Starting phenix.real_space_refine on Wed Mar 4 00:33:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7scj_25036/03_2026/7scj_25036.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scj_25036/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7scj_25036/03_2026/7scj_25036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scj_25036/03_2026/7scj_25036.map" model { file = "/net/cci-nas-00/data/ceres_data/7scj_25036/03_2026/7scj_25036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scj_25036/03_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-5986/lib/python3.9/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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 3 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: 2.29, per 1000 atoms: 0.25 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: 0.77 Conformation dependent library (CDL) restraints added in 472.4 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: 0.33 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: 1.57 Time building geometry restraints manager: 1.05 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 - 24.04: 5571 24.04 - 48.09: 198 48.09 - 72.13: 39 72.13 - 96.17: 21 96.17 - 120.21: 11 Dihedral angle restraints: 5840 sinusoidal: 2500 harmonic: 3340 Sorted by residual: dihedral pdb=" C3 NDG D 3 " pdb=" C4 NDG D 3 " pdb=" C5 NDG D 3 " pdb=" O5 NDG D 3 " ideal model delta sinusoidal sigma weight residual 53.31 -66.90 120.21 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C3 NDG D 3 " pdb=" C4 NDG D 3 " pdb=" C5 NDG D 3 " pdb=" C6 NDG D 3 " ideal model delta sinusoidal sigma weight residual 287.69 173.81 113.88 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" O4 NDG D 3 " pdb=" C4 NDG D 3 " pdb=" C5 NDG D 3 " pdb=" O5 NDG D 3 " ideal model delta sinusoidal sigma weight residual 286.72 174.60 112.12 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 5837 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: 1.140 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.160 Find NCS groups from input model: 0.060 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 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 : 14.792 120.214 3655 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 covalent geometry : bond 0.00373 ( 9585) covalent geometry : angle 0.60242 (13034) SS BOND : bond 0.01288 ( 9) SS BOND : angle 1.48692 ( 18) hydrogen bonds : bond 0.18619 ( 291) hydrogen bonds : angle 6.57352 ( 825) link_ALPHA1-4 : bond 0.00343 ( 1) link_ALPHA1-4 : angle 1.31741 ( 3) link_BETA1-4 : bond 0.02246 ( 3) link_BETA1-4 : angle 6.50132 ( 9) link_NAG-ASN : bond 0.06807 ( 2) link_NAG-ASN : angle 4.30665 ( 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 : 0.336 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: 0.1111 time to fit residues: 39.6365 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 : 0.328 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.143303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125167 restraints weight = 12687.553| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.27 r_work: 0.3481 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9600 Z= 0.130 Angle : 0.582 8.197 13070 Z= 0.294 Chirality : 0.044 0.199 1434 Planarity : 0.004 0.064 1644 Dihedral : 12.878 91.056 1452 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % 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: -0.18 (0.52), residues: 108 loop : -0.66 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 covalent geometry : bond 0.00282 ( 9585) covalent geometry : angle 0.57087 (13034) SS BOND : bond 0.00282 ( 9) SS BOND : angle 0.72955 ( 18) hydrogen bonds : bond 0.04485 ( 291) hydrogen bonds : angle 5.31858 ( 825) link_ALPHA1-4 : bond 0.01750 ( 1) link_ALPHA1-4 : angle 2.15139 ( 3) link_BETA1-4 : bond 0.01686 ( 3) link_BETA1-4 : angle 3.61431 ( 9) link_NAG-ASN : bond 0.01469 ( 2) link_NAG-ASN : angle 2.34056 ( 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 265 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 248 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8088 (m-10) cc_final: 0.7765 (m-10) REVERT: A 261 LYS cc_start: 0.8126 (ttpp) cc_final: 0.7906 (ttmm) REVERT: A 291 ASP cc_start: 0.6954 (p0) cc_final: 0.6706 (p0) REVERT: A 359 MET cc_start: 0.8342 (mpp) cc_final: 0.7846 (mpp) REVERT: A 399 ASP cc_start: 0.7491 (t0) cc_final: 0.7287 (t0) REVERT: A 420 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7126 (tt0) REVERT: A 600 ASP cc_start: 0.6927 (t0) cc_final: 0.6103 (t0) REVERT: A 603 LYS cc_start: 0.7739 (mppt) cc_final: 0.7196 (mppt) REVERT: A 714 TYR cc_start: 0.7859 (p90) cc_final: 0.7197 (p90) REVERT: A 715 MET cc_start: 0.7496 (tpp) cc_final: 0.7245 (tpp) REVERT: B 99 ASN cc_start: 0.7935 (p0) cc_final: 0.7678 (p0) REVERT: B 182 ARG cc_start: 0.7474 (mmm-85) cc_final: 0.7262 (mmm-85) REVERT: B 188 LEU cc_start: 0.7690 (mm) cc_final: 0.7325 (mt) REVERT: B 265 TYR cc_start: 0.7779 (m-80) cc_final: 0.7276 (m-80) REVERT: B 333 ASP cc_start: 0.7820 (m-30) cc_final: 0.7529 (m-30) REVERT: B 416 ASP cc_start: 0.7872 (m-30) cc_final: 0.7436 (m-30) REVERT: B 522 ARG cc_start: 0.7763 (ptm160) cc_final: 0.7504 (ttp-170) outliers start: 17 outliers final: 9 residues processed: 252 average time/residue: 0.1008 time to fit residues: 34.8368 Evaluate side-chains 248 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 239 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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: 3.9990 chunk 9 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.0170 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3811 r_free = 0.3811 target = 0.140789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122519 restraints weight = 12765.641| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.26 r_work: 0.3440 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9600 Z= 0.185 Angle : 0.599 8.293 13070 Z= 0.301 Chirality : 0.045 0.200 1434 Planarity : 0.004 0.044 1644 Dihedral : 11.637 80.194 1452 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.48 % Allowed : 13.69 % Favored : 83.83 % 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: 0.65 (0.26), residues: 377 sheet: -0.57 (0.50), residues: 114 loop : -0.78 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 149 TYR 0.025 0.002 TYR A 634 PHE 0.026 0.002 PHE A 250 TRP 0.014 0.002 TRP A 711 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9585) covalent geometry : angle 0.58848 (13034) SS BOND : bond 0.00322 ( 9) SS BOND : angle 0.68800 ( 18) hydrogen bonds : bond 0.04654 ( 291) hydrogen bonds : angle 5.09982 ( 825) link_ALPHA1-4 : bond 0.01352 ( 1) link_ALPHA1-4 : angle 1.73657 ( 3) link_BETA1-4 : bond 0.01440 ( 3) link_BETA1-4 : angle 3.81403 ( 9) link_NAG-ASN : bond 0.00648 ( 2) link_NAG-ASN : angle 2.27413 ( 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 265 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8194 (m-10) cc_final: 0.7858 (m-10) REVERT: A 105 ASP cc_start: 0.7458 (t0) cc_final: 0.7118 (t0) REVERT: A 160 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7701 (m) REVERT: A 215 MET cc_start: 0.6853 (ptp) cc_final: 0.6525 (ptp) REVERT: A 261 LYS cc_start: 0.8211 (ttpp) cc_final: 0.7955 (ttmm) REVERT: A 264 LEU cc_start: 0.7013 (tp) cc_final: 0.6767 (tt) REVERT: A 319 TYR cc_start: 0.7835 (t80) cc_final: 0.7581 (t80) REVERT: A 420 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7192 (tt0) REVERT: A 705 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7461 (mtt) REVERT: A 714 TYR cc_start: 0.7921 (p90) cc_final: 0.7185 (p90) REVERT: A 715 MET cc_start: 0.7494 (tpp) cc_final: 0.7280 (tpp) REVERT: A 721 GLN cc_start: 0.6034 (pm20) cc_final: 0.5524 (pt0) REVERT: A 722 MET cc_start: 0.7066 (ptp) cc_final: 0.6748 (ptt) REVERT: B 99 ASN cc_start: 0.7945 (p0) cc_final: 0.7690 (p0) REVERT: B 129 GLU cc_start: 0.6512 (mm-30) cc_final: 0.6207 (tp30) REVERT: B 182 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.7350 (mmm-85) REVERT: B 188 LEU cc_start: 0.7698 (mm) cc_final: 0.7355 (mt) REVERT: B 252 TYR cc_start: 0.8267 (m-10) cc_final: 0.8058 (m-10) REVERT: B 265 TYR cc_start: 0.7720 (m-80) cc_final: 0.7150 (m-80) REVERT: B 333 ASP cc_start: 0.7866 (m-30) cc_final: 0.7552 (m-30) REVERT: B 354 GLU cc_start: 0.7174 (mp0) cc_final: 0.6763 (mp0) REVERT: B 357 ASP cc_start: 0.7939 (t0) cc_final: 0.7651 (t0) REVERT: B 394 TRP cc_start: 0.7503 (t-100) cc_final: 0.7268 (t-100) REVERT: B 416 ASP cc_start: 0.7948 (m-30) cc_final: 0.7546 (m-30) outliers start: 25 outliers final: 15 residues processed: 248 average time/residue: 0.0965 time to fit residues: 33.3788 Evaluate side-chains 249 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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: 0.0570 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 chunk 74 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3832 r_free = 0.3832 target = 0.142397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.123973 restraints weight = 12900.220| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.30 r_work: 0.3449 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9600 Z= 0.122 Angle : 0.557 8.827 