Starting phenix.real_space_refine on Wed Jul 30 23:41:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ona_16984/07_2025/8ona_16984.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ona_16984/07_2025/8ona_16984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ona_16984/07_2025/8ona_16984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ona_16984/07_2025/8ona_16984.map" model { file = "/net/cci-nas-00/data/ceres_data/8ona_16984/07_2025/8ona_16984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ona_16984/07_2025/8ona_16984.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 8217 2.51 5 N 2154 2.21 5 O 2421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12900 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4188 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 29, 'TRANS': 493} Chain breaks: 1 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Restraints were copied for chains: C, B, D, F Time building chain proxies: 8.95, per 1000 atoms: 0.69 Number of scatterers: 12900 At special positions: 0 Unit cell: (107.31, 104.244, 133.882, 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 108 16.00 O 2421 8.00 N 2154 7.00 C 8217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 405 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 401 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 350 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 401 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 401 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 399 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS C 360 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 360 " - pdb=" SG CYS B 368 " 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=3, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 180 " " NAG A 602 " - " ASN A 299 " " NAG A 603 " - " ASN A 392 " " NAG A 604 " - " ASN A 444 " " NAG A 605 " - " ASN A 460 " " NAG B 601 " - " ASN B 180 " " NAG B 602 " - " ASN B 299 " " NAG B 603 " - " ASN B 392 " " NAG B 604 " - " ASN B 444 " " NAG B 605 " - " ASN B 460 " " NAG C 601 " - " ASN C 180 " " NAG C 602 " - " ASN C 299 " " NAG C 603 " - " ASN C 392 " " NAG C 604 " - " ASN C 444 " " NAG C 605 " - " ASN C 460 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.6 seconds 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2988 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 9 sheets defined 49.6% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 17 through 24 removed outlier: 4.449A pdb=" N LYS A 21 " --> pdb=" O HIS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 58 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.546A pdb=" N ILE A 107 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 124 removed outlier: 3.663A pdb=" N LYS A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.675A pdb=" N PHE A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.657A pdb=" N CYS A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 365 through 390 removed outlier: 4.224A pdb=" N THR A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 398 Processing helix chain 'A' and resid 423 through 435 Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.665A pdb=" N PHE A 443 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 493 through 509 Processing helix chain 'A' and resid 512 through 529 Processing helix chain 'B' and resid 3 through 14 Processing helix chain 'B' and resid 17 through 24 removed outlier: 4.450A pdb=" N LYS B 21 " --> pdb=" O HIS B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 58 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.546A pdb=" N ILE B 107 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 124 removed outlier: 3.663A pdb=" N LYS B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 136 through 144 Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.676A pdb=" N PHE B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.658A pdb=" N CYS B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 365 through 390 removed outlier: 4.224A pdb=" N THR B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 398 Processing helix chain 'B' and resid 423 through 435 Processing helix chain 'B' and resid 438 through 444 removed outlier: 3.665A pdb=" N PHE B 443 " --> pdb=" O ASN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 493 through 509 Processing helix chain 'B' and resid 512 through 529 Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 17 through 24 removed outlier: 4.450A pdb=" N LYS C 21 " --> pdb=" O HIS C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 58 Processing helix chain 'C' and resid 86 through 100 Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.546A pdb=" N ILE C 107 " --> pdb=" O PHE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 124 removed outlier: 3.663A pdb=" N LYS C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 136 through 144 Processing helix chain 'C' and resid 145 through 153 removed outlier: 3.675A pdb=" N PHE C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 180 through 184 Processing helix chain 'C' and resid 314 through 332 removed outlier: 3.657A pdb=" N CYS C 318 " --> pdb=" O ARG C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 365 through 390 removed outlier: 4.224A pdb=" N THR C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 398 Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 438 through 444 removed outlier: 3.665A pdb=" N PHE C 443 " --> pdb=" O ASN C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 493 through 509 Processing helix chain 'C' and resid 512 through 529 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 178 removed outlier: 6.455A pdb=" N ILE A 222 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS A 172 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER A 220 " --> pdb=" O CYS A 172 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR A 174 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A 218 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 279 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 189 removed outlier: 6.458A pdb=" N ASN A 195 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN A 81 " --> pdb=" O ASN A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 68 Processing sheet with id=AA5, first strand: chain 'B' and resid 177 through 178 removed outlier: 6.455A pdb=" N ILE B 222 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N CYS B 172 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B 220 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR B 174 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY B 218 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE B 279 " --> pdb=" O PHE B 471 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 189 removed outlier: 6.457A pdb=" N ASN B 195 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN B 81 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 61 through 68 Processing sheet with id=AA8, first strand: chain 'C' and resid 177 through 178 removed outlier: 6.454A pdb=" N ILE C 222 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N CYS C 172 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER C 220 " --> pdb=" O CYS C 172 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR C 174 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY C 218 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE C 279 " --> pdb=" O PHE C 471 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 189 removed outlier: 6.458A pdb=" N ASN C 195 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN C 81 " --> pdb=" O ASN C 195 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.20 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3176 1.33 - 1.45: 2854 1.45 - 1.58: 7035 1.58 - 1.70: 0 1.70 - 1.82: 162 Bond restraints: 13227 Sorted by residual: bond pdb=" N GLN B 13 " pdb=" CA GLN B 13 " ideal model delta sigma weight residual 1.456 1.504 -0.048 1.18e-02 7.18e+03 1.65e+01 bond pdb=" N GLN C 13 " pdb=" CA GLN C 13 " ideal model delta sigma weight residual 1.456 1.503 -0.048 1.18e-02 7.18e+03 1.62e+01 bond pdb=" N GLN A 13 " pdb=" CA GLN A 13 " ideal model delta sigma weight residual 1.456 1.503 -0.047 1.18e-02 7.18e+03 1.61e+01 