Starting phenix.real_space_refine on Thu Sep 18 01:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ona_16984/09_2025/8ona_16984.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ona_16984/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ona_16984/09_2025/8ona_16984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ona_16984/09_2025/8ona_16984.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ona_16984/09_2025/8ona_16984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ona_16984/09_2025/8ona_16984.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "D" 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: B, C, E, F Time building chain proxies: 3.47, per 1000 atoms: 0.27 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 B 80 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 401 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 401 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 399 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 360 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 360 " - pdb=" SG CYS C 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: 1.13 Conformation dependent library (CDL) restraints added in 552.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.42 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: 2.12 Time building geometry restraints manager: 1.51 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.240 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B 102 TYR 0.014 0.002 TYR B 414 PHE 0.024 0.001 PHE A 33 TRP 0.013 0.002 TRP B 34 HIS 0.005 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00444 (13227) covalent geometry : angle 0.73838 (17910) SS BOND : bond 0.00228 ( 24) SS BOND : angle 0.78473 ( 48) hydrogen bonds : bond 0.13738 ( 670) hydrogen bonds : angle 6.15669 ( 1893) Misc. bond : bond 0.10386 ( 3) link_NAG-ASN : bond 0.00215 ( 15) link_NAG-ASN : angle 2.68325 ( 45) *********************** 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 : 0.543 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: 0.7003 time to fit residues: 373.1367 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 : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.122606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.109466 restraints weight = 17401.180| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.96 r_work: 0.3262 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 13269 Z= 0.160 Angle : 0.704 16.739 18003 Z= 0.355 Chirality : 0.046 0.254 1950 Planarity : 0.005 0.038 2307 Dihedral : 5.280 36.463 2040 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.50 % Allowed : 13.85 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.21), residues: 1563 helix: 0.98 (0.20), residues: 690 sheet: 0.97 (0.29), residues: 279 loop : 0.67 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 351 TYR 0.015 0.001 TYR B 118 PHE 0.023 0.002 PHE B 431 TRP 0.016 0.002 TRP A 349 HIS 0.004 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00374 (13227) covalent geometry : angle 0.67144 (17910) SS BOND : bond 0.00433 ( 24) SS BOND : angle 3.62329 ( 48) hydrogen bonds : bond 0.04350 ( 670) hydrogen bonds : angle 4.78858 ( 1893) Misc. bond : bond 0.00032 ( 3) link_NAG-ASN : bond 0.00629 ( 15) link_NAG-ASN : angle 2.18464 ( 45) *********************** 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 458 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 423 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.7414 (OUTLIER) cc_final: 0.7214 (p0) REVERT: A 44 MET cc_start: 0.7758 (ttt) cc_final: 0.7477 (ttt) REVERT: A 49 MET cc_start: 0.7365 (ttt) cc_final: 0.7041 (tmm) REVERT: A 62 LYS cc_start: 0.7901 (ttpp) cc_final: 0.7681 (tttp) REVERT: A 100 ASP cc_start: 0.7973 (t0) cc_final: 0.7624 (t0) REVERT: A 203 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 280 SER cc_start: 0.8661 (t) cc_final: 0.8420 (p) REVERT: A 301 SER cc_start: 0.8556 (t) cc_final: 0.8125 (p) REVERT: A 302 ASP cc_start: 0.7766 (p0) cc_final: 0.7477 (p0) REVERT: A 336 VAL cc_start: 0.8373 (p) cc_final: 0.8049 (t) REVERT: A 373 MET cc_start: 0.8079 (mmp) cc_final: 0.7824 (mmm) REVERT: A 380 LYS cc_start: 0.7823 (mtpt) cc_final: 0.7588 (mtpt) REVERT: A 438 LYS cc_start: 0.8541 (mttt) cc_final: 0.8328 (mttm) REVERT: A 440 ASN cc_start: 0.7448 (p0) cc_final: 0.7219 (t0) REVERT: A 465 GLU cc_start: 0.7950 (tp30) cc_final: 0.7676 (tp30) REVERT: A 470 ASP cc_start: 0.8055 (m-30) cc_final: 0.7683 (m-30) REVERT: A 521 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8169 (tm-30) REVERT: B 15 THR cc_start: 0.7859 (p) cc_final: 0.7602 (p) REVERT: B 44 MET cc_start: 0.7797 (ttt) cc_final: 0.7431 (ttt) REVERT: B 49 MET cc_start: 0.7447 (ttt) cc_final: 0.6738 (tmm) REVERT: B 61 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8177 (ttpp) REVERT: B 62 LYS cc_start: 0.7912 (ttpp) cc_final: 0.7698 (tttp) REVERT: B 121 LYS cc_start: 0.8498 (ttpp) cc_final: 0.8204 (tttm) REVERT: B 135 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7671 (mt-10) REVERT: B 156 GLU cc_start: 0.8073 (tt0) cc_final: 0.7810 (tt0) REVERT: B 203 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7482 (mm-30) REVERT: B 244 GLU cc_start: 0.7718 (tp30) cc_final: 0.7489 (tp30) REVERT: B 288 ARG cc_start: 0.8262 (mtp85) cc_final: 0.7944 (mtm-85) REVERT: B 293 ILE cc_start: 0.7944 (mm) cc_final: 0.7633 (mt) REVERT: B 303 LYS cc_start: 0.8638 (mtmt) cc_final: 0.8329 (mtpp) REVERT: B 310 THR cc_start: 