Starting phenix.real_space_refine on Fri Jun 13 04:21:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ev9_28623/06_2025/8ev9_28623_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ev9_28623/06_2025/8ev9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ev9_28623/06_2025/8ev9_28623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ev9_28623/06_2025/8ev9_28623.map" model { file = "/net/cci-nas-00/data/ceres_data/8ev9_28623/06_2025/8ev9_28623_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ev9_28623/06_2025/8ev9_28623_neut.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.41, per 1000 atoms: 0.91 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: 3.83 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.61 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: 4.60 Time building geometry restraints manager: 4.51 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 609 or resid 801 through 802)) selection = (chain 'B' and (resid 159 through 391 or resid 393 through 609 or resid 801 thro \ ugh 802)) selection = (chain 'C' and (resid 159 through 260 or resid 270 through 391 or resid 393 thro \ ugh 609 or resid 801 through 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 40.950 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.750 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.003 TRP A 171 HIS 0.006 0.002 HIS D 251 PHE 0.028 0.003 PHE C 301 TYR 0.023 0.003 TYR C 354 ARG 0.014 0.001 ARG D 636 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 3) link_NAG-ASN : angle 2.05492 ( 9) hydrogen bonds : bond 0.11469 ( 901) hydrogen bonds : angle 5.94920 ( 2644) covalent geometry : bond 0.01035 (15013) covalent geometry : angle 1.16038 (20381) *********************** 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 : 1.656 Fit side-chains revert: symmetry clash REVERT: A 198 GLU cc_start: 0.7561 (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: 0.6394 (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: 0.7060 (ttp) REVERT: C 417 ILE cc_start: 0.8358 (mm) cc_final: 0.8137 (mt) REVERT: C 442 ASP cc_start: 0.7492 (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: 0.7535 (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: 0.7694 (mt0) outliers start: 7 outliers final: 3 residues processed: 190 average time/residue: 0.2979 time to fit residues: 81.1494 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 : 1.561 ------------------------------------------------------------------------------- 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 148 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.202153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.166717 restraints weight = 23522.841| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.89 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1328 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= 0.131 Angle : 0.540 8.042 20390 Z= 0.286 Chirality : 0.040 0.187 2319 Planarity : 0.005 0.073 2504 Dihedral : 13.166 150.462 2172 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.63 % Allowed : 17.20 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 1766 helix: -0.47 (0.13), residues: 1164 sheet: -2.27 (0.61), residues: 54 loop : -1.62 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 171 HIS 0.010 0.001 HIS D 339 PHE 0.018 0.001 PHE D 270 TYR 0.019 0.001 TYR D 252 ARG 0.007 0.000 ARG A 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00043 ( 3) link_NAG-ASN : angle 1.96786 ( 9) hydrogen bonds : bond 0.04181 ( 901) hydrogen bonds : angle 4.34579 ( 2644) covalent geometry : bond 0.00292 (15013) covalent geometry : angle 0.53836 (20381) *********************** 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 194 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 1.572 Fit side-chains REVERT: A 569 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7463 (ttt180) REVERT: B 507 ASP cc_start: 0.7965 (m-30) cc_final: 0.7724 (m-30) REVERT: C 402 MET cc_start: 0.7487 (ttp) cc_final: 0.7227 (ttp) REVERT: C 414 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7760 (mm-40) REVERT: C 418 ASP cc_start: 0.7740 (m-30) cc_final: 0.7487 (m-30) REVERT: D 353 VAL cc_start: 0.8445 (t) cc_final: 0.8047 (m) REVERT: D 428 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.6175 (m-80) REVERT: D 607 ASN cc_start: 0.7329 (m-40) cc_final: 0.7015 (m-40) outliers start: 26 outliers final: 12 residues processed: 186 average time/residue: 0.2748 time to fit residues: 75.8104 Evaluate side-chains 162 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 B residue 204 LEU Chi-restraints excluded: chain B residue 425 GLN 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 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 73 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 127 optimal weight: 0.3980 chunk 136 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN 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 = 0.4271 r_free = 0.4271 target = 0.204301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149055 restraints weight = 21915.946| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.95 r_work: 0.3413 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1677 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= 0.121 Angle : 0.504 7.811 20390 Z= 0.265 Chirality : 0.040 0.164 2319 Planarity : 0.004 0.062 2504 Dihedral : 12.801 153.211 2162 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.06 % Allowed : 17.82 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 1766 helix: 0.58 (0.15), residues: 1162 sheet: -2.61 (0.58), residues: 54 loop : -1.30 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 171 HIS 0.003 0.001 HIS D 251 PHE 0.020 0.001 PHE D 590 TYR 0.022 0.001 TYR A 423 ARG 0.006 0.000 ARG A 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 3) link_NAG-ASN : angle 2.09005 ( 9) hydrogen bonds : bond 0.03901 ( 901) hydrogen bonds : angle 4.00930 ( 2644) covalent geometry : bond 0.00271 (15013) covalent geometry : angle 0.50239 (20381) *********************** 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 190 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.749 Fit side-chains REVERT: A 569 ARG cc_start: 0.7958 (ttp80) cc_final: 0.6659 (mtt-85) REVERT: B 507 ASP cc_start: 0.8637 (m-30) cc_final: 0.8280 (m-30) REVERT: C 402 MET cc_start: 0.7862 (ttp) cc_final: 0.7617 (ttp) REVERT: C 442 ASP cc_start: 0.7991 (m-30) cc_final: 0.7704 (m-30) REVERT: C 496 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6769 (mm) REVERT: C 581 LYS cc_start: 0.6490 (tttt) cc_final: 0.6093 (tptm) REVERT: D 428 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.6562 (m-80) REVERT: D 538 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7776 (mm) REVERT: D 607 ASN cc_start: 0.7308 (m-40) cc_final: 0.7008 (m-40) outliers start: 33 outliers final: 16 residues processed: 179 average time/residue: 0.2494 time to fit residues: 68.8496 Evaluate side-chains 157 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 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 480 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 496 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 85 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 165 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 175 optimal weight: 30.0000 chunk 123 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN C 523 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 = 0.4236 r_free = 0.4236 target = 0.201949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145898 restraints weight = 22278.942| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.85 r_work: 0.3428 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15016 Z= 0.133 Angle : 0.501 7.613 20390 Z= 0.265 Chirality : 0.040 0.163 2319 Planarity : 0.004 0.061 2504 Dihedral : 12.648 153.504 2162 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.94 % Allowed : 18.26 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1766 helix: 1.01 (0.15), residues: 1167 sheet: -2.35 (0.58), residues: 54 loop : -1.17 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 171 HIS 0.003 0.001 HIS D 251 PHE 0.018 0.001 PHE D 590 TYR 0.018 0.001 TYR A 423 ARG 0.004 0.000 ARG A 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 3) link_NAG-ASN : angle 1.99497 ( 9) hydrogen bonds : bond 0.03876 ( 901) hydrogen bonds : angle 3.90811 ( 2644) covalent geometry : bond 0.00306 (15013) covalent geometry : angle 0.49922 (20381) *********************** 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 184 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.600 Fit side-chains REVERT: A 414 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6408 (mp10) REVERT: A 569 ARG cc_start: 0.8095 (ttp80) cc_final: 0.6790 (mtt-85) REVERT: B 368 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: B 507 ASP cc_start: 0.8801 (m-30) cc_final: 0.8503 (m-30) REVERT: C 402 MET cc_start: 0.8066 (ttp) cc_final: 0.7796 (ttp) REVERT: C 414 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7737 (tp40) REVERT: C 442 ASP cc_start: 0.8175 (m-30) cc_final: 0.7906 (m-30) REVERT: C 496 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6905 (mm) REVERT: D 538 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8014 (mm) REVERT: D 607 ASN cc_start: 0.7352 (m-40) cc_final: 0.7138 (m-40) outliers start: 31 outliers final: 18 residues processed: 175 average time/residue: 0.2405 time to fit residues: 64.7679 Evaluate side-chains 166 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.493 ------------------------------------------------------------------------------- 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 472 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 368 GLU Chi-restraints excluded: chain B residue 480 VAL 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 