" N ALA A 393 " pdb=" CA ALA A 393 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA GLY B 367 " pdb=" C GLY B 367 " pdb=" N GLU B 368 " pdb=" CA GLU B 368 " ideal model delta harmonic sigma weight residual 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 8993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 2314 0.356 - 0.712: 1 0.712 - 1.068: 0 1.068 - 1.424: 0 1.424 - 1.780: 4 Chirality restraints: 2319 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 7.92e+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 7.91e+01 chirality pdb=" C4' PCG D 901 " pdb=" C3' PCG D 901 " pdb=" C5' PCG D 901 " pdb=" O4' PCG D 901 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.90e+01 ... (remaining 2316 not shown) Planarity restraints: 2507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.062 5.00e-02 4.00e+02 9.34e-02 1.39e+01 pdb=" N PRO D 273 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 411 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO D 412 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 412 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 412 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 369 " 0.044 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO A 370 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.036 5.00e-02 4.00e+02 ... (remaining 2504 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 132 2.59 - 3.17: 11539 3.17 - 3.75: 23513 3.75 - 4.32: 31180 4.32 - 4.90: 52695 Nonbonded interactions: 119059 Sorted by model distance: nonbonded pdb=" CG2 ILE D 236 " pdb=" CD PRO D 237 " model vdw 2.017 3.860 nonbonded pdb=" OD1 ASP A 432 " pdb=" N LEU A 433 " model vdw 2.117 3.120 nonbonded pdb=" CB ARG A 564 " pdb=" O1A PCG A 802 " model vdw 2.292 3.440 nonbonded pdb=" CA ARG A 564 " pdb=" O1A PCG A 802 " model vdw 2.315 3.470 nonbonded pdb=" OG1 THR D 605 " pdb=" N2 PCG D 901 " model vdw 2.315 3.120 ... (remaining 119054 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 260 or resid 270 through 391 or resid 393 thro \ ugh 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 260 or resid 270 through 391 or resid 393 thro \ ugh 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.370 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.010 0.117 15016 Z= 0.435 Angle : 1.161 18.285 20390 Z= 0.581 Chirality : 0.098 1.780 2319 Planarity : 0.008 0.093 2504 Dihedral : 17.527 129.678 5622 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.44 % Allowed : 15.45 % 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: -4.23 (0.14), residues: 1766 helix: -2.85 (0.09), residues: 1158 sheet: -2.25 (0.63), residues: 53 loop : -2.25 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 636 TYR 0.023 0.003 TYR C 354 PHE 0.028 0.003 PHE C 301 TRP 0.031 0.003 TRP A 171 HIS 0.006 0.002 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.01035 (15013) covalent geometry : angle 1.16038 (20381) hydrogen bonds : bond 0.11469 ( 901) hydrogen bonds : angle 5.94920 ( 2644) link_NAG-ASN : bond 0.00368 ( 3) link_NAG-ASN : angle 2.05492 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 184 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 198 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7330 (mt-10) REVERT: A 272 GLU cc_start: 0.7121 (mp0) cc_final: 0.6895 (mp0) REVERT: A 414 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.5380 (mp10) REVERT: B 410 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6392 (tmm160) REVERT: B 499 ARG cc_start: 0.7686 (ttp80) cc_final: 0.7339 (ptt-90) REVERT: B 521 ILE cc_start: 0.8566 (mt) cc_final: 0.8191 (mm) REVERT: C 402 MET cc_start: 0.7322 (ttp) cc_final: 0.7062 (ttp) REVERT: C 417 ILE cc_start: 0.8358 (mm) cc_final: 0.8136 (mt) REVERT: C 442 ASP cc_start: 0.7491 (m-30) cc_final: 0.7180 (m-30) REVERT: C 575 ASP cc_start: 0.8418 (t0) cc_final: 0.8195 (t0) REVERT: D 336 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7318 (mt-10) REVERT: D 484 GLU cc_start: 0.6934 (mp0) cc_final: 0.6572 (mm-30) REVERT: D 570 GLN cc_start: 0.7985 (mt0) cc_final: 0.7687 (mt0) outliers start: 7 outliers final: 3 residues processed: 190 average time/residue: 0.1290 time to fit residues: 35.3515 Evaluate side-chains 157 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 152 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 456 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.0270 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 276 ASN A 299 ASN A 473 HIS B 196 GLN B 229 GLN B 276 ASN B 317 ASN B 398 ASN B 414 GLN C 229 GLN C 317 ASN C 398 ASN C 407 ASN C 414 GLN C 484 GLN C 523 ASN D 232 ASN D 339 HIS D 365 HIS D 367 ASN D 426 ASN D 452 GLN D 453 ASN D 566 HIS D 570 GLN D 602 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.202997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.159980 