bond pdb=" C ASP A 5 " pdb=" O ASP A 5 " ideal model delta sigma weight residual 1.235 1.277 -0.042 1.26e-02 6.30e+03 1.10e+01 bond pdb=" C ASP B 5 " pdb=" O ASP B 5 " ideal model delta sigma weight residual 1.235 1.277 -0.041 1.26e-02 6.30e+03 1.07e+01 ... (remaining 13222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 17275 1.81 - 3.61: 529 3.61 - 5.42: 85 5.42 - 7.23: 15 7.23 - 9.04: 6 Bond angle restraints: 17910 Sorted by residual: angle pdb=" C GLU C 12 " pdb=" N GLN C 13 " pdb=" CA GLN C 13 " ideal model delta sigma weight residual 122.73 113.82 8.91 1.61e+00 3.86e-01 3.06e+01 angle pdb=" C GLU B 12 " pdb=" N GLN B 13 " pdb=" CA GLN B 13 " ideal model delta sigma weight residual 122.73 113.83 8.90 1.61e+00 3.86e-01 3.05e+01 angle pdb=" C GLU A 12 " pdb=" N GLN A 13 " pdb=" CA GLN A 13 " ideal model delta sigma weight residual 122.73 113.86 8.87 1.61e+00 3.86e-01 3.03e+01 angle pdb=" C GLN C 13 " pdb=" N THR C 14 " pdb=" CA THR C 14 " ideal model delta sigma weight residual 122.64 113.60 9.04 1.70e+00 3.46e-01 2.83e+01 angle pdb=" C GLN A 13 " pdb=" N THR A 14 " pdb=" CA THR A 14 " ideal model delta sigma weight residual 122.64 113.62 9.02 1.70e+00 3.46e-01 2.81e+01 ... (remaining 17905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 7277 15.80 - 31.59: 694 31.59 - 47.39: 150 47.39 - 63.18: 27 63.18 - 78.98: 21 Dihedral angle restraints: 8169 sinusoidal: 3540 harmonic: 4629 Sorted by residual: dihedral pdb=" CA MET A 16 " pdb=" C MET A 16 " pdb=" N HIS A 17 " pdb=" CA HIS A 17 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA MET B 16 " pdb=" C MET B 16 " pdb=" N HIS B 17 " pdb=" CA HIS B 17 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA MET C 16 " pdb=" C MET C 16 " pdb=" N HIS C 17 " pdb=" CA HIS C 17 " ideal model delta harmonic sigma weight residual 180.00 -160.24 -19.76 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 8166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1733 0.081 - 0.162: 199 0.162 - 0.243: 9 0.243 - 0.324: 3 0.324 - 0.404: 6 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CA ARG C 102 " pdb=" N ARG C 102 " pdb=" C ARG C 102 " pdb=" CB ARG C 102 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA ARG A 102 " pdb=" N ARG A 102 " pdb=" C ARG A 102 " pdb=" CB ARG A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA ARG B 102 " pdb=" N ARG B 102 " pdb=" C ARG B 102 " pdb=" CB ARG B 102 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 1947 not shown) Planarity restraints: 2322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 248 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C ALA C 248 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA C 248 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL C 249 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 248 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C ALA A 248 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA A 248 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL A 249 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 248 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.19e+00 pdb=" C ALA B 248 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA B 248 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL B 249 " -0.017 2.00e-02 2.50e+03 ... (remaining 2319 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4302 2.84 - 3.35: 12172 3.35 - 3.87: 21415 3.87 - 4.38: 25047 4.38 - 4.90: 42554 Nonbonded interactions: 105490 Sorted by model distance: nonbonded pdb=" O PRO C 20 " pdb=" OD1 ASN C 24 " model vdw 2.322 3.040 nonbonded pdb=" O PRO B 20 " pdb=" OD1 ASN B 24 " model vdw 2.322 3.040 nonbonded pdb=" O PRO A 20 " pdb=" OD1 ASN A 24 " model vdw 2.322 3.040 nonbonded pdb=" OE1 GLN A 48 " pdb=" OE1 GLN A 504 " model vdw 2.361 3.040 nonbonded pdb=" OE1 GLN C 48 " pdb=" OE1 GLN C 504 " model vdw 2.362 3.040 ... (remaining 105485 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 32.730 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 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 : 0.005 0.104 13269 Z= 0.312 Angle : 0.750 9.037 18003 Z= 0.436 Chirality : 0.052 0.404 1950 Planarity : 0.004 0.029 2307 Dihedral : 13.104 78.976 5109 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.43 % Allowed : 7.49 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1563 helix: 0.16 (0.19), residues: 684 sheet: 1.09 (0.30), residues: 279 loop : 0.59 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 34 HIS 0.005 0.001 HIS B 376 PHE 0.024 0.001 PHE A 33 TYR 0.014 0.002 TYR B 414 ARG 0.003 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 15) link_NAG-ASN : angle 2.68325 ( 45) hydrogen bonds : bond 0.13738 ( 670) hydrogen bonds : angle 6.15669 ( 1893) SS BOND : bond 0.00228 ( 24) SS BOND : angle 0.78473 ( 48) covalent geometry : bond 0.00444 (13227) covalent geometry : angle 0.73838 (17910) Misc. bond : bond 0.10386 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 493 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7599 (ttt) cc_final: 0.7225 (ttt) REVERT: A 49 MET cc_start: 0.6342 (ttt) cc_final: 0.6038 (ttp) REVERT: A 61 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7667 (ttmm) REVERT: A 100 ASP cc_start: 0.7278 (t0) cc_final: 0.6722 (t0) REVERT: A 111 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 120 LYS cc_start: 0.7799 (mttt) cc_final: 0.7550 (tppp) REVERT: A 138 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7445 (mt-10) REVERT: A 203 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 232 LYS cc_start: 0.8380 (mttt) cc_final: 0.8086 (mttm) REVERT: A 271 GLU cc_start: 0.7437 (pt0) cc_final: 0.7225 (pt0) REVERT: A 288 ARG cc_start: 0.7311 (mtp85) cc_final: 0.6768 (mtm-85) REVERT: A 290 ASN cc_start: 0.7792 (m110) cc_final: 0.7591 (m-40) REVERT: A 302 ASP cc_start: 0.7303 (p0) cc_final: 0.6937 (p0) REVERT: A 303 LYS cc_start: 0.7634 (mtmt) cc_final: 0.7370 (mtmt) REVERT: A 380 LYS cc_start: 0.6968 (mtpt) cc_final: 0.6720 (mtpt) REVERT: A 388 LYS cc_start: 0.7247 (mtpp) cc_final: 0.7018 (mtpp) REVERT: A 409 SER cc_start: 0.7501 (m) cc_final: 0.7062 (t) REVERT: A 411 ASP cc_start: 0.7684 (m-30) cc_final: 0.7285 (m-30) REVERT: A 438 LYS cc_start: 0.8094 (mttt) cc_final: 0.7818 (mttp) REVERT: A 440 ASN cc_start: 0.7226 (p0) cc_final: 0.6602 (t0) REVERT: A 465 GLU cc_start: 0.7711 (tp30) cc_final: 0.7496 (tp30) REVERT: A 470 ASP cc_start: 0.7746 (m-30) cc_final: 0.7252 (m-30) REVERT: B 10 PHE cc_start: 0.6376 (t80) cc_final: 0.6023 (t80) REVERT: B 21 LYS cc_start: 0.7265 (tppp) cc_final: 0.6955 (mmtt) REVERT: B 33 PHE cc_start: 0.7398 (t80) cc_final: 0.7149 (t80) REVERT: B 44 MET cc_start: 0.7439 (ttt) cc_final: 0.6852 (ttt) REVERT: B 60 PRO cc_start: 0.7894 (Cg_endo) cc_final: 0.7633 (Cg_exo) REVERT: B 61 LYS cc_start: 0.8018 (ttmt) cc_final: 0.7513 (mtpp) REVERT: B 62 LYS cc_start: 0.6305 (ttpp) cc_final: 0.6079 (tttp) REVERT: B 100 ASP cc_start: 0.7176 (t0) cc_final: 0.6607 (t70) REVERT: B 135 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 138 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7296 (mp0) REVERT: B 141 GLN cc_start: 0.8124 (mm110) cc_final: 0.7877 (mm110) REVERT: B 156 GLU cc_start: 0.7726 (tt0) cc_final: 0.7498 (tt0) REVERT: B 171 ASN cc_start: 0.8276 (t0) cc_final: 0.8056 (m-40) REVERT: B 203 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 232 LYS cc_start: 0.8211 (mttt) cc_final: 0.7902 (mttp) REVERT: B 244 GLU cc_start: 0.7871 (tp30) cc_final: 0.7668 (tp30) REVERT: B 288 ARG cc_start: 0.7142 (mtp85) cc_final: 0.6751 (mtm110) REVERT: B 301 SER cc_start: 0.6940 (t) cc_final: 0.6600 (p) REVERT: B 303 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7312 (mtpp) REVERT: B 308 ASP cc_start: 0.7746 (m-30) cc_final: 0.7514 (p0) REVERT: B 310 THR cc_start: 0.8384 (p) cc_final: 0.7780 (t) REVERT: B 311 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6481 (mm-30) REVERT: B 329 GLU cc_start: 0.7453 (tt0) cc_final: 0.7140 (tt0) REVERT: B 353 ASP cc_start: 0.7528 (p0) cc_final: 0.7230 (p0) REVERT: B 380 LYS cc_start: 0.7046 (mtpt) cc_final: 0.6841 (mtpt) REVERT: B 402 PHE cc_start: 0.7967 (m-80) cc_final: 0.7636 (m-80) REVERT: B 425 GLU cc_start: 0.7451 (tp30) cc_final: 0.7138 (mm-30) REVERT: B 440 ASN cc_start: 0.7348 (p0) cc_final: 0.7120 (m-40) REVERT: B 462 SER cc_start: 0.8231 (m) cc_final: 0.7773 (p) REVERT: B 465 GLU cc_start: 0.7664 (tp30) cc_final: 0.7462 (tp30) REVERT: B 466 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7040 (mm-30) REVERT: B 492 TYR cc_start: 0.7852 (t80) cc_final: 0.7159 (t80) REVERT: B 518 GLU cc_start: 0.7175 (tp30) cc_final: 0.6958 (tp30) REVERT: C 7 MET cc_start: 0.6814 (ttm) cc_final: 0.6596 (ttm) REVERT: C 10 PHE cc_start: 0.6183 (t80) cc_final: 0.5851 (t80) REVERT: C 33 PHE cc_start: 0.7353 (t80) cc_final: 0.7052 (t80) REVERT: C 61 LYS cc_start: 0.7886 (ttmt) cc_final: 0.7547 (ttmm) REVERT: C 66 GLU cc_start: 0.7472 (pt0) cc_final: 0.6812 (pm20) REVERT: C 99 GLU cc_start: 0.7502 (tt0) cc_final: 0.7237 (tt0) REVERT: C 100 ASP cc_start: 0.7379 (t0) cc_final: 0.6845 (t70) REVERT: C 120 LYS cc_start: 0.7695 (mttt) cc_final: 0.7408 (ttmm) REVERT: C 138 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7464 (mp0) REVERT: C 142 GLU cc_start: 0.7499 (tt0) cc_final: 0.7223 (tt0) REVERT: C 156 GLU cc_start: 0.7688 (tt0) cc_final: 0.7267 (pm20) REVERT: C 178 ARG cc_start: 0.7384 (ttm170) cc_final: 0.7000 (ttp-170) REVERT: C 181 LYS cc_start: 0.7705 (mtmm) cc_final: 0.7236 (mtpp) REVERT: C 232 LYS cc_start: 0.8394 (mttt) cc_final: 0.8033 (mttp) REVERT: C 249 VAL cc_start: 0.8242 (m) cc_final: 0.8012 (m) REVERT: C 288 ARG cc_start: 0.7201 (mtp85) cc_final: 0.6772 (mtm110) REVERT: C 303 LYS cc_start: 0.7695 (mtmt) cc_final: 0.7369 (mtmt) REVERT: C 346 ASN cc_start: 0.7610 (m-40) cc_final: 0.7362 (m-40) REVERT: C 441 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7062 (mm-30) REVERT: C 462 SER cc_start: 0.8179 (m) cc_final: 0.7817 (t) REVERT: C 463 ASN cc_start: 0.7933 (t0) cc_final: 0.7243 (t0) REVERT: C 465 GLU cc_start: 0.7788 (tp30) cc_final: 0.7518 (tp30) REVERT: C 466 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7265 (mm-30) REVERT: C 470 ASP cc_start: 0.7767 (m-30) cc_final: 0.7556 (m-30) REVERT: C 480 ASP cc_start: 0.7265 (m-30) cc_final: 0.6881 (m-30) REVERT: C 487 GLN cc_start: 0.7708 (tt0) cc_final: 0.7374 (tt0) REVERT: C 492 TYR cc_start: 0.7659 (t80) cc_final: 0.6990 (t80) REVERT: C 494 ARG cc_start: 0.6765 (ttp-110) cc_final: 0.6553 (ttp-110) outliers start: 6 outliers final: 0 residues processed: 496 average time/residue: 1.3983 time to fit residues: 746.4161 Evaluate side-chains 396 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 ASN A 297 HIS A 495 ASN B 48 GLN B 173 HIS ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN C 48 GLN C 91 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN C 297 HIS C 319 GLN C 324 GLN C 482 ASN C 496 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.108262 restraints weight = 17229.471| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.94 r_work: 0.3242 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 13269 Z= 0.218 Angle : 0.731 15.444 18003 Z= 0.371 Chirality : 0.048 0.261 1950 Planarity : 0.005 0.041 2307 Dihedral : 5.328 36.994 2040 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.71 % Allowed : 13.49 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1563 helix: 0.88 (0.20), residues: 690 sheet: 0.91 (0.28), residues: 279 loop : 0.63 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 349 HIS 0.006 0.001 HIS B 260 PHE 0.024 0.002 PHE B 431 TYR 0.016 0.002 TYR A 414 ARG 0.006 0.001 ARG C 351 Details of bonding type rmsd link_NAG-ASN : bond 0.00684 ( 15) link_NAG-ASN : angle 2.21879 ( 45) hydrogen bonds : bond 0.04530 ( 670) hydrogen bonds : angle 4.80782 ( 1893) SS BOND : bond 0.00515 ( 24) SS BOND : angle 3.81684 ( 48) covalent geometry : bond 0.00512 (13227) covalent geometry : angle 0.69721 (17910) Misc. bond : bond 0.00118 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 424 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8769 (tptt) cc_final: 0.8479 (mmtp) REVERT: A 44 MET cc_start: 0.7755 (ttt) cc_final: 0.7500 (ttt) REVERT: A 49 MET cc_start: 0.7388 (ttt) cc_final: 0.7161 (ttp) REVERT: A 62 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7700 (tttp) REVERT: A 102 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.7903 (mtm-85) REVERT: A 203 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7525 (mm-30) REVERT: A 301 SER cc_start: 0.8550 (t) cc_final: 0.8145 (p) REVERT: A 302 ASP cc_start: 0.7766 (p0) cc_final: 0.7484 (p0) REVERT: A 336 VAL cc_start: 0.8410 (p) cc_final: 0.8096 (t) REVERT: A 373 MET cc_start: 0.8076 (mmp) cc_final: 0.7816 (mmm) REVERT: A 380 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7592 (mtpt) REVERT: A 438 LYS cc_start: 0.8549 (mttt) cc_final: 0.8331 (mttm) REVERT: A 440 ASN cc_start: 0.7504 (p0) cc_final: 0.7174 (t0) REVERT: A 465 GLU cc_start: 0.7882 (tp30) cc_final: 0.7645 (tp30) REVERT: A 466 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7940 (mm-30) REVERT: A 470 ASP cc_start: 0.8057 (m-30) cc_final: 0.7695 (m-30) REVERT: A 521 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8161 (tm-30) REVERT: B 15 THR cc_start: 0.7993 (p) cc_final: 0.7727 (p) REVERT: B 44 MET cc_start: 0.7807 (ttt) cc_final: 0.7456 (ttt) REVERT: B 49 MET cc_start: 0.7476 (ttt) cc_final: 0.6756 (tmm) REVERT: B 61 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8241 (ttpp) REVERT: B 62 LYS cc_start: 0.7953 (ttpp) cc_final: 0.7737 (tttp) REVERT: B 121 LYS cc_start: 0.8519 (ttpp) cc_final: 0.8226 (tttm) REVERT: B 135 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7747 (mt-10) REVERT: B 156 GLU cc_start: 0.8040 (tt0) cc_final: 0.7777 (tt0) REVERT: B 203 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7510 (mm-30) REVERT: B 244 GLU cc_start: 0.7732 (tp30) cc_final: 0.7483 (tp30) REVERT: B 303 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8313 (mtpp) REVERT: B 329 GLU cc_start: 0.8232 (tt0) cc_final: 0.8010 (tt0) REVERT: B 363 THR cc_start: 0.8382 (m) cc_final: 0.8087 (t) REVERT: B 370 GLN cc_start: 0.8186 (mt0) cc_final: 0.7697 (mm110) REVERT: B 380 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7656 (mtpt) REVERT: B 441 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: B 466 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 492 TYR cc_start: 0.8687 (t80) cc_final: 0.8146 (t80) REVERT: B 521 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8247 (tm-30) REVERT: C 51 GLU cc_start: 0.7331 (tp30) cc_final: 0.7043 (tm-30) REVERT: C 61 LYS cc_start: 0.8255 (ttmt) cc_final: 0.8018 (ttmm) REVERT: C 62 LYS cc_start: 0.7988 (ttpp) cc_final: 0.7712 (ttmm) REVERT: C 141 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8514 (mm-40) REVERT: C 142 GLU cc_start: 0.8175 (tt0) cc_final: 0.7921 (tt0) REVERT: C 156 GLU cc_start: 0.7998 (tt0) cc_final: 0.7753 (tt0) REVERT: C 229 MET cc_start: 0.8837 (pmm) cc_final: 0.8529 (pmm) REVERT: C 288 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7918 (mtm-85) REVERT: C 301 SER cc_start: 0.8475 (t) cc_final: 0.8192 (p) REVERT: C 346 ASN cc_start: 0.8050 (m-40) cc_final: 0.7790 (m-40) REVERT: C 380 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7781 (mtpp) REVERT: C 432 ASP cc_start: 0.8366 (t70) cc_final: 0.8078 (t0) REVERT: C 438 LYS cc_start: 0.8515 (mttt) cc_final: 0.8204 (mttm) REVERT: C 462 SER cc_start: 0.8748 (m) cc_final: 0.8404 (t) REVERT: C 463 ASN cc_start: 0.8698 (t0) cc_final: 0.8108 (t0) REVERT: C 465 GLU cc_start: 0.7974 (tp30) cc_final: 0.7762 (tp30) REVERT: C 466 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7891 (mm-30) REVERT: C 470 ASP cc_start: 0.8005 (m-30) cc_final: 0.7779 (m-30) REVERT: C 492 TYR cc_start: 0.8628 (t80) cc_final: 0.8375 (t80) REVERT: C 521 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8048 (tm-30) outliers start: 38 outliers final: 13 residues processed: 445 average time/residue: 1.3909 time to fit residues: 667.1152 Evaluate side-chains 403 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 388 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 363 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN B 482 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.108675 restraints weight = 17522.073| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.96 r_work: 0.3249 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13269 