Starting phenix.real_space_refine on Sat Sep 12 00:20:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w4c_65624/09_2026/9w4c_65624.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w4c_65624/09_2026/9w4c_65624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w4c_65624/09_2026/9w4c_65624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w4c_65624/09_2026/9w4c_65624.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w4c_65624/09_2026/9w4c_65624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w4c_65624/09_2026/9w4c_65624.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.156 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 7716 2.51 5 N 2052 2.21 5 O 2358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12210 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 4014 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 14, 'TRANS': 477} Chain breaks: 1 Chain: "B" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 4014 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 14, 'TRANS': 477} Chain breaks: 1 Chain: "C" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 4014 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 14, 'TRANS': 477} Chain breaks: 1 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.25, per 1000 atoms: 0.27 Number of scatterers: 12210 At special positions: 0 Unit cell: (88.35, 88.35, 134.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2358 8.00 N 2052 7.00 C 7716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 393 " - pdb=" SG CYS A 403 " distance=2.03 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 436 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 403 " distance=2.04 Simple disulfide: pdb=" SG CYS B 418 " - pdb=" SG CYS B 436 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 365 " distance=2.03 Simple disulfide: pdb=" SG CYS C 393 " - pdb=" SG CYS C 403 " distance=2.03 Simple disulfide: pdb=" SG CYS C 418 " - pdb=" SG CYS C 436 " distance=2.03 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 495 " 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 NAG-ASN " NAG A 701 " - " ASN A 104 " " NAG A 702 " - " ASN A 293 " " NAG A 703 " - " ASN A 361 " " NAG A 704 " - " ASN A 526 " " NAG B 701 " - " ASN B 104 " " NAG B 702 " - " ASN B 293 " " NAG B 703 " - " ASN B 361 " " NAG B 704 " - " ASN B 526 " " NAG C 701 " - " ASN C 104 " " NAG C 702 " - " ASN C 293 " " NAG C 703 " - " ASN C 361 " " NAG C 704 " - " ASN C 526 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 589.8 milliseconds 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2886 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 9 sheets defined 37.9% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.675A pdb=" N LEU A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 102 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 122 through 137 Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.557A pdb=" N LYS A 204 " --> pdb=" O HIS A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 211 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 239 through 274 removed outlier: 3.518A pdb=" N TYR A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 295 through 298 Processing helix chain 'A' and resid 311 through 320 removed outlier: 4.257A pdb=" N ALA A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.543A pdb=" N ILE A 531 " --> pdb=" O PHE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 removed outlier: 4.723A pdb=" N GLN A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 562 through 568 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.701A pdb=" N LEU B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 102 Processing helix chain 'B' and resid 113 through 122 Processing helix chain 'B' and resid 122 through 137 Processing helix chain 'B' and resid 192 through 205 removed outlier: 3.796A pdb=" N ASN B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 211 Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 239 through 274 Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 295 through 298 Processing helix chain 'B' and resid 311 through 320 removed outlier: 4.122A pdb=" N ALA B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 417 through 424 Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 551 through 558 Processing helix chain 'B' and resid 562 through 568 Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.666A pdb=" N LEU C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 102 Processing helix chain 'C' and resid 113 through 122 Processing helix chain 'C' and resid 122 through 138 removed outlier: 3.983A pdb=" N HIS C 138 " --> pdb=" O ASN C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 204 removed outlier: 3.562A pdb=" N LYS C 204 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 211 Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 239 through 274 removed outlier: 3.577A pdb=" N TYR C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 294 Processing helix chain 'C' and resid 295 through 298 Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.796A pdb=" N MET C 313 " --> pdb=" O ASN C 309 