13070 Z= 0.280 Chirality : 0.044 0.188 1434 Planarity : 0.004 0.046 1644 Dihedral : 10.029 78.557 1452 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.78 % Allowed : 14.19 % 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: -0.25 (0.25), residues: 1113 helix: 0.87 (0.27), residues: 373 sheet: -0.49 (0.51), residues: 109 loop : -0.71 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 149 TYR 0.019 0.001 TYR B 265 PHE 0.031 0.001 PHE A 250 TRP 0.014 0.001 TRP A 445 HIS 0.003 0.000 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9585) covalent geometry : angle 0.54890 (13034) SS BOND : bond 0.00177 ( 9) SS BOND : angle 0.62851 ( 18) hydrogen bonds : bond 0.03872 ( 291) hydrogen bonds : angle 4.85616 ( 825) link_ALPHA1-4 : bond 0.01431 ( 1) link_ALPHA1-4 : angle 1.50913 ( 3) link_BETA1-4 : bond 0.01505 ( 3) link_BETA1-4 : angle 3.13021 ( 9) link_NAG-ASN : bond 0.00578 ( 2) link_NAG-ASN : angle 2.08657 ( 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 261 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8173 (m-10) cc_final: 0.7866 (m-10) REVERT: A 105 ASP cc_start: 0.7383 (t0) cc_final: 0.6975 (t0) REVERT: A 160 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7667 (m) REVERT: A 166 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7872 (mm) REVERT: A 215 MET cc_start: 0.6756 (ptp) cc_final: 0.6435 (ptp) REVERT: A 420 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7172 (tt0) REVERT: A 447 LYS cc_start: 0.8311 (mttm) cc_final: 0.7955 (ttmm) REVERT: A 599 TRP cc_start: 0.7708 (t-100) cc_final: 0.7496 (t-100) REVERT: A 714 TYR cc_start: 0.7874 (p90) cc_final: 0.7356 (p90) REVERT: A 715 MET cc_start: 0.7406 (tpp) cc_final: 0.7137 (tpp) REVERT: A 721 GLN cc_start: 0.5952 (pm20) cc_final: 0.5511 (pt0) REVERT: B 99 ASN cc_start: 0.7921 (p0) cc_final: 0.7652 (p0) REVERT: B 182 ARG cc_start: 0.7537 (mmm-85) cc_final: 0.6923 (mmm-85) REVERT: B 188 LEU cc_start: 0.7671 (mm) cc_final: 0.7354 (mt) REVERT: B 265 TYR cc_start: 0.7463 (m-80) cc_final: 0.6754 (m-80) REVERT: B 313 GLN cc_start: 0.7824 (mm-40) cc_final: 0.6885 (tm-30) REVERT: B 333 ASP cc_start: 0.7869 (m-30) cc_final: 0.7601 (m-30) REVERT: B 354 GLU cc_start: 0.7156 (mp0) cc_final: 0.6580 (mp0) REVERT: B 357 ASP cc_start: 0.7893 (t0) cc_final: 0.7602 (t0) REVERT: B 377 LEU cc_start: 0.7804 (mt) cc_final: 0.7574 (mt) REVERT: B 378 GLN cc_start: 0.7398 (mm-40) cc_final: 0.6970 (mp10) REVERT: B 394 TRP cc_start: 0.7459 (t-100) cc_final: 0.7206 (t-100) REVERT: B 416 ASP cc_start: 0.7930 (m-30) cc_final: 0.7722 (m-30) REVERT: B 522 ARG cc_start: 0.7800 (ptm160) cc_final: 0.7410 (ptm160) REVERT: B 687 MET cc_start: 0.7884 (tpp) cc_final: 0.7527 (tpp) outliers start: 28 outliers final: 17 residues processed: 243 average time/residue: 0.1018 time to fit residues: 33.7095 Evaluate side-chains 247 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 314 ARG 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 656 LEU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 90 optimal weight: 0.0870 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN A 601 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.142094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123960 restraints weight = 12872.986| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.23 r_work: 0.3469 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9600 Z= 0.126 Angle : 0.561 9.108 13070 Z= 0.281 Chirality : 0.044 0.214 1434 Planarity : 0.004 0.047 1644 Dihedral : 9.245 73.285 1452 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.08 % Allowed : 14.09 % Favored : 82.84 % 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: 0.88 (0.27), residues: 376 sheet: -0.63 (0.51), residues: 111 loop : -0.73 (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 0.031 0.001 PHE A 250 TRP 0.015 0.001 TRP A 711 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9585) covalent geometry : angle 0.55332 (13034) SS BOND : bond 0.00189 ( 9) SS BOND : angle 0.64451 ( 18) hydrogen bonds : bond 0.03759 ( 291) hydrogen bonds : angle 4.73710 ( 825) link_ALPHA1-4 : bond 0.01258 ( 1) link_ALPHA1-4 : angle 1.56728 ( 3) link_BETA1-4 : bond 0.01277 ( 3) link_BETA1-4 : angle 3.01191 ( 9) link_NAG-ASN : bond 0.00525 ( 2) link_NAG-ASN : angle 1.90905 ( 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 267 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8219 (m-10) cc_final: 0.7805 (m-80) REVERT: A 105 ASP cc_start: 0.7356 (t0) cc_final: 0.6962 (t0) REVERT: A 108 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8310 (mt) REVERT: A 160 