0.8752 (p) cc_final: 0.8420 (t) REVERT: B 311 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6879 (mm-30) REVERT: B 347 ILE cc_start: 0.8484 (mm) cc_final: 0.8271 (tp) REVERT: B 370 GLN cc_start: 0.8182 (mt0) cc_final: 0.7687 (mm110) REVERT: B 380 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7644 (mtpt) REVERT: B 441 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: B 466 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7712 (mm-30) REVERT: B 492 TYR cc_start: 0.8645 (t80) cc_final: 0.8086 (t80) REVERT: B 521 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8235 (tm-30) REVERT: C 10 PHE cc_start: 0.7997 (t80) cc_final: 0.7788 (t80) REVERT: C 51 GLU cc_start: 0.7309 (tp30) cc_final: 0.7053 (tm-30) REVERT: C 61 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7950 (ttmm) REVERT: C 62 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7701 (ttmm) REVERT: C 95 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7909 (mtt180) REVERT: C 141 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8484 (mm-40) REVERT: C 142 GLU cc_start: 0.8153 (tt0) cc_final: 0.7896 (tt0) REVERT: C 156 GLU cc_start: 0.7997 (tt0) cc_final: 0.7759 (tt0) REVERT: C 288 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7917 (mtm-85) REVERT: C 301 SER cc_start: 0.8451 (t) cc_final: 0.8162 (p) REVERT: C 346 ASN cc_start: 0.8011 (m-40) cc_final: 0.7758 (m-40) REVERT: C 380 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7766 (mtpp) REVERT: C 432 ASP cc_start: 0.8383 (t70) cc_final: 0.8098 (t0) REVERT: C 438 LYS cc_start: 0.8499 (mttt) cc_final: 0.8262 (mttt) REVERT: C 462 SER cc_start: 0.8706 (m) cc_final: 0.8359 (t) REVERT: C 463 ASN cc_start: 0.8662 (t0) cc_final: 0.8068 (t0) REVERT: C 465 GLU cc_start: 0.7983 (tp30) cc_final: 0.7780 (tp30) REVERT: C 466 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7918 (mm-30) REVERT: C 470 ASP cc_start: 0.8003 (m-30) cc_final: 0.7768 (m-30) REVERT: C 492 TYR cc_start: 0.8550 (t80) cc_final: 0.8209 (t80) REVERT: C 521 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8051 (tm-30) outliers start: 35 outliers final: 13 residues processed: 443 average time/residue: 0.6631 time to fit residues: 316.8543 Evaluate side-chains 409 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 393 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN 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 B residue 520 LEU 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 104 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 85 optimal weight: 0.0270 chunk 118 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- 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 ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS B 324 GLN B 482 ASN C 13 GLN C 152 ASN C 482 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.120924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107857 restraints weight = 17712.983| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.97 r_work: 0.3256 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13269 Z= 0.218 Angle : 0.668 9.986 18003 Z= 0.342 Chirality : 0.047 0.270 1950 Planarity : 0.005 0.049 2307 Dihedral : 5.276 33.031 2040 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.78 % Allowed : 15.99 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.21), residues: 1563 helix: 1.22 (0.20), residues: 687 sheet: 0.78 (0.28), residues: 279 loop : 0.54 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 55 TYR 0.015 0.002 TYR C 118 PHE 0.018 0.002 PHE B 431 TRP 0.016 0.002 TRP C 349 HIS 0.006 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00506 (13227) covalent geometry : angle 0.64854 (17910) SS BOND : bond 0.00654 ( 24) SS BOND : angle 2.52608 ( 48) hydrogen bonds : bond 0.04631 ( 670) hydrogen bonds : angle 4.62812 ( 1893) Misc. bond : bond 0.00056 ( 3) link_NAG-ASN : bond 0.00619 ( 15) link_NAG-ASN : angle 2.08848 ( 45) *********************** 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 445 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 392 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8040 (mmmm) cc_final: 0.7790 (tptp) REVERT: A 44 MET cc_start: 0.7808 (ttt) cc_final: 0.7533 (ttt) REVERT: A 49 MET cc_start: 0.7432 (ttt) cc_final: 0.6998 (tmm) REVERT: A 102 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.8010 (mtm-85) REVERT: A 203 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7550 (mm-30) REVERT: A 288 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7850 (mtm-85) REVERT: A 301 SER cc_start: 0.8505 (t) cc_final: 0.8160 (p) REVERT: A 302 ASP cc_start: 0.7783 (p0) cc_final: 0.7518 (p0) REVERT: A 336 VAL cc_start: 0.8420 (p) cc_final: 0.8146 (t) REVERT: A 373 MET cc_start: 0.8163 (mmp) cc_final: 0.7879 (mmm) REVERT: A 380 LYS cc_start: 0.7624 (mtpt) cc_final: 0.7393 (mtpt) REVERT: A 409 SER cc_start: 0.8608 (m) cc_final: 0.8358 (t) REVERT: A 411 ASP cc_start: 0.8087 (m-30) cc_final: 0.7663 (m-30) REVERT: A 440 ASN cc_start: 0.7427 (p0) cc_final: 0.7115 (t0) REVERT: A 465 GLU cc_start: 0.7963 (tp30) cc_final: 0.7745 (tp30) REVERT: A 470 ASP cc_start: 0.8053 (m-30) cc_final: 0.7675 (m-30) REVERT: A 521 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8061 (tm-30) REVERT: B 44 MET cc_start: 0.7805 (ttt) cc_final: 0.7433 (ttt) REVERT: B 49 MET cc_start: 0.7517 (ttt) cc_final: 0.7284 (tmm) REVERT: B 62 LYS cc_start: 0.7933 (ttpp) cc_final: 0.7721 (tttp) REVERT: B 66 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7683 (pt0) REVERT: B 121 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8195 (tttm) REVERT: B 135 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7710 (mt-10) REVERT: B 156 GLU cc_start: 0.8055 (tt0) cc_final: 0.7805 (tt0) REVERT: B 203 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7528 (mm-30) REVERT: B 288 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7997 (mtm-85) REVERT: B 303 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8387 (mtpp) REVERT: B 363 THR cc_start: 0.8368 (m) cc_final: 0.8060 (t) REVERT: B 370 GLN cc_start: 0.8194 (mt0) cc_final: 0.7730 (mm110) REVERT: B 380 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7670 (mtpt) REVERT: B 441 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: B 466 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7741 (mm-30) REVERT: B 492 TYR cc_start: 0.8701 (t80) cc_final: 0.8231 (t80) REVERT: B 521 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8111 (tm-30) REVERT: C 10 PHE cc_start: 0.8156 (t80) cc_final: 0.7820 (t80) REVERT: C 51 GLU cc_start: 0.7353 (tp30) cc_final: 0.7038 (tm-30) REVERT: C 61 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7938 (mtpm) REVERT: C 62 LYS cc_start: 0.7944 (ttpp) cc_final: 0.7561 (tttp) REVERT: C 141 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8483 (mm110) REVERT: C 142 GLU cc_start: 0.8135 (tt0) cc_final: 0.7846 (tt0) REVERT: C 156 GLU cc_start: 0.7987 (tt0) cc_final: 0.7750 (tt0) REVERT: C 203 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7359 (mm-30) REVERT: C 288 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7921 (mtm-85) REVERT: C 301 SER cc_start: 0.8477 (t) cc_final: 0.8182 (p) REVERT: C 323 MET cc_start: 0.8350 (mtm) cc_final: 0.8136 (mtm) REVERT: C 346 ASN cc_start: 0.8062 (m-40) cc_final: 0.7784 (m-40) REVERT: C 363 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.7993 (p) REVERT: C 366 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7435 (mt-10) REVERT: C 370 GLN cc_start: 0.8173 (mt0) cc_final: 0.7925 (mm110) REVERT: C 380 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7806 (mmtp) REVERT: C 432 ASP cc_start: 0.8381 (t0) cc_final: 0.8108 (t0) REVERT: C 438 LYS cc_start: 0.8532 (mttt) cc_final: 0.8241 (mttm) REVERT: C 462 SER cc_start: 0.8737 (m) cc_final: 0.8390 (t) REVERT: C 463 ASN cc_start: 0.8695 (t0) cc_final: 0.8102 (t0) REVERT: C 466 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7897 (mm-30) REVERT: C 470 ASP cc_start: 0.8013 (m-30) cc_final: 0.7769 (m-30) REVERT: C 492 TYR cc_start: 0.8647 (t80) cc_final: 0.8394 (t80) REVERT: C 521 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8015 (tm-30) outliers start: 53 outliers final: 24 residues processed: 411 average time/residue: 0.6850 time to fit residues: 302.4868 Evaluate side-chains 411 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 383 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 A residue 400 ASN 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 66 GLU 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 478 ILE Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 19 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 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 501 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 109 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 482 ASN C 482 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109862 restraints weight = 17562.129| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.96 r_work: 0.3276 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2652 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= 0.140 Angle : 0.621 14.013 18003 Z= 0.317 Chirality : 0.044 0.262 1950 Planarity : 0.005 0.051 2307 Dihedral : 5.007 30.942 2040 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.86 % Allowed : 17.56 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.21), residues: 1563 helix: 1.45 (0.20), residues: 690 sheet: 0.87 (0.28), residues: 276 loop : 0.46 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 383 TYR 0.014 0.001 TYR A 118 PHE 0.019 0.001 PHE B 431 TRP 0.015 0.002 TRP A 349 HIS 0.003 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00317 (13227) covalent geometry : angle 0.59697 (17910) SS BOND : bond 0.00564 ( 24) SS BOND : angle 2.93710 ( 48) hydrogen bonds : bond 0.04011 ( 670) hydrogen bonds : angle 4.50496 ( 1893) Misc. bond : bond 0.00025 ( 3) link_NAG-ASN : bond 0.00548 ( 15) link_NAG-ASN : angle 1.86922 ( 45) *********************** 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 : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 THR cc_start: 0.8025 (p) cc_final: 0.7819 (p) REVERT: A 44 MET cc_start: 0.7652 (ttt) cc_final: 0.7356 (ttt) REVERT: A 49 MET cc_start: 0.7388 (ttt) cc_final: 0.7000 (tmm) REVERT: A 102 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7904 (mtm180) REVERT: A 288 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7845 (mtm-85) REVERT: A 302 ASP cc_start: 0.7775 (p0) cc_final: 0.7516 (p0) REVERT: A 336 VAL cc_start: 0.8418 (p) cc_final: 0.8161 (t) REVERT: A 373 MET cc_start: 0.8126 (mmp) cc_final: 0.7818 (mmm) REVERT: A 380 LYS cc_start: 0.7437 (mtpt) cc_final: 0.7155 (mttp) REVERT: A 386 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8315 (mtmt) REVERT: A 465 GLU cc_start: 0.7958 (tp30) cc_final: 0.7726 (tp30) REVERT: A 470 ASP cc_start: 0.7978 (m-30) cc_final: 0.7662 (m-30) REVERT: A 521 