Starting phenix.real_space_refine on Thu Jul 2 17:55:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7scj_25036/07_2026/7scj_25036.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scj_25036/07_2026/7scj_25036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7scj_25036/07_2026/7scj_25036.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7scj_25036/07_2026/7scj_25036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7scj_25036/07_2026/7scj_25036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scj_25036/07_2026/7scj_25036.map" model { file = "/net/cci-nas-00/data/ceres_data/7scj_25036/07_2026/7scj_25036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scj_25036/07_2026/7scj_25036.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 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 45 5.16 5 C 5991 2.51 5 N 1562 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4596 Classifications: {'peptide': 563} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 537} Chain breaks: 3 Chain: "B" Number of atoms: 4596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4596 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 533} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'BDP': 1, 'NDG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.79, per 1000 atoms: 0.19 Number of scatterers: 9336 At special positions: 0 Unit cell: (98.532, 86.112, 110.124, 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 45 16.00 P 4 15.00 O 1734 8.00 N 1562 7.00 C 5991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=1.99 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " distance=2.03 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 ALPHA1-4 " BDP D 2 " - " NDG D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NDG D 1 " - " BDP D 2 " NAG-ASN " NAG A 901 " - " ASN A 330 " " NAG C 1 " - " ASN B 637 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 310.0 milliseconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 14 sheets defined 37.2% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.714A pdb=" N CYS A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 141 Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.536A pdb=" N PHE A 226 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 303 through 308 removed outlier: 4.011A pdb=" N HIS A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 4.326A pdb=" N ASP A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 397 through 416 Processing helix chain 'A' and resid 418 through 432 Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.731A pdb=" N TRP A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 446' Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 571 through 585 removed outlier: 3.706A pdb=" N SER A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 639 through 649 removed outlier: 3.917A pdb=" N LYS A 643 " --> pdb=" O PRO A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 699 through 713 removed outlier: 3.934A pdb=" N SER A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 166 through 176 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.989A pdb=" N LEU B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 312' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.743A pdb=" N ASP B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.608A pdb=" N MET B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 381 through 399 Processing helix chain 'B' and resid 402 through 419 Processing helix chain 'B' and resid 420 through 423 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 467 through 478 removed outlier: 3.765A pdb=" N ARG B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 523 removed outlier: 3.938A pdb=" N ARG B 522 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 523 " --> pdb=" O SER B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 removed outlier: 3.704A pdb=" N GLU B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 Processing helix chain 'B' and resid 615 through 624 Processing helix chain 'B' and resid 627 through 640 Processing helix chain 'B' and resid 669 through 685 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 145 removed outlier: 6.052A pdb=" N VAL A 116 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE A 154 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE A 193 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N HIS A 190 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA A 217 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 192 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 163 removed outlier: 7.161A pdb=" N TYR A 196 " --> pdb=" O ARG A 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 297 removed outlier: 6.386A pdb=" N LEU A 264 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU A 295 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE A 266 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR A 297 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY A 268 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 265 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS A 334 " --> pdb=" O VAL A 358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 517 removed outlier: 6.575A pdb=" N PHE A 480 " --> pdb=" O CYS A 510 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN A 512 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 594 through 595 Processing sheet with id=AA6, first strand: chain 'A' and resid 599 through 600 Processing sheet with id=AA7, first strand: chain 'A' and resid 724 through 726 removed outlier: 6.522A pdb=" N LYS B 645 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 536 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 535 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 461 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE B 