Starting phenix.real_space_refine on Fri Jun 13 02:28:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eva_28624/06_2025/8eva_28624_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eva_28624/06_2025/8eva_28624.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/8eva_28624/06_2025/8eva_28624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eva_28624/06_2025/8eva_28624.map" model { file = "/net/cci-nas-00/data/ceres_data/8eva_28624/06_2025/8eva_28624_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eva_28624/06_2025/8eva_28624_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= 0.034 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 9514 2.51 5 N 2373 2.21 5 O 2634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 194 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: 14591 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3634 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3623 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 444, 3623 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 bond proxies already assigned to first conformer: 3692 Chain: "B" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3563 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 14, 'TRANS': 420} Chain breaks: 2 Chain: "C" Number of atoms: 3681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3681 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 14, 'TRANS': 437} Chain: "D" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3579 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 12, 'TRANS': 424} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 392 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 392 " occ=0.50 Time building chain proxies: 10.45, per 1000 atoms: 0.72 Number of scatterers: 14591 At special positions: 0 Unit cell: (110.39, 107.07, 126.16, 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 2634 8.00 N 2373 7.00 C 9514 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: 3.79 Conformation dependent library (CDL) restraints added in 2.3 seconds 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3358 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 13 sheets defined 66.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 166 through 193 Proline residue: A 178 - end of helix removed outlier: 3.845A pdb=" N ASP A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.705A 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 247 through 255 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.948A pdb=" N PHE A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.210A 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 407 Processing helix chain 'A' and resid 407 through 427 Processing helix chain 'A' and resid 430 through 448 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 461 through 473 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 487 through 498 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 592 through 608 Processing helix chain 'B' and resid 166 through 193 Proline residue: B 178 - end of helix removed outlier: 4.074A pdb=" N TYR B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 223 Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.990A pdb=" N LYS B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 279 Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.321A 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 Processing helix chain 'B' and resid 407 through 428 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: 3.750A pdb=" N ILE B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 498 Processing helix chain 'B' and resid 580 through 590 removed outlier: 3.902A pdb=" N LEU B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 611 removed outlier: 4.355A pdb=" N LYS B 595 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 193 Proline residue: C 178 - end of helix removed outlier: 3.926A pdb=" N ASP C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 removed outlier: 3.691A pdb=" N TYR C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 222 Processing helix chain 'C' and resid 235 through 245 Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 259 through 267 removed outlier: 3.518A pdb=" N GLY C 267 " --> pdb=" O TYR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 removed outlier: 4.063A pdb=" N VAL C 273 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 278 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 293 removed outlier: 3.917A 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: 3.612A 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 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 478 removed outlier: 5.754A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 498 Processing helix chain 'C' and resid 549 through 554 removed outlier: 4.149A pdb=" N LEU C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN C 554 " --> pdb=" O ILE C 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 549 through 554' Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 592 through 