486 CYS Chi-restraints excluded: chain C residue 496 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 307 ILE Chi-restraints excluded: chain D residue 506 VAL 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 123 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 155 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 118 optimal weight: 0.0370 chunk 2 optimal weight: 0.6980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 345 HIS C 414 GLN C 523 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 = 0.4261 r_free = 0.4261 target = 0.203536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139465 restraints weight = 20197.570| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.11 r_work: 0.3404 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2000 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= 0.123 Angle : 0.481 7.425 20390 Z= 0.255 Chirality : 0.040 0.160 2319 Planarity : 0.004 0.060 2504 Dihedral : 12.535 153.720 2162 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.38 % Allowed : 18.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1766 helix: 1.24 (0.15), residues: 1169 sheet: -2.25 (0.58), residues: 54 loop : -1.05 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 373 HIS 0.004 0.001 HIS D 251 PHE 0.017 0.001 PHE D 590 TYR 0.017 0.001 TYR A 423 ARG 0.004 0.000 ARG A 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 3) link_NAG-ASN : angle 1.88583 ( 9) hydrogen bonds : bond 0.03761 ( 901) hydrogen bonds : angle 3.82217 ( 2644) covalent geometry : bond 0.00280 (15013) covalent geometry : angle 0.47995 (20381) *********************** 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 191 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 1.540 Fit side-chains REVERT: A 414 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6073 (mp10) REVERT: A 569 ARG cc_start: 0.7943 (ttp80) cc_final: 0.6619 (ttt-90) REVERT: B 368 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: B 507 ASP cc_start: 0.8676 (m-30) cc_final: 0.8346 (m-30) REVERT: C 402 MET cc_start: 0.7923 (ttp) cc_final: 0.7589 (ttp) REVERT: C 414 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7720 (mm-40) REVERT: C 418 ASP cc_start: 0.8252 (m-30) cc_final: 0.7691 (m-30) REVERT: C 442 ASP cc_start: 0.8022 (m-30) cc_final: 0.7722 (m-30) REVERT: C 496 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6816 (mm) REVERT: C 581 LYS cc_start: 0.6747 (tttt) cc_final: 0.6369 (tptm) REVERT: D 428 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.6554 (m-80) REVERT: D 461 ASP cc_start: 0.7076 (t0) cc_final: 0.6807 (t0) REVERT: D 538 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8023 (mm) REVERT: D 561 MET cc_start: 0.7624 (tpp) cc_final: 0.7413 (tpt) REVERT: D 607 ASN cc_start: 0.7332 (m-40) cc_final: 0.7104 (m-40) outliers start: 38 outliers final: 19 residues processed: 183 average time/residue: 0.2274 time to fit residues: 64.8084 Evaluate side-chains 172 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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 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 368 GLU Chi-restraints excluded: chain B residue 480 VAL 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 419 SER Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 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 307 ILE Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 0.0570 chunk 151 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN C 523 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 = 0.4221 r_free = 0.4221 target = 0.200527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.142512 restraints weight = 23662.794| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.95 r_work: 0.3390 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15016 Z= 0.160 Angle : 0.506 7.152 20390 Z= 0.268 Chirality : 0.041 0.159 2319 Planarity : 0.004 0.055 2504 Dihedral : 12.512 154.416 2162 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.25 % Allowed : 18.82 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1766 helix: 1.24 (0.15), residues: 1169 sheet: -2.34 (0.58), residues: 49 loop : -1.08 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 373 HIS 0.004 0.001 HIS D 251 PHE 0.018 0.001 PHE B 301 TYR 0.015 0.001 TYR A 423 ARG 0.004 0.000 ARG A 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00122 ( 3) link_NAG-ASN : angle 1.82802 ( 9) hydrogen bonds : bond 0.03947 ( 901) hydrogen bonds : angle 3.86659 ( 2644) covalent geometry : bond 0.00380 (15013) covalent geometry : angle 0.50471 (20381) *********************** 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 189 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 1.550 Fit side-chains REVERT: A 414 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6604 (mp10) REVERT: A 569 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7467 (ttp-110) REVERT: B 368 