456 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU B 486 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA B 458 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B 488 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 460 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 510 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.598A pdb=" N LEU B 212 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 217 through 218 removed outlier: 4.749A pdb=" N PHE B 217 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 254 through 257 removed outlier: 7.161A pdb=" N LEU B 254 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LEU B 283 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER B 256 " --> pdb=" O LEU B 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 298 through 301 removed outlier: 3.546A pdb=" N GLN B 304 " --> pdb=" O HIS B 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 317 through 320 removed outlier: 6.755A pdb=" N CYS B 318 " --> pdb=" O VAL B 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 570 through 574 removed outlier: 3.655A pdb=" N LYS B 579 " --> pdb=" O ASP B 574 " (cutoff:3.500A) 291 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 1.10 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: 2933 1.34 - 1.46: 1705 1.46 - 1.58: 4872 1.58 - 1.69: 5 1.69 - 1.81: 70 Bond restraints: 9585 Sorted by residual: bond pdb=" O1A UDP A 902 " pdb=" PA UDP A 902 " ideal model delta sigma weight residual 1.482 1.524 -0.042 1.00e-02 1.00e+04 1.76e+01 bond pdb=" N VAL A 265 " pdb=" CA VAL A 265 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.14e-02 7.69e+03 9.58e+00 bond pdb=" N GLU B 397 " pdb=" CA GLU B 397 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.35e-02 5.49e+03 7.53e+00 bond pdb=" O3A UDP A 902 " pdb=" PB UDP A 902 " ideal model delta sigma weight residual 1.584 1.611 -0.027 1.00e-02 1.00e+04 7.16e+00 bond pdb=" O2A UDP A 902 " pdb=" PA UDP A 902 " ideal model delta sigma weight residual 1.527 1.481 0.046 1.80e-02 3.09e+03 6.43e+00 ... (remaining 9580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 12702 1.66 - 3.32: 272 3.32 - 4.98: 45 4.98 - 6.63: 13 6.63 - 8.29: 2 Bond angle restraints: 13034 Sorted by residual: angle pdb=" O3A UDP A 902 " pdb=" PB UDP A 902 " pdb=" O3B UDP A 902 " ideal model delta sigma weight residual 112.01 103.72 8.29 1.00e+00 1.00e+00 6.88e+01 angle pdb=" O5' UDP A 902 " pdb=" PA UDP A 902 " pdb=" O1A UDP A 902 " ideal model delta sigma weight residual 106.70 111.11 -4.41 1.00e+00 1.00e+00 1.95e+01 angle pdb=" O5' UDP A 902 " pdb=" PA UDP A 902 " pdb=" O2A UDP A 902 " ideal model delta sigma weight residual 110.83 106.99 3.84 1.00e+00 1.00e+00 1.47e+01 angle pdb=" C TYR A 262 " pdb=" CA TYR A 262 " pdb=" CB TYR A 262 " ideal model delta sigma weight residual 112.43 105.20 7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" C TYR B 399 " pdb=" CA TYR B 399 " pdb=" CB TYR B 399 " ideal model delta sigma weight residual 109.65 115.28 -5.63 1.68e+00 3.54e-01 1.12e+01 ... (remaining 13029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 5197 15.25 - 30.51: 329 30.51 - 45.76: 81 45.76 - 61.02: 15 61.02 - 76.27: 6 Dihedral angle restraints: 5628 sinusoidal: 2288 harmonic: 3340 Sorted by residual: dihedral pdb=" CB CYS B 96 " pdb=" SG CYS B 96 " pdb=" SG CYS B 151 " pdb=" CB CYS B 151 " ideal model delta sinusoidal sigma weight residual -86.00 -58.37 -27.63 1 1.00e+01 1.00e-02 1.09e+01 dihedral pdb=" CA ARG B 322 " pdb=" CB ARG B 322 " pdb=" CG ARG B 322 " pdb=" CD ARG B 322 " ideal model delta sinusoidal sigma weight residual -60.00 -111.39 51.39 3 1.50e+01 4.44e-03 9.01e+00 dihedral pdb=" CB LYS A 479 " pdb=" CG LYS A 479 " pdb=" CD LYS A 479 " pdb=" CE LYS A 479 " ideal model delta sinusoidal sigma weight residual 60.00 111.26 -51.26 3 1.50e+01 4.44e-03 8.99e+00 ... (remaining 5625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1419 0.129 - 0.257: 10 0.257 - 0.386: 3 0.386 - 0.515: 1 0.515 - 0.643: 1 Chirality restraints: 1434 Sorted by residual: chirality pdb=" C1 BDP D 2 " pdb=" O4 NDG D 1 " pdb=" C2 BDP D 2 " pdb=" O5 BDP D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-02 2.50e+03 1.03e+03 chirality pdb=" C1 NDG D 3 " pdb=" O4 BDP D 2 " pdb=" C2 NDG D 3 " pdb=" O5 NDG D 3 " both_signs ideal model delta sigma weight residual False 2.40 1.94 0.46 2.00e-02 2.50e+03 5.18e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.67e+00 ... (remaining 1431 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NDG D 3 " 0.183 2.00e-02 2.50e+03 1.57e-01 3.09e+02 pdb=" C7 NDG D 3 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NDG D 3 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NDG D 3 " -0.259 2.00e-02 2.50e+03 pdb=" O7 NDG D 3 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NDG D 1 " 0.073 2.00e-02 2.50e+03 6.12e-02 4.68e+01 pdb=" C7 NDG D 1 " -0.017 2.00e-02 2.50e+03 pdb=" C8 NDG D 1 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NDG D 1 " -0.100 2.00e-02 2.50e+03 pdb=" O7 NDG D 1 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 330 " 0.043 2.00e-02 2.50e+03 4.30e-02 2.31e+01 pdb=" CG ASN A 330 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 330 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 330 " -0.064 2.00e-02 2.50e+03 pdb=" C1 NAG A 901 " 0.053 2.00e-02 2.50e+03 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 725 2.74 - 3.28: 9357 3.28 - 3.82: 15558 3.82 - 4.36: 18907 4.36 - 4.90: 32053 Nonbonded interactions: 76600 Sorted by model distance: nonbonded pdb=" OG1 THR A 673 " pdb=" OD1 ASP A 725 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR B 130 " pdb=" O PRO B 155 " model vdw 2.204 3.040 nonbonded pdb=" NZ LYS A 400 " pdb=" O TYR B 421 " model vdw 2.210 3.120 nonbonded pdb=" O GLU B 548 " pdb=" OH TYR B 566 " model vdw 2.231 3.040 nonbonded pdb=" O ASP A 164 " pdb=" OG SER A 167 " model vdw 2.234 3.040 ... (remaining 76595 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 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: 1.040 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.800 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 9600 Z= 0.205 Angle : 0.635 15.063 13070 Z= 0.331 Chirality : 0.051 0.643 1434 Planarity : 0.006 0.157 1644 Dihedral : 11.118 76.269 3443 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.25), residues: 1113 helix: 0.86 (0.28), residues: 366 sheet: -0.41 (0.51), residues: 110 loop : -0.71 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 384 TYR 0.033 0.002 TYR B 399 PHE 0.012 0.001 PHE B 400 TRP 0.012 0.001 TRP A 711 HIS 0.002 0.001 HIS B 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.20 ( 9585) covalent geometry : angle 0.60242 / 0.32 (13034) SS BOND : bond 0.01288 / 0.64 ( 9) SS BOND : angle 1.48692 / 0.77 ( 18) hydrogen bonds : bond 0.18619 / 11.58 ( 291) hydrogen bonds : angle 6.57352 / 4.39 ( 825) link_ALPHA1-4 : bond 0.00343 / 0.18 ( 1) link_ALPHA1-4 : angle 1.31741 / 0.53 ( 3) link_BETA1-4 : bond 0.02246 / 0.83 ( 3) link_BETA1-4 : angle 6.50132 / 3.49 ( 9) link_NAG-ASN : bond 0.06807 / 3.58 ( 2) link_NAG-ASN : angle 4.30665 / 2.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.7867 (m-10) cc_final: 0.7593 (m-10) REVERT: A 115 LYS cc_start: 0.7464 (mmmm) cc_final: 0.7214 (mttm) REVERT: A 125 GLU cc_start: 0.6568 (mt-10) cc_final: 0.6169 (mt-10) REVERT: A 225 ASN cc_start: 0.8047 (m110) cc_final: 0.7811 (m110) REVERT: A 261 LYS cc_start: 0.7545 (ttpp) cc_final: 0.7305 (ttpp) REVERT: A 291 ASP cc_start: 0.6459 (p0) cc_final: 0.6249 (p0) REVERT: A 359 MET cc_start: 0.7948 (mpp) cc_final: 0.7498 (mpp) REVERT: A 420 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6669 (tt0) REVERT: A 455 LEU cc_start: 0.7969 (mt) cc_final: 0.7755 (mt) REVERT: A 471 ASN cc_start: 0.6771 (m110) cc_final: 0.6554 (m-40) REVERT: A 715 MET cc_start: 0.6937 (tpp) cc_final: 0.6582 (tpp) REVERT: B 99 ASN cc_start: 0.7745 (p0) cc_final: 0.7448 (p0) REVERT: B 135 MET cc_start: 0.6968 (mmp) cc_final: 0.6692 (mmp) REVERT: B 188 LEU cc_start: 0.7393 (mm) cc_final: 0.7000 (mt) REVERT: B 265 TYR cc_start: 0.7228 (m-80) cc_final: 0.6894 (m-80) REVERT: B 267 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7450 (mm-30) REVERT: B 270 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6948 (mm-30) REVERT: B 333 ASP cc_start: 0.7318 (m-30) cc_final: 0.6931 (m-30) REVERT: B 357 ASP cc_start: 0.7261 (t0) cc_final: 0.6967 (t0) REVERT: B 416 ASP cc_start: 0.7494 (m-30) cc_final: 0.7229 (m-30) REVERT: B 549 LEU cc_start: 0.7901 (mm) cc_final: 0.7584 (mp) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.0978 time to fit residues: 35.1723 Evaluate side-chains 239 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.0060 chunk 5 optimal weight: 0.0170 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.4434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 HIS ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN A 388 GLN A 706 ASN B 102 ASN B 301 HIS B 618 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125131 restraints weight = 12676.716| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.27 r_work: 0.3479 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9600 Z= 0.130 Angle : 0.570 8.512 13070 Z= 0.292 Chirality : 0.043 0.224 1434 Planarity : 0.004 0.054 1644 Dihedral : 3.963 16.639 1240 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.69 % Allowed : 10.22 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.25), residues: 1113 helix: 0.82 (0.27), residues: 374 sheet: -0.17 (0.52), residues: 108 loop : -0.66 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 149 TYR 0.021 0.002 TYR A 634 PHE 0.025 0.001 PHE A 250 TRP 0.014 0.001 TRP B 556 HIS 0.004 0.001 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 9585) covalent geometry : angle 0.55704 / 0.29 (13034) SS BOND : bond 0.00284 / 0.19 ( 9) SS BOND : angle 0.72580 / 0.43 ( 18) hydrogen bonds : bond 0.04569 / 2.92 ( 291) hydrogen bonds : angle 5.32989 / 3.54 ( 825) link_ALPHA1-4 : bond 0.01384 / 0.73 ( 1) link_ALPHA1-4 : angle 2.54486 / 1.12 ( 3) link_BETA1-4 : bond 0.01384 / 0.52 ( 3) link_BETA1-4 : angle 3.89211 / 1.87 ( 9) link_NAG-ASN : bond 0.01179 / 0.62 ( 2) link_NAG-ASN : angle 2.31740 / 1.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 247 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8083 (m-10) cc_final: 0.7760 (m-10) REVERT: A 261 LYS cc_start: 0.8129 (ttpp) cc_final: 0.7907 (ttmm) REVERT: A 291 ASP cc_start: 0.6955 (p0) cc_final: 0.6707 (p0) REVERT: A 359 MET cc_start: 0.8343 (mpp) cc_final: 0.7844 (mpp) REVERT: A 399 ASP cc_start: 0.7496 (t0) cc_final: 0.7295 (t0) REVERT: A 420 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7134 (tt0) REVERT: A 600 ASP cc_start: 0.6933 (t0) cc_final: 0.6107 (t0) REVERT: A 603 LYS cc_start: 0.7740 (mppt) cc_final: 0.7195 (mppt) REVERT: A 714 TYR cc_start: 0.7861 (p90) cc_final: 0.7205 (p90) REVERT: A 715 MET cc_start: 0.7492 (tpp) cc_final: 0.7247 (tpp) REVERT: B 99 ASN cc_start: 0.7935 (p0) cc_final: 0.7677 (p0) REVERT: B 182 ARG cc_start: 0.7499 (mmm-85) cc_final: 0.7284 (mmm-85) REVERT: B 188 LEU cc_start: 0.7692 (mm) cc_final: 0.7329 (mt) REVERT: B 265 TYR cc_start: 0.7779 (m-80) cc_final: 0.7284 (m-80) REVERT: B 333 ASP cc_start: 0.7828 (m-30) cc_final: 0.7540 (m-30) REVERT: B 416 ASP cc_start: 0.7874 (m-30) cc_final: 0.7395 (m-30) outliers start: 17 outliers final: 9 residues processed: 251 average time/residue: 0.0939 time to fit residues: 32.4938 Evaluate side-chains 245 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 236 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 HIS ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.140828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122395 restraints weight = 12752.120| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.27 r_work: 0.3435 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9600 Z= 0.166 Angle : 0.571 9.206 13070 Z= 0.291 Chirality : 0.044 0.183 1434 Planarity : 0.004 0.044 1644 Dihedral : 4.001 14.941 1240 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.58 % Allowed : 13.10 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.25), residues: 1113 helix: 0.66 (0.26), residues: 377 sheet: -0.55 (0.50), residues: 114 loop : -0.75 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 149 TYR 0.021 0.002 TYR A 634 PHE 0.027 0.002 PHE A 250 TRP 0.013 0.002 TRP B 394 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 9585) covalent geometry : angle 0.55724 / 0.29 (13034) SS BOND : bond 0.00299 / 0.20 ( 9) SS BOND : angle 0.68031 / 0.40 ( 18) hydrogen bonds : bond 0.04510 / 2.86 ( 291) hydrogen bonds : angle 5.05613 / 3.34 ( 825) link_ALPHA1-4 : bond 0.00816 / 0.43 ( 1) link_ALPHA1-4 : angle 2.40686 / 1.04 ( 3) link_BETA1-4 : bond 0.01190 / 0.45 ( 3) link_BETA1-4 : angle 4.13088 / 1.96 ( 9) link_NAG-ASN : bond 0.00729 / 0.38 ( 2) link_NAG-ASN : angle 2.16407 / 1.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8167 (m-10) cc_final: 0.7849 (m-10) REVERT: A 105 ASP cc_start: 0.7451 (t0) cc_final: 0.7088 (t0) REVERT: A 160 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7677 (m) REVERT: A 166 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7886 (mm) REVERT: A 215 MET cc_start: 0.6782 (ptp) cc_final: 0.6452 (ptp) REVERT: A 319 TYR cc_start: 0.7817 (t80) cc_final: 0.7568 (t80) REVERT: A 420 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7159 (tt0) REVERT: A 447 LYS cc_start: 0.8259 (mttm) cc_final: 0.8012 (ttmm) REVERT: A 705 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7448 (mtt) REVERT: A 714 TYR cc_start: 0.7970 (p90) cc_final: 0.7246 (p90) REVERT: A 715 MET cc_start: 0.7510 (tpp) cc_final: 0.7297 (tpp) REVERT: A 721 GLN cc_start: 0.6050 (pm20) cc_final: 0.5534 (pt0) REVERT: A 722 MET cc_start: 0.7012 (ptp) cc_final: 0.6709 (ptt) REVERT: B 99 ASN cc_start: 0.7961 (p0) cc_final: 0.7713 (p0) REVERT: B 129 GLU cc_start: 0.6435 (mm-30) cc_final: 0.6169 (tp30) REVERT: B 188 LEU cc_start: 0.7689 (mm) cc_final: 0.7360 (mt) REVERT: B 252 TYR cc_start: 0.8268 (m-10) cc_final: 0.8056 (m-10) REVERT: B 265 TYR cc_start: 0.7730 (m-80) cc_final: 0.7137 (m-80) REVERT: B 313 GLN cc_start: 0.7889 (mm-40) cc_final: 0.6944 (tm-30) REVERT: B 333 ASP cc_start: 0.7820 (m-30) cc_final: 0.7514 (m-30) REVERT: B 354 GLU cc_start: 0.7193 (mp0) cc_final: 0.6790 (mp0) REVERT: B 357 ASP cc_start: 0.7891 (t0) cc_final: 0.7608 (t0) REVERT: B 378 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7059 (mp10) REVERT: B 394 TRP cc_start: 0.7460 (t-100) cc_final: 0.7230 (t-100) REVERT: B 416 ASP cc_start: 0.7962 (m-30) cc_final: 0.7560 (m-30) outliers start: 26 outliers final: 15 residues processed: 244 average time/residue: 0.0942 time to fit residues: 32.2657 Evaluate side-chains 247 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 229 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 692 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.0770 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 111 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 HIS A 316 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** 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 = 0.3806 r_free = 0.3806 target = 0.140677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122140 restraints weight = 12933.476| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.30 r_work: 0.3424 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9600 Z= 0.154 Angle : 0.561 8.716 13070 Z= 0.286 Chirality : 0.043 0.177 1434 Planarity : 0.004 0.047 1644 Dihedral : 3.999 15.394 1240 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.68 % Allowed : 14.29 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1113 helix: 0.74 (0.26), residues: 376 sheet: -0.51 (0.51), residues: 109 loop : -0.76 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 163 TYR 0.021 0.002 TYR A 634 PHE 0.029 0.002 PHE A 250 TRP 0.013 0.002 TRP B 396 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9585) covalent geometry : angle 0.54846 / 0.28 (13034) SS BOND : bond 0.00387 / 0.22 ( 9) SS BOND : angle 0.65239 / 0.38 ( 18) hydrogen bonds : bond 0.04173 / 2.64 ( 291) hydrogen bonds : angle 4.94556 / 3.25 ( 825) link_ALPHA1-4 : bond 0.00742 / 0.39 ( 1) link_ALPHA1-4 : angle 2.33805 / 1.01 ( 3) link_BETA1-4 : bond 0.01124 / 0.42 ( 3) link_BETA1-4 : angle 3.91160 / 1.85 ( 9) link_NAG-ASN : bond 0.00551 / 0.29 ( 2) link_NAG-ASN : angle 2.04321 / 1.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8172 (m-10) cc_final: 0.7730 (m-80) REVERT: A 105 ASP cc_start: 0.7433 (t0) cc_final: 0.7027 (t0) REVERT: A 160 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7701 (m) REVERT: A 179 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7810 (mm-40) REVERT: A 215 MET cc_start: 0.6782 (ptp) cc_final: 0.6449 (ptp) REVERT: A 261 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7888 (ttmm) REVERT: A 264 LEU cc_start: 0.7070 (tp) cc_final: 0.6865 (tt) REVERT: A 420 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7184 (tt0) REVERT: A 714 TYR cc_start: 0.7931 (p90) cc_final: 0.7335 (p90) REVERT: A 715 MET cc_start: 0.7459 (tpp) cc_final: 0.7203 (tpp) REVERT: A 721 GLN cc_start: 0.5973 (pm20) cc_final: 0.5495 (pt0) REVERT: B 99 ASN cc_start: 0.7933 (p0) cc_final: 0.7699 (p0) REVERT: B 129 GLU cc_start: 0.6497 (mm-30) cc_final: 0.6171 (tp30) REVERT: B 182 ARG cc_start: 0.7510 (mmm-85) cc_final: 0.6916 (mmm-85) REVERT: B 188 LEU cc_start: 0.7630 (mm) cc_final: 0.7307 (mt) REVERT: B 265 TYR cc_start: 0.7449 (m-80) cc_final: 0.6700 (m-80) REVERT: B 313 GLN cc_start: 0.7865 (mm-40) cc_final: 0.6970 (tm-30) REVERT: B 333 ASP cc_start: 0.7856 (m-30) cc_final: 0.7557 (m-30) REVERT: B 354 GLU cc_start: 0.7214 (mp0) cc_final: 0.6652 (mp0) REVERT: B 357 ASP cc_start: 0.7850 (t0) cc_final: 0.7553 (t0) REVERT: B 370 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.7014 (mtt) REVERT: B 378 GLN cc_start: 0.7445 (mm-40) cc_final: 0.7008 (mp10) REVERT: B 394 TRP cc_start: 0.7459 (t-100) cc_final: 0.7218 (t-100) REVERT: B 416 ASP cc_start: 0.7960 (m-30) cc_final: 0.7509 (m-30) outliers start: 27 outliers final: 19 residues processed: 246 average time/residue: 0.0899 time to fit residues: 30.2009 Evaluate side-chains 246 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 692 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 95 optimal weight: 0.0060 chunk 4 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 90 optimal weight: 0.0070 chunk 66 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 overall best weight: 0.1752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 HIS ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN A 406 GLN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 HIS ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125111 restraints weight = 12857.885| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.22 r_work: 0.3460 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 9600 Z= 0.105 Angle : 0.544 8.898 13070 Z= 0.277 Chirality : 0.042 0.210 1434 Planarity : 0.004 0.047 1644 Dihedral : 3.859 14.790 1240 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.68 % Allowed : 14.58 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.25), residues: 1113 helix: 0.86 (0.27), residues: 377 sheet: -0.58 (0.50), residues: 109 loop : -0.69 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.024 0.001 TYR A 629 PHE 0.030 0.001 PHE A 250 TRP 0.020 0.001 TRP A 599 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 9585) covalent geometry : angle 0.53335 / 0.27 (13034) SS BOND : bond 0.00137 / 0.09 ( 9) SS BOND : angle 0.59587 / 0.34 ( 18) hydrogen bonds : bond 0.03567 / 2.24 ( 291) hydrogen bonds : angle 4.79824 / 3.15 ( 825) link_ALPHA1-4 : bond 0.00788 / 0.41 ( 1) link_ALPHA1-4 : angle 2.13823 / 0.99 ( 3) link_BETA1-4 : bond 0.01261 / 0.48 ( 3) link_BETA1-4 : angle 3.65846 / 1.69 ( 9) link_NAG-ASN : bond 0.00548 / 0.29 ( 2) link_NAG-ASN : angle 1.81580 / 0.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8128 (m-10) cc_final: 0.7691 (m-80) REVERT: A 105 ASP cc_start: 0.7334 (t0) cc_final: 0.6850 (t0) REVERT: A 160 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7679 (m) REVERT: A 166 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7841 (mm) REVERT: A 179 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7817 (mm-40) REVERT: A 215 MET cc_start: 0.6670 (ptp) cc_final: 0.6399 (ptp) REVERT: A 261 LYS cc_start: 0.8074 (ttpp) cc_final: 0.7850 (ttmm) REVERT: A 291 ASP cc_start: 0.7196 (p0) cc_final: 0.6854 (p0) REVERT: A 420 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7197 (tt0) REVERT: A 714 TYR cc_start: 0.7895 (p90) cc_final: 0.7432 (p90) REVERT: A 715 MET cc_start: 0.7443 (tpp) cc_final: 0.7201 (tpp) REVERT: A 721 GLN cc_start: 0.5825 (pm20) cc_final: 0.5422 (pt0) REVERT: B 99 ASN cc_start: 0.7931 (p0) cc_final: 0.7685 (p0) REVERT: B 182 ARG cc_start: 0.7464 (mmm-85) cc_final: 0.6879 (mmm-85) REVERT: B 188 LEU cc_start: 0.7700 (mm) cc_final: 0.7406 (mt) REVERT: B 265 TYR cc_start: 0.7362 (m-80) cc_final: 0.6617 (m-80) REVERT: B 313 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7473 (tp40) REVERT: B 333 ASP cc_start: 0.7836 (m-30) cc_final: 0.7545 (m-30) REVERT: B 354 GLU cc_start: 0.7129 (mp0) cc_final: 0.6554 (mp0) REVERT: B 357 ASP cc_start: 0.7795 (t0) cc_final: 0.7502 (t0) REVERT: B 378 GLN cc_start: 0.7366 (mm-40) cc_final: 0.6966 (mp10) REVERT: B 384 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7919 (tm-30) REVERT: B 394 TRP cc_start: 0.7378 (t-100) cc_final: 0.7103 (t-100) REVERT: B 416 ASP cc_start: 0.7887 (m-30) cc_final: 0.7452 (m-30) REVERT: B 446 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8054 (mp) REVERT: B 522 ARG cc_start: 0.7659 (ptm160) cc_final: 0.7334 (ttp-170) outliers start: 27 outliers final: 14 residues processed: 251 average time/residue: 0.0901 time to fit residues: 31.2585 Evaluate side-chains 250 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 0.0980 chunk 15 optimal weight: 0.0980 chunk 58 optimal weight: 0.9990 chunk 109 optimal weight: 0.1980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 HIS ** B 678 ASN ** 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 = 0.3826 r_free = 0.3826 target = 0.142371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124024 restraints weight = 12933.404| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.29 r_work: 0.3440 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9600 Z= 0.121 Angle : 0.557 9.303 13070 Z= 0.281 Chirality : 0.042 0.194 1434 Planarity : 0.004 0.047 1644 Dihedral : 3.803 14.785 1240 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.78 % Allowed : 14.78 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.25), residues: 1113 helix: 0.84 (0.27), residues: 378 sheet: -0.62 (0.51), residues: 109 loop : -0.70 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 588 TYR 0.022 0.001 TYR B 265 PHE 0.030 0.001 PHE A 250 TRP 0.014 0.001 TRP A 445 HIS 0.002 0.000 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9585) covalent geometry : angle 0.54707 / 0.28 (13034) SS BOND : bond 0.00211 / 0.14 ( 9) SS BOND : angle 0.61551 / 0.36 ( 18) hydrogen bonds : bond 0.03675 / 2.33 ( 291) hydrogen bonds : angle 4.75164 / 3.12 ( 825) link_ALPHA1-4 : bond 