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7921 (tm-30) REVERT: B 23 ILE cc_start: 0.8440 (mm) cc_final: 0.8017 (tt) REVERT: B 44 MET cc_start: 0.7717 (ttt) cc_final: 0.7457 (ttt) REVERT: B 49 MET cc_start: 0.7552 (ttt) cc_final: 0.7292 (tmm) REVERT: B 121 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8166 (tttm) REVERT: B 156 GLU cc_start: 0.8039 (tt0) cc_final: 0.7785 (tt0) REVERT: B 203 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7512 (mm-30) REVERT: B 288 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7913 (mtm-85) REVERT: B 301 SER cc_start: 0.8760 (m) cc_final: 0.8423 (p) REVERT: B 303 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8385 (mtpp) REVERT: B 336 VAL cc_start: 0.8376 (p) cc_final: 0.8046 (t) REVERT: B 347 ILE cc_start: 0.8546 (tp) cc_final: 0.8333 (tp) REVERT: B 370 GLN cc_start: 0.8194 (mt0) cc_final: 0.7701 (mm110) REVERT: B 440 ASN cc_start: 0.7389 (p0) cc_final: 0.7014 (p0) REVERT: B 441 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: B 463 ASN cc_start: 0.8623 (t0) cc_final: 0.8203 (t0) REVERT: B 466 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 492 TYR cc_start: 0.8701 (t80) cc_final: 0.8229 (t80) REVERT: B 521 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8201 (tm-30) REVERT: C 16 MET cc_start: 0.7643 (ptp) cc_final: 0.7432 (ptm) REVERT: C 22 VAL cc_start: 0.8805 (t) cc_final: 0.8573 (p) REVERT: C 51 GLU cc_start: 0.7385 (tp30) cc_final: 0.7074 (tm-30) REVERT: C 141 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8476 (mm110) REVERT: C 156 GLU cc_start: 0.8001 (tt0) cc_final: 0.7762 (tt0) REVERT: C 203 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7379 (mm-30) REVERT: C 288 ARG cc_start: 0.8198 (mtp85) cc_final: 0.7852 (mtm180) REVERT: C 312 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7989 (ttp-170) REVERT: C 323 MET cc_start: 0.8300 (mtm) cc_final: 0.8096 (mtm) REVERT: C 346 ASN cc_start: 0.8067 (m-40) cc_final: 0.7787 (m-40) REVERT: C 355 ASN cc_start: 0.7957 (m-40) cc_final: 0.7660 (p0) REVERT: C 363 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.7948 (p) REVERT: C 370 GLN cc_start: 0.8185 (mt0) cc_final: 0.7739 (mp10) REVERT: C 380 LYS cc_start: 0.7911 (mtpt) cc_final: 0.7710 (mmtp) REVERT: C 438 LYS cc_start: 0.8534 (mttt) cc_final: 0.8250 (mttm) REVERT: C 462 SER cc_start: 0.8736 (m) cc_final: 0.8388 (t) REVERT: C 463 ASN cc_start: 0.8676 (t0) cc_final: 0.8093 (t0) REVERT: C 466 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7913 (mm-30) REVERT: C 492 TYR cc_start: 0.8669 (t80) cc_final: 0.8468 (t80) REVERT: C 521 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7925 (tm-30) outliers start: 40 outliers final: 16 residues processed: 395 average time/residue: 0.7319 time to fit residues: 309.6858 Evaluate side-chains 387 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 367 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 C residue 7 MET Chi-restraints excluded: chain C residue 19 VAL 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 Chi-restraints excluded: chain C residue 501 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 75 optimal weight: 0.9990 chunk 56 optimal weight: 0.0370 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- 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 B 297 HIS B 482 ASN C 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.122923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109822 restraints weight = 17575.723| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.95 r_work: 0.3274 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13269 Z= 0.154 Angle : 0.635 16.527 18003 Z= 0.321 Chirality : 0.044 0.262 1950 Planarity : 0.005 0.055 2307 Dihedral : 4.822 26.831 2040 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.71 % Allowed : 18.70 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.21), residues: 1563 helix: 1.56 (0.20), residues: 687 sheet: 0.88 (0.28), residues: 276 loop : 0.45 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 178 TYR 0.014 0.001 TYR B 118 PHE 0.026 0.001 PHE B 33 TRP 0.015 0.002 TRP C 349 HIS 0.003 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00354 (13227) covalent geometry : angle 0.60907 (17910) SS BOND : bond 0.00581 ( 24) SS BOND : angle 3.10833 ( 48) hydrogen bonds : bond 0.04089 ( 670) hydrogen bonds : angle 4.47399 ( 1893) Misc. bond : bond 0.00032 ( 3) link_NAG-ASN : bond 0.00541 ( 15) link_NAG-ASN : angle 1.84885 ( 45) *********************** 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 407 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 369 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7634 (ttt) cc_final: 0.7330 (ttt) REVERT: A 49 MET cc_start: 0.7402 (ttt) cc_final: 0.7034 (tmm) REVERT: A 102 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7934 (mtm180) REVERT: A 178 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7755 (mtm-85) REVERT: A 203 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7581 (mm-30) REVERT: A 288 ARG cc_start: 0.8215 (mtp85) cc_final: 0.7980 (mtp180) REVERT: A 289 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7713 (ttt90) REVERT: A 302 ASP cc_start: 0.7781 (p0) cc_final: 0.7525 (p0) REVERT: A 373 MET cc_start: 0.8135 (mmp) cc_final: 0.7871 (mmm) REVERT: A 380 LYS cc_start: 0.7323 (mtpt) cc_final: 0.7058 (mttp) REVERT: A 393 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.8042 (m) REVERT: A 406 ASP cc_start: 0.7846 (t0) cc_final: 0.7417 (t0) REVERT: A 425 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7493 (mt-10) REVERT: A 465 GLU cc_start: 0.7948 (tp30) cc_final: 0.7713 (tp30) REVERT: A 470 ASP cc_start: 0.7967 (m-30) cc_final: 0.7638 (m-30) REVERT: A 521 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7868 (tm-30) REVERT: B 22 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8647 (p) REVERT: B 44 MET cc_start: 0.7702 (ttt) cc_final: 0.7429 (ttt) REVERT: B 121 LYS cc_start: 0.8521 (ttpp) cc_final: 0.8151 (tttp) REVERT: B 156 GLU cc_start: 0.8074 (tt0) cc_final: 0.7812 (tt0) REVERT: B 203 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7511 (mm-30) REVERT: B 213 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: B 288 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7965 (mtm-85) REVERT: B 297 HIS cc_start: 0.7640 (m90) cc_final: 0.7346 (m-70) REVERT: B 301 SER cc_start: 0.8739 (m) cc_final: 0.8402 (p) REVERT: B 303 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8399 (mtpp) REVERT: B 347 ILE cc_start: 0.8525 (tp) cc_final: 0.8305 (tp) REVERT: B 370 GLN cc_start: 0.8188 (mt0) cc_final: 0.7696 (mm110) REVERT: B 380 LYS cc_start: 0.7454 (mtpt) cc_final: 0.7103 (mmtp) REVERT: B 381 CYS cc_start: 0.6549 (m) cc_final: 0.6127 (t) REVERT: B 440 ASN cc_start: 0.7360 (p0) cc_final: 0.7020 (p0) REVERT: B 441 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: B 463 ASN cc_start: 0.8609 (t0) cc_final: 0.8124 (t0) REVERT: B 466 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7751 (mm-30) REVERT: B 492 TYR cc_start: 0.8692 (t80) cc_final: 0.8206 (t80) REVERT: B 521 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8212 (tm-30) REVERT: C 16 MET cc_start: 0.7666 (ptp) cc_final: 0.7446 (ptm) REVERT: C 22 VAL cc_start: 0.8799 (t) cc_final: 0.8566 (p) REVERT: C 141 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8463 (mm110) REVERT: C 156 GLU cc_start: 0.7974 (tt0) cc_final: 0.7744 (pm20) REVERT: C 203 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7411 (mm-30) REVERT: C 288 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7794 (mtm-85) REVERT: C 323 MET cc_start: 0.8316 (mtm) cc_final: 0.8112 (mtm) REVERT: C 346 ASN cc_start: 0.8101 (m-40) cc_final: 0.7807 (m-40) REVERT: C 355 ASN cc_start: 0.7924 (m-40) cc_final: 0.7639 (p0) REVERT: C 363 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.7943 (p) REVERT: C 370 GLN cc_start: 0.8193 (mt0) cc_final: 0.7746 (mp10) REVERT: C 380 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7739 (mmtp) REVERT: C 438 LYS cc_start: 0.8537 (mttt) cc_final: 0.8241 (mttm) REVERT: C 462 SER cc_start: 0.8754 (m) cc_final: 0.8402 (t) REVERT: C 463 ASN cc_start: 0.8690 (t0) cc_final: 0.8093 (t0) REVERT: C 466 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7934 (mm-30) REVERT: C 521 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7913 (tm-30) outliers start: 38 outliers final: 20 residues processed: 387 average time/residue: 0.7251 time to fit residues: 300.9789 Evaluate side-chains 389 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 362 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 22 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 213 GLU 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 529 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 49 MET 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 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 480 ASP 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 108 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 297 HIS 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 = 0.123167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.110110 restraints weight = 17406.357| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.94 r_work: 0.3272 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 13269 Z= 0.148 Angle : 0.635 16.622 18003 Z= 0.319 Chirality : 0.044 0.257 1950 Planarity : 0.005 0.058 2307 Dihedral : 4.730 26.579 2040 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.64 % Allowed : 19.13 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.21), residues: 1563 helix: 1.62 (0.20), residues: 687 sheet: 0.90 (0.28), residues: 276 loop : 0.42 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 178 TYR 0.014 0.001 TYR A 118 PHE 0.019 0.001 PHE B 431 TRP 0.021 0.002 TRP C 508 HIS 0.003 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00346 (13227) covalent geometry : angle 0.60909 (17910) SS BOND : bond 0.00595 ( 24) SS BOND : angle 3.10206 ( 48) hydrogen bonds : bond 0.03960 ( 670) hydrogen bonds : angle 4.41426 ( 1893) Misc. bond : bond 0.00030 ( 3) link_NAG-ASN : bond 0.00519 ( 15) link_NAG-ASN : angle 1.80087 ( 45) *********************** 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: 37 poor density : 379 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8816 (mmtm) cc_final: 0.8599 (tppt) REVERT: A 44 MET cc_start: 0.7623 (ttt) cc_final: 0.7319 (ttt) REVERT: A 49 MET cc_start: 0.7394 (ttt) cc_final: 0.7065 (tmm) REVERT: A 102 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7926 (mtm180) REVERT: A 178 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7797 (mtm-85) REVERT: A 288 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7952 (mtp180) REVERT: A 289 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7669 (ttt90) REVERT: A 302 ASP cc_start: 0.7743 (p0) cc_final: 0.7499 (p0) REVERT: A 373 MET cc_start: 0.8115 (mmp) cc_final: 0.7856 (mmm) REVERT: A 380 