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 417 through 424 Processing helix chain 'C' and resid 510 through 514 Processing helix chain 'C' and resid 526 through 531 removed outlier: 3.521A pdb=" N ILE C 531 " --> pdb=" O PHE C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 558 Processing helix chain 'C' and resid 562 through 568 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 77 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 77 current: chain 'A' and resid 332 through 343 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 332 through 343 current: chain 'A' and resid 374 through 378 removed outlier: 5.642A pdb=" N ASN A 383 " --> pdb=" O SER A 378 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 383 through 387 current: chain 'A' and resid 401 through 403 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 401 through 403 current: chain 'B' and resid 475 through 480 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 475 through 480 current: chain 'B' and resid 502 through 506 Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 358 removed outlier: 9.121A pdb=" N ASN A 547 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG A 442 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 465 through 471 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 475 through 480 current: chain 'A' and resid 502 through 506 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 502 through 506 current: chain 'C' and resid 333 through 343 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 333 through 343 current: chain 'C' and resid 374 through 378 removed outlier: 5.728A pdb=" N ASN C 383 " --> pdb=" O SER C 378 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 383 through 387 current: chain 'C' and resid 401 through 403 Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 49 Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 77 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 77 current: chain 'B' and resid 333 through 343 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 333 through 343 current: chain 'B' and resid 374 through 378 removed outlier: 5.643A pdb=" N ASN B 383 " --> pdb=" O SER B 378 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 383 through 387 current: chain 'B' and resid 401 through 403 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 401 through 403 current: chain 'C' and resid 475 through 480 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 475 through 480 current: chain 'C' and resid 502 through 506 Processing sheet with id=AA7, first strand: chain 'B' and resid 357 through 358 removed outlier: 9.350A pdb=" N ASN B 547 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG B 442 " --> pdb=" O ASN B 547 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 46 through 50 removed outlier: 4.692A pdb=" N VAL C 484 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 358 430 hydrogen bonds defined for protein. 1203 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: 1.91 Time building geometry restraints manager: 1.28 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: 4031 1.34 - 1.46: 2446 1.46 - 1.58: 5811 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 12423 Sorted by residual: bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.73e+00 bond pdb=" C1 NAG C 702 " pdb=" O5 NAG C 702 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.82e+00 bond pdb=" C1 NAG B 702 " pdb=" O5 NAG B 702 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C1 NAG C 704 " pdb=" O5 NAG C 704 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.70e+00 ... (remaining 12418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 16161 1.25 - 2.51: 542 2.51 - 3.76: 107 3.76 - 5.02: 16 5.02 - 6.27: 4 Bond angle restraints: 16830 Sorted by residual: angle pdb=" CA CYS A 393 " pdb=" CB CYS A 393 " pdb=" SG CYS A 393 " ideal model delta sigma weight residual 114.40 120.29 -5.89 2.30e+00 1.89e-01 6.55e+00 angle pdb=" CA GLN C 330 " pdb=" CB GLN C 330 " pdb=" CG GLN C 330 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.45e+00 angle pdb=" C LEU A 402 " pdb=" N CYS A 403 " pdb=" CA CYS A 403 " ideal model delta sigma weight residual 122.99 119.73 3.26 1.41e+00 5.03e-01 5.34e+00 angle pdb=" C VAL C 294 " pdb=" CA VAL C 294 " pdb=" CB VAL C 294 " ideal model delta sigma weight residual 111.85 108.98 2.87 1.27e+00 6.20e-01 5.09e+00 angle pdb=" N GLN A 330 " pdb=" CA GLN A 330 " pdb=" C GLN A 330 " ideal model delta sigma weight residual 113.21 110.66 2.55 1.15e+00 7.56e-01 4.92e+00 ... (remaining 16825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.08: 7296 23.08 - 46.15: 385 46.15 - 69.23: 47 69.23 - 92.31: 41 92.31 - 115.39: 34 Dihedral angle restraints: 7803 sinusoidal: 3387 harmonic: 4416 Sorted by residual: dihedral pdb=" CA PRO A 329 " pdb=" C PRO A 329 " pdb=" N GLN A 330 " pdb=" CA GLN A 330 " ideal model delta harmonic sigma weight residual 180.00 156.58 23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA GLU A 211 " pdb=" C GLU A 211 " pdb=" N GLN A 212 " pdb=" CA GLN A 212 " ideal model delta harmonic sigma weight residual 180.00 158.74 21.26 