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: C 402 MET cc_start: 0.8169 (ttp) cc_final: 0.7776 (ttp) REVERT: C 414 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7807 (mm-40) REVERT: C 418 ASP cc_start: 0.8360 (m-30) cc_final: 0.7822 (m-30) REVERT: C 442 ASP cc_start: 0.8275 (m-30) cc_final: 0.7987 (m-30) REVERT: C 496 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6854 (mm) REVERT: C 581 LYS cc_start: 0.6719 (tttt) cc_final: 0.6344 (tptm) REVERT: D 336 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7558 (tt0) REVERT: D 461 ASP cc_start: 0.7165 (t0) cc_final: 0.6884 (t0) REVERT: D 538 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8045 (mm) REVERT: D 561 MET cc_start: 0.7739 (tpp) cc_final: 0.7521 (tpt) REVERT: D 607 ASN cc_start: 0.7323 (m-40) cc_final: 0.7107 (m-40) outliers start: 36 outliers final: 26 residues processed: 180 average time/residue: 0.2341 time to fit residues: 65.5253 Evaluate side-chains 179 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.656 ------------------------------------------------------------------------------- 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 368 GLU Chi-restraints excluded: chain B residue 401 SER 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 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 419 SER 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 486 CYS Chi-restraints excluded: chain C residue 496 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 307 ILE Chi-restraints excluded: chain D residue 453 ASN Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 105 optimal weight: 0.0070 chunk 20 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.202830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149600 restraints weight = 23170.718| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.00 r_work: 0.3409 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15016 Z= 0.112 Angle : 0.470 6.994 20390 Z= 0.249 Chirality : 0.040 0.149 2319 Planarity : 0.004 0.057 2504 Dihedral : 12.435 154.705 2162 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.25 % Allowed : 19.26 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.20), residues: 1766 helix: 1.45 (0.15), residues: 1170 sheet: -2.09 (0.58), residues: 54 loop : -1.00 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 373 HIS 0.004 0.001 HIS D 251 PHE 0.015 0.001 PHE D 590 TYR 0.016 0.001 TYR A 423 ARG 0.004 0.000 ARG A 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 3) link_NAG-ASN : angle 1.77356 ( 9) hydrogen bonds : bond 0.03689 ( 901) hydrogen bonds : angle 3.76775 ( 2644) covalent geometry : bond 0.00250 (15013) covalent geometry : angle 0.46857 (20381) *********************** 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 : 1.748 Fit side-chains REVERT: A 347 ARG cc_start: 0.7958 (ptm-80) cc_final: 0.7586 (ptt90) REVERT: A 414 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6233 (mp10) REVERT: A 569 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7337 (ttp-110) REVERT: B 368 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: B 406 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8290 (mtt) REVERT: C 402 MET cc_start: 0.7934 (ttp) cc_final: 0.7589 (ttp) REVERT: C 414 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7422 (tp40) REVERT: C 418 ASP cc_start: 0.8222 (m-30) cc_final: 0.7784 (m-30) REVERT: C 442 ASP cc_start: 0.8110 (m-30) cc_final: 0.7811 (m-30) REVERT: C 496 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6776 (mm) REVERT: C 581 LYS cc_start: 0.6720 (tttt) cc_final: 0.6354 (tptm) REVERT: D 344 ILE cc_start: 0.7634 (tt) cc_final: 0.7288 (pt) REVERT: D 428 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.6536 (m-80) REVERT: D 461 ASP cc_start: 0.7012 (t0) cc_final: 0.6732 (t0) REVERT: D 538 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8001 (mm) REVERT: D 561 MET cc_start: 0.7650 (tpp) cc_final: 0.7427 (tpt) REVERT: D 607 ASN cc_start: 0.7328 (m-40) cc_final: 0.7105 (m-40) outliers start: 36 outliers final: 22 residues processed: 183 average time/residue: 0.2530 time to fit residues: 70.9691 Evaluate side-chains 181 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 429 VAL 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 368 GLU Chi-restraints excluded: chain B residue 406 MET 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 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 536 MET Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 66 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN ** D 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4258 r_free = 0.4258 target = 0.204957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.171553 restraints weight = 25203.637| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 3.71 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15016 Z= 0.120 Angle : 0.471 7.101 20390 Z= 0.250 Chirality : 0.040 0.157 2319 Planarity : 0.004 0.053 2504 Dihedral : 12.389 153.811 2162 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.38 % Allowed : 19.45 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 1766 helix: 1.50 (0.15), residues: 1175 sheet: -1.93 (0.61), residues: 54 loop : -0.97 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 373 HIS 0.004 0.001 HIS D 251 PHE 0.042 0.001 PHE D 590 TYR 0.015 0.001 TYR A 423 ARG 0.003 0.000 ARG A 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 3) link_NAG-ASN : angle 1.72857 ( 9) hydrogen bonds : bond 0.03666 ( 901) hydrogen bonds : angle 3.74173 ( 2644) covalent geometry : bond 0.00275 (15013) covalent geometry : angle 0.47014 (20381) *********************** 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 204 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 1.693 Fit side-chains REVERT: A 414 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6357 (mp10) REVERT: B 368 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: B 406 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7942 (mtt) REVERT: C 402 MET cc_start: 0.7598 (ttp) cc_final: 0.7168 (ttp) REVERT: C 414 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7674 (tp40) REVERT: C 418 ASP cc_start: 0.7753 (m-30) cc_final: 0.7462 (m-30) REVERT: C 496 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7220 (mm) REVERT: D 344 ILE cc_start: 0.7183 (tt) cc_final: 0.6959 (pt) REVERT: D 428 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6120 (m-80) REVERT: D 484 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6185 (mp0) REVERT: D 538 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8192 (mm) REVERT: D 607 ASN cc_start: 0.7271 (m-40) cc_final: 0.7011 (m-40) outliers start: 38 outliers final: 22 residues processed: 194 average time/residue: 0.2681 time to fit residues: 80.2714 Evaluate side-chains 183 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 2.195 ------------------------------------------------------------------------------- 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 429 VAL 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 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 368 GLU Chi-restraints excluded: chain B residue 406 MET 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 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 82 optimal weight: 0.0070 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN C 473 HIS ** D 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4268 r_free = 0.4268 target = 0.205936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.172683 restraints weight = 29086.586| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 4.05 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3943 r_free = 0.3943 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3943 r_free = 0.3943 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2350 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= 0.111 Angle : 0.472 7.279 20390 Z= 0.249 Chirality : 0.040 0.279 2319 Planarity : 0.004 0.053 2504 Dihedral : 12.334 153.152 2162 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.94 % Allowed : 19.95 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1766 helix: 1.57 (0.15), residues: 1181 sheet: -1.71 (0.62), residues: 54 loop : -0.89 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 171 HIS 0.004 0.001 HIS D 251 PHE 0.037 0.001 PHE D 590 TYR 0.014 0.001 TYR A 423 ARG 0.005 0.000 ARG B 499 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 3) link_NAG-ASN : angle 1.66945 ( 9) hydrogen bonds : bond 0.03582 ( 901) hydrogen bonds : angle 3.71033 ( 2644) covalent geometry : bond 0.00249 (15013) covalent geometry : angle 0.47089 (20381) *********************** 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 189 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 1.585 Fit side-chains REVERT: A 414 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6251 (mp10) REVERT: A 569 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7532 (ttt-90) REVERT: A 583 ASP cc_start: 0.7689 (m-30) cc_final: 0.7435 (m-30) REVERT: B 368 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: B 402 MET cc_start: 0.7042 (ttp) cc_final: 0.6788 (ttt) REVERT: C 402 MET cc_start: 0.7670 (ttp) cc_final: 0.7262 (ttp) REVERT: C 414 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7741 (tp40) REVERT: C 418 ASP cc_start: 0.7722 (m-30) cc_final: 0.7441 (m-30) REVERT: C 496 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7227 (mm) REVERT: D 428 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6128 (m-80) REVERT: D 484 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6105 (mp0) REVERT: D 538 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8201 (mm) REVERT: D 607 ASN cc_start: 0.7296 (m-40) cc_final: 0.7021 (m-40) outliers start: 31 outliers final: 21 residues processed: 182 average time/residue: 0.2760 time to fit residues: 78.1102 Evaluate