LYS cc_start: 0.7399 (mtpt) cc_final: 0.7153 (mttp) REVERT: A 381 CYS cc_start: 0.6670 (OUTLIER) cc_final: 0.6198 (t) REVERT: A 465 GLU cc_start: 0.7930 (tp30) cc_final: 0.7709 (tp30) REVERT: A 470 ASP cc_start: 0.7910 (m-30) cc_final: 0.7511 (m-30) REVERT: A 521 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7631 (tm-30) REVERT: B 44 MET cc_start: 0.7676 (ttt) cc_final: 0.7399 (ttt) REVERT: B 121 LYS cc_start: 0.8521 (ttpp) cc_final: 0.8171 (tttp) REVERT: B 156 GLU cc_start: 0.8043 (tt0) cc_final: 0.7790 (tt0) REVERT: B 178 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7577 (ttm170) REVERT: B 203 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 213 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7507 (pt0) REVERT: B 288 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7959 (mtm-85) REVERT: B 297 HIS cc_start: 0.7716 (m90) cc_final: 0.7465 (m-70) REVERT: B 301 SER cc_start: 0.8726 (m) cc_final: 0.8356 (p) REVERT: B 303 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8400 (mtpp) REVERT: B 347 ILE cc_start: 0.8576 (tp) cc_final: 0.8362 (tp) REVERT: B 370 GLN cc_start: 0.8181 (mt0) cc_final: 0.7689 (mm110) REVERT: B 380 LYS cc_start: 0.7473 (mtpt) cc_final: 0.7113 (mmtp) REVERT: B 381 CYS cc_start: 0.6544 (m) cc_final: 0.6127 (t) REVERT: B 440 ASN cc_start: 0.7324 (p0) cc_final: 0.6654 (p0) REVERT: B 441 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: B 463 ASN cc_start: 0.8621 (t0) cc_final: 0.8170 (t0) REVERT: B 466 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7671 (mm-30) REVERT: B 492 TYR cc_start: 0.8687 (t80) cc_final: 0.8191 (t80) REVERT: B 521 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8152 (tm-30) REVERT: C 16 MET cc_start: 0.7631 (ptp) cc_final: 0.7421 (ptm) REVERT: C 141 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8443 (mm110) REVERT: C 156 GLU cc_start: 0.7946 (tt0) cc_final: 0.7735 (pm20) REVERT: C 203 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7448 (mm-30) REVERT: C 288 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7816 (mtm-85) REVERT: C 312 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7963 (ttp-170) REVERT: C 323 MET cc_start: 0.8307 (mtm) cc_final: 0.8099 (mtm) REVERT: C 346 ASN cc_start: 0.8100 (m-40) cc_final: 0.7798 (m-40) REVERT: C 355 ASN cc_start: 0.7911 (m-40) cc_final: 0.7668 (p0) REVERT: C 363 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.7962 (p) REVERT: C 370 GLN cc_start: 0.8156 (mt0) cc_final: 0.7729 (mp10) REVERT: C 438 LYS cc_start: 0.8514 (mttt) cc_final: 0.8255 (mttm) REVERT: C 462 SER cc_start: 0.8755 (m) cc_final: 0.8401 (t) REVERT: C 463 ASN cc_start: 0.8703 (t0) cc_final: 0.8107 (t0) REVERT: C 466 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7945 (mm-30) REVERT: C 521 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7904 (tm-30) outliers start: 37 outliers final: 20 residues processed: 395 average time/residue: 0.7138 time to fit residues: 302.5916 Evaluate side-chains 396 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 370 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 381 CYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 213 GLU 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 529 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 19 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 57 PHE 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 492 TYR 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 107 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS B 290 ASN C 290 ASN C 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.122620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109676 restraints weight = 17538.606| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.96 r_work: 0.3274 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13269 Z= 0.150 Angle : 0.621 11.313 18003 Z= 0.314 Chirality : 0.044 0.258 1950 Planarity : 0.005 0.061 2307 Dihedral : 4.649 27.062 2040 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.71 % Allowed : 19.84 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.21), residues: 1563 helix: 1.64 (0.20), residues: 687 sheet: 0.97 (0.28), residues: 276 loop : 0.43 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 178 TYR 0.014 0.001 TYR A 118 PHE 0.025 0.001 PHE B 33 TRP 0.015 0.002 TRP C 349 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00350 (13227) covalent geometry : angle 0.59846 (17910) SS BOND : bond 0.00507 ( 24) SS BOND : angle 2.87115 ( 48) hydrogen bonds : bond 0.03908 ( 670) hydrogen bonds : angle 4.38202 ( 1893) Misc. bond : bond 0.00032 ( 3) link_NAG-ASN : bond 0.00507 ( 15) link_NAG-ASN : angle 1.76357 ( 45) *********************** 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 414 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 376 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7630 (ttt) cc_final: 0.7332 (ttt) REVERT: A 49 MET cc_start: 0.7388 (ttt) cc_final: 0.7048 (tmm) REVERT: A 102 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.7944 (mtm180) REVERT: A 178 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7795 (mtm-85) REVERT: A 288 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7973 (mtp180) REVERT: A 289 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7691 (ttt90) REVERT: A 302 ASP cc_start: 0.7759 (p0) cc_final: 0.7520 (p0) REVERT: A 373 MET cc_start: 0.8085 (mmp) cc_final: 0.7835 (mmm) REVERT: A 380 LYS cc_start: 0.7299 (mtpt) cc_final: 