609 Processing helix chain 'D' and resid 215 through 242 Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 249 through 271 removed outlier: 3.866A pdb=" N ILE D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 275 removed outlier: 3.810A 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: 3.973A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 330 through 345 removed outlier: 4.293A pdb=" N PHE D 334 " --> pdb=" O LYS D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 379 removed outlier: 4.057A 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 449 removed outlier: 3.594A pdb=" N PHE D 432 " --> pdb=" O PHE D 428 " (cutoff:3.500A) 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: 3.964A pdb=" N LEU D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 521 removed outlier: 3.938A pdb=" N VAL D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 526 removed outlier: 3.958A pdb=" N LYS D 526 " --> pdb=" O ASP D 523 " (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 Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.598A pdb=" N ASP A 575 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510 removed outlier: 6.311A pdb=" N ILE A 568 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 228 Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 503 removed outlier: 3.510A pdb=" N PHE B 547 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 508 through 510 removed outlier: 7.109A pdb=" N ILE B 568 " --> pdb=" O ILE B 509 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 567 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'C' and resid 499 through 502 Processing sheet with id=AA9, first strand: chain 'C' and resid 508 through 510 removed outlier: 7.010A pdb=" N ILE C 568 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 514 through 515 removed outlier: 3.725A pdb=" N ASP C 514 " --> pdb=" O ARG C 564 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 277 through 279 removed outlier: 4.090A pdb=" N PHE D 277 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 282 " --> pdb=" O ARG D 279 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AB4, first strand: chain 'D' and resid 550 through 552 removed outlier: 6.652A pdb=" N PHE D 550 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA D 610 " --> pdb=" O PHE D 550 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS D 552 " --> pdb=" O VAL D 608 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2683 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: 4.37 Time building geometry restraints manager: 4.47 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: 4442 1.34 - 1.46: 3247 1.46 - 1.58: 7147 1.58 - 1.70: 0 1.70 - 1.81: 105 Bond restraints: 14941 Sorted by residual: bond pdb=" O5' PCG D 901 " pdb=" PA PCG D 901 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.41e+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 3.38e+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 3.37e+01 bond pdb=" O5' PCG A 802 " pdb=" PA PCG A 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 A 802 " pdb=" PA PCG A 802 " ideal model delta sigma weight residual 1.617 1.513 0.104 2.00e-02 2.50e+03 2.71e+01 ... (remaining 14936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 20075 3.67 - 7.33: 150 7.33 - 11.00: 43 11.00 - 14.67: 4 14.67 - 18.34: 12 Bond angle restraints: 20284 Sorted by residual: angle pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " pdb=" C5' PCG B 802 " ideal model delta sigma weight residual 109.85 128.19 -18.34 3.00e+00 1.11e-01 3.74e+01 angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 109.85 128.11 -18.26 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " pdb=" C5' PCG A 802 " ideal model delta sigma weight residual 109.85 128.09 -18.24 3.00e+00 1.11e-01 3.70e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 109.85 128.09 -18.24 3.00e+00 1.11e-01 3.70e+01 angle pdb=" O1A PCG B 802 " pdb=" PA PCG B 802 " pdb=" O5' PCG B 802 " ideal model delta sigma weight residual 102.28 117.96 -15.68 3.00e+00 1.11e-01 2.73e+01 ... (remaining 20279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 8289 25.94 - 51.87: 579 51.87 - 77.80: 51 77.80 - 103.74: 12 103.74 - 129.67: 16 Dihedral angle restraints: 8947 sinusoidal: 3725 harmonic: 5222 Sorted by residual: dihedral pdb=" C3' PCG C 802 " pdb=" O3' PCG C 802 " pdb=" PA PCG C 802 " pdb=" O2A PCG C 802 " ideal model delta sinusoidal sigma weight residual 279.09 149.42 129.67 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C3' PCG B 802 " pdb=" O3' PCG B 802 " pdb=" PA PCG B 802 " pdb=" O2A PCG B 802 " ideal model delta sinusoidal sigma weight residual 279.09 149.44 129.65 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C3' PCG D 901 " pdb=" O3' PCG D 901 " pdb=" PA PCG D 901 " pdb=" O2A PCG D 901 " ideal model delta sinusoidal sigma weight residual 279.09 149.46 129.63 1 3.00e+01 1.11e-03 1.75e+01 ... (remaining 8944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 2305 0.356 - 0.712: 0 0.712 - 1.067: 0 1.067 - 1.423: 0 1.423 - 