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA GLU C 211 " pdb=" C GLU C 211 " pdb=" N GLN C 212 " pdb=" CA GLN C 212 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 7800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1769 0.072 - 0.144: 196 0.144 - 0.216: 6 0.216 - 0.288: 1 0.288 - 0.360: 2 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C1 NAG C 703 " pdb=" ND2 ASN C 361 " pdb=" C2 NAG C 703 " pdb=" O5 NAG C 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 104 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 361 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1971 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 361 " -0.018 2.00e-02 2.50e+03 1.69e-02 3.57e+00 pdb=" CG ASN C 361 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN C 361 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 361 " 0.017 2.00e-02 2.50e+03 pdb=" C1 NAG C 703 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 527 " 0.009 2.00e-02 2.50e+03 1.32e-02 3.04e+00 pdb=" CG PHE A 527 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 527 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 527 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 527 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 527 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 527 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 527 " 0.008 2.00e-02 2.50e+03 1.19e-02 2.48e+00 pdb=" CG PHE C 527 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE C 527 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 527 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 527 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 527 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 527 " 0.000 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1632 2.76 - 3.29: 11762 3.29 - 3.83: 21145 3.83 - 4.36: 25169 4.36 - 4.90: 42547 Nonbonded interactions: 102255 Sorted by model distance: nonbonded pdb=" OG SER A 378 " pdb=" OD1 ASP A 380 " model vdw 2.224 3.040 nonbonded pdb=" OG SER B 378 " pdb=" OD1 ASP B 380 " model vdw 2.267 3.040 nonbonded pdb=" O MET A 291 " pdb=" OG1 THR A 295 " model vdw 2.277 3.040 nonbonded pdb=" O ASP C 217 " pdb=" NH2 ARG C 286 " model vdw 2.285 3.120 nonbonded pdb=" O ASP A 217 " pdb=" NH2 ARG A 286 " model vdw 2.286 3.120 ... (remaining 102250 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.670 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: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.030 Process input model: 12.150 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.003 0.051 12450 Z= 0.140 Angle : 0.562 7.123 16896 Z= 0.293 Chirality : 0.045 0.360 1974 Planarity : 0.003 0.029 2148 Dihedral : 17.432 115.385 4872 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.49 (0.22), residues: 1464 helix: 2.29 (0.24), residues: 483 sheet: 0.37 (0.27), residues: 369 loop : -1.37 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 529 TYR 0.023 0.002 TYR C 274 PHE 0.029 0.001 PHE A 527 TRP 0.007 0.001 TRP A 71 HIS 0.006 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (12423) covalent geometry : angle 0.53885 / 0.29 (16830) SS BOND : bond 0.00223 / 0.12 ( 15) SS BOND : angle 2.23251 / 1.54 ( 30) hydrogen bonds : bond 0.13990 / 8.73 ( 430) hydrogen bonds : angle 5.36136 / 3.76 ( 1203) link_NAG-ASN : bond 0.00779 / 0.54 ( 12) link_NAG-ASN : angle 2.92255 / 1.97 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 360 ASN cc_start: 0.7151 (m-40) cc_final: 0.6778 (m-40) REVERT: A 433 MET cc_start: 0.8400 (mmp) cc_final: 0.8142 (mmm) REVERT: A 463 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6774 (mm-30) REVERT: B 266 ASP cc_start: 0.7268 (m-30) cc_final: 0.7045 (m-30) REVERT: B 293 ASN cc_start: 0.7314 (t0) cc_final: 0.6916 (t0) REVERT: C 360 ASN cc_start: 0.7206 (m-40) cc_final: 0.6996 (m-40) REVERT: C 402 LEU cc_start: 0.7298 (mt) cc_final: 0.7065 (mt) REVERT: C 548 ASN cc_start: 0.7861 (p0) cc_final: 0.7521 (t0) outliers start: 0 outliers final: 1 residues processed: 307 average time/residue: 0.5175 time to fit residues: 174.2030 Evaluate side-chains 222 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 419 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 HIS A 314 HIS A 360 ASN A 364 ASN B 102 ASN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS B 314 HIS B 413 ASN B 512 ASN C 102 ASN C 229 HIS C 314 HIS ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.160799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131152 restraints weight = 13308.763| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.87 r_work: 0.3286 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12450 Z= 0.128 Angle : 0.547 9.124 16896 Z= 0.273 Chirality : 0.045 0.312 1974 Planarity : 0.004 0.049 2148 Dihedral : 9.022 97.097 1853 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.25 % Allowed : 11.67 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.22), residues: 1464 helix: 2.07 (0.24), residues: 507 sheet: 0.17 (0.27), residues: 390 loop : -1.21 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 382 TYR 0.022 0.001 TYR B 274 PHE 0.023 0.001 PHE A 527 TRP 0.008 