0.00754 / 0.40 ( 1) link_ALPHA1-4 : angle 2.17937 / 0.99 ( 3) link_BETA1-4 : bond 0.01172 / 0.44 ( 3) link_BETA1-4 : angle 3.62000 / 1.69 ( 9) link_NAG-ASN : bond 0.00514 / 0.27 ( 2) link_NAG-ASN : angle 1.77473 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8158 (m-10) cc_final: 0.7727 (m-80) REVERT: A 105 ASP cc_start: 0.7393 (t0) cc_final: 0.6899 (t0) REVERT: A 160 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7681 (m) REVERT: A 166 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7899 (mm) REVERT: A 179 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7834 (mm-40) REVERT: A 215 MET cc_start: 0.6733 (ptp) cc_final: 0.6421 (ptp) REVERT: A 261 LYS cc_start: 0.8110 (ttpp) cc_final: 0.7832 (ttpp) REVERT: A 291 ASP cc_start: 0.7330 (p0) cc_final: 0.6901 (p0) REVERT: A 420 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7152 (tt0) REVERT: A 714 TYR cc_start: 0.7901 (p90) cc_final: 0.7423 (p90) REVERT: A 715 MET cc_start: 0.7459 (tpp) cc_final: 0.7205 (tpp) REVERT: A 721 GLN cc_start: 0.5967 (pm20) cc_final: 0.5578 (pt0) REVERT: A 722 MET cc_start: 0.7086 (ptp) cc_final: 0.6830 (ptt) REVERT: B 99 ASN cc_start: 0.7969 (p0) cc_final: 0.7730 (p0) REVERT: B 182 ARG cc_start: 0.7544 (mmm-85) cc_final: 0.6955 (mmm-85) REVERT: B 188 LEU cc_start: 0.7684 (mm) cc_final: 0.7398 (mt) REVERT: B 265 TYR cc_start: 0.7472 (m-80) cc_final: 0.6842 (m-80) REVERT: B 313 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7472 (tp40) REVERT: B 333 ASP cc_start: 0.7868 (m-30) cc_final: 0.7565 (m-30) REVERT: B 354 GLU cc_start: 0.7156 (mp0) cc_final: 0.6561 (mp0) REVERT: B 357 ASP cc_start: 0.7821 (t0) cc_final: 0.7536 (t0) REVERT: B 378 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6938 (mp10) REVERT: B 384 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.6944 (tm-30) REVERT: B 394 TRP cc_start: 0.7424 (t-100) cc_final: 0.7089 (t-100) REVERT: B 416 ASP cc_start: 0.7931 (m-30) cc_final: 0.7512 (m-30) outliers start: 28 outliers final: 19 residues processed: 248 average time/residue: 0.1035 time to fit residues: 35.2186 Evaluate side-chains 255 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 0.0770 chunk 46 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 HIS ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 HIS ** B 678 ASN ** 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 = 0.3828 r_free = 0.3828 target = 0.142568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.124565 restraints weight = 13004.409| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.23 r_work: 0.3461 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9600 Z= 0.119 Angle : 0.558 9.913 13070 Z= 0.281 Chirality : 0.043 0.189 1434 Planarity : 0.004 0.047 1644 Dihedral : 3.796 15.049 1240 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.98 % Allowed : 15.08 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.25), residues: 1113 helix: 0.87 (0.27), residues: 378 sheet: -0.58 (0.52), residues: 109 loop : -0.68 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 179 TYR 0.020 0.001 TYR A 629 PHE 0.011 0.001 PHE A 345 TRP 0.013 0.001 TRP B 396 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9585) covalent geometry : angle 0.54808 / 0.28 (13034) SS BOND : bond 0.00207 / 0.14 ( 9) SS BOND : angle 0.63223 / 0.38 ( 18) hydrogen bonds : bond 0.03538 / 2.24 ( 291) hydrogen bonds : angle 4.72135 / 3.10 ( 825) link_ALPHA1-4 : bond 0.00679 / 0.36 ( 1) link_ALPHA1-4 : angle 2.16649 / 0.97 ( 3) link_BETA1-4 : bond 0.01165 / 0.44 ( 3) link_BETA1-4 : angle 3.56561 / 1.66 ( 9) link_NAG-ASN : bond 0.00497 / 0.26 ( 2) link_NAG-ASN : angle 1.75570 / 0.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8175 (m-10) cc_final: 0.7741 (m-80) REVERT: A 115 LYS cc_start: 0.7702 (mtpp) cc_final: 0.7463 (mtpp) REVERT: A 160 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7730 (m) REVERT: A 166 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7921 (mm) REVERT: A 179 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7811 (mm-40) REVERT: A 215 MET cc_start: 0.6700 (ptp) cc_final: 0.6442 (ptp) REVERT: A 261 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7849 (ttpp) REVERT: A 291 ASP cc_start: 0.7259 (p0) cc_final: 0.6842 (p0) REVERT: A 420 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7189 (tt0) REVERT: A 453 PHE cc_start: 0.8237 (m-80) cc_final: 0.7985 (m-80) REVERT: A 579 PHE cc_start: 0.8231 (t80) cc_final: 0.7811 (t80) REVERT: A 705 MET cc_start: 0.7603 (mtm) cc_final: 0.7380 (mtt) REVERT: A 714 TYR cc_start: 0.7880 (p90) cc_final: 0.7401 (p90) REVERT: A 715 MET cc_start: 0.7453 (tpp) cc_final: 0.7203 (tpp) REVERT: A 721 GLN cc_start: 0.5950 (pm20) cc_final: 0.5576 (pt0) REVERT: B 92 ASP cc_start: 0.8085 (t70) cc_final: 0.7768 (t0) REVERT: B 99 ASN cc_start: 0.7987 (p0) cc_final: 0.7755 (p0) REVERT: B 182 ARG cc_start: 0.7571 (mmm-85) cc_final: 0.6992 (mmm-85) REVERT: B 188 LEU cc_start: 0.7725 (mm) cc_final: 0.7432 (mt) REVERT: B 265 TYR cc_start: 0.7468 (m-80) cc_final: 0.6821 (m-80) REVERT: B 267 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7587 (mm-30) REVERT: B 313 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7447 (tp40) REVERT: B 333 ASP cc_start: 0.7843 (m-30) cc_final: 0.7538 (m-30) REVERT: B 354 GLU cc_start: 0.7117 (mp0) cc_final: 0.6539 (mp0) REVERT: B 357 ASP cc_start: 0.7820 (t0) cc_final: 0.7542 (t0) REVERT: B 384 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: B 394 TRP cc_start: 0.7394 (t-100) cc_final: 0.7055 (t-100) REVERT: B 412 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: B 416 ASP cc_start: 0.7930 (m-30) cc_final: 0.7577 (m-30) REVERT: B 522 ARG cc_start: 0.7869 (ptm160) cc_final: 0.7378 (ttp-170) outliers start: 30 outliers final: 16 residues processed: 247 average time/residue: 0.1034 time to fit residues: 35.2551 