1.779: 4 Chirality restraints: 2309 Sorted by residual: chirality pdb=" C4' PCG B 802 " pdb=" C3' PCG B 802 " pdb=" C5' PCG B 802 " pdb=" O4' PCG B 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.91e+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 7.91e+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 ... (remaining 2306 not shown) Planarity restraints: 2494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO D 273 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 369 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO A 370 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 502 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO D 503 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 503 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 503 " 0.037 5.00e-02 4.00e+02 ... (remaining 2491 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2650 2.77 - 3.30: 13362 3.30 - 3.83: 25074 3.83 - 4.37: 28114 4.37 - 4.90: 49075 Nonbonded interactions: 118275 Sorted by model distance: nonbonded pdb=" O MET C 585 " pdb=" OG1 THR C 589 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASP D 529 " pdb=" OG SER D 634 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR A 259 " pdb=" O VAL A 273 " model vdw 2.315 3.040 nonbonded pdb=" ND2 ASN A 317 " pdb=" OD1 ASP A 384 " model vdw 2.334 3.120 nonbonded pdb=" OE1 GLN A 604 " pdb=" NZ LYS A 608 " model vdw 2.334 3.120 ... (remaining 118270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 258 or resid 270 through 391 or resid 393 thro \ ugh 554 or resid 562 through 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 258 or resid 270 through 391 or resid 393 thro \ ugh 554 or resid 562 through 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=0.50 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.820 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 14944 Z= 0.313 Angle : 1.025 18.336 20293 Z= 0.506 Chirality : 0.091 1.779 2309 Planarity : 0.008 0.080 2491 Dihedral : 17.842 129.674 5589 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.82 % Allowed : 16.03 % Favored : 83.16 % 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: -3.78 (0.15), residues: 1755 helix: -2.32 (0.11), residues: 1153 sheet: -2.33 (0.63), residues: 60 loop : -2.49 (0.22), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 171 HIS 0.005 0.001 HIS D 251 PHE 0.019 0.002 PHE C 192 TYR 0.022 0.002 TYR B 354 ARG 0.007 0.000 ARG A 481 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 3) link_NAG-ASN : angle 2.28980 ( 9) hydrogen bonds : bond 0.11641 ( 925) hydrogen bonds : angle 5.54726 ( 2683) covalent geometry : bond 0.00677 (14941) covalent geometry : angle 1.02411 (20284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LYS cc_start: 0.8306 (mtpp) cc_final: 0.8059 (mtmt) REVERT: A 599 GLU cc_start: 0.7332 (tt0) cc_final: 0.6836 (tm-30) REVERT: B 392 PHE cc_start: 0.7506 (t80) cc_final: 0.7254 (t80) REVERT: B 463 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7622 (pptt) REVERT: C 193 ASP cc_start: 0.8303 (t70) cc_final: 0.7982 (t0) REVERT: C 439 ARG cc_start: 0.7737 (mtm180) cc_final: 0.7376 (mtp85) REVERT: C 524 GLU cc_start: 0.7288 (tp30) cc_final: 0.7054 (tp30) REVERT: C 563 ARG cc_start: 0.5732 (OUTLIER) cc_final: 0.5493 (mtp85) REVERT: D 352 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7201 (mtt90) REVERT: D 443 ASP cc_start: 0.8451 (t0) cc_final: 0.8240 (t0) REVERT: D 453 ASN cc_start: 0.8425 (m-40) cc_final: 0.8012 (m110) REVERT: D 497 ASP cc_start: 0.7679 (t0) cc_final: 0.7418 (t0) outliers start: 13 outliers final: 7 residues processed: 212 average time/residue: 0.3473 time to fit residues: 105.8862 Evaluate side-chains 172 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 563 ARG Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 456 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 158 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 405 ASN A 523 ASN B 196 GLN B 237 ASN B 317 ASN B 345 HIS B 422 GLN B 447 ASN B 484 GLN C 248 GLN C 299 ASN C 317 ASN C 567 ASN C 604 GLN D 230 ASN D 232 ASN D 276 GLN D 326 ASN D 340 HIS D 365 HIS D 367 ASN D 426 ASN D 453 ASN D 531 GLN D 630 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.196673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149634 restraints weight = 18797.390| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.96 r_work: 0.3246 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14944 Z= 0.129 Angle : 0.540 7.664 20293 Z= 0.286 Chirality : 0.040 0.152 2309 Planarity : 0.005 0.061 2491 Dihedral : 13.225 154.218 2173 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.01 % Allowed : 18.92 % Favored : 79.07 % 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 (0.18), residues: 1755 helix: -0.15 (0.14), residues: 1158 sheet: -1.95 (0.63), residues: 58 loop : -1.90 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 445 HIS 0.004 0.001 HIS B 473 PHE 0.019 0.001 PHE C 413 TYR 0.015 0.001 TYR B 352 ARG 0.003 0.000 ARG A 569 