0.001 TRP B 71 HIS 0.003 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (12423) covalent geometry : angle 0.52810 / 0.27 (16830) SS BOND : bond 0.00324 / 0.17 ( 15) SS BOND : angle 1.39687 / 0.95 ( 30) hydrogen bonds : bond 0.02910 / 1.86 ( 430) hydrogen bonds : angle 4.29286 / 3.02 ( 1203) link_NAG-ASN : bond 0.00707 / 0.44 ( 12) link_NAG-ASN : angle 2.85723 / 1.95 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 131 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: A 365 CYS cc_start: 0.8048 (m) cc_final: 0.7776 (m) REVERT: A 433 MET cc_start: 0.8119 (mmp) cc_final: 0.7846 (mmm) REVERT: A 434 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.6921 (p0) REVERT: A 463 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7000 (mm-30) REVERT: A 500 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7931 (mptt) REVERT: B 433 MET cc_start: 0.8196 (mmp) cc_final: 0.7982 (mmm) REVERT: B 463 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7123 (mm-30) REVERT: C 127 ILE cc_start: 0.8915 (mm) cc_final: 0.8615 (mp) REVERT: C 131 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: C 291 MET cc_start: 0.9117 (mtp) cc_final: 0.8699 (mtp) REVERT: C 360 ASN cc_start: 0.7524 (m-40) cc_final: 0.7322 (m-40) REVERT: C 423 PHE cc_start: 0.8725 (t80) cc_final: 0.8522 (t80) REVERT: C 463 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6975 (mm-30) REVERT: C 500 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7800 (mptt) outliers start: 31 outliers final: 15 residues processed: 275 average time/residue: 0.4792 time to fit residues: 145.6156 Evaluate side-chains 247 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 500 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 133 ASN B 133 ASN B 206 ASN B 547 ASN C 246 ASN C 547 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.157303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.127429 restraints weight = 13311.806| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.87 r_work: 0.3202 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12450 Z= 0.176 Angle : 0.540 6.486 16896 Z= 0.279 Chirality : 0.044 0.235 1974 Planarity : 0.004 0.063 2148 Dihedral : 6.652 89.227 1851 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.48 % Allowed : 13.41 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1464 helix: 1.98 (0.23), residues: 507 sheet: 0.09 (0.27), residues: 390 loop : -1.25 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 529 TYR 0.019 0.001 TYR A 274 PHE 0.018 0.002 PHE A 527 TRP 0.013 0.002 TRP B 71 HIS 0.005 0.001 HIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (12423) covalent geometry : angle 0.52485 / 0.28 (16830) SS BOND : bond 0.00492 / 0.26 ( 15) SS BOND : angle 1.93665 / 1.36 ( 30) hydrogen bonds : bond 0.03439 / 2.20 ( 430) hydrogen bonds : angle 4.32353 / 3.03 ( 1203) link_NAG-ASN : bond 0.00613 / 0.35 ( 12) link_NAG-ASN : angle 2.25619 / 1.52 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: A 433 MET cc_start: 0.8230 (mmp) cc_final: 0.7943 (mmm) REVERT: A 500 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7907 (mptt) REVERT: B 307 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7986 (tm-30) REVERT: B 463 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7160 (mm-30) REVERT: B 500 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7853 (mptt) REVERT: B 558 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8428 (mtp) REVERT: C 127 ILE cc_start: 0.8950 (mm) cc_final: 0.8656 (mp) REVERT: C 131 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: C 291 MET cc_start: 0.9141 (mtp) cc_final: 0.8753 (mtp) REVERT: C 360 ASN cc_start: 0.7597 (m-40) cc_final: 0.7387 (m-40) REVERT: C 423 PHE cc_start: 0.8807 (t80) cc_final: 0.8592 (t80) REVERT: C 500 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7785 (mptt) REVERT: C 566 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7759 (mtt180) outliers start: 48 outliers final: 23 residues processed: 263 average time/residue: 0.5068 time to fit residues: 146.5935 Evaluate side-chains 255 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 566 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 23 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 90 optimal weight: 0.0020 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN B 206 ASN C 254 GLN ** C 552 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 = 0.3765 r_free = 0.3765 target = 0.160159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.130791 restraints weight = 13261.788| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.85 r_work: 0.3306 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12450 Z= 0.099 Angle : 0.464 6.757 16896 Z= 0.242 Chirality : 0.042 0.207 1974 Planarity : 0.003 0.066 2148 Dihedral : 6.024 86.055 1851 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.75 % Allowed : 16.01 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.22), residues: 1464 helix: 2.11 (0.23), residues: 507 sheet: 0.18 (0.27), residues: 390 loop : -1.16 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 382 TYR 0.021 0.001 TYR C 274 PHE 0.013 0.001 PHE B 539 TRP 0.008 0.001 TRP