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7730 (m) REVERT: A 166 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7962 (mm) REVERT: A 215 MET cc_start: 0.6733 (ptp) cc_final: 0.6449 (ptp) REVERT: A 261 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7847 (ttmm) REVERT: A 420 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7222 (tt0) REVERT: A 705 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7365 (mtt) REVERT: A 714 TYR cc_start: 0.7782 (p90) cc_final: 0.7322 (p90) REVERT: A 715 MET cc_start: 0.7429 (tpp) cc_final: 0.7150 (tpp) REVERT: A 721 GLN cc_start: 0.5930 (pm20) cc_final: 0.5563 (pt0) REVERT: B 99 ASN cc_start: 0.7991 (p0) cc_final: 0.7770 (p0) REVERT: B 182 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.6976 (mmm-85) REVERT: B 188 LEU cc_start: 0.7720 (mm) cc_final: 0.7415 (mt) REVERT: B 265 TYR cc_start: 0.7388 (m-80) cc_final: 0.6703 (m-80) REVERT: B 313 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7497 (tp40) REVERT: B 333 ASP cc_start: 0.7865 (m-30) cc_final: 0.7566 (m-30) REVERT: B 354 GLU cc_start: 0.7123 (mp0) cc_final: 0.6558 (mp0) REVERT: B 357 ASP cc_start: 0.7805 (t0) cc_final: 0.7521 (t0) REVERT: B 377 LEU cc_start: 0.7831 (mt) cc_final: 0.7575 (mt) REVERT: B 378 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6986 (mp10) REVERT: B 384 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7940 (tm-30) REVERT: B 388 MET cc_start: 0.7641 (mtm) cc_final: 0.7279 (mtp) REVERT: B 394 TRP cc_start: 0.7426 (t-100) cc_final: 0.7168 (t-100) REVERT: B 416 ASP cc_start: 0.7928 (m-30) cc_final: 0.7475 (m-30) REVERT: B 522 ARG cc_start: 0.7798 (ptm160) cc_final: 0.7420 (ttp-170) outliers start: 31 outliers final: 20 residues processed: 247 average time/residue: 0.1027 time to fit residues: 34.5617 Evaluate side-chains 254 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU 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 314 ARG 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 656 LEU Chi-restraints excluded: chain A residue 705 MET 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 430 ASN 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 638 VAL Chi-restraints excluded: chain B residue 692 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123238 restraints weight = 12942.431| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.21 r_work: 0.3453 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2139 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= 0.153 Angle : 0.575 8.345 13070 Z= 0.291 Chirality : 0.044 0.206 1434 Planarity : 0.004 0.047 1644 Dihedral : 8.848 68.657 1452 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.37 % Allowed : 14.09 % Favored : 82.54 % 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: -0.38 (0.25), residues: 1113 helix: 0.79 (0.26), residues: 377 sheet: -0.69 (0.48), residues: 121 loop : -0.80 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 588 TYR 0.019 0.002 TYR B 143 PHE 0.029 0.002 PHE A 250 TRP 0.020 0.001 TRP A 599 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9585) covalent geometry : angle 0.56847 (13034) SS BOND : bond 0.00242 ( 9) SS BOND : angle 0.63057 ( 18) hydrogen bonds : bond 0.04001 ( 291) hydrogen bonds : angle 4.80561 ( 825) link_ALPHA1-4 : bond 0.01087 ( 1) link_ALPHA1-4 : angle 1.57219 ( 3) link_BETA1-4 : bond 0.01172 ( 3) link_BETA1-4 : angle 2.85786 ( 9) link_NAG-ASN : bond 0.00481 ( 2) link_NAG-ASN : angle 1.86716 ( 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 264 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8245 (m-10) cc_final: 0.7833 (m-80) REVERT: A 105 ASP cc_start: 0.7373 (t0) cc_final: 0.6976 (t0) REVERT: A 108 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8324 (mt) REVERT: A 160 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7742 (m) REVERT: A 166 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8028 (mm) REVERT: A 215 MET cc_start: 0.6792 (ptp) cc_final: 0.6484 (ptp) REVERT: A 291 ASP cc_start: 0.7350 (p0) cc_final: 0.6931 (p0) REVERT: A 420 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7171 (tt0) REVERT: A 705 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7363 (mtt) REVERT: A 714 TYR cc_start: 0.7791 (p90) cc_final: 0.7305 (p90) REVERT: A 715 MET cc_start: 0.7432 (tpp) cc_final: 0.7154 (tpp) REVERT: A 721 GLN cc_start: 0.5887 (pm20) cc_final: 0.5537 (pt0) REVERT: B 99 ASN cc_start: 0.8002 (p0) cc_final: 0.7771 (p0) REVERT: B 135 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7043 (mmp) REVERT: B 182 ARG cc_start: 0.7640 (mmm-85) cc_final: 0.7048 (mmm-85) REVERT: B 188 LEU cc_start: 0.7722 (mm) cc_final: 0.7416 (mt) REVERT: B 265 TYR cc_start: 0.7430 (m-80) cc_final: 0.6831 (m-80) REVERT: B 313 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7534 (tp40) REVERT: B 333 ASP cc_start: 0.7898 (m-30) cc_final: 0.7590 (m-30) REVERT: B 354 GLU cc_start: 0.7153 (mp0) cc_final: 0.6585 (mp0) REVERT: B 357 ASP cc_start: 0.7813 (t0) cc_final: 0.7527 (t0) REVERT: B 377 LEU cc_start: 0.7872 (mt) cc_final: 0.7626 (mt) REVERT: B 384 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: B 394 TRP cc_start: 0.7434 (t-100) cc_final: 0.7149 (t-100) REVERT: B 412 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.6356 (tm-30) REVERT: B 416 ASP cc_start: 0.7921 (m-30) cc_final: 0.7539 (m-30) REVERT: B 446 LEU cc_start: 0.8298 (mm) cc_final: 0.8086 (mp) outliers start: 34 outliers final: 21 residues processed: 243 average time/residue: 0.0991 time to fit residues: 33.1780 Evaluate side-chains 258 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 108 LEU 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 252 LYS 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 395 SER 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 A residue 656 LEU Chi-restraints excluded: chain A residue 705 MET 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 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 Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 692 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.1980 chunk 29 optimal weight: 0.0470 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123700 restraints weight = 12968.861| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.29 r_work: 0.3445 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9600 Z= 0.131 Angle : 0.576 10.004 13070 Z= 0.293 Chirality : 0.044 0.218 1434 Planarity : 0.004 0.047 1644 Dihedral : 8.448 65.599 1452 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.47 % Allowed : 14.48 % Favored : 82.04 % 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: -0.33 (0.25), residues: 1113 helix: 0.83 (0.27), residues: 376 sheet: -0.64 (0.51), residues: 110 loop : -0.78 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 179 TYR 0.017 0.002 TYR B 265 PHE 0.012 0.001 PHE A 143 TRP 0.014 0.001 TRP A 599 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9585) covalent geometry : angle 0.57065 (13034) SS BOND : bond 0.00188 ( 9) SS BOND : angle 0.56140 ( 18) hydrogen bonds : bond 0.03742 ( 291) hydrogen bonds : angle 4.78992 ( 825) link_ALPHA1-4 : bond 0.01115 ( 1) link_ALPHA1-4 : angle 1.64016 ( 3) link_BETA1-4 : bond 0.01119 ( 3) link_BETA1-4 : angle 2.73134 ( 9) link_NAG-ASN : bond 0.00497 ( 2) link_NAG-ASN : angle 1.70111 ( 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 269 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8233 (m-10) cc_final: 0.7806 (m-80) REVERT: A 160 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7686 (m) REVERT: A 166 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7983 (mm) REVERT: A 215 MET cc_start: 0.6784 (ptp) cc_final: 0.6477 (ptp) REVERT: A 291 ASP cc_start: 0.7342 (p0) cc_final: 0.6915 (p0) REVERT: A 420 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7166 (tt0) REVERT: A 453 PHE cc_start: 0.8297 (m-80) cc_final: 0.7983 (m-80) REVERT: A 579 PHE cc_start: 0.8212 (t80) cc_final: 0.7788 (t80) REVERT: A 634 TYR cc_start: 0.8287 (t80) cc_final: 0.8005 (t80) REVERT: A 714 TYR cc_start: 0.7835 (p90) cc_final: 0.7400 (p90) REVERT: A 715 MET cc_start: 0.7468 (tpp) cc_final: 0.7193 (tpp) REVERT: A 721 GLN cc_start: 0.5980 (pm20) cc_final: 0.5615 (pt0) REVERT: B 92 ASP cc_start: 0.8035 (t70) cc_final: 0.7778 (t0) REVERT: B 99 ASN cc_start: 0.7959 (p0) cc_final: 0.7714 (p0) REVERT: B 135 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6979 (mmp) REVERT: B 182 ARG cc_start: 0.7619 (mmm-85) cc_final: 0.7001 (mmm-85) REVERT: B 188 LEU cc_start: 0.7693 (mm) cc_final: 0.7405 (mt) REVERT: B 265 TYR cc_start: 0.7525 (m-80) cc_final: 0.6713 (m-80) REVERT: B 313 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7540 (tp40) REVERT: B 333 ASP cc_start: 0.7875 (m-30) cc_final: 0.7565 (m-30) REVERT: B 354 GLU cc_start: 0.7127 (mp0) cc_final: 0.6570 (mp0) REVERT: B 357 ASP cc_start: 0.7865 (t0) cc_final: 0.7604 (t0) REVERT: B 377 LEU cc_start: 0.7790 (mt) cc_final: 0.7521 (mt) REVERT: B 378 GLN cc_start: 0.7463 (mm110) cc_final: 0.6987 (mp10) REVERT: B 384 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: B 412 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.6280 (tm-30) REVERT: B 416 ASP cc_start: 0.7969 (m-30) cc_final: 