Evaluate side-chains 253 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 HIS ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.141052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122718 restraints weight = 12813.617| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.28 r_work: 0.3418 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9600 Z= 0.155 Angle : 0.577 9.337 13070 Z= 0.292 Chirality : 0.044 0.197 1434 Planarity : 0.004 0.047 1644 Dihedral : 3.907 16.728 1240 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.88 % Allowed : 15.18 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1113 helix: 0.78 (0.27), residues: 377 sheet: -0.68 (0.51), residues: 110 loop : -0.72 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.021 0.002 TYR A 319 PHE 0.026 0.002 PHE A 250 TRP 0.012 0.001 TRP A 711 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 9585) covalent geometry : angle 0.56675 / 0.29 (13034) SS BOND : bond 0.00236 / 0.14 ( 9) SS BOND : angle 0.62213 / 0.36 ( 18) hydrogen bonds : bond 0.03875 / 2.44 ( 291) hydrogen bonds : angle 4.74531 / 3.12 ( 825) link_ALPHA1-4 : bond 0.00569 / 0.30 ( 1) link_ALPHA1-4 : angle 2.27196 / 0.98 ( 3) link_BETA1-4 : bond 0.01095 / 0.41 ( 3) link_BETA1-4 : angle 3.62782 / 1.70 ( 9) link_NAG-ASN : bond 0.00491 / 0.26 ( 2) link_NAG-ASN : angle 1.85095 / 0.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8231 (m-10) cc_final: 0.7803 (m-80) REVERT: A 160 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7727 (m) REVERT: A 166 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7888 (mm) REVERT: A 179 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7835 (mm-40) REVERT: A 215 MET cc_start: 0.6783 (ptp) cc_final: 0.6473 (ptp) REVERT: A 261 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7792 (ttpp) REVERT: A 291 ASP cc_start: 0.7264 (p0) cc_final: 0.6887 (p0) REVERT: A 420 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7191 (tt0) REVERT: A 453 PHE cc_start: 0.8292 (m-80) cc_final: 0.7991 (m-80) REVERT: A 579 PHE cc_start: 0.8202 (t80) cc_final: 0.7786 (t80) REVERT: A 714 TYR cc_start: 0.7906 (p90) cc_final: 0.7469 (p90) REVERT: A 715 MET cc_start: 0.7462 (tpp) cc_final: 0.7179 (tpp) REVERT: A 721 GLN cc_start: 0.5932 (pm20) cc_final: 0.5587 (pt0) REVERT: B 92 ASP cc_start: 0.8084 (t70) cc_final: 0.7810 (t0) REVERT: B 99 ASN cc_start: 0.7973 (p0) cc_final: 0.7741 (p0) REVERT: B 135 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7025 (mmp) REVERT: B 182 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.7000 (mmm-85) REVERT: B 188 LEU cc_start: 0.7669 (mm) cc_final: 0.7381 (mt) REVERT: B 265 TYR cc_start: 0.7536 (m-80) cc_final: 0.7001 (m-80) REVERT: B 313 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7503 (tp40) REVERT: B 333 ASP cc_start: 0.7854 (m-30) cc_final: 0.7549 (m-30) REVERT: B 354 GLU cc_start: 0.7155 (mp0) cc_final: 0.6572 (mp0) REVERT: B 357 ASP cc_start: 0.7869 (t0) cc_final: 0.7631 (t0) REVERT: B 378 GLN cc_start: 0.7444 (mm110) cc_final: 0.6962 (mp10) REVERT: B 384 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: B 412 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.6227 (tm-30) REVERT: B 416 ASP cc_start: 0.7975 (m-30) cc_final: 0.7606 (m-30) REVERT: B 522 ARG cc_start: 0.7900 (ptm160) cc_final: 0.7365 (ttp-170) outliers start: 29 outliers final: 18 residues processed: 246 average time/residue: 0.1069 time to fit residues: 36.1020 Evaluate side-chains 259 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 81 optimal weight: 0.0670 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123708 restraints weight = 12790.270| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.22 r_work: 0.3434 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9600 Z= 0.135 Angle : 0.577 9.258 13070 Z= 0.292 Chirality : 0.043 0.170 1434 Planarity : 0.004 0.046 1644 Dihedral : 3.902 16.777 1240 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.78 % Allowed : 15.87 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1113 helix: 0.87 (0.27), residues: 376 sheet: -0.67 (0.51), residues: 109 loop : -0.75 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 179 TYR 0.019 0.002 TYR B 265 PHE 0.020 0.001 PHE A 250 TRP 0.028 0.001 TRP B 394 HIS 0.005 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 9585) covalent geometry : angle 0.56754 / 0.29 (13034) SS BOND : bond 0.00204 / 0.12 ( 9) SS BOND : angle 0.61780 / 0.36 ( 18) hydrogen bonds : bond 0.03705 / 2.33 ( 291) hydrogen bonds : angle 4.72120 / 3.10 ( 825) link_ALPHA1-4 : bond 0.00620 / 0.33 ( 1) link_ALPHA1-4 : angle 2.23018 / 0.98 ( 3) link_BETA1-4 : bond 0.01146 / 0.43 ( 3) link_BETA1-4 : angle 3.56613 / 1.65 ( 9) link_NAG-ASN : bond 0.00490 / 0.26 ( 2) link_NAG-ASN : angle 1.81931 / 0.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8234 (m-10) cc_final: 0.7813 (m-80) REVERT: A 160 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7749 (m) REVERT: A 166 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7858 (mm) REVERT: A 179 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7805 (mm-40) REVERT: A 215 MET cc_start: 0.6788 (ptp) cc_final: 0.6483 (ptp) REVERT: A 261 LYS cc_start: 0.8118 (ttpp) cc_final: 0.7793 (ttpp) REVERT: A 291 ASP cc_start: 0.7236 (p0) cc_final: 0.6847 (p0) REVERT: A 420 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7210 (tt0) REVERT: A 453 PHE cc_start: 0.8254 (m-80) cc_final: 0.7958 (m-80) REVERT: A 579 PHE cc_start: 0.8178 (t80) cc_final: 0.7760 (t80) REVERT: A 705 MET cc_start: 0.7412 (mtm) cc_final: 0.7204 (mtt) REVERT: A 714 TYR cc_start: 0.7860 (p90) cc_final: 0.7497 (p90) REVERT: A 715 MET cc_start: 0.7446 (tpp) cc_final: 0.7180 (tpp) REVERT: A 721 GLN cc_start: 0.5967 (pm20) cc_final: 0.5620 (pt0) REVERT: B 92 ASP cc_start: 0.8082 (t70) cc_final: 0.7790 (t0) REVERT: B 99 