B 71 HIS 0.002 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (12423) covalent geometry : angle 0.45094 / 0.24 (16830) SS BOND : bond 0.00258 / 0.15 ( 15) SS BOND : angle 1.27628 / 0.87 ( 30) hydrogen bonds : bond 0.02673 / 1.71 ( 430) hydrogen bonds : angle 4.12705 / 2.88 ( 1203) link_NAG-ASN : bond 0.00472 / 0.29 ( 12) link_NAG-ASN : angle 2.10740 / 1.44 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 365 CYS cc_start: 0.7826 (m) cc_final: 0.7474 (m) REVERT: A 434 ASN cc_start: 0.7226 (OUTLIER) cc_final: 0.6971 (p0) REVERT: B 307 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: B 433 MET cc_start: 0.8251 (mmp) cc_final: 0.8038 (mmm) REVERT: B 463 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7168 (mm-30) REVERT: B 500 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7803 (mptt) REVERT: C 127 ILE cc_start: 0.8950 (mm) cc_final: 0.8655 (mp) REVERT: C 131 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: C 230 LEU cc_start: 0.8701 (mt) cc_final: 0.8257 (mp) REVERT: C 291 MET cc_start: 0.9114 (mtp) cc_final: 0.8714 (mtp) REVERT: C 566 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7724 (mtt180) outliers start: 38 outliers final: 13 residues processed: 264 average time/residue: 0.5036 time to fit residues: 146.7614 Evaluate side-chains 244 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 566 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 13 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 413 ASN A 512 ASN A 548 ASN B 206 ASN C 43 ASN ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.156295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126433 restraints weight = 13299.234| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.86 r_work: 0.3192 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12450 Z= 0.195 Angle : 0.560 11.510 16896 Z= 0.287 Chirality : 0.045 0.329 1974 Planarity : 0.004 0.068 2148 Dihedral : 6.211 84.983 1851 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.70 % Allowed : 16.67 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.22), residues: 1464 helix: 2.00 (0.23), residues: 507 sheet: 0.01 (0.27), residues: 393 loop : -1.30 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 382 TYR 0.027 0.002 TYR C 274 PHE 0.013 0.002 PHE A 527 TRP 0.014 0.002 TRP B 71 HIS 0.004 0.001 HIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.19 (12423) covalent geometry : angle 0.53509 / 0.28 (16830) SS BOND : bond 0.00481 / 0.25 ( 15) SS BOND : angle 2.17127 / 1.49 ( 30) hydrogen bonds : bond 0.03396 / 2.18 ( 430) hydrogen bonds : angle 4.31950 / 3.03 ( 1203) link_NAG-ASN : bond 0.00794 / 0.43 ( 12) link_NAG-ASN : angle 3.03669 / 1.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8251 (ptm) REVERT: A 131 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: A 365 CYS cc_start: 0.7850 (m) cc_final: 0.7446 (m) REVERT: A 500 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7904 (mptt) REVERT: B 84 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8008 (mt-10) REVERT: B 194 ASP cc_start: 0.7842 (m-30) cc_final: 0.7558 (m-30) REVERT: B 463 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7298 (mm-30) REVERT: B 500 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7887 (mptt) REVERT: B 558 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8435 (mtp) REVERT: C 64 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8344 (ptm) REVERT: C 127 ILE cc_start: 0.8959 (mm) cc_final: 0.8638 (mp) REVERT: C 131 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: C 230 LEU cc_start: 0.8840 (mt) cc_final: 0.8456 (mp) REVERT: C 357 MET cc_start: 0.9009 (ptt) cc_final: 0.8807 (ptt) REVERT: C 423 PHE cc_start: 0.8825 (t80) cc_final: 0.8577 (t80) REVERT: C 500 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7798 (mptt) REVERT: C 566 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7749 (mtt180) outliers start: 51 outliers final: 27 residues processed: 267 average time/residue: 0.5259 time to fit residues: 154.1153 Evaluate side-chains 257 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 566 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 71 optimal weight: 0.0010 chunk 6 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 63 GLN B 206 ASN B 246 ASN B 379 GLN C 43 ASN C 225 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.159624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130190 restraints weight = 13269.011| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.84 r_work: 0.3295 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12450 Z= 0.107 Angle : 0.488 11.703 16896 Z= 0.252 Chirality : 0.043 0.309 1974 Planarity : 0.003 0.070 2148 Dihedral : 5.876 83.044 1851 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.83 % Allowed : 18.48 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.22), residues: 1464 helix: 2.11 (0.23), residues: 507 sheet: 0.08 (0.27), residues: 393 loop : -1.23 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 382 TYR 0.017 0.001 TYR C 274 PHE 0.011 0.001 PHE B 539 TRP 0.008 0.001 TRP A 71 HIS 0.002 0.001 HIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (12423) covalent geometry : angle 0.46573 / 0.25 (16830) SS BOND : bond 0.00246 / 0.13 ( 15) SS BOND : angle 1.36562 / 0.95 ( 30) hydrogen bonds : bond 0.02729 / 1.73 ( 430) hydrogen bonds : angle 4.13295 / 2.89 ( 1203) link_NAG-ASN : bond 0.00693 / 0.38 ( 12) link_NAG-ASN : angle 2.99896 / 1.