0.7616 (m-30) REVERT: B 431 ASP cc_start: 0.7799 (m-30) cc_final: 0.7309 (m-30) REVERT: B 446 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8104 (mp) outliers start: 35 outliers final: 21 residues processed: 244 average time/residue: 0.0997 time to fit residues: 33.4660 Evaluate side-chains 255 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 314 ARG Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 GLU 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 272 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 412 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 0.5980 chunk 14 optimal weight: 0.0370 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN ** 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 = 0.3827 r_free = 0.3827 target = 0.142373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124181 restraints weight = 12804.289| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.27 r_work: 0.3447 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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 0.066 9600 Z= 0.127 Angle : 0.576 9.361 13070 Z= 0.292 Chirality : 0.043 0.216 1434 Planarity : 0.004 0.047 1644 Dihedral : 8.150 62.951 1452 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.47 % Allowed : 14.88 % Favored : 81.65 % 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: -0.31 (0.25), residues: 1113 helix: 0.87 (0.27), residues: 376 sheet: -0.65 (0.51), residues: 111 loop : -0.77 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.023 0.002 TYR B 265 PHE 0.019 0.001 PHE A 250 TRP 0.025 0.001 TRP B 394 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9585) covalent geometry : angle 0.57054 (13034) SS BOND : bond 0.00229 ( 9) SS BOND : angle 0.68227 ( 18) hydrogen bonds : bond 0.03677 ( 291) hydrogen bonds : angle 4.75196 ( 825) link_ALPHA1-4 : bond 0.01140 ( 1) link_ALPHA1-4 : angle 1.61525 ( 3) link_BETA1-4 : bond 0.01050 ( 3) link_BETA1-4 : angle 2.58456 ( 9) link_NAG-ASN : bond 0.00418 ( 2) link_NAG-ASN : angle 1.79498 ( 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 266 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8225 (m-10) cc_final: 0.7807 (m-80) REVERT: A 160 THR cc_start: 0.8006 (OUTLIER) cc_final: 0.7696 (m) REVERT: A 166 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7997 (mm) REVERT: A 215 MET cc_start: 0.6820 (ptp) cc_final: 0.6498 (ptp) REVERT: A 264 LEU cc_start: 0.7161 (tt) cc_final: 0.6858 (tp) REVERT: A 291 ASP cc_start: 0.7302 (p0) cc_final: 0.6913 (p0) REVERT: A 420 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7184 (tt0) REVERT: A 453 PHE cc_start: 0.8304 (m-80) cc_final: 0.7977 (m-80) REVERT: A 579 PHE cc_start: 0.8193 (t80) cc_final: 0.7768 (t80) REVERT: A 714 TYR cc_start: 0.7866 (p90) cc_final: 0.7426 (p90) REVERT: A 715 MET cc_start: 0.7434 (tpp) cc_final: 0.7172 (tpp) REVERT: A 721 GLN cc_start: 0.5947 (pm20) cc_final: 0.5604 (pt0) REVERT: B 92 ASP cc_start: 0.8055 (t70) cc_final: 0.7784 (t0) REVERT: B 99 ASN cc_start: 0.7950 (p0) cc_final: 0.7712 (p0) REVERT: B 135 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6990 (mmp) REVERT: B 182 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7024 (mmm-85) REVERT: B 188 LEU cc_start: 0.7682 (mm) cc_final: 0.7396 (mt) REVERT: B 265 TYR cc_start: 0.7489 (m-80) cc_final: 0.6858 (m-80) REVERT: B 267 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7697 (mm-30) REVERT: B 270 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7373 (mm-30) REVERT: B 313 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7512 (tp40) REVERT: B 333 ASP cc_start: 0.7872 (m-30) cc_final: 0.7565 (m-30) REVERT: B 357 ASP cc_start: 0.7882 (t0) cc_final: 0.7642 (t0) REVERT: B 377 LEU cc_start: 0.7776 (mt) cc_final: 0.7514 (mt) REVERT: B 378 GLN cc_start: 0.7386 (mm110) cc_final: 0.6903 (mp10) REVERT: B 384 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: B 412 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.6265 (tm-30) REVERT: B 416 ASP cc_start: 0.7953 (m-30) cc_final: 0.7576 (m-30) REVERT: B 522 ARG cc_start: 0.7963 (ptm160) cc_final: 0.7693 (ptm160) outliers start: 35 outliers final: 20 residues processed: 245 average time/residue: 0.0956 time to fit residues: 32.5014 Evaluate side-chains 251 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 223 THR 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 A residue 656 LEU 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 Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 chunk 5 optimal weight: 0.0040 chunk 81 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN ** 