Z= 0.213 Angle : 0.660 9.363 18003 Z= 0.338 Chirality : 0.047 0.275 1950 Planarity : 0.005 0.056 2307 Dihedral : 5.286 33.907 2040 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.07 % Allowed : 16.27 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1563 helix: 1.17 (0.20), residues: 687 sheet: 0.77 (0.28), residues: 279 loop : 0.51 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 349 HIS 0.005 0.001 HIS A 297 PHE 0.032 0.002 PHE A 33 TYR 0.016 0.002 TYR C 326 ARG 0.004 0.001 ARG C 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 15) link_NAG-ASN : angle 2.06544 ( 45) hydrogen bonds : bond 0.04652 ( 670) hydrogen bonds : angle 4.62012 ( 1893) SS BOND : bond 0.00993 ( 24) SS BOND : angle 2.40693 ( 48) covalent geometry : bond 0.00489 (13227) covalent geometry : angle 0.64162 (17910) Misc. bond : bond 0.00040 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 394 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7777 (ttt) cc_final: 0.7490 (ttt) REVERT: A 49 MET cc_start: 0.7410 (ttt) cc_final: 0.7004 (tmm) REVERT: A 102 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.8068 (mtm-85) REVERT: A 203 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7596 (mm-30) REVERT: A 288 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7925 (mtm-85) REVERT: A 301 SER cc_start: 0.8481 (t) cc_final: 0.8144 (p) REVERT: A 302 ASP cc_start: 0.7785 (p0) cc_final: 0.7503 (p0) REVERT: A 336 VAL cc_start: 0.8437 (p) cc_final: 0.8158 (t) REVERT: A 373 MET cc_start: 0.8169 (mmp) cc_final: 0.7887 (mmm) REVERT: A 380 LYS cc_start: 0.7627 (mtpt) cc_final: 0.7405 (mtpt) REVERT: A 440 ASN cc_start: 0.7404 (p0) cc_final: 0.7037 (t0) REVERT: A 441 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7486 (mm-30) REVERT: A 465 GLU cc_start: 0.7947 (tp30) cc_final: 0.7698 (tp30) REVERT: A 470 ASP cc_start: 0.8023 (m-30) cc_final: 0.7673 (m-30) REVERT: A 521 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8023 (tm-30) REVERT: B 44 MET cc_start: 0.7819 (ttt) cc_final: 0.7449 (ttt) REVERT: B 49 MET cc_start: 0.7484 (ttt) cc_final: 0.6768 (tmm) REVERT: B 62 LYS cc_start: 0.7940 (ttpp) cc_final: 0.7727 (tttp) REVERT: B 121 LYS cc_start: 0.8513 (ttpp) cc_final: 0.8201 (tttm) REVERT: B 135 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7700 (mt-10) REVERT: B 156 GLU cc_start: 0.8056 (tt0) cc_final: 0.7806 (tt0) REVERT: B 203 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7555 (mm-30) REVERT: B 288 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7918 (mtm-85) REVERT: B 303 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8410 (mtpp) REVERT: B 329 GLU cc_start: 0.8253 (tt0) cc_final: 0.8023 (tt0) REVERT: B 363 THR cc_start: 0.8353 (m) cc_final: 0.8076 (t) REVERT: B 370 GLN cc_start: 0.8226 (mt0) cc_final: 0.7742 (mm110) REVERT: B 441 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: B 466 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7741 (mm-30) REVERT: B 492 TYR cc_start: 0.8708 (t80) cc_final: 0.8227 (t80) REVERT: B 521 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8200 (tm-30) REVERT: C 22 VAL cc_start: 0.8866 (t) cc_final: 0.8616 (p) REVERT: C 51 GLU cc_start: 0.7396 (tp30) cc_final: 0.7052 (tm-30) REVERT: C 61 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7836 (mtpm) REVERT: C 141 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8496 (mm110) REVERT: C 142 GLU cc_start: 0.8152 (tt0) cc_final: 0.7862 (tt0) REVERT: C 156 GLU cc_start: 0.7967 (tt0) cc_final: 0.7732 (tt0) REVERT: C 203 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7392 (mm-30) REVERT: C 288 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7913 (mtm-85) REVERT: C 301 SER cc_start: 0.8483 (t) cc_final: 0.8184 (p) REVERT: C 323 MET cc_start: 0.8347 (mtm) cc_final: 0.8146 (mtm) REVERT: C 346 ASN cc_start: 0.8052 (m-40) cc_final: 0.7777 (m-40) REVERT: C 355 ASN cc_start: 0.8015 (m-40) cc_final: 0.7716 (p0) REVERT: C 363 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8008 (p) REVERT: C 366 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7427 (mt-10) REVERT: C 370 GLN cc_start: 0.8143 (mt0) cc_final: 0.7934 (mm110) REVERT: C 380 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7764 (mmtp) REVERT: C 438 LYS cc_start: 0.8529 (mttt) cc_final: 0.8251 (mttm) REVERT: C 462 SER cc_start: 0.8749 (m) cc_final: 0.8400 (t) REVERT: C 463 ASN cc_start: 0.8713 (t0) cc_final: 0.8122 (t0) REVERT: C 466 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7870 (mm-30) REVERT: C 521 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7994 (tm-30) outliers start: 43 outliers final: 22 residues processed: 411 average time/residue: 1.4343 time to fit residues: 632.6653 Evaluate side-chains 405 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 380 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 501 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 24 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS B 297 HIS B 482 ASN C 13 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.109791 restraints weight = 17355.468| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.95 r_work: 0.3271 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13269 Z= 0.138 Angle : 0.633 15.002 18003 Z= 0.323 Chirality : 0.044 0.261 1950 Planarity : 0.005 0.057 2307 Dihedral : 5.014 29.304 2040 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.86 % Allowed : 17.92 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.21), residues: 1563 helix: 1.44 (0.20), residues: 690 sheet: 0.87 (0.29), residues: 270 loop : 0.42 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 34 HIS 0.003 0.001 HIS B 260 PHE 0.017 0.001 PHE B 431 TYR 0.015 0.001 TYR B 118 ARG 0.005 0.000 ARG B 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 15) link_NAG-ASN : angle 1.84692 ( 45) hydrogen bonds : bond 0.04088 ( 670) hydrogen bonds : angle 4.51634 ( 1893) SS BOND : bond 0.00628 ( 24) SS BOND : angle 3.15548 ( 48) covalent geometry : bond 0.00310 (13227) covalent geometry : angle 0.60673 (17910) Misc. bond : bond 0.00023 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 381 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 THR cc_start: 0.8075 (p) cc_final: 0.7855 (p) REVERT: A 44 MET cc_start: 0.7637 (ttt) cc_final: 0.7347 (ttt) REVERT: A 49 MET cc_start: 0.7346 (ttt) cc_final: 0.6961 (tmm) REVERT: A 102 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7945 (mtm180) REVERT: A 178 ARG cc_start: 0.7979 (ttm170) cc_final: 0.7778 (mtm-85) REVERT: A 288 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7841 (mtm-85) REVERT: A 302 ASP cc_start: 0.7789 (p0) cc_final: 0.7537 (p0) REVERT: A 373 MET cc_start: 0.8133 (mmp) cc_final: 0.7824 (mmm) REVERT: A 380 LYS cc_start: 0.7445 (mtpt) cc_final: 0.7158 (mttp) REVERT: A 386 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8319 (mtmt) REVERT: A 465 GLU cc_start: 0.7915 (tp30) cc_final: 0.7697 (tp30) REVERT: A 470 ASP cc_start: 0.7972 (m-30) cc_final: 0.7641 (m-30) REVERT: A 521 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7897 (tm-30) REVERT: B 44 MET cc_start: 0.7683 (ttt) cc_final: 0.7433 (ttt) REVERT: B 49 MET cc_start: 0.7517 (ttt) cc_final: 0.7258 (tmm) REVERT: B 121 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8160 (tttm) REVERT: B 156 GLU cc_start: 0.8067 (tt0) cc_final: 0.7795 (tt0) REVERT: B 203 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7541 (mm-30) REVERT: B 288 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7541 (mtm-85) REVERT: B 297 HIS cc_start: 0.7696 (m90) cc_final: 0.7424 (m-70) REVERT: B 301 SER cc_start: 0.8743 (m) cc_final: 0.8421 (p) REVERT: B 303 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8373 (mtpp) REVERT: B 329 GLU cc_start: 0.8215 (tt0) cc_final: 0.7953 (tt0) REVERT: B 347 ILE cc_start: 0.8535 (tp) cc_final: 0.8313 (tp) REVERT: B 370 GLN cc_start: 0.8252 (mt0) cc_final: 0.7752 (mm110) REVERT: B 381 CYS cc_start: 0.6574 (m) cc_final: 0.6171 (t) REVERT: B 441 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: B 463 ASN cc_start: 0.8590 (t0) cc_final: 0.8162 (t0) REVERT: B 466 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 492 TYR cc_start: 0.8688 (t80) cc_final: 0.8205 (t80) REVERT: B 