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8135 (ptm) REVERT: A 500 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7909 (mptt) REVERT: A 548 ASN cc_start: 0.8335 (t0) cc_final: 0.7768 (m-40) REVERT: B 84 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8071 (mt-10) REVERT: B 307 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: B 360 ASN cc_start: 0.7637 (m-40) cc_final: 0.6676 (p0) REVERT: B 463 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7187 (mm-30) REVERT: B 500 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7868 (mptt) REVERT: C 64 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8278 (ptm) REVERT: C 127 ILE cc_start: 0.8945 (mm) cc_final: 0.8645 (mp) REVERT: C 131 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: C 211 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: C 230 LEU cc_start: 0.8819 (mt) cc_final: 0.8426 (mp) REVERT: C 291 MET cc_start: 0.9140 (mtp) cc_final: 0.8724 (mtp) REVERT: C 357 MET cc_start: 0.9038 (ptt) cc_final: 0.8816 (ptt) REVERT: C 500 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8314 (mppt) REVERT: C 566 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7751 (mtt180) outliers start: 39 outliers final: 15 residues processed: 268 average time/residue: 0.5504 time to fit residues: 161.8385 Evaluate side-chains 248 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 566 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 145 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 37 optimal weight: 0.0570 chunk 68 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 63 GLN B 206 ASN ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.157179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126538 restraints weight = 12868.851| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.89 r_work: 0.3202 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12450 Z= 0.161 Angle : 0.541 11.497 16896 Z= 0.279 Chirality : 0.044 0.314 1974 Planarity : 0.004 0.073 2148 Dihedral : 5.989 82.206 1851 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.70 % Allowed : 18.62 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.22), residues: 1464 helix: 2.08 (0.23), residues: 504 sheet: 0.14 (0.27), residues: 378 loop : -1.39 (0.22), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 382 TYR 0.022 0.001 TYR C 274 PHE 0.011 0.001 PHE C 539 TRP 0.012 0.001 TRP A 71 HIS 0.004 0.001 HIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (12423) covalent geometry : angle 0.51803 / 0.27 (16830) SS BOND : bond 0.00449 / 0.26 ( 15) SS BOND : angle 2.06522 / 1.50 ( 30) hydrogen bonds : bond 0.03109 / 1.99 ( 430) hydrogen bonds : angle 4.22069 / 2.96 ( 1203) link_NAG-ASN : bond 0.00673 / 0.36 ( 12) link_NAG-ASN : angle 2.90277 / 1.92 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 0.465 Fit side-chains REVERT: A 64 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8242 (ptm) REVERT: A 131 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: A 500 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7921 (mptt) REVERT: B 84 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8069 (mt-10) REVERT: B 194 ASP cc_start: 0.7811 (m-30) cc_final: 0.7544 (m-30) REVERT: B 463 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7223 (mm-30) REVERT: B 500 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7892 (mptt) REVERT: C 127 ILE cc_start: 0.8955 (mm) cc_final: 0.8642 (mp) REVERT: C 131 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: C 291 MET cc_start: 0.9150 (mtp) cc_final: 0.8755 (mtp) REVERT: C 500 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8378 (mppt) REVERT: C 540 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6744 (mm-30) REVERT: C 566 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7704 (mtt180) outliers start: 51 outliers final: 22 residues processed: 272 average time/residue: 0.5121 time to fit residues: 152.8271 Evaluate side-chains 255 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 566 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 72 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 126 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.0010 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 63 GLN B 206 ASN B 246 ASN C 43 ASN C 119 GLN C 225 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.159192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.129881 restraints weight = 13249.260| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.83 r_work: 0.3232 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12450 Z= 0.125 Angle : 0.522 11.399 16896 Z= 0.270 Chirality : 0.043 0.317 1974 Planarity : 0.004 0.073 2148 Dihedral : 5.855 80.886 1851 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.04 % Allowed : 19.57 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.22), residues: 1464 helix: 2.12 (0.23), residues: 504 sheet: -0.05 (0.27), residues: 393 loop : -1.27 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 529 TYR 0.020 0.001 TYR B 274 PHE 0.011 0.001 PHE B 539 TRP 0.009 0.001 TRP A 71 HIS 0.003 0.001 HIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (12423) covalent geometry : angle 0.49844 / 0.26 (16830) SS BOND : bond 0.00348 / 0.18 ( 15) SS BOND : angle 2.10897 / 1.77 ( 30) hydrogen bonds : bond 0.02831 / 1.81 ( 430) hydrogen bonds : angle 4.16872 / 2.92 ( 1203) link_NAG-ASN : bond 0.00652 / 0.34 ( 12) link_NAG-ASN : angle 2.85546 / 1.89 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 time to evaluate : 0.440 Fit side-chains REVERT: A 64 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8136 (ptm) REVERT: A 131 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: A 500 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7906 (mptt) REVERT: A 548 ASN cc_start: 0.8422 (t0) cc_final: 0.7946 (m110) REVERT: B 84 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8145 (mt-10) REVERT: B 194 ASP cc_start: 0.7779 (m-30) cc_final: 0.7512 (m-30) REVERT: B 360 ASN cc_start: 0.7617 (m-40) cc_final: 0.6647 (p0) REVERT: B 463 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7160 (mm-30) REVERT: B 500 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7895 (mptt) REVERT: B 539 PHE cc_start: 0.8568 (m-80) cc_final: 0.8333 (m-80) REVERT: B 558 MET cc_start: 0.8680 (mtm) cc_final: 0.8474 (mtp) REVERT: C 127 ILE cc_start: 0.8941 (mm) cc_final: 0.8632 (mp) REVERT: C 131 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: C 291 MET cc_start: 0.9131 (mtp) cc_final: 0.8732 (mtp) REVERT: C 500 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8325 (mppt) REVERT: C 540 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6604 (mm-30) REVERT: C 548 ASN cc_start: 0.8118 (p0) cc_final: 0.7434 (t0) REVERT: C 566 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7711 (mtt180) outliers start: 42 outliers final: 23 residues processed: 270 average time/residue: 0.5098 time to fit residues: 151.4569 Evaluate side-chains 262 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 566 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 34 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 chunk 90 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 ASN B 547 ASN ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.160457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130486 restraints weight = 13154.766| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.88 r_work: 0.3237 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12450 Z= 0.113 Angle : 0.526 11.218 16896 Z= 0.270 Chirality : 0.043 0.320 1974 Planarity : 0.004 0.073 2148 Dihedral : 5.799 79.623 1851 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.68 % Allowed : 20.43 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.22), residues: 1464 helix: 2.14 (0.23), residues: 507 sheet: 0.12 (0.27), residues: 378 loop : -1.38 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 382 TYR 0.020 0.001 TYR B 274 PHE 0.018 0.001 PHE C 423 TRP 0.008 0.001 TRP A 71 HIS 0.003 0.001 HIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (12423) covalent geometry : angle 0.50088 / 0.26 (16830) SS BOND : bond 0.00285 / 0.14 ( 15) SS BOND : angle 2.43219 / 1.72 ( 30) hydrogen bonds : bond 0.02659 / 1.70 ( 430) hydrogen bonds : angle 4.10796 / 2.87 ( 1203) link_NAG-ASN : bond 0.00643 / 0.34 ( 12) link_NAG-ASN : angle 2.80315 / 1.85 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 0.598 Fit side-chains REVERT: A 101 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7846 (mptm) REVERT: A 131 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: A 500 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7912 (mptt) REVERT: A 548 ASN cc_start: 0.8352 (t0) cc_final: 0.7877 (m110) REVERT: B 84 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8096 (mt-10) REVERT: B 194 ASP cc_start: 0.7764 (m-30) cc_final: 0.7477 (m-30) REVERT: B 360 ASN cc_start: 0.7566 (m-40) cc_final: 0.6569 (p0) REVERT: B 463 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7142 (mm-30) REVERT: B 500 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7892 (mptt) REVERT: C 64 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8202 (ptm) REVERT: C 127 ILE cc_start: 0.8924 (mm) cc_final: 0.8622 (mp) REVERT: C 131 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: C 144 ASN cc_start: 0.7925 (t0) cc_final: 0.7687 (m110) REVERT: C 291 MET cc_start: 0.9139 (mtp) cc_final: 0.8710 (mtp) REVERT: C 419 ASP cc_start: 0.7905 (p0) cc_final: 0.7636 (p0) REVERT: C 500 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8337 (mppt) REVERT: C 529 ARG cc_start: 0.7940 (mtp85) cc_final: 0.7576 (mtp180) REVERT: C 540 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6566 (mm-30) REVERT: C 548 ASN cc_start: 0.8103 (p0) cc_final: 0.7476 (t0) REVERT: C 566 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7685 (mtt180) outliers start: 37 outliers final: 20 residues processed: 272 average time/residue: 0.5230 time to fit residues: 156.6561 Evaluate side-chains 261 