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 = 0.3839 r_free = 0.3839 target = 0.143222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125029 restraints weight = 12725.994| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.27 r_work: 0.3476 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9600 Z= 0.119 Angle : 0.583 9.869 13070 Z= 0.295 Chirality : 0.043 0.205 1434 Planarity : 0.004 0.046 1644 Dihedral : 7.926 61.553 1452 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.78 % Allowed : 15.67 % Favored : 81.55 % 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: 0.80 (0.27), residues: 382 sheet: -0.64 (0.51), residues: 111 loop : -0.76 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.033 0.002 TYR A 319 PHE 0.016 0.001 PHE A 250 TRP 0.017 0.001 TRP B 394 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9585) covalent geometry : angle 0.57816 (13034) SS BOND : bond 0.00171 ( 9) SS BOND : angle 0.63331 ( 18) hydrogen bonds : bond 0.03526 ( 291) hydrogen bonds : angle 4.72613 ( 825) link_ALPHA1-4 : bond 0.01201 ( 1) link_ALPHA1-4 : angle 1.64965 ( 3) link_BETA1-4 : bond 0.01044 ( 3) link_BETA1-4 : angle 2.49919 ( 9) link_NAG-ASN : bond 0.00487 ( 2) link_NAG-ASN : angle 1.69620 ( 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 253 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8222 (m-10) cc_final: 0.7809 (m-80) REVERT: A 160 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7685 (m) REVERT: A 166 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7998 (mm) REVERT: A 215 MET cc_start: 0.6789 (ptp) cc_final: 0.6497 (ptp) REVERT: A 264 LEU cc_start: 0.7167 (tt) cc_final: 0.6873 (tp) REVERT: A 291 ASP cc_start: 0.7289 (p0) cc_final: 0.6908 (p0) REVERT: A 420 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7241 (tt0) REVERT: A 453 PHE cc_start: 0.8286 (m-80) cc_final: 0.7981 (m-80) REVERT: A 579 PHE cc_start: 0.8176 (t80) cc_final: 0.7732 (t80) REVERT: A 705 MET cc_start: 0.7593 (mtm) cc_final: 0.7365 (mtm) REVERT: A 714 TYR cc_start: 0.7840 (p90) cc_final: 0.7474 (p90) REVERT: A 715 MET cc_start: 0.7411 (tpp) cc_final: 0.7158 (tpp) REVERT: A 721 GLN cc_start: 0.6237 (pm20) cc_final: 0.5845 (pt0) REVERT: B 92 ASP cc_start: 0.8122 (t70) cc_final: 0.7841 (t0) REVERT: B 99 ASN cc_start: 0.7945 (p0) cc_final: 0.7694 (p0) REVERT: B 135 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6968 (mmp) REVERT: B 182 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.7033 (mmm-85) REVERT: B 188 LEU cc_start: 0.7675 (mm) cc_final: 0.7394 (mt) REVERT: B 265 TYR cc_start: 0.7448 (m-80) cc_final: 0.6831 (m-80) REVERT: B 267 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7689 (mm-30) REVERT: B 270 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7395 (mm-30) REVERT: B 313 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7400 (tp40) REVERT: B 333 ASP cc_start: 0.7833 (m-30) cc_final: 0.7523 (m-30) REVERT: B 357 ASP cc_start: 0.7869 (t0) cc_final: 0.7630 (t0) REVERT: B 377 LEU cc_start: 0.7712 (mt) cc_final: 0.7444 (mt) REVERT: B 378 GLN cc_start: 0.7360 (mm110) cc_final: 0.6852 (mp10) REVERT: B 394 TRP cc_start: 0.7439 (t-100) cc_final: 0.7192 (t-100) REVERT: B 412 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.6237 (tm-30) REVERT: B 416 ASP cc_start: 0.7927 (m-30) cc_final: 0.7571 (m-30) REVERT: B 522 ARG cc_start: 0.7896 (ptm160) cc_final: 0.7386 (ttp-170) outliers start: 28 outliers final: 19 residues processed: 236 average time/residue: 0.0946 time to fit residues: 30.8173 Evaluate side-chains 243 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 223 THR 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 A residue 656 LEU 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 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 14 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 0.0370 chunk 4 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN ** 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 = 0.3836 r_free = 0.3836 target = 0.143047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124809 restraints weight = 12828.479| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.28 r_work: 0.3471 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9600 Z= 0.128 Angle : 0.585 9.778 13070 Z= 0.296 Chirality : 0.043 0.191 1434 Planarity : 0.004 0.046 1644 Dihedral : 7.803 60.420 1452 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.28 % Allowed : 16.37 % 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: -0.35 (0.25), residues: 1113 helix: 0.79 (0.27), residues: 381 sheet: -0.62 (0.51), residues: 