521 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8229 (tm-30) REVERT: C 10 PHE cc_start: 0.8101 (t80) cc_final: 0.7773 (t80) REVERT: C 61 LYS cc_start: 0.8100 (ttmt) cc_final: 0.7784 (ttmm) REVERT: C 141 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8475 (mm110) REVERT: C 156 GLU cc_start: 0.8001 (tt0) cc_final: 0.7775 (pm20) REVERT: C 171 ASN cc_start: 0.8355 (m-40) cc_final: 0.8115 (m-40) REVERT: C 203 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7416 (mm-30) REVERT: C 288 ARG cc_start: 0.8184 (mtp85) cc_final: 0.7785 (mtm-85) REVERT: C 293 ILE cc_start: 0.7967 (mm) cc_final: 0.7593 (mt) REVERT: C 323 MET cc_start: 0.8307 (mtm) cc_final: 0.8086 (mtm) REVERT: C 346 ASN cc_start: 0.8078 (m-40) cc_final: 0.7793 (m-40) REVERT: C 355 ASN cc_start: 0.7978 (m-40) cc_final: 0.7684 (p0) REVERT: C 363 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.7955 (p) REVERT: C 370 GLN cc_start: 0.8147 (mt0) cc_final: 0.7791 (mp10) REVERT: C 438 LYS cc_start: 0.8547 (mttt) cc_final: 0.8249 (mttm) REVERT: C 462 SER cc_start: 0.8736 (m) cc_final: 0.8444 (p) REVERT: C 463 ASN cc_start: 0.8683 (t0) cc_final: 0.8090 (t0) REVERT: C 466 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7914 (mm-30) REVERT: C 521 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7920 (tm-30) outliers start: 40 outliers final: 16 residues processed: 396 average time/residue: 1.4151 time to fit residues: 602.2637 Evaluate side-chains 381 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 361 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109032 restraints weight = 17595.782| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.95 r_work: 0.3260 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13269 Z= 0.186 Angle : 0.635 13.082 18003 Z= 0.323 Chirality : 0.045 0.264 1950 Planarity : 0.005 0.060 2307 Dihedral : 4.908 27.017 2040 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.64 % Allowed : 18.70 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.21), residues: 1563 helix: 1.50 (0.20), residues: 687 sheet: 0.84 (0.28), residues: 276 loop : 0.39 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 508 HIS 0.004 0.001 HIS B 260 PHE 0.026 0.002 PHE B 33 TYR 0.015 0.001 TYR C 118 ARG 0.004 0.000 ARG A 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 15) link_NAG-ASN : angle 1.87208 ( 45) hydrogen bonds : bond 0.04227 ( 670) hydrogen bonds : angle 4.46693 ( 1893) SS BOND : bond 0.00521 ( 24) SS BOND : angle 2.61083 ( 48) covalent geometry : bond 0.00433 (13227) covalent geometry : angle 0.61467 (17910) Misc. bond : bond 0.00038 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 365 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8048 (mmmm) cc_final: 0.7770 (tptp) REVERT: A 15 THR cc_start: 0.8085 (p) cc_final: 0.7874 (p) REVERT: A 44 MET cc_start: 0.7660 (ttt) cc_final: 0.7368 (ttt) REVERT: A 49 MET cc_start: 0.7409 (ttt) cc_final: 0.7022 (tmm) REVERT: A 102 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.7986 (mtm180) REVERT: A 178 ARG cc_start: 0.8006 (ttm170) cc_final: 0.7781 (mtm-85) REVERT: A 203 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 288 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7860 (mtm180) REVERT: A 289 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7733 (ttt90) REVERT: A 302 ASP cc_start: 0.7815 (p0) cc_final: 0.7557 (p0) REVERT: A 373 MET cc_start: 0.8120 (mmp) cc_final: 0.7806 (mmm) REVERT: A 380 LYS cc_start: 0.7354 (mtpt) cc_final: 0.7082 (mttp) REVERT: A 393 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.8056 (m) REVERT: A 465 GLU cc_start: 0.7927 (tp30) cc_final: 0.7707 (tp30) REVERT: A 470 ASP cc_start: 0.7953 (m-30) cc_final: 0.7651 (m-30) REVERT: A 521 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 44 MET cc_start: 0.7695 (ttt) cc_final: 0.7462 (ttt) REVERT: B 121 LYS cc_start: 0.8520 (ttpp) cc_final: 0.8158 (tttm) REVERT: B 156 GLU cc_start: 0.8050 (tt0) cc_final: 0.7797 (tt0) REVERT: B 203 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7560 (mm-30) REVERT: B 288 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7894 (mtm-85) REVERT: B 301 SER cc_start: 0.8699 (m) cc_final: 0.8431 (p) REVERT: B 303 LYS cc_start: 0.8741 (mtmt) cc_final: 0.8396 (mtpp) REVERT: B 329 GLU cc_start: 0.8218 (tt0) cc_final: 0.7943 (tt0) REVERT: B 347 ILE cc_start: 0.8537 (tp) cc_final: 0.8324 (tp) REVERT: B 363 THR cc_start: 0.8344 (m) cc_final: 0.8020 (t) REVERT: B 370 GLN cc_start: 0.8219 (mt0) cc_final: 0.7702 (mm110) REVERT: B 380 LYS cc_start: 0.7602 (mtpt) cc_final: 0.7250 (mmtp) REVERT: B 440 ASN cc_start: 0.7390 (p0) cc_final: 0.7085 (p0) REVERT: B 441 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: B 463 ASN cc_start: 0.8636 (t0) cc_final: 0.8173 (t0) REVERT: B 466 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7749 (mm-30) REVERT: B 492 TYR cc_start: 0.8688 (t80) cc_final: 0.8169 (t80) REVERT: B 521 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8265 (tm-30) REVERT: C 10 PHE cc_start: 0.8127 (t80) cc_final: 0.7776 (t80) REVERT: C 46 CYS cc_start: 0.7689 (m) cc_final: 0.7416 (t) REVERT: C 110 SER cc_start: 0.8384 (t) cc_final: 0.8082 (p) REVERT: C 141 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8476 (mm110) REVERT: C 156 GLU cc_start: 0.7966 (tt0) cc_final: 0.7737 (pm20) REVERT: C 203 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7448 (mm-30) REVERT: C 288 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7840 (mtm180) REVERT: C 323 MET cc_start: 0.8323 (mtm) cc_final: 0.8113 (mtm) REVERT: C 346 ASN cc_start: 0.8064 (m-40) cc_final: 0.7794 (m-40) REVERT: C 355 ASN cc_start: 0.7954 (m-40) cc_final: 0.7689 (p0) REVERT: C 363 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.7968 (p) REVERT: C 370 GLN cc_start: 0.8147 (mt0) cc_final: 0.7753 (mp10) REVERT: C 438 LYS cc_start: 0.8506 (mttt) cc_final: 0.8168 (mttm) REVERT: C 462 SER cc_start: 0.8764 (m) cc_final: 0.8416 (t) REVERT: C 463 ASN cc_start: 0.8695 (t0) cc_final: 0.8091 (t0) REVERT: C 466 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7913 (mm-30) REVERT: C 516 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7957 (mm) REVERT: C 521 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7914 (tm-30) outliers start: 37 outliers final: 19 residues processed: 380 average time/residue: 1.4796 time to fit residues: 603.7397 Evaluate side-chains 385 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 360 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 136 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.123422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.110309 restraints weight = 17687.031| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.97 r_work: 0.3280 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13269 Z= 0.144 Angle : 0.639 16.704 18003 Z= 0.322 Chirality : 0.044 0.258 1950 Planarity : 0.005 0.058 2307 Dihedral : 4.772 26.568 2040 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.14 % Allowed : 18.42 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.21), residues: 1563 helix: 1.54 (0.20), residues: 690 sheet: 0.87 (0.28), residues: 276 loop : 0.38 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 508 HIS 0.004 0.001 HIS C 376 PHE 0.017 0.001 PHE B 431 TYR 0.014 0.001 TYR A 118 ARG 0.004 0.000 ARG A 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 15) link_NAG-ASN : angle 1.77032 ( 45) hydrogen bonds : bond 0.03977 ( 670) hydrogen bonds : angle 4.47125 ( 1893) SS BOND : bond 0.00533 ( 24) SS BOND : angle 3.15578 ( 48) covalent geometry : bond 0.00333 (13227) covalent geometry : angle 0.61320 (17910) Misc. bond : bond 0.00025 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 372 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8052 (mmmm) cc_final: 0.7812 (tptp) REVERT: A 44 MET cc_start: 0.7626 (ttt) cc_final: 0.7320 (ttt) REVERT: A 49 MET cc_start: 0.7408 (ttt) cc_final: 0.7063 (tmm) REVERT: A 102 ARG cc_start: 0.8241 (mtm-85) cc_final: 0.7970 (mtm180) REVERT: A 288 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7874 (mtm180) REVERT: A 289 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7719 (ttt90) REVERT: A 302 ASP cc_start: 0.7804 (p0) cc_final: 0.7537 (p0) REVERT: A 373 