ASN cc_start: 0.7945 (p0) cc_final: 0.7707 (p0) REVERT: B 135 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.7011 (mmp) REVERT: B 182 ARG cc_start: 0.7617 (mmm-85) cc_final: 0.7038 (mmm-85) REVERT: B 188 LEU cc_start: 0.7675 (mm) cc_final: 0.7391 (mt) REVERT: B 265 TYR cc_start: 0.7518 (m-80) cc_final: 0.6971 (m-80) REVERT: B 313 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7485 (tp40) REVERT: B 333 ASP cc_start: 0.7835 (m-30) cc_final: 0.7530 (m-30) REVERT: B 354 GLU cc_start: 0.7150 (mp0) cc_final: 0.6610 (mp0) REVERT: B 357 ASP cc_start: 0.7829 (t0) cc_final: 0.7599 (t0) REVERT: B 377 LEU cc_start: 0.7812 (mt) cc_final: 0.7378 (mt) REVERT: B 378 GLN cc_start: 0.7461 (mm110) cc_final: 0.6981 (mp10) REVERT: B 384 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: B 412 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.6271 (tm-30) REVERT: B 416 ASP cc_start: 0.7937 (m-30) cc_final: 0.7597 (m-30) REVERT: B 522 ARG cc_start: 0.7877 (ptm160) cc_final: 0.7508 (ptm160) outliers start: 28 outliers final: 20 residues processed: 246 average time/residue: 0.1069 time to fit residues: 36.3110 Evaluate side-chains 254 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122533 restraints weight = 12904.939| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.22 r_work: 0.3429 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9600 Z= 0.171 Angle : 0.597 9.151 13070 Z= 0.303 Chirality : 0.044 0.168 1434 Planarity : 0.004 0.046 1644 Dihedral : 3.992 16.911 1240 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.58 % Allowed : 16.17 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.25), residues: 1113 helix: 0.76 (0.27), residues: 375 sheet: -0.71 (0.51), residues: 109 loop : -0.82 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.037 0.002 TYR A 319 PHE 0.018 0.002 PHE A 250 TRP 0.023 0.002 TRP B 394 HIS 0.005 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 9585) covalent geometry : angle 0.58757 / 0.30 (13034) SS BOND : bond 0.00235 / 0.13 ( 9) SS BOND : angle 0.64714 / 0.37 ( 18) hydrogen bonds : bond 0.03952 / 2.48 ( 291) hydrogen bonds : angle 4.78881 / 3.15 ( 825) link_ALPHA1-4 : bond 0.00520 / 0.27 ( 1) link_ALPHA1-4 : angle 2.27646 / 0.98 ( 3) link_BETA1-4 : bond 0.01073 / 0.41 ( 3) link_BETA1-4 : angle 3.60443 / 1.68 ( 9) link_NAG-ASN : bond 0.00475 / 0.25 ( 2) link_NAG-ASN : angle 1.86465 / 0.93 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8253 (m-10) cc_final: 0.7838 (m-80) REVERT: A 166 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7950 (mm) REVERT: A 215 MET cc_start: 0.6811 (ptp) cc_final: 0.6523 (ptp) REVERT: A 261 LYS cc_start: 0.8148 (ttpp) cc_final: 0.7823 (ttpp) REVERT: A 291 ASP cc_start: 0.7239 (p0) cc_final: 0.6855 (p0) REVERT: A 411 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6912 (mp) REVERT: A 420 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7190 (tt0) REVERT: A 453 PHE cc_start: 0.8254 (m-80) cc_final: 0.8001 (m-80) REVERT: A 579 PHE cc_start: 0.8202 (t80) cc_final: 0.7788 (t80) REVERT: A 705 MET cc_start: 0.7429 (mtm) cc_final: 0.7223 (mtt) REVERT: A 714 TYR cc_start: 0.7838 (p90) cc_final: 0.7457 (p90) REVERT: A 715 MET cc_start: 0.7473 (tpp) cc_final: 0.7198 (tpp) REVERT: A 721 GLN cc_start: 0.5994 (pm20) cc_final: 0.5667 (pt0) REVERT: B 92 ASP cc_start: 0.8107 (t70) cc_final: 0.7779 (t0) REVERT: B 99 ASN cc_start: 0.7967 (p0) cc_final: 0.7744 (p0) REVERT: B 135 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7047 (mmp) REVERT: B 188 LEU cc_start: 0.7701 (mm) cc_final: 0.7400 (mt) REVERT: B 265 TYR cc_start: 0.7523 (m-80) cc_final: 0.6988 (m-80) REVERT: B 313 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7490 (tp40) REVERT: B 333 ASP cc_start: 0.7856 (m-30) cc_final: 0.7553 (m-30) REVERT: B 354 GLU cc_start: 0.7170 (mp0) cc_final: 0.6637 (mp0) REVERT: B 357 ASP cc_start: 0.7828 (t0) cc_final: 0.7605 (t0) REVERT: B 377 LEU cc_start: 0.7859 (mt) cc_final: 0.7431 (mt) REVERT: B 378 GLN cc_start: 0.7475 (mm110) cc_final: 0.7018 (mp10) REVERT: B 384 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: B 412 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.6301 (tm-30) REVERT: B 416 ASP cc_start: 0.7939 (m-30) cc_final: 0.7589 (m-30) REVERT: B 522 ARG cc_start: 0.7897 (ptm160) cc_final: 0.7553 (ptm160) outliers start: 26 outliers final: 20 residues processed: 246 average time/residue: 0.1043 time to fit residues: 35.4196 Evaluate side-chains 261 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.122686 restraints weight = 12765.150| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.21 r_work: 0.3432 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.004 0.056 9600 Z= 0.156 Angle : 0.599 9.076 13070 Z= 0.304 Chirality : 0.044 0.168 1434 Planarity : 0.004 0.046 1644 Dihedral : 4.017 16.915 1240 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.48 % Allowed : 16.57 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.25), residues: 1113 helix: 0.74 (0.27), residues: 375 sheet: -0.69 (0.51), residues: 109 loop : -0.85 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.036 0.002 TYR A 319 PHE 0.017 0.002 PHE A 250 TRP 0.020 0.002 TRP B 394 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 9585) covalent geometry : angle 0.58907 / 0.30 (13034) SS BOND : bond 0.00205 / 0.11 ( 9) SS BOND : angle 0.64175 / 0.37 ( 18) hydrogen bonds : bond 0.03909 / 2.45 ( 291) hydrogen bonds : angle 4.78116 / 3.14 ( 825) link_ALPHA1-4 : bond 0.00542 / 0.29 ( 1) link_ALPHA1-4 : angle 2.29027 / 0.99 ( 3) link_BETA1-4 : bond 0.01107 / 0.42 ( 3) link_BETA1-4 : angle 3.59059 / 1.67 ( 9) link_NAG-ASN : bond 0.00493 / 0.26 ( 2) link_NAG-ASN : angle 1.83645 / 0.91 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2394.18 seconds wall clock time: 41 minutes 47.95 seconds (2507.95 seconds total)