side-chains 183 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 3.215 ------------------------------------------------------------------------------- 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 430 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 529 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 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 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU 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 538 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 141 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 36 optimal weight: 0.2980 chunk 150 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 61 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN ** D 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4252 r_free = 0.4252 target = 0.204000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.169097 restraints weight = 24941.740| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.93 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3930 r_free = 0.3930 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3930 r_free = 0.3930 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2419 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= 0.105 Angle : 0.470 7.144 20390 Z= 0.247 Chirality : 0.040 0.241 2319 Planarity : 0.004 0.054 2504 Dihedral : 12.256 152.950 2160 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.94 % Allowed : 19.95 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1766 helix: 1.64 (0.15), residues: 1182 sheet: -1.50 (0.58), residues: 64 loop : -0.82 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 171 HIS 0.004 0.001 HIS D 251 PHE 0.036 0.001 PHE D 590 TYR 0.014 0.001 TYR A 423 ARG 0.005 0.000 ARG B 499 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 3) link_NAG-ASN : angle 1.64658 ( 9) hydrogen bonds : bond 0.03528 ( 901) hydrogen bonds : angle 3.66670 ( 2644) covalent geometry : bond 0.00233 (15013) covalent geometry : angle 0.46853 (20381) ********************** 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: 31 poor density : 159 time to evaluate : 1.734 Fit side-chains REVERT: A 414 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6019 (mp10) REVERT: A 418 ASP cc_start: 0.7090 (t0) cc_final: 0.6853 (m-30) REVERT: A 569 ARG cc_start: 0.7779 (ttp80) cc_final: 0.7496 (ttt-90) REVERT: B 368 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: B 402 MET cc_start: 0.6954 (ttp) cc_final: 0.6665 (ttt) REVERT: C 402 MET cc_start: 0.7570 (ttp) cc_final: 0.7174 (ttp) REVERT: C 418 ASP cc_start: 0.7707 (m-30) cc_final: 0.7450 (m-30) REVERT: D 428 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6094 (m-80) REVERT: D 484 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6135 (mp0) REVERT: D 538 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8171 (mm) REVERT: D 607 ASN cc_start: 0.7291 (m-40) cc_final: 0.7030 (m-40) outliers start: 31 outliers final: 22 residues processed: 183 average time/residue: 0.2592 time to fit residues: 74.0674 Evaluate side-chains 184 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 430 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 529 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 368 GLU Chi-restraints excluded: chain B residue 401 SER 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 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU 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 538 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 128 optimal weight: 30.0000 chunk 11 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 162 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN D 566 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.199450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138633 restraints weight = 23680.792| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.33 r_work: 0.3362 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2408 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= 0.128 Angle : 0.484 7.287 20390 Z= 0.255 Chirality : 0.041 0.255 2319 Planarity : 0.004 0.053 2504 Dihedral : 12.258 153.261 2160 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.00 % Allowed : 19.89 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1766 helix: 1.61 (0.15), residues: 1181 sheet: -1.45 (0.59), residues: 64 loop : -0.80 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 373 HIS 0.004 0.001 HIS D 251 PHE 0.014 0.001 PHE B 301 TYR 0.013 0.001 TYR A 423 ARG 0.005 0.000 ARG B 499 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 3) link_NAG-ASN : angle 1.63043 ( 9) hydrogen bonds : bond 0.03632 ( 901) hydrogen bonds : angle 3.68533 ( 2644) covalent geometry : bond 0.00298 (15013) covalent geometry : angle 0.48264 (20381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7784.67 seconds wall clock time: 136 minutes 7.97 seconds (8167.97 seconds total)