MET cc_start: 0.8105 (mmp) cc_final: 0.7834 (mmm) REVERT: A 380 LYS cc_start: 0.7348 (mtpt) cc_final: 0.7093 (mttp) REVERT: A 393 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8062 (m) REVERT: A 406 ASP cc_start: 0.7885 (t0) cc_final: 0.7484 (t0) REVERT: A 465 GLU cc_start: 0.7939 (tp30) cc_final: 0.7727 (tp30) REVERT: A 470 ASP cc_start: 0.7902 (m-30) cc_final: 0.7501 (m-30) REVERT: A 521 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7613 (tm-30) REVERT: B 44 MET cc_start: 0.7702 (ttt) cc_final: 0.7413 (ttt) REVERT: B 121 LYS cc_start: 0.8512 (ttpp) cc_final: 0.8132 (tttm) REVERT: B 156 GLU cc_start: 0.8039 (tt0) cc_final: 0.7790 (tt0) REVERT: B 203 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 213 GLU cc_start: 0.7764 (pt0) cc_final: 0.7397 (pt0) REVERT: B 288 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7876 (mtm110) REVERT: B 297 HIS cc_start: 0.7641 (m90) cc_final: 0.7408 (m-70) REVERT: B 301 SER cc_start: 0.8731 (m) cc_final: 0.8351 (p) REVERT: B 303 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8384 (mtpp) REVERT: B 329 GLU cc_start: 0.8161 (tt0) cc_final: 0.7904 (tt0) REVERT: B 347 ILE cc_start: 0.8538 (tp) cc_final: 0.8319 (tp) REVERT: B 370 GLN cc_start: 0.8174 (mt0) cc_final: 0.7660 (mm110) REVERT: B 380 LYS cc_start: 0.7439 (mtpt) cc_final: 0.7123 (mmtp) REVERT: B 381 CYS cc_start: 0.6614 (m) cc_final: 0.6105 (t) REVERT: B 441 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: B 463 ASN cc_start: 0.8634 (t0) cc_final: 0.8147 (t0) REVERT: B 466 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 492 TYR cc_start: 0.8674 (t80) cc_final: 0.8146 (t80) REVERT: B 521 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8165 (tm-30) REVERT: C 10 PHE cc_start: 0.8090 (t80) cc_final: 0.7726 (t80) REVERT: C 22 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8531 (t) REVERT: C 141 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8427 (mm110) REVERT: C 156 GLU cc_start: 0.7946 (tt0) cc_final: 0.7714 (pm20) REVERT: C 203 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7467 (mm-30) REVERT: C 288 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7822 (mtm-85) REVERT: C 293 ILE cc_start: 0.7629 (mt) cc_final: 0.7399 (mt) REVERT: C 323 MET cc_start: 0.8297 (mtm) cc_final: 0.8084 (mtm) REVERT: C 346 ASN cc_start: 0.8051 (m-40) cc_final: 0.7768 (m-40) REVERT: C 355 ASN cc_start: 0.7930 (m-40) cc_final: 0.7699 (p0) REVERT: C 363 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.7962 (p) REVERT: C 370 GLN cc_start: 0.8130 (mt0) cc_final: 0.7740 (mp10) REVERT: C 380 LYS cc_start: 0.8006 (mmtp) cc_final: 0.7795 (mmtp) REVERT: C 438 LYS cc_start: 0.8480 (mttt) cc_final: 0.8190 (mttm) REVERT: C 441 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7600 (mm-30) REVERT: C 462 SER cc_start: 0.8759 (m) cc_final: 0.8405 (t) REVERT: C 463 ASN cc_start: 0.8701 (t0) cc_final: 0.8088 (t0) REVERT: C 466 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7917 (mm-30) REVERT: C 516 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7957 (mm) REVERT: C 521 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7870 (tm-30) outliers start: 44 outliers final: 22 residues processed: 389 average time/residue: 1.4548 time to fit residues: 609.3690 Evaluate side-chains 395 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 366 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS A 297 HIS B 152 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.110090 restraints weight = 17502.808| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.96 r_work: 0.3279 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13269 Z= 0.150 Angle : 0.639 13.565 18003 Z= 0.323 Chirality : 0.044 0.256 1950 Planarity : 0.005 0.060 2307 Dihedral : 4.730 27.239 2040 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.78 % Allowed : 19.84 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1563 helix: 1.57 (0.20), residues: 687 sheet: 0.94 (0.29), residues: 276 loop : 0.40 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 34 HIS 0.003 0.001 HIS A 297 PHE 0.025 0.001 PHE B 33 TYR 0.014 0.001 TYR A 118 ARG 0.006 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 15) link_NAG-ASN : angle 1.77931 ( 45) hydrogen bonds : bond 0.03940 ( 670) hydrogen bonds : angle 4.42717 ( 1893) SS BOND : bond 0.00558 ( 24) SS BOND : angle 3.07713 ( 48) covalent geometry : bond 0.00350 (13227) covalent geometry : angle 0.61374 (17910) Misc. bond : bond 0.00028 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 365 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7602 (ttt) cc_final: 0.7292 (ttt) REVERT: A 49 MET cc_start: 0.7369 (ttt) cc_final: 0.6885 (tmm) REVERT: A 102 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7997 (mtm180) REVERT: A 203 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 288 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7973 (mtp180) REVERT: A 289 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7732 (ttt90) REVERT: A 302 ASP cc_start: 0.7716 (p0) cc_final: 0.7480 (p0) REVERT: A 373 MET cc_start: 0.8098 (mmp) cc_final: 0.7842 (mmm) REVERT: A 465 GLU cc_start: 0.7949 (tp30) cc_final: 0.7734 (tp30) REVERT: A 470 ASP cc_start: 0.7909 (m-30) cc_final: 0.7604 (m-30) REVERT: A 521 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7659 (tm-30) REVERT: B 44 MET cc_start: 0.7663 (ttt) cc_final: 0.7392 (ttt) REVERT: B 156 GLU cc_start: 0.8065 (tt0) cc_final: 0.7818 (tt0) REVERT: B 288 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7892 (mtm110) REVERT: B 301 SER cc_start: 0.8709 (m) cc_final: 0.8340 (p) REVERT: B 303 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8330 (mtpp) REVERT: B 326 TYR cc_start: 0.8611 (m-80) cc_final: 0.8032 (m-10) REVERT: B 329 GLU cc_start: 0.8143 (tt0) cc_final: 0.7907 (tt0) REVERT: B 347 ILE cc_start: 0.8593 (tp) cc_final: 0.8376 (tp) REVERT: B 370 GLN cc_start: 0.8184 (mt0) cc_final: 0.7772 (mm110) REVERT: B 380 LYS cc_start: 0.7452 (mtpt) cc_final: 0.7145 (mmtp) REVERT: B 441 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: B 463 ASN cc_start: 0.8655 (t0) cc_final: 0.8120 (t0) REVERT: B 466 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7810 (mm-30) REVERT: B 492 TYR cc_start: 0.8699 (t80) cc_final: 0.8163 (t80) REVERT: B 521 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8165 (tm-30) REVERT: C 10 PHE cc_start: 0.8156 (t80) cc_final: 0.7797 (t80) REVERT: C 22 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8583 (t) REVERT: C 110 SER cc_start: 0.8378 (t) cc_final: 0.8108 (p) REVERT: C 141 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8360 (mm-40) REVERT: C 156 GLU cc_start: 0.7938 (tt0) cc_final: 0.7720 (pm20) REVERT: C 203 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7489 (mm-30) REVERT: C 288 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7814 (mtm-85) REVERT: C 318 CYS cc_start: 0.7904 (t) cc_final: 0.7579 (t) REVERT: C 323 MET cc_start: 0.8297 (mtm) cc_final: 0.8080 (mtm) REVERT: C 346 ASN cc_start: 0.8059 (m-40) cc_final: 0.7765 (m-40) REVERT: C 363 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.7965 (p) REVERT: C 370 GLN cc_start: 0.8156 (mt0) cc_final: 0.7923 (mm110) REVERT: C 380 LYS cc_start: 0.8030 (mmtp) cc_final: 0.7821 (mmtp) REVERT: C 438 LYS cc_start: 0.8474 (mttt) cc_final: 0.8185 (mttm) REVERT: C 462 SER cc_start: 0.8763 (m) cc_final: 0.8407 (t) REVERT: C 463 ASN cc_start: 0.8707 (t0) cc_final: 0.8070 (t0) REVERT: C 466 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7950 (mm-30) REVERT: C 516 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7959 (mm) REVERT: C 521 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7858 (tm-30) outliers start: 39 outliers final: 19 residues processed: 382 average time/residue: 1.5223 time to fit residues: 623.9671 Evaluate side-chains 387 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 362 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 143 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 112 optimal weight: 0.0770 chunk 96 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS B 297 HIS C 13 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.111579 restraints weight = 17641.192| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.98 