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 3) link_NAG-ASN : angle 2.16771 ( 9) hydrogen bonds : bond 0.04240 ( 925) hydrogen bonds : angle 4.43207 ( 2683) covalent geometry : bond 0.00282 (14941) covalent geometry : angle 0.53829 (20284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5840 (OUTLIER) cc_final: 0.3866 (t80) REVERT: A 344 GLU cc_start: 0.7287 (tp30) cc_final: 0.6801 (tt0) REVERT: A 391 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.5656 (mp) REVERT: A 418 ASP cc_start: 0.6824 (m-30) cc_final: 0.6290 (p0) REVERT: A 448 LYS cc_start: 0.8690 (mtpp) cc_final: 0.8335 (mtmt) REVERT: A 599 GLU cc_start: 0.8182 (tt0) cc_final: 0.7073 (tm-30) REVERT: B 270 TYR cc_start: 0.4841 (OUTLIER) cc_final: 0.3915 (p90) REVERT: B 392 PHE cc_start: 0.7801 (t80) cc_final: 0.7563 (t80) REVERT: B 514 ASP cc_start: 0.8567 (t0) cc_final: 0.7963 (m-30) REVERT: C 193 ASP cc_start: 0.8690 (t70) cc_final: 0.8351 (t0) REVERT: C 223 ARG cc_start: 0.8059 (mtt-85) cc_final: 0.7613 (mtm-85) REVERT: C 426 PHE cc_start: 0.5286 (OUTLIER) cc_final: 0.4559 (t80) REVERT: C 439 ARG cc_start: 0.7993 (mtm180) cc_final: 0.7564 (mtp180) REVERT: C 549 GLU cc_start: 0.7702 (pt0) cc_final: 0.7085 (pt0) REVERT: D 443 ASP cc_start: 0.8634 (t0) cc_final: 0.8231 (t0) REVERT: D 497 ASP cc_start: 0.8381 (t0) cc_final: 0.7976 (t0) outliers start: 32 outliers final: 12 residues processed: 209 average time/residue: 0.2633 time to fit residues: 82.4327 Evaluate side-chains 189 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 155 optimal weight: 0.2980 chunk 40 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.193231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131012 restraints weight = 19690.437| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.43 r_work: 0.3285 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14944 Z= 0.173 Angle : 0.556 8.516 20293 Z= 0.292 Chirality : 0.042 0.156 2309 Planarity : 0.004 0.047 2491 Dihedral : 12.931 150.701 2152 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.26 % Allowed : 20.62 % Favored : 77.12 % 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: -0.33 (0.19), residues: 1755 helix: 0.58 (0.15), residues: 1161 sheet: -1.85 (0.64), residues: 58 loop : -1.71 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 PHE 0.024 0.001 PHE D 516 TYR 0.017 0.001 TYR B 352 ARG 0.004 0.000 ARG B 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00091 ( 3) link_NAG-ASN : angle 2.19549 ( 9) hydrogen bonds : bond 0.04359 ( 925) hydrogen bonds : angle 4.29267 ( 2683) covalent geometry : bond 0.00404 (14941) covalent geometry : angle 0.55448 (20284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5930 (OUTLIER) cc_final: 0.4193 (t80) REVERT: A 344 GLU cc_start: 0.7201 (tp30) cc_final: 0.6673 (tt0) REVERT: A 391 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.5636 (mp) REVERT: A 418 ASP cc_start: 0.6816 (m-30) cc_final: 0.6297 (p0) REVERT: A 448 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8343 (mtmt) REVERT: A 599 GLU cc_start: 0.8218 (tt0) cc_final: 0.7099 (tm-30) REVERT: B 161 VAL cc_start: 0.8682 (t) cc_final: 0.8470 (m) REVERT: B 238 ARG cc_start: 0.7773 (mmm-85) cc_final: 0.7323 (ttp80) REVERT: B 270 TYR cc_start: 0.4749 (OUTLIER) cc_final: 0.3814 (p90) REVERT: B 392 PHE cc_start: 0.7838 (t80) cc_final: 0.7520 (t80) REVERT: B 425 GLN cc_start: 0.6744 (mp10) cc_final: 0.6424 (mp10) REVERT: B 514 ASP cc_start: 0.8603 (t0) cc_final: 0.8030 (m-30) REVERT: B 570 SER cc_start: 0.9007 (m) cc_final: 0.8224 (p) REVERT: C 193 ASP cc_start: 0.8590 (t70) cc_final: 0.8235 (t0) REVERT: C 223 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.7571 (mtm-85) REVERT: C 426 PHE cc_start: 0.5257 (OUTLIER) cc_final: 0.4594 (t80) REVERT: C 439 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7543 (mtp180) REVERT: D 352 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7761 (mtm-85) REVERT: D 443 ASP cc_start: 0.8685 (t0) cc_final: 0.8255 (t0) REVERT: D 497 ASP cc_start: 0.8444 (t0) cc_final: 0.7997 (t0) REVERT: D 607 ASN cc_start: 0.8151 (m-40) cc_final: 0.7941 (m-40) REVERT: D 608 VAL cc_start: 0.8803 (t) cc_final: 0.8556 (p) outliers start: 36 outliers final: 15 residues processed: 207 average time/residue: 0.2599 time to fit residues: 79.4144 Evaluate side-chains 194 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 55 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 135 optimal weight: 0.0050 chunk 26 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN C 604 GLN D 531 GLN D 570 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.196173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3516 r_free = 0.3516 target = 0.131058 restraints weight = 20490.726| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.57 r_work: 0.3310 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 14944 Z= 0.134 Angle : 0.518 8.079 20293 Z= 0.271 Chirality : 0.040 0.151 2309 Planarity : 0.004 0.041 2491 Dihedral : 12.735 151.690 2152 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.26 % Allowed : 21.81 % Favored : 75.93 % 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: 0.27 (0.20), residues: 1755 helix: 1.07 (0.15), residues: 1161 sheet: -1.73 (0.64), residues: 58 loop : -1.54 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 PHE 0.016 0.001 PHE C 413 TYR 0.018 0.001 TYR C 546 ARG 0.004 0.000 ARG D 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 3) link_NAG-ASN : angle 2.09774 ( 9) hydrogen bonds : bond 0.04086 ( 925) hydrogen bonds : angle 4.10866 ( 2683) covalent geometry : bond 0.00309 (14941) covalent geometry : angle 0.51633 (20284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5956 (OUTLIER) cc_final: 0.4494 (t80) REVERT: A 418 ASP cc_start: 0.6747 (m-30) cc_final: 0.6367 (p0) REVERT: A 448 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8148 (ptpp) REVERT: A 599 GLU cc_start: 0.8152 (tt0) cc_final: 0.7126 (tm-30) REVERT: B 238 ARG cc_start: 0.7744 (mmm-85) cc_final: 0.7462 (ttp80) REVERT: B 270 TYR cc_start: 0.4836 (OUTLIER) cc_final: 0.3915 (p90) REVERT: B 392 PHE cc_start: 0.7820 (t80) cc_final: 0.7476 (t80) REVERT: B 425 GLN cc_start: 0.6717 (mp10) cc_final: 0.6508 (mp10) REVERT: B 514 ASP cc_start: 0.8684 (t0) cc_final: 0.8058 (m-30) REVERT: B 570 SER cc_start: 0.8993 (m) cc_final: 0.8217 (p) REVERT: C 193 ASP cc_start: 0.8482 (t70) cc_final: 0.8133 (t0) REVERT: C 223 ARG cc_start: 0.7942 (mtt-85) cc_final: 0.7575 (mtm-85) REVERT: C 426 PHE cc_start: 0.5338 (OUTLIER) cc_final: 0.4523 (t80) REVERT: C 439 ARG cc_start: 0.7923 (mtm180) cc_final: 0.7523 (mtp180) REVERT: D 279 ARG cc_start: 0.8408 (tmm-80) cc_final: 0.8065 (ttp-170) REVERT: D 352 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7728 (mtm-85) REVERT: D 443 ASP cc_start: 0.8683 (t0) cc_final: 0.8263 (t0) REVERT: D 497 ASP cc_start: 0.8463 (t0) cc_final: 0.8030 (t0) REVERT: D 607 ASN cc_start: 0.8142 (m-40) cc_final: 0.7936 (m-40) REVERT: D 608 VAL cc_start: 0.8856 (t) cc_final: 0.8617 (p) REVERT: D 639 MET cc_start: 0.6542 (mmm) cc_final: 0.6309 (mmm) outliers start: 36 outliers final: 13 residues processed: 203 average time/residue: 0.2935 time to fit residues: 87.7633 Evaluate side-chains 184 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 14 optimal weight: 0.0570 chunk 142 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 overall best weight: 1.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.196774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126210 restraints weight = 25606.464| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.82 r_work: 0.3274 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14944 Z= 0.146 Angle : 0.526 8.310 20293 Z= 0.274 Chirality : 0.041 0.151 2309 Planarity : 0.004 0.037 2491 Dihedral : 12.648 151.902 2152 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.26 % Allowed : 22.19 % Favored : 75.55 % 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: 0.52 (0.20), residues: 1755 helix: 1.26 (0.15), residues: 1153 sheet: -1.18 (0.65), residues: 63 loop : -1.46 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 PHE 0.015 0.001 PHE D 516 TYR 0.014 0.001 TYR B 352 ARG 0.004 0.000 ARG D 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 3) link_NAG-ASN : angle 2.08029 ( 9) hydrogen bonds : bond 0.04112 ( 925) hydrogen bonds : angle 4.08541 ( 2683) covalent geometry : bond 0.00341 (14941) covalent geometry : angle 0.52427 (20284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 1.634 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5905 (OUTLIER) cc_final: 0.4548 (t80) REVERT: A 418 ASP cc_start: 0.6820 (m-30) cc_final: 0.6431 (p0) REVERT: A 448 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8160 (ptpp) REVERT: B 238 ARG cc_start: 0.7717 (mmm-85) cc_final: 0.7507 (ttp80) REVERT: B 270 TYR cc_start: 0.4797 (OUTLIER) cc_final: 0.3853 (p90) REVERT: B 392 PHE cc_start: 0.7837 (t80) cc_final: 0.7494 (t80) REVERT: B 425 GLN cc_start: 0.6569 (mp10) cc_final: 0.6236 (mp10) REVERT: B 514 ASP cc_start: 0.8727 (t0) cc_final: 0.8050 (m-30) REVERT: B 570 SER cc_start: 0.8987 (m) cc_final: 0.8179 (p) REVERT: C 223 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.7582 (mtm-85) REVERT: C 426 PHE cc_start: 0.5426 (OUTLIER) cc_final: 0.4669 (t80) REVERT: C 439 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7494 (mtp180) REVERT: C 455 GLU cc_start: 0.8169 (mp0) cc_final: 0.7858 (mp0) REVERT: D 279 ARG cc_start: 0.8398 (tmm-80) cc_final: 0.8060 (ttp-170) REVERT: D 352 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7730 (mtm-85) REVERT: D 443 ASP cc_start: 0.8627 (t0) cc_final: 0.8181 (t0) REVERT: D 497 ASP cc_start: 0.8537 (t0) cc_final: 0.8107 (t0) REVERT: D 531 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.6447 (mm110) REVERT: D 608 VAL cc_start: 0.8854 (t) cc_final: 0.8578 (p) outliers start: 36 outliers final: 18 residues processed: 201 average time/residue: 0.2676 time to fit residues: 79.8203 Evaluate side-chains 191 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 125 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.194884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.128022 