restraints weight = 18730.807| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 3.54 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15016 Z= 0.127 Angle : 0.537 8.170 20390 Z= 0.285 Chirality : 0.040 0.184 2319 Planarity : 0.005 0.075 2504 Dihedral : 13.160 151.952 2172 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.63 % Allowed : 16.89 % Favored : 81.49 % 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: -1.48 (0.18), residues: 1766 helix: -0.50 (0.13), residues: 1164 sheet: -2.28 (0.61), residues: 54 loop : -1.61 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 223 TYR 0.018 0.001 TYR D 252 PHE 0.018 0.001 PHE D 590 TRP 0.018 0.001 TRP A 171 HIS 0.010 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00268 (15013) covalent geometry : angle 0.53581 (20381) hydrogen bonds : bond 0.04151 ( 901) hydrogen bonds : angle 4.34657 ( 2644) link_NAG-ASN : bond 0.00052 ( 3) link_NAG-ASN : angle 1.96402 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.420 Fit side-chains REVERT: A 569 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7306 (ttt180) REVERT: B 507 ASP cc_start: 0.8000 (m-30) cc_final: 0.7739 (m-30) REVERT: C 402 MET cc_start: 0.7477 (ttp) cc_final: 0.7245 (ttp) REVERT: D 353 VAL cc_start: 0.8444 (t) cc_final: 0.8034 (m) REVERT: D 428 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6274 (m-80) REVERT: D 607 ASN cc_start: 0.7427 (m-40) cc_final: 0.7083 (m-40) outliers start: 26 outliers final: 10 residues processed: 187 average time/residue: 0.1217 time to fit residues: 33.6270 Evaluate side-chains 157 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 129 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 317 ASN C 317 ASN C 414 GLN C 523 ASN D 426 ASN D 453 ASN D 566 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.195863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.162153 restraints weight = 29245.736| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.96 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3849 r_free = 0.3849 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3849 r_free = 0.3849 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 15016 Z= 0.380 Angle : 0.739 9.865 20390 Z= 0.384 Chirality : 0.049 0.189 2319 Planarity : 0.005 0.075 2504 Dihedral : 13.101 156.662 2162 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.81 % Allowed : 17.64 % Favored : 79.55 % 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: -1.17 (0.18), residues: 1766 helix: -0.21 (0.14), residues: 1168 sheet: -2.44 (0.61), residues: 49 loop : -1.64 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 223 TYR 0.022 0.003 TYR C 352 PHE 0.026 0.002 PHE B 301 TRP 0.017 0.003 TRP C 335 HIS 0.004 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00928 (15013) covalent geometry : angle 0.73766 (20381) hydrogen bonds : bond 0.05348 ( 901) hydrogen bonds : angle 4.61929 ( 2644) link_NAG-ASN : bond 0.00182 ( 3) link_NAG-ASN : angle 2.21904 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 414 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.6558 (mp10) REVERT: B 368 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: C 414 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7473 (tp40) REVERT: C 418 ASP cc_start: 0.7944 (m-30) cc_final: 0.7564 (m-30) REVERT: D 424 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8019 (tp) REVERT: D 538 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8216 (mm) REVERT: D 545 TYR cc_start: 0.8480 (m-80) cc_final: 0.8249 (m-80) REVERT: D 607 ASN cc_start: 0.7360 (m-40) cc_final: 0.7054 (m110) outliers start: 45 outliers final: 25 residues processed: 196 average time/residue: 0.1046 time to fit residues: 31.6046 Evaluate side-chains 184 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 129 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN B 317 ASN C 345 HIS C 414 GLN C 523 ASN D 426 ASN D 453 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.200521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146262 restraints weight = 23661.450| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.11 r_work: 0.3346 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15016 Z= 0.154 Angle : 0.537 7.507 20390 Z= 0.283 Chirality : 0.042 0.217 2319 Planarity : 0.004 0.073 2504 Dihedral : 12.751 155.216 2162 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.19 % Allowed : 19.39 % Favored : 78.42 % 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: -0.24 (0.19), residues: 1766 helix: 0.58 (0.15), residues: 1167 sheet: -2.32 (0.62), residues: 44 loop : -1.43 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 223 TYR 0.019 0.001 TYR A 423 PHE 0.017 0.001 PHE D 590 TRP 0.017 0.001 TRP A 171 HIS 0.003 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00362 (15013) covalent