r_work: 0.3297 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13269 Z= 0.134 Angle : 0.646 13.939 18003 Z= 0.323 Chirality : 0.043 0.253 1950 Planarity : 0.005 0.062 2307 Dihedral : 4.632 28.647 2040 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.64 % Allowed : 20.06 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.21), residues: 1563 helix: 1.66 (0.20), residues: 687 sheet: 1.03 (0.29), residues: 270 loop : 0.35 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 508 HIS 0.003 0.001 HIS B 297 PHE 0.016 0.001 PHE B 431 TYR 0.013 0.001 TYR B 118 ARG 0.004 0.000 ARG A 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 15) link_NAG-ASN : angle 1.70856 ( 45) hydrogen bonds : bond 0.03764 ( 670) hydrogen bonds : angle 4.42445 ( 1893) SS BOND : bond 0.00509 ( 24) SS BOND : angle 3.17248 ( 48) covalent geometry : bond 0.00308 (13227) covalent geometry : angle 0.62032 (17910) Misc. bond : bond 0.00026 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 368 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7603 (ttt) cc_final: 0.7304 (ttt) REVERT: A 49 MET cc_start: 0.7320 (ttt) cc_final: 0.7009 (tmm) REVERT: A 102 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7972 (mtm180) REVERT: A 288 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7965 (mtp180) REVERT: A 289 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7748 (ttt90) REVERT: A 302 ASP cc_start: 0.7686 (p0) cc_final: 0.7457 (p0) REVERT: A 370 GLN cc_start: 0.7823 (mm110) cc_final: 0.7463 (mp10) REVERT: A 373 MET cc_start: 0.8049 (mmp) cc_final: 0.7807 (mmm) REVERT: A 386 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8273 (mtmt) REVERT: A 462 SER cc_start: 0.8708 (m) cc_final: 0.8294 (p) REVERT: A 465 GLU cc_start: 0.7981 (tp30) cc_final: 0.7763 (tp30) REVERT: A 470 ASP cc_start: 0.7861 (m-30) cc_final: 0.7512 (m-30) REVERT: A 521 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7633 (tm-30) REVERT: B 121 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8228 (tttp) REVERT: B 156 GLU cc_start: 0.8050 (tt0) cc_final: 0.7797 (tt0) REVERT: B 178 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7771 (mtm-85) REVERT: B 213 GLU cc_start: 0.7663 (pt0) cc_final: 0.7348 (pt0) REVERT: B 288 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7890 (mtm110) REVERT: B 301 SER cc_start: 0.8691 (m) cc_final: 0.8290 (p) REVERT: B 303 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8333 (mtpp) REVERT: B 326 TYR cc_start: 0.8566 (m-80) cc_final: 0.7978 (m-10) REVERT: B 329 GLU cc_start: 0.8131 (tt0) cc_final: 0.7903 (tt0) REVERT: B 347 ILE cc_start: 0.8508 (tp) cc_final: 0.8275 (tp) REVERT: B 370 GLN cc_start: 0.8157 (mt0) cc_final: 0.7723 (mm110) REVERT: B 380 LYS cc_start: 0.7255 (mtpt) cc_final: 0.6982 (mmtp) REVERT: B 381 CYS cc_start: 0.6342 (m) cc_final: 0.5870 (t) REVERT: B 441 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: B 463 ASN cc_start: 0.8646 (t0) cc_final: 0.8111 (t0) REVERT: B 466 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7838 (mm-30) REVERT: B 492 TYR cc_start: 0.8659 (t80) cc_final: 0.8120 (t80) REVERT: B 521 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8158 (tm-30) REVERT: C 10 PHE cc_start: 0.8146 (t80) cc_final: 0.7795 (t80) REVERT: C 22 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8590 (t) REVERT: C 62 LYS cc_start: 0.7867 (ttpp) cc_final: 0.7528 (ttpp) REVERT: C 110 SER cc_start: 0.8364 (t) cc_final: 0.8077 (p) REVERT: C 141 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8351 (mm-40) REVERT: C 156 GLU cc_start: 0.7882 (tt0) cc_final: 0.7671 (pm20) REVERT: C 203 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7662 (tp30) REVERT: C 288 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7825 (mtm-85) REVERT: C 323 MET cc_start: 0.8323 (mtm) cc_final: 0.8112 (mtm) REVERT: C 346 ASN cc_start: 0.8036 (m-40) cc_final: 0.7736 (m-40) REVERT: C 363 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.7933 (p) REVERT: C 370 GLN cc_start: 0.8129 (mt0) cc_final: 0.7901 (mm110) REVERT: C 380 LYS cc_start: 0.7993 (mmtp) cc_final: 0.7762 (mmtp) REVERT: C 441 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7698 (mm-30) REVERT: C 462 SER cc_start: 0.8757 (m) cc_final: 0.8391 (t) REVERT: C 463 ASN cc_start: 0.8704 (t0) cc_final: 0.8069 (t0) REVERT: C 466 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7918 (mm-30) REVERT: C 495 ASN cc_start: 0.8286 (t0) cc_final: 0.7901 (t0) REVERT: C 516 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7949 (mm) REVERT: C 521 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7841 (tm-30) outliers start: 37 outliers final: 21 residues processed: 383 average time/residue: 1.4889 time to fit residues: 611.6783 Evaluate side-chains 385 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 357 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 2 optimal weight: 0.0270 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 53 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.125151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111986 restraints weight = 17452.685| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.96 r_work: 0.3300 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13269 Z= 0.126 Angle : 0.650 12.334 18003 Z= 0.324 Chirality : 0.043 0.250 1950 Planarity : 0.005 0.058 2307 Dihedral : 4.594 32.164 2040 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.28 % Allowed : 21.41 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.21), residues: 1563 helix: 1.65 (0.20), residues: 687 sheet: 1.04 (0.29), residues: 276 loop : 0.36 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 508 HIS 0.002 0.000 HIS A 260 PHE 0.022 0.001 PHE B 33 TYR 0.013 0.001 TYR B 118 ARG 0.005 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 15) link_NAG-ASN : angle 1.69213 ( 45) hydrogen bonds : bond 0.03668 ( 670) hydrogen bonds : angle 4.41071 ( 1893) SS BOND : bond 0.00569 ( 24) SS BOND : angle 3.23383 ( 48) covalent geometry : bond 0.00284 (13227) covalent geometry : angle 0.62373 (17910) Misc. bond : bond 0.00013 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 354 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7612 (ttt) cc_final: 0.7295 (ttt) REVERT: A 49 MET cc_start: 0.7321 (ttt) cc_final: 0.6852 (tmm) REVERT: A 102 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7956 (mtm180) REVERT: A 288 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7958 (mtm-85) REVERT: A 289 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7758 (ttt90) REVERT: A 302 ASP cc_start: 0.7655 (p0) cc_final: 0.7415 (p0) REVERT: A 370 GLN cc_start: 0.7783 (mm110) cc_final: 0.7436 (mp10) REVERT: A 373 MET cc_start: 0.8047 (mmp) cc_final: 0.7818 (mmm) REVERT: A 386 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8278 (mtmt) REVERT: A 411 ASP cc_start: 0.8102 (m-30) cc_final: 0.7896 (t0) REVERT: A 462 SER cc_start: 0.8764 (m) cc_final: 0.8352 (p) REVERT: A 465 GLU cc_start: 0.8000 (tp30) cc_final: 0.7772 (tp30) REVERT: A 470 ASP cc_start: 0.7881 (m-30) cc_final: 0.7499 (m-30) REVERT: A 507 LEU cc_start: 0.8901 (tm) cc_final: 0.8700 (tp) REVERT: A 521 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7586 (tm-30) REVERT: B 29 MET cc_start: 0.7083 (ppp) cc_final: 0.6805 (ppp) REVERT: B 121 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8224 (tttp) REVERT: B 156 GLU cc_start: 0.8037 (tt0) cc_final: 0.7790 (tt0) REVERT: B 178 ARG cc_start: 0.8020 (mtm-85) cc_final: 0.7617 (ttm170) REVERT: B 213 GLU cc_start: 0.7631 (pt0) cc_final: 0.7407 (pt0) REVERT: B 301 SER cc_start: 0.8672 (m) cc_final: 0.8264 (p) REVERT: B 303 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8326 (mtpp) REVERT: B 326 TYR cc_start: 0.8563 (m-80) cc_final: 0.8041 (m-10) REVERT: B 329 GLU cc_start: 0.8106 (tt0) cc_final: 0.7882 (tt0) REVERT: B 347 ILE cc_start: 0.8482 (tp) cc_final: 0.8259 (tp) REVERT: B 370 GLN cc_start: 0.8138 (mt0) cc_final: 0.7634 (mm110) REVERT: B 380 LYS cc_start: 0.7221 (mtpt) cc_final: 0.6990 (mmtp) REVERT: B 463 ASN cc_start: 0.8640 (t0) cc_final: 0.8082 (t0) REVERT: B 466 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7835 (mm-30) REVERT: B 492 TYR cc_start: 0.8633 (t80) cc_final: 