restraints weight = 24484.029| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.78 r_work: 0.3263 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14944 Z= 0.139 Angle : 0.513 8.298 20293 Z= 0.269 Chirality : 0.041 0.149 2309 Planarity : 0.004 0.036 2491 Dihedral : 12.571 152.055 2152 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.89 % Allowed : 21.94 % Favored : 75.17 % 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: 0.69 (0.20), residues: 1755 helix: 1.39 (0.15), residues: 1153 sheet: -1.19 (0.64), residues: 63 loop : -1.38 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 PHE 0.010 0.001 PHE D 590 TYR 0.014 0.001 TYR B 352 ARG 0.002 0.000 ARG B 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 3) link_NAG-ASN : angle 2.02591 ( 9) hydrogen bonds : bond 0.04042 ( 925) hydrogen bonds : angle 4.03699 ( 2683) covalent geometry : bond 0.00320 (14941) covalent geometry : angle 0.51173 (20284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5978 (OUTLIER) cc_final: 0.4729 (t80) REVERT: A 391 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.5673 (mp) REVERT: A 418 ASP cc_start: 0.6771 (m-30) cc_final: 0.6414 (p0) REVERT: A 448 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8155 (ptpp) REVERT: B 238 ARG cc_start: 0.7686 (mmm-85) cc_final: 0.7422 (ttp80) REVERT: B 270 TYR cc_start: 0.4845 (OUTLIER) cc_final: 0.3855 (p90) REVERT: B 392 PHE cc_start: 0.7828 (t80) cc_final: 0.7457 (t80) REVERT: B 425 GLN cc_start: 0.6449 (mp10) cc_final: 0.6110 (mp10) REVERT: B 511 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7502 (mttt) REVERT: B 519 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7225 (ttp) REVERT: B 570 SER cc_start: 0.8972 (m) cc_final: 0.8192 (p) REVERT: C 223 ARG cc_start: 0.7944 (mtt-85) cc_final: 0.7584 (mtm-85) REVERT: C 402 MET cc_start: 0.6394 (tmm) cc_final: 0.6189 (tmm) REVERT: C 426 PHE cc_start: 0.5383 (OUTLIER) cc_final: 0.4634 (t80) REVERT: C 439 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7510 (mtp180) REVERT: C 455 GLU cc_start: 0.8157 (mp0) cc_final: 0.7859 (mp0) REVERT: D 279 ARG cc_start: 0.8386 (tmm-80) cc_final: 0.8048 (ttp-170) REVERT: D 443 ASP cc_start: 0.8605 (t0) cc_final: 0.8163 (t0) REVERT: D 497 ASP cc_start: 0.8554 (t0) cc_final: 0.8128 (t0) REVERT: D 608 VAL cc_start: 0.8839 (t) cc_final: 0.8574 (p) outliers start: 46 outliers final: 26 residues processed: 211 average time/residue: 0.2562 time to fit residues: 81.2993 Evaluate side-chains 201 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 151 optimal weight: 0.5980 chunk 169 optimal weight: 0.0370 chunk 110 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 127 optimal weight: 20.0000 chunk 85 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN D 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.198990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150222 restraints weight = 18276.213| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.92 r_work: 0.3255 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14944 Z= 0.110 Angle : 0.490 8.237 20293 Z= 0.255 Chirality : 0.039 0.145 2309 Planarity : 0.003 0.036 2491 Dihedral : 12.401 152.680 2148 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.07 % Allowed : 22.75 % Favored : 75.17 % 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: 0.99 (0.21), residues: 1755 helix: 1.61 (0.15), residues: 1156 sheet: -1.23 (0.64), residues: 63 loop : -1.21 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 445 HIS 0.004 0.001 HIS B 473 PHE 0.012 0.001 PHE D 590 TYR 0.011 0.001 TYR B 184 ARG 0.002 0.000 ARG B 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00037 ( 3) link_NAG-ASN : angle 1.88325 ( 9) hydrogen bonds : bond 0.03732 ( 925) hydrogen bonds : angle 3.90292 ( 2683) covalent geometry : bond 0.00243 (14941) covalent geometry : angle 0.48800 (20284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5762 (OUTLIER) cc_final: 0.4673 (t80) REVERT: A 391 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.5560 (mp) REVERT: A 425 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6255 (mm110) REVERT: A 448 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8101 (ptpp) REVERT: B 238 ARG cc_start: 0.7688 (mmm-85) cc_final: 0.7464 (ttp80) REVERT: B 270 TYR cc_start: 0.4836 (OUTLIER) cc_final: 0.3939 (p90) REVERT: B 392 PHE cc_start: 0.7757 (t80) cc_final: 0.7412 (t80) REVERT: B 425 GLN cc_start: 0.6377 (mp10) cc_final: 0.6062 (mp10) REVERT: B 511 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7513 (mmtp) REVERT: B 519 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7152 (ttp) REVERT: B 570 SER cc_start: 0.8937 (m) cc_final: 0.8146 (p) REVERT: C 193 ASP cc_start: 0.8326 (t70) cc_final: 0.8043 (t0) REVERT: C 223 ARG cc_start: 0.8010 (mtt-85) cc_final: 0.7650 (mtm-85) REVERT: D 279 ARG cc_start: 0.8367 (tmm-80) cc_final: 0.8049 (ttp-170) REVERT: D 443 ASP cc_start: 0.8531 (t0) cc_final: 0.8108 (t0) REVERT: D 497 ASP cc_start: 0.8581 (t0) cc_final: 0.8158 (t0) REVERT: D 