geometry : angle 0.53556 (20381) hydrogen bonds : bond 0.04173 ( 901) hydrogen bonds : angle 4.13608 ( 2644) link_NAG-ASN : bond 0.00084 ( 3) link_NAG-ASN : angle 2.06202 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.499 Fit side-chains REVERT: A 414 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6132 (mp10) REVERT: A 569 ARG cc_start: 0.7595 (ttp-110) cc_final: 0.6477 (mtt180) REVERT: B 580 SER cc_start: 0.7716 (OUTLIER) cc_final: 0.7173 (p) REVERT: C 414 GLN cc_start: 0.8380 (mm110) cc_final: 0.7652 (mm-40) REVERT: C 418 ASP cc_start: 0.8328 (m-30) cc_final: 0.7727 (m-30) REVERT: C 442 ASP cc_start: 0.8033 (m-30) cc_final: 0.7759 (m-30) REVERT: C 581 LYS cc_start: 0.6463 (tttt) cc_final: 0.6060 (tptm) REVERT: D 561 MET cc_start: 0.7541 (tpt) cc_final: 0.7159 (tpt) REVERT: D 607 ASN cc_start: 0.7296 (m-40) cc_final: 0.6999 (m-40) outliers start: 35 outliers final: 22 residues processed: 191 average time/residue: 0.1101 time to fit residues: 32.0570 Evaluate side-chains 175 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 513 ASP Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 24 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 152 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 ASN D 426 ASN D 453 ASN D 566 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.201206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 141)---------------| | r_work = 0.3590 r_free = 0.3590 target = 0.137399 restraints weight = 22202.723| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.95 r_work: 0.3335 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15016 Z= 0.143 Angle : 0.512 6.814 20390 Z= 0.271 Chirality : 0.041 0.203 2319 Planarity : 0.004 0.063 2504 Dihedral : 12.611 153.590 2162 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.00 % Allowed : 20.14 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.20), residues: 1766 helix: 0.96 (0.15), residues: 1169 sheet: -2.54 (0.59), residues: 49 loop : -1.24 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.023 0.001 TYR D 252 PHE 0.015 0.001 PHE D 590 TRP 0.015 0.001 TRP D 373 HIS 0.004 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00334 (15013) covalent geometry : angle 0.51004 (20381) hydrogen bonds : bond 0.04028 ( 901) hydrogen bonds : angle 3.98455 ( 2644) link_NAG-ASN : bond 0.00092 ( 3) link_NAG-ASN : angle 1.94631 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.587 Fit side-chains REVERT: A 247 THR cc_start: 0.7067 (p) cc_final: 0.6843 (t) REVERT: A 414 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6185 (mp10) REVERT: B 580 SER cc_start: 0.7688 (OUTLIER) cc_final: 0.7102 (p) REVERT: C 414 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7586 (mm-40) REVERT: C 418 ASP cc_start: 0.8287 (m-30) cc_final: 0.7660 (m-30) REVERT: C 442 ASP cc_start: 0.8018 (m-30) cc_final: 0.7634 (m-30) REVERT: D 561 MET cc_start: 0.7527 (tpt) cc_final: 0.7138 (tpt) REVERT: D 607 ASN cc_start: 0.7216 (m-40) cc_final: 0.6945 (m-40) outliers start: 32 outliers final: 20 residues processed: 174 average time/residue: 0.1090 time to fit residues: 29.2993 Evaluate side-chains 170 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 504 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 61 optimal weight: 0.1980 chunk 36 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 0.0170 chunk 37 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 HIS C 523 ASN D 426 ASN D 453 ASN D 566 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.202231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.167512 restraints weight = 25258.288| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 4.01 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15016 Z= 0.110 Angle : 0.477 6.705 20390 Z= 0.253 Chirality : 0.040 0.191 2319 Planarity : 0.004 0.062 2504 Dihedral : 12.472 153.021 2162 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.88 % Allowed : 20.70 % Favored : 77.42 % 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: 0.64 (0.20), residues: 1766 helix: 1.26 (0.15), residues: 1174 sheet: -2.25 (0.60), residues: 54 loop : -1.07 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.021 0.001 TYR D 252 PHE 0.012 0.001 PHE D 590 TRP 0.014 0.001 TRP A 171 HIS 0.004 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00245 (15013) covalent geometry : angle 0.47574 (20381) hydrogen bonds : bond 0.03710 ( 901) hydrogen bonds : angle 3.80637 ( 2644) link_NAG-ASN : bond 0.00087 ( 3) link_NAG-ASN : angle 1.81898 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.488 Fit side-chains REVERT: A 414 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.6350 (mp10) REVERT: B 368 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: C 414 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7808 (mm-40) REVERT: C 418 ASP cc_start: 0.7796 (m-30) cc_final: 0.7522 (m-30) REVERT: C 581 LYS cc_start: 0.7011 (tttt) cc_final: 0.6698 (tptm) REVERT: D 607 ASN cc_start: 0.7339 (m-40) cc_final: 0.7013 (m-40) outliers start: 30 outliers final: 22 residues processed: 180 average time/residue: 0.1053 time to fit residues: 29.2883 Evaluate side-chains 177 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 453 ASN Chi-restraints excluded: chain D residue 504 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 148 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 523 ASN D 426 ASN D 453 ASN D 566 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.204243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.170847 restraints weight = 24665.920| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.76 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15016 Z= 0.124 Angle : 0.486 6.762 20390 Z= 0.257 Chirality : 0.041 0.188 2319 Planarity : 0.004 0.059 2504 Dihedral : 12.434 152.882 2162 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.25 % Allowed : 20.58 % Favored : 77.17 % 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: 0.77 (0.20), residues: 1766 helix: 1.33 (0.15), residues: 1182 sheet: -2.15 (0.61), residues: 54 loop : -1.01 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.018 0.001 TYR D 252 PHE 0.014 0.001 PHE D 432 TRP 0.013 0.001 TRP D 373 HIS 0.004 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00282 (15013) covalent geometry : angle 0.48484 (20381) hydrogen bonds : bond 0.03748 ( 901) hydrogen bonds : angle 3.78535 ( 2644) link_NAG-ASN : bond 0.00092 ( 3) link_NAG-ASN : angle 1.75609 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.525 Fit side-chains REVERT: A 414 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.6373 (mp10) REVERT: B 368 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: C 414 GLN cc_start: 0.8161 (mm110) cc_final: 0.7773 (mm-40) REVERT: C 418 ASP cc_start: 0.7767 (m-30) cc_final: 0.7489 (m-30) REVERT: D 607 ASN cc_start: 0.7277 (m-40) cc_final: 0.6953 (m-40) outliers start: 36 outliers final: 29 residues processed: 189 average time/residue: 0.1036 time to fit residues: 30.2675 Evaluate side-chains 182 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 91 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 0.0370 chunk 56 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 523 ASN D 426 ASN D 453 ASN D 566 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.204802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.171782 restraints weight = 27892.138| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.88 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15016 Z= 0.116 Angle : 0.479 6.774 20390 Z= 0.253 Chirality : 0.040 0.183 2319 Planarity : 0.004 0.054 2504 Dihedral : 12.380 152.721 2162 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.69 % Allowed : 20.14 % Favored : 77.17 % 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: 0.94 (0.20), residues: 1766 helix: 1.46 (0.15), residues: 1176 sheet: -1.99 (0.62), residues: 54 loop : -0.92 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.026 0.001 TYR A 508 PHE 0.015 0.001 PHE C 413 TRP 0.013 0.001 TRP D 373 HIS 0.004 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00264 (15013) covalent geometry : angle 0.47755 (20381) hydrogen bonds : bond 0.03678 ( 901) hydrogen bonds : angle 3.74721 ( 2644) link_NAG-ASN : bond 0.00094 ( 3) link_NAG-ASN : angle 1.70724 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 0.559 Fit side-chains REVERT: A 414 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.6444 (mp10) REVERT: B 368 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: D 428 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6072 (m-80) REVERT: D 484 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: D 607 ASN cc_start: 0.7336 (m-40) cc_final: 0.7053 (m-40) outliers start: 43 outliers final: 35 residues processed: 186 average time/residue: 0.1072 time to fit residues: 30.6792 Evaluate side-chains 187 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 453 ASN Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.0980 chunk 156 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 30.