0.8033 (t80) REVERT: B 521 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8049 (tm-30) REVERT: C 10 PHE cc_start: 0.8149 (t80) cc_final: 0.7762 (t80) REVERT: C 46 CYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7498 (t) REVERT: C 55 ARG cc_start: 0.7600 (tmt90) cc_final: 0.7249 (tmt170) REVERT: C 62 LYS cc_start: 0.7854 (ttpp) cc_final: 0.7529 (ttpp) REVERT: C 110 SER cc_start: 0.8352 (t) cc_final: 0.8093 (p) REVERT: C 141 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8382 (mm-40) REVERT: C 203 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7657 (tp30) REVERT: C 236 ILE cc_start: 0.8908 (mm) cc_final: 0.8665 (mp) REVERT: C 288 ARG cc_start: 0.8168 (mtp85) cc_final: 0.7826 (mtm-85) REVERT: C 323 MET cc_start: 0.8298 (mtm) cc_final: 0.8081 (mtm) REVERT: C 370 GLN cc_start: 0.8093 (mt0) cc_final: 0.7890 (mm110) REVERT: C 441 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7695 (mm-30) REVERT: C 462 SER cc_start: 0.8749 (m) cc_final: 0.8377 (t) REVERT: C 463 ASN cc_start: 0.8667 (t0) cc_final: 0.8019 (t0) REVERT: C 466 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7878 (mm-30) REVERT: C 495 ASN cc_start: 0.8291 (t0) cc_final: 0.7914 (t0) REVERT: C 516 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7968 (mm) REVERT: C 521 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7787 (tm-30) outliers start: 32 outliers final: 21 residues processed: 369 average time/residue: 1.4967 time to fit residues: 591.6889 Evaluate side-chains 377 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 351 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 73 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN ** C 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.120233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107472 restraints weight = 17494.629| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.89 r_work: 0.3283 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13269 Z= 0.199 Angle : 0.696 12.815 18003 Z= 0.351 Chirality : 0.045 0.262 1950 Planarity : 0.005 0.056 2307 Dihedral : 4.667 32.933 2040 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.78 % Allowed : 21.77 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.21), residues: 1563 helix: 1.43 (0.20), residues: 690 sheet: 1.09 (0.29), residues: 276 loop : 0.34 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 508 HIS 0.004 0.001 HIS A 376 PHE 0.022 0.002 PHE A 33 TYR 0.016 0.002 TYR A 118 ARG 0.007 0.001 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 15) link_NAG-ASN : angle 1.75237 ( 45) hydrogen bonds : bond 0.04162 ( 670) hydrogen bonds : angle 4.42521 ( 1893) SS BOND : bond 0.00425 ( 24) SS BOND : angle 3.38320 ( 48) covalent geometry : bond 0.00468 (13227) covalent geometry : angle 0.66959 (17910) Misc. bond : bond 0.00043 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 357 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ILE cc_start: 0.8386 (mp) cc_final: 0.8154 (mp) REVERT: A 44 MET cc_start: 0.7633 (ttt) cc_final: 0.7325 (ttt) REVERT: A 49 MET cc_start: 0.7335 (ttt) cc_final: 0.6877 (tmm) REVERT: A 102 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.7981 (mtm180) REVERT: A 178 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7735 (mtm-85) REVERT: A 288 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7940 (mtp180) REVERT: A 289 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7743 (ttt90) REVERT: A 302 ASP cc_start: 0.7692 (p0) cc_final: 0.7456 (p0) REVERT: A 352 ASP cc_start: 0.7855 (t0) cc_final: 0.7603 (t0) REVERT: A 370 GLN cc_start: 0.7821 (mm110) cc_final: 0.7474 (mp10) REVERT: A 373 MET cc_start: 0.8106 (mmp) cc_final: 0.7804 (mmm) REVERT: A 465 GLU cc_start: 0.7947 (tp30) cc_final: 0.7720 (tp30) REVERT: A 470 ASP cc_start: 0.7904 (m-30) cc_final: 0.7554 (m-30) REVERT: A 507 LEU cc_start: 0.8934 (tm) cc_final: 0.8734 (tp) REVERT: A 521 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7566 (tm-30) REVERT: B 29 MET cc_start: 0.7117 (ppp) cc_final: 0.6806 (ppp) REVERT: B 121 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8185 (tttp) REVERT: B 156 GLU cc_start: 0.8042 (tt0) cc_final: 0.7794 (tt0) REVERT: B 288 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7622 (mtm-85) REVERT: B 297 HIS cc_start: 0.7583 (m90) cc_final: 0.7323 (m-70) REVERT: B 301 SER cc_start: 0.8685 (m) cc_final: 0.8298 (p) REVERT: B 303 LYS cc_start: 0.8607 (mtmt) cc_final: 0.8315 (mtpp) REVERT: B 326 TYR cc_start: 0.8606 (m-80) cc_final: 0.8073 (m-10) REVERT: B 329 GLU cc_start: 0.8141 (tt0) cc_final: 0.7912 (tt0) REVERT: B 347 ILE cc_start: 0.8511 (tp) cc_final: 0.8296 (tp) REVERT: B 370 GLN cc_start: 0.8158 (mt0) cc_final: 0.7725 (mm110) REVERT: B 380 LYS cc_start: 0.7281 (mtpt) cc_final: 0.7046 (mmtp) REVERT: B 463 ASN cc_start: 0.8634 (t0) cc_final: 0.8116 (t0) REVERT: B 466 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7830 (mm-30) REVERT: B 480 ASP cc_start: 0.7830 (m-30) cc_final: 0.7266 (p0) REVERT: B 492 TYR cc_start: 0.8688 (t80) cc_final: 0.8125 (t80) REVERT: B 521 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7639 (tm-30) REVERT: C 10 PHE cc_start: 0.8250 (t80) cc_final: 0.7897 (t80) REVERT: C 22 VAL cc_start: 0.8788 (t) cc_final: 0.8573 (p) REVERT: C 46 CYS cc_start: 0.7874 (m) cc_final: 0.7549 (t) REVERT: C 62 LYS cc_start: 0.7920 (ttpp) cc_final: 0.7600 (ttpp) REVERT: C 110 SER cc_start: 0.8364 (t) cc_final: 0.8095 (p) REVERT: C 141 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8374 (mm-40) REVERT: C 203 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7723 (tp30) REVERT: C 236 ILE cc_start: 0.8922 (mm) cc_final: 0.8680 (mp) REVERT: C 288 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7796 (mtm-85) REVERT: C 323 MET cc_start: 0.8323 (mtm) cc_final: 0.8107 (mtm) REVERT: C 346 ASN cc_start: 0.8023 (m-40) cc_final: 0.7716 (m-40) REVERT: C 363 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.7942 (p) REVERT: C 370 GLN cc_start: 0.8124 (mt0) cc_final: 0.7923 (mm110) REVERT: C 381 CYS cc_start: 0.6630 (m) cc_final: 0.6192 (t) REVERT: C 402 PHE cc_start: 0.8515 (m-80) cc_final: 0.8257 (m-80) REVERT: C 462 SER cc_start: 0.8751 (m) cc_final: 0.8390 (t) REVERT: C 463 ASN cc_start: 0.8684 (t0) cc_final: 0.8058 (t0) REVERT: C 466 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7858 (mm-30) REVERT: C 516 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8040 (mm) REVERT: C 521 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7751 (tm-30) outliers start: 25 outliers final: 22 residues processed: 366 average time/residue: 1.5205 time to fit residues: 598.6946 Evaluate side-chains 380 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 354 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 26 optimal weight: 0.9980 chunk 117 optimal weight: 0.0270 chunk 126 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 89 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 0.0170 overall best weight: 0.2374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN ** C 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111002 restraints weight = 17339.735| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.87 r_work: 0.3317 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13269 Z= 0.118 Angle : 0.645 11.707 18003 Z= 0.322 Chirality : 0.043 0.247 1950 Planarity : 0.005 0.056 2307 Dihedral : 4.491 29.619 2040 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.78 % Allowed : 22.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.21), residues: 1563 helix: 1.65 (0.20), residues: 687 sheet: 1.10 (0.29), residues: 276 loop : 0.36 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 219 HIS 0.002 0.001 HIS C 17 PHE 0.023 0.001 PHE B 33 TYR 0.016 0.001 TYR A 118 ARG 0.005 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 15) link_NAG-ASN : angle 1.58487 ( 45) hydrogen bonds : bond 0.03514 ( 670) hydrogen bonds : angle 4.39188 ( 1893) SS BOND : bond 0.00402 ( 24) SS BOND : angle 2.93076 ( 48) covalent geometry : bond 0.00269 (13227) covalent geometry : angle 0.62378 (17910) Misc. bond : bond 0.00013 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12046.23 seconds wall clock time: 205 minutes 53.14 seconds (12353.14 seconds total)