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 566 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 92 optimal weight: 0.0870 chunk 117 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 144 optimal weight: 0.0270 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN B 246 ASN ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN ** C 552 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 = 0.3777 r_free = 0.3777 target = 0.161267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131219 restraints weight = 12936.373| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.89 r_work: 0.3255 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12450 Z= 0.105 Angle : 0.527 11.083 16896 Z= 0.272 Chirality : 0.043 0.318 1974 Planarity : 0.004 0.071 2148 Dihedral : 5.663 78.091 1851 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.25 % Allowed : 21.67 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1464 helix: 2.22 (0.23), residues: 507 sheet: 0.14 (0.27), residues: 375 loop : -1.34 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 292 TYR 0.024 0.001 TYR B 274 PHE 0.008 0.001 PHE A 469 TRP 0.007 0.001 TRP B 71 HIS 0.002 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 (12423) covalent geometry : angle 0.50408 / 0.27 (16830) SS BOND : bond 0.00220 / 0.11 ( 15) SS BOND : angle 2.23283 / 1.54 ( 30) hydrogen bonds : bond 0.02499 / 1.60 ( 430) hydrogen bonds : angle 4.05722 / 2.83 ( 1203) link_NAG-ASN : bond 0.00625 / 0.33 ( 12) link_NAG-ASN : angle 2.73751 / 1.81 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 0.452 Fit side-chains REVERT: A 64 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8038 (ptm) REVERT: A 131 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: A 433 MET cc_start: 0.8072 (mmp) cc_final: 0.7809 (mmm) REVERT: A 434 ASN cc_start: 0.7162 (OUTLIER) cc_final: 0.6950 (p0) REVERT: A 463 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6744 (mm-30) REVERT: A 500 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7952 (mptt) REVERT: A 548 ASN cc_start: 0.8250 (t0) cc_final: 0.7726 (m110) REVERT: B 84 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8028 (mt-10) REVERT: B 194 ASP cc_start: 0.7723 (m-30) cc_final: 0.7459 (m-30) REVERT: B 292 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.8157 (ttm170) REVERT: B 360 ASN cc_start: 0.7534 (m-40) cc_final: 0.6543 (p0) REVERT: B 463 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7154 (mm-30) REVERT: B 500 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8113 (mppt) REVERT: B 558 MET cc_start: 0.8688 (mtm) cc_final: 0.8365 (ttm) REVERT: C 64 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8191 (ptm) REVERT: C 127 ILE cc_start: 0.8922 (mm) cc_final: 0.8626 (mp) REVERT: C 131 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: C 291 MET cc_start: 0.9130 (mtp) cc_final: 0.8715 (mtp) REVERT: C 419 ASP cc_start: 0.7864 (p0) cc_final: 0.7583 (p0) REVERT: C 423 PHE cc_start: 0.8750 (t80) cc_final: 0.8535 (t80) REVERT: C 500 LYS cc_start: 0.8567 (mptt) cc_final: 0.8288 (mppt) REVERT: C 529 ARG cc_start: 0.7931 (mtp85) cc_final: 0.7594 (mtp180) REVERT: C 540 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6563 (mm-30) REVERT: C 548 ASN cc_start: 0.8104 (p0) cc_final: 0.7532 (t0) REVERT: C 566 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7716 (mtt180) outliers start: 31 outliers final: 15 residues processed: 265 average time/residue: 0.5054 time to fit residues: 147.5305 Evaluate side-chains 256 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 566 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 133 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 129 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 113 optimal weight: 0.0370 chunk 126 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN C 225 ASN ** C 552 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 = 0.3772 r_free = 0.3772 target = 0.160738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130600 restraints weight = 12890.204| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.89 r_work: 0.3252 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12450 Z= 0.115 Angle : 0.537 10.728 16896 Z= 0.277 Chirality : 0.043 0.317 1974 Planarity : 0.004 0.070 2148 Dihedral : 5.656 77.085 1851 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.10 % Allowed : 22.54 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1464 helix: 2.26 (0.23), residues: 507 sheet: 0.15 (0.27), residues: 375 loop : -1.33 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 529 TYR 0.029 0.001 TYR B 274 PHE 0.020 0.001 PHE B 539 TRP 0.008 0.001 TRP B 71 HIS 0.003 0.001 HIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (12423) covalent geometry : angle 0.51463 / 0.27 (16830) SS BOND : bond 0.00287 / 0.14 ( 15) SS BOND : angle 2.24178 / 1.58 ( 30) hydrogen bonds : bond 0.02592 / 1.67 ( 430) hydrogen bonds : angle 4.07229 / 2.85 ( 1203) link_NAG-ASN : bond 0.00630 / 0.34 ( 12) link_NAG-ASN : angle 2.68546 / 1.77 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4582.03 seconds wall clock time: 78 minutes 55.14 seconds (4735.14 seconds total)