111 loop : -0.78 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.035 0.002 TYR A 319 PHE 0.017 0.001 PHE A 250 TRP 0.016 0.001 TRP B 394 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9585) covalent geometry : angle 0.58058 (13034) SS BOND : bond 0.00176 ( 9) SS BOND : angle 0.61965 ( 18) hydrogen bonds : bond 0.03578 ( 291) hydrogen bonds : angle 4.72506 ( 825) link_ALPHA1-4 : bond 0.01139 ( 1) link_ALPHA1-4 : angle 1.62808 ( 3) link_BETA1-4 : bond 0.00992 ( 3) link_BETA1-4 : angle 2.44518 ( 9) link_NAG-ASN : bond 0.00505 ( 2) link_NAG-ASN : angle 1.68442 ( 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 249 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8239 (m-10) cc_final: 0.7826 (m-80) REVERT: A 160 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7683 (m) REVERT: A 166 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8003 (mm) REVERT: A 215 MET cc_start: 0.6778 (ptp) cc_final: 0.6494 (ptp) REVERT: A 264 LEU cc_start: 0.7183 (tt) cc_final: 0.6958 (tp) REVERT: A 291 ASP cc_start: 0.7279 (p0) cc_final: 0.6928 (p0) REVERT: A 388 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.7079 (pt0) REVERT: A 420 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7251 (tt0) REVERT: A 453 PHE cc_start: 0.8290 (m-80) cc_final: 0.7990 (m-80) REVERT: A 579 PHE cc_start: 0.8172 (t80) cc_final: 0.7723 (t80) REVERT: A 634 TYR cc_start: 0.8246 (t80) cc_final: 0.8001 (t80) REVERT: A 705 MET cc_start: 0.7599 (mtm) cc_final: 0.7362 (mtm) REVERT: A 714 TYR cc_start: 0.7838 (p90) cc_final: 0.7450 (p90) REVERT: A 715 MET cc_start: 0.7426 (tpp) cc_final: 0.7167 (tpp) REVERT: A 721 GLN cc_start: 0.5905 (pm20) cc_final: 0.5567 (pt0) REVERT: B 92 ASP cc_start: 0.8159 (t70) cc_final: 0.7864 (t0) REVERT: B 99 ASN cc_start: 0.7960 (p0) cc_final: 0.7732 (p0) REVERT: B 135 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6997 (mmp) REVERT: B 188 LEU cc_start: 0.7669 (mm) cc_final: 0.7391 (mt) REVERT: B 265 TYR cc_start: 0.7502 (m-80) cc_final: 0.6915 (m-80) REVERT: B 267 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7691 (mm-30) REVERT: B 270 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7410 (mm-30) REVERT: B 313 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7438 (tp40) REVERT: B 333 ASP cc_start: 0.7822 (m-30) cc_final: 0.7512 (m-30) REVERT: B 357 ASP cc_start: 0.7900 (t0) cc_final: 0.7670 (t0) REVERT: B 377 LEU cc_start: 0.7708 (mt) cc_final: 0.7454 (mt) REVERT: B 378 GLN cc_start: 0.7371 (mm110) cc_final: 0.6870 (mp10) REVERT: B 394 TRP cc_start: 0.7445 (t-100) cc_final: 0.7200 (t-100) REVERT: B 412 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.6220 (tm-30) REVERT: B 416 ASP cc_start: 0.7942 (m-30) cc_final: 0.7578 (m-30) REVERT: B 522 ARG cc_start: 0.7891 (ptm160) cc_final: 0.7348 (ttp-170) outliers start: 23 outliers final: 18 residues processed: 235 average time/residue: 0.1030 time to fit residues: 33.1930 Evaluate side-chains 249 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 223 THR 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 587 GLU Chi-restraints excluded: chain A residue 656 LEU 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 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 Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3817 r_free = 0.3817 target = 0.141597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123383 restraints weight = 12732.110| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.26 r_work: 0.3451 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9600 Z= 0.162 Angle : 0.606 9.621 13070 Z= 0.307 Chirality : 0.045 0.230 1434 Planarity : 0.004 0.046 1644 Dihedral : 7.807 61.311 1452 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % 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: -0.44 (0.25), residues: 1113 helix: 0.81 (0.27), residues: 375 sheet: -0.88 (0.48), residues: 126 loop : -0.84 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.036 0.002 TYR A 319 PHE 0.018 0.002 PHE A 250 TRP 0.015 0.002 TRP B 394 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9585) covalent geometry : angle 0.60077 (13034) SS BOND : bond 0.00203 ( 9) SS BOND : angle 0.65043 ( 18) hydrogen bonds : bond 0.03922 ( 291) hydrogen bonds : angle 4.79594 ( 825) link_ALPHA1-4 : bond 0.01117 ( 1) link_ALPHA1-4 : angle 1.66407 ( 3) link_BETA1-4 : bond 0.00956 ( 3) link_BETA1-4 : angle 2.47350 ( 9) link_NAG-ASN : bond 0.00481 ( 2) link_NAG-ASN : angle 1.76980 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2291.88 seconds wall clock time: 39 minutes 58.38 seconds (2398.38 seconds total)