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN D 426 ASN D 453 ASN D 566 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.201638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146587 restraints weight = 20660.395| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.89 r_work: 0.3414 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15016 Z= 0.135 Angle : 0.493 6.897 20390 Z= 0.261 Chirality : 0.041 0.181 2319 Planarity : 0.004 0.052 2504 Dihedral : 12.371 153.001 2162 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.44 % Allowed : 20.76 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.20), residues: 1766 helix: 1.45 (0.15), residues: 1173 sheet: -1.82 (0.63), residues: 54 loop : -0.84 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 499 TYR 0.026 0.001 TYR A 508 PHE 0.015 0.001 PHE B 301 TRP 0.013 0.001 TRP D 373 HIS 0.004 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00315 (15013) covalent geometry : angle 0.49143 (20381) hydrogen bonds : bond 0.03760 ( 901) hydrogen bonds : angle 3.77124 ( 2644) link_NAG-ASN : bond 0.00101 ( 3) link_NAG-ASN : angle 1.69161 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.571 Fit side-chains REVERT: A 414 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.6678 (mp10) REVERT: A 494 LEU cc_start: 0.8112 (mm) cc_final: 0.7895 (mm) REVERT: B 368 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: C 414 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7642 (tp40) REVERT: D 428 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: D 607 ASN cc_start: 0.7342 (m-40) cc_final: 0.7122 (m-40) outliers start: 39 outliers final: 34 residues processed: 183 average time/residue: 0.1041 time to fit residues: 29.6882 Evaluate side-chains 188 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 453 ASN Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 28 optimal weight: 8.9990 chunk 137 optimal weight: 0.6980 chunk 162 optimal weight: 0.0370 chunk 175 optimal weight: 30.0000 chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 86 optimal weight: 0.0270 chunk 51 optimal weight: 0.7980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN D 453 ASN D 566 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.203031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.166859 restraints weight = 27137.830| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 4.46 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15016 Z= 0.106 Angle : 0.476 6.600 20390 Z= 0.252 Chirality : 0.040 0.177 2319 Planarity : 0.004 0.053 2504 Dihedral : 12.328 152.544 2162 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.31 % Allowed : 20.76 % Favored : 76.92 % 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: 1.11 (0.21), residues: 1766 helix: 1.56 (0.15), residues: 1173 sheet: -1.70 (0.64), residues: 54 loop : -0.78 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 499 TYR 0.023 0.001 TYR A 508 PHE 0.013 0.001 PHE C 413 TRP 0.015 0.001 TRP D 373 HIS 0.005 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00232 (15013) covalent geometry : angle 0.47523 (20381) hydrogen bonds : bond 0.03630 ( 901) hydrogen bonds : angle 3.72026 ( 2644) link_NAG-ASN : bond 0.00092 ( 3) link_NAG-ASN : angle 1.67496 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.516 Fit side-chains REVERT: A 368 GLU cc_start: 0.6509 (mm-30) cc_final: 0.6272 (mm-30) REVERT: A 414 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6389 (mp10) REVERT: B 368 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: C 414 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7785 (tp40) REVERT: D 484 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6225 (mp0) REVERT: D 607 ASN cc_start: 0.7372 (m-40) cc_final: 0.7055 (m110) outliers start: 37 outliers final: 30 residues processed: 181 average time/residue: 0.1053 time to fit residues: 29.7943 Evaluate side-chains 183 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 29 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 122 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 72 optimal weight: 0.0980 chunk 127 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN D 453 ASN D 566 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.203196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147361 restraints weight = 19154.753| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.84 r_work: 0.3436 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15016 Z= 0.107 Angle : 0.477 6.817 20390 Z= 0.250 Chirality : 0.041 0.357 2319 Planarity : 0.004 0.051 2504 Dihedral : 12.290 152.478 2162 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.19 % Allowed : 20.89 % Favored : 76.92 % 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: 1.17 (0.21), residues: 1766 helix: 1.60 (0.15), residues: 1171 sheet: -1.56 (0.59), residues: 64 loop : -0.73 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 499 TYR 0.021 0.001 TYR A 508 PHE 0.012 0.001 PHE D 590 TRP 0.013 0.001 TRP D 373 HIS 0.005 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00236 (15013) covalent geometry : angle 0.47593 (20381) hydrogen bonds : bond 0.03569 ( 901) hydrogen bonds : angle 3.69884 ( 2644) link_NAG-ASN : bond 0.00102 ( 3) link_NAG-ASN : angle 1.63156 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3182.76 seconds wall clock time: 55 minutes 21.07 seconds (3321.07 seconds total)