531 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6715 (mm-40) REVERT: D 608 VAL cc_start: 0.8865 (t) cc_final: 0.8600 (p) outliers start: 33 outliers final: 16 residues processed: 208 average time/residue: 0.2899 time to fit residues: 89.7581 Evaluate side-chains 192 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 69 optimal weight: 2.9990 chunk 141 optimal weight: 0.0570 chunk 92 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 chunk 72 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 170 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 425 GLN B 537 GLN C 299 ASN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.197621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.132615 restraints weight = 25256.088| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.71 r_work: 0.3363 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14944 Z= 0.102 Angle : 0.494 9.199 20293 Z= 0.256 Chirality : 0.039 0.175 2309 Planarity : 0.003 0.035 2491 Dihedral : 12.334 152.763 2148 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.14 % Allowed : 23.26 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1755 helix: 1.77 (0.15), residues: 1157 sheet: -1.34 (0.67), residues: 53 loop : -1.13 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 445 HIS 0.004 0.001 HIS B 473 PHE 0.012 0.001 PHE D 590 TYR 0.010 0.001 TYR C 546 ARG 0.002 0.000 ARG B 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00052 ( 3) link_NAG-ASN : angle 1.74090 ( 9) hydrogen bonds : bond 0.03620 ( 925) hydrogen bonds : angle 3.82092 ( 2683) covalent geometry : bond 0.00217 (14941) covalent geometry : angle 0.49240 (20284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 1.552 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5731 (OUTLIER) cc_final: 0.4881 (t80) REVERT: A 425 GLN cc_start: 0.6684 (OUTLIER) cc_final: 0.6354 (mm110) REVERT: A 448 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8149 (ptpp) REVERT: B 270 TYR cc_start: 0.4931 (OUTLIER) cc_final: 0.4086 (p90) REVERT: B 392 PHE cc_start: 0.7624 (t80) cc_final: 0.7326 (t80) REVERT: B 425 GLN cc_start: 0.6254 (mp10) cc_final: 0.5986 (mp10) REVERT: B 519 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7069 (ttp) REVERT: B 570 SER cc_start: 0.8869 (m) cc_final: 0.8092 (p) REVERT: C 193 ASP cc_start: 0.8204 (t70) cc_final: 0.7886 (t0) REVERT: C 223 ARG cc_start: 0.7858 (mtt-85) cc_final: 0.7559 (mtm-85) REVERT: C 439 ARG cc_start: 0.7879 (mtm-85) cc_final: 0.7368 (mtp85) REVERT: D 279 ARG cc_start: 0.8329 (tmm-80) cc_final: 0.7996 (ttp-170) REVERT: D 443 ASP cc_start: 0.8426 (t0) cc_final: 0.8133 (t0) REVERT: D 497 ASP cc_start: 0.8527 (t0) cc_final: 0.8135 (t0) REVERT: D 531 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6631 (mm-40) REVERT: D 608 VAL cc_start: 0.8852 (t) cc_final: 0.8600 (p) outliers start: 34 outliers final: 22 residues processed: 202 average time/residue: 0.2669 time to fit residues: 81.4697 Evaluate side-chains 190 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 159 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 34 optimal weight: 0.0170 chunk 68 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.199253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129623 restraints weight = 25387.011| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.89 r_work: 0.3308 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 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 = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14944 Z= 0.113 Angle : 0.503 9.227 20293 Z= 0.260 Chirality : 0.040 0.149 2309 Planarity : 0.003 0.034 2491 Dihedral : 12.316 152.620 2148 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.51 % Allowed : 22.88 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1755 helix: 1.80 (0.15), residues: 1157 sheet: -1.17 (0.68), residues: 53 loop : -1.08 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 445 HIS 0.004 0.001 HIS B 473 PHE 0.021 0.001 PHE C 413 TYR 0.019 0.001 TYR C 546 ARG 0.003 0.000 ARG B 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 3) link_NAG-ASN : angle 1.70320 ( 9) hydrogen bonds : bond 0.03681 ( 925) hydrogen bonds : angle 3.80725 ( 2683) covalent geometry : bond 0.00253 (14941) covalent geometry : angle 0.50230 (20284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5701 (OUTLIER) cc_final: 0.4892 (t80) REVERT: A 384 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: A 395 ILE cc_start: 0.5608 (OUTLIER) cc_final: 0.4948 (mm) REVERT: A 425 GLN cc_start: 0.6769 (OUTLIER) cc_final: 0.6409 (mm110) REVERT: A 448 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8171 (ptpp) REVERT: B 270 TYR cc_start: 0.4951 (OUTLIER) cc_final: 0.4038 (p90) REVERT: B 392 PHE cc_start: 0.7695 (t80) cc_final: 0.7388 (t80) REVERT: B 425 GLN cc_start: 0.6151 (mp10) cc_final: 0.5889 (mp10) REVERT: B 518 GLU cc_start: 0.6468 (tt0) cc_final: 0.5783 (pt0) REVERT: B 519 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7089 (ttp) REVERT: B 570 SER cc_start: 0.8925 (m) cc_final: 0.8187 (p) REVERT: C 193 ASP cc_start: 0.8233 (t70) cc_final: 0.7914 (t0) REVERT: C 223 ARG cc_start: 0.7886 (mtt-85) cc_final: 0.7575 (mtm-85) REVERT: C 439 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7401 (mtp180) REVERT: C 577 PHE cc_start: 0.8435 (m-10) cc_final: 0.8176 (m-10) REVERT: D 279 ARG cc_start: 0.8299 (tmm-80) cc_final: 0.7958 (ttp-170) REVERT: D 443 ASP cc_start: 0.8516 (t0) cc_final: 0.8158 (t0) REVERT: D 497 ASP cc_start: 0.8548 (t0) cc_final: 0.8144 (t0) REVERT: D 531 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6669 (mm-40) REVERT: D 608 VAL cc_start: 0.8869 (t) cc_final: 0.8599 (p) outliers start: 40 outliers final: 27 residues processed: 204 average time/residue: 0.2626 time to fit residues: 82.6285 Evaluate side-chains 200 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 59 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 ASN D 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.196852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127599 restraints weight = 29703.710| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.32 r_work: 0.3252 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14944 Z= 0.153 Angle : 0.544 9.388 20293 Z= 0.280 Chirality : 0.041 0.189 2309 Planarity : 0.003 0.034 2491 Dihedral : 12.361 153.583 2148 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.33 % Allowed : 23.00 % Favored : 74.67 % 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: 1.11 (0.20), residues: 1755 helix: 1.68 (0.15), residues: 1154 sheet: -1.49 (0.65), residues: 58 loop : -1.06 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 445 HIS 0.003 0.001 HIS D 251 PHE 0.020 0.001 PHE C 413 TYR 0.014 0.001 TYR B 352 ARG 0.003 0.000 ARG B 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 3) link_NAG-ASN : angle 1.75184 ( 9) hydrogen bonds : bond 0.03955 ( 925) hydrogen bonds : angle 3.91433 ( 2683) covalent geometry : bond 0.00361 (14941) covalent geometry : angle 0.54296 (20284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 1.517 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5726 (OUTLIER) cc_final: 0.4831 (t80) REVERT: A 384 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.7544 (m-30) REVERT: A 395 ILE cc_start: 0.5678 (OUTLIER) cc_final: 0.5111 (pt) REVERT: A 425 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6594 (mm110) REVERT: A 448 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8187 (ptpp) REVERT: A 604 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8049 (pp30) REVERT: B 229 GLN cc_start: 0.7869 (mt0) cc_final: 0.7653 (mt0) REVERT: B 270 TYR cc_start: 0.4914 (OUTLIER) cc_final: 0.3946 (p90) REVERT: B 392 PHE cc_start: 0.7802 (t80) cc_final: 0.7447 (t80) REVERT: B 425 GLN cc_start: 0.6131 (mp10) cc_final: 0.5877 (mp10) REVERT: B 519 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7061 (ttp) REVERT: B 570 SER cc_start: 0.8965 (m) cc_final: 0.8216 (p) REVERT: C 193 ASP cc_start: 0.8255 (t70) cc_final: 0.7929 (t0) REVERT: C 223 ARG cc_start: 0.7956 (mtt-85) cc_final: 0.7617 (mtm-85) REVERT: C 426 PHE cc_start: 0.5599 (OUTLIER) cc_final: 0.4808 (t80) REVERT: C 439 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7418 (mtp180) REVERT: D 279 ARG cc_start: 0.8351 (tmm-80) cc_final: 0.8013 (ttp-170) REVERT: D 443 ASP cc_start: 0.8559 (t0) cc_final: 0.8170 (t0) REVERT: D 497 ASP cc_start: 0.8553 (t0) cc_final: 0.8159 (t0) REVERT: D 531 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6674 (mm-40) REVERT: D 608 VAL cc_start: 0.8861 (t) cc_final: 0.8580 (p) outliers start: 37 outliers final: 26 residues processed: 200 average time/residue: 0.2309 time to fit residues: 70.5056 Evaluate side-chains 202 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 604 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 168 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 29 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.192305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127981 restraints weight = 19126.328| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.23 r_work: 0.3277 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.005 0.048 14944 Z= 0.218 Angle : 0.605 12.004 20293 Z= 0.313 Chirality : 0.044 0.167 2309 Planarity : 0.004 0.034 2491 Dihedral : 12.466 154.416 2148 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.45 % Allowed : 22.69 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.20), residues: 1755 helix: 1.39 (0.15), residues: 1153 sheet: -1.22 (0.64), residues: 65 loop : -1.19 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 445 HIS 0.003 0.001 HIS D 251 PHE 0.018 0.002 PHE C 413 TYR 0.017 0.002 TYR B 352 ARG 0.003 0.000 ARG B 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 3) link_NAG-ASN : angle 1.96469 ( 9) hydrogen bonds : bond 0.04472 ( 925) hydrogen bonds : angle 4.14144 ( 2683) covalent geometry : bond 0.00522 (14941) covalent geometry : angle 0.60386 (20284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8202.11 seconds wall clock time: 143 minutes 25.20 seconds (8605.20 seconds total)