0.7046 (mttp) REVERT: A 462 SER cc_start: 0.8709 (m) cc_final: 0.8295 (p) REVERT: A 465 GLU cc_start: 0.7936 (tp30) cc_final: 0.7728 (tp30) REVERT: A 470 ASP cc_start: 0.7921 (m-30) cc_final: 0.7582 (m-30) REVERT: A 521 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7662 (tm-30) REVERT: B 10 PHE cc_start: 0.7885 (t80) cc_final: 0.7610 (t80) REVERT: B 156 GLU cc_start: 0.8062 (tt0) cc_final: 0.7810 (tt0) REVERT: B 178 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7637 (ttm170) REVERT: B 213 GLU cc_start: 0.7927 (pt0) cc_final: 0.7438 (pt0) REVERT: B 288 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7978 (mtm-85) REVERT: B 301 SER cc_start: 0.8701 (m) cc_final: 0.8325 (p) REVERT: B 303 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8328 (mtpp) REVERT: B 312 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7219 (ttm170) REVERT: B 347 ILE cc_start: 0.8564 (tp) cc_final: 0.8350 (tp) REVERT: B 370 GLN cc_start: 0.8180 (mt0) cc_final: 0.7669 (mm110) REVERT: B 380 LYS cc_start: 0.7466 (mtpt) cc_final: 0.7126 (mmtp) REVERT: B 438 LYS cc_start: 0.8626 (mttt) cc_final: 0.8365 (mttt) REVERT: B 440 ASN cc_start: 0.7303 (p0) cc_final: 0.7037 (p0) REVERT: B 441 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: B 463 ASN cc_start: 0.8619 (t0) cc_final: 0.8104 (t0) REVERT: B 466 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7690 (mm-30) REVERT: B 492 TYR cc_start: 0.8655 (t80) cc_final: 0.8139 (t80) REVERT: B 521 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8197 (tm-30) REVERT: C 16 MET cc_start: 0.7645 (ptp) cc_final: 0.7428 (ptm) REVERT: C 110 SER cc_start: 0.8377 (t) cc_final: 0.8097 (p) REVERT: C 141 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8421 (mm110) REVERT: C 156 GLU cc_start: 0.7920 (tt0) cc_final: 0.7693 (pm20) REVERT: C 203 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7458 (mm-30) REVERT: C 288 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7814 (mtm-85) REVERT: C 312 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7992 (ttp-170) REVERT: C 318 CYS cc_start: 0.7896 (t) cc_final: 0.7587 (t) REVERT: C 323 MET cc_start: 0.8301 (mtm) cc_final: 0.8094 (mtm) REVERT: C 346 ASN cc_start: 0.8068 (m-40) cc_final: 0.7774 (m-40) REVERT: C 355 ASN cc_start: 0.7911 (m-40) cc_final: 0.7675 (p0) REVERT: C 363 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.7931 (p) REVERT: C 370 GLN cc_start: 0.8153 (mt0) cc_final: 0.7859 (mm110) REVERT: C 438 LYS cc_start: 0.8433 (mttt) cc_final: 0.8118 (mttm) REVERT: C 462 SER cc_start: 0.8756 (m) cc_final: 0.8393 (t) REVERT: C 463 ASN cc_start: 0.8701 (t0) cc_final: 0.8103 (t0) REVERT: C 466 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7942 (mm-30) REVERT: C 521 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7845 (tm-30) outliers start: 38 outliers final: 20 residues processed: 395 average time/residue: 0.7208 time to fit residues: 305.4439 Evaluate side-chains 395 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 369 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 529 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 19 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 270 THR 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 492 TYR Chi-restraints excluded: chain C residue 501 ILE 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 155 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN B 297 HIS C 376 HIS C 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.124001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.111054 restraints weight = 17392.799| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.94 r_work: 0.3283 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13269 Z= 0.143 Angle : 0.650 14.337 18003 Z= 0.324 Chirality : 0.044 0.256 1950 Planarity : 0.005 0.063 2307 Dihedral : 4.591 26.155 2040 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.71 % Allowed : 19.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.21), residues: 1563 helix: 1.63 (0.20), residues: 687 sheet: 1.04 (0.29), residues: 276 loop : 0.38 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 178 TYR 0.013 0.001 TYR B 118 PHE 0.018 0.001 PHE B 431 TRP 0.019 0.002 TRP B 508 HIS 0.003 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00331 (13227) covalent geometry : angle 0.62356 (17910) SS BOND : bond 0.00598 ( 24) SS BOND : angle 3.22367 ( 48) hydrogen bonds : bond 0.03836 ( 670) hydrogen bonds : angle 4.42554 ( 1893) Misc. bond : bond 0.00025 ( 3) link_NAG-ASN : bond 0.00523 ( 15) link_NAG-ASN : angle 1.72198 ( 45) *********************** 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 412 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 374 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7607 (ttt) cc_final: 0.7297 (ttt) REVERT: A 49 MET cc_start: 0.7367 (ttt) cc_final: 0.7045 (tmm) REVERT: A 102 ARG cc_start: 0.8227 (mtm-85) cc_final: 0.7966 (mtm180) REVERT: A 288 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7887 (mtm180) REVERT: A 289 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7718 (ttt90) REVERT: A 302 ASP cc_start: 0.7760 (p0) cc_final: 0.7522 (p0) REVERT: A 373 MET cc_start: 0.8079 (mmp) cc_final: 0.7836 (mmm) REVERT: A 462 SER cc_start: 0.8689 (m) cc_final: 0.8286 (p) REVERT: A 470 ASP cc_start: 0.7876 (m-30) cc_final: 0.7487 (m-30) REVERT: A 507 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8744 (tm) REVERT: A 521 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7641 (tm-30) REVERT: B 10 PHE cc_start: 0.7873 (t80) cc_final: 0.7586 (t80) REVERT: B 22 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8523 (p) REVERT: B 121 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8188 (tttp) REVERT: B 156 GLU cc_start: 0.8067 (tt0) cc_final: 0.7816 (tt0) REVERT: B 178 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7696 (mtt180) REVERT: B 213 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7565 (pt0) REVERT: B 288 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7989 (mtm-85) REVERT: B 297 HIS cc_start: 0.7563 (m90) cc_final: 0.7327 (m-70) REVERT: B 301 SER cc_start: 0.8690 (m) cc_final: 0.8307 (p) REVERT: B 303 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8339 (mtpp) REVERT: B 308 ASP cc_start: 0.7772 (p0) cc_final: 0.7502 (p0) REVERT: B 326 TYR cc_start: 0.8626 (m-80) cc_final: 0.8018 (m-10) REVERT: B 347 ILE cc_start: 0.8522 (tp) cc_final: 0.8298 (tp) REVERT: B 370 GLN cc_start: 0.8177 (mt0) cc_final: 0.7768 (mm110) REVERT: B 380 LYS cc_start: 0.7336 (mtpt) cc_final: 0.7042 (mmtp) REVERT: B 381 CYS cc_start: 0.6480 (m) cc_final: 0.5970 (t) REVERT: B 438 LYS cc_start: 0.8634 (mttt) cc_final: 0.8413 (mttt) REVERT: B 440 ASN cc_start: 0.7271 (p0) cc_final: 0.6744 (p0) REVERT: B 441 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: B 463 ASN cc_start: 0.8631 (t0) cc_final: 0.8103 (t0) REVERT: B 466 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7694 (mm-30) REVERT: B 492 TYR cc_start: 0.8651 (t80) cc_final: 0.8125 (t80) REVERT: B 521 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8155 (tm-30) REVERT: C 16 MET cc_start: 0.7608 (ptp) cc_final: 0.7378 (ptm) REVERT: C 110 SER cc_start: 0.8363 (t) cc_final: 0.8095 (p) REVERT: C 141 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8430 (mm110) REVERT: C 156 GLU cc_start: 0.7909 (tt0) cc_final: 0.7699 (pm20) REVERT: C 203 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7632 (tp30) REVERT: C 288 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7826 (mtm-85) REVERT: C 323 MET cc_start: 0.8315 (mtm) cc_final: 0.8107 (mtm) REVERT: C 346 ASN cc_start: 0.8063 (m-40) cc_final: 0.7767 (m-40) REVERT: C 363 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.7947 (p) REVERT: C 370 GLN cc_start: 0.8144 (mt0) cc_final: 0.7846 (mm110) REVERT: C 440 ASN cc_start: 0.7704 (m-40) cc_final: 0.7416 (m-40) REVERT: C 462 SER cc_start: 0.8757 (m) cc_final: 0.8397 (t) REVERT: C 463 ASN cc_start: 0.8712 (t0) cc_final: 0.8089 (t0) REVERT: C 466 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7929 (mm-30) REVERT: C 521 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7848 (tm-30) outliers start: 38 outliers final: 23 residues processed: 387 average time/residue: 0.6901 time to fit residues: 285.9864 Evaluate side-chains 394 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 363 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 507 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 213 GLU 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 19 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 57 PHE Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 270 THR 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 492 TYR Chi-restraints excluded: chain C residue 501 ILE 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 7 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 57 optimal weight: 0.0470 chunk 13 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 482 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111244 restraints weight = 17465.275| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.95 r_work: 0.3300 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13269 Z= 0.131 Angle : 0.652 12.627 18003 Z= 0.325 Chirality : 0.044 0.253 1950 Planarity : 0.005 0.062 2307 Dihedral : 4.574 32.285 2040 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.50 % Allowed : 20.77 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.21), residues: 1563 helix: 1.66 (0.20), residues: 687 sheet: 1.08 (0.29), residues: 276 loop : 0.35 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 178 TYR 0.013 0.001 TYR B 118 PHE 0.024 0.001 PHE B 33 TRP 0.021 0.002 TRP C 508 HIS 0.004 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00300 (13227) covalent geometry : angle 0.62567 (17910) SS BOND : bond 0.00471 ( 24) SS BOND : angle 3.29872 ( 48) hydrogen bonds : bond 0.03762 ( 670) hydrogen bonds : angle 4.41804 ( 1893) Misc. bond : bond 0.00013 ( 3) link_NAG-ASN : bond 0.00571 ( 15) link_NAG-ASN : angle 1.69826 ( 45) *********************** 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 391 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 356 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ILE cc_start: 0.8293 (mp) cc_final: 0.8052 (mp) REVERT: A 44 MET cc_start: 0.7611 (ttt) cc_final: 0.7293 (ttt) REVERT: A 49 MET cc_start: 0.7323 (ttt) cc_final: 0.6830 (tmm) REVERT: A 102 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7932 (mtm180) REVERT: A 288 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7966 (mtm-85) REVERT: A 289 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7720 (ttt90) REVERT: A 302 ASP cc_start: 0.7762 (p0) cc_final: 0.7500 (p0) REVERT: A 370 GLN cc_start: 0.7796 (mm110) cc_final: 0.7442 (mp10) REVERT: A 373 MET cc_start: 0.8047 (mmp) cc_final: 0.7807 (mmm) REVERT: A 462 SER cc_start: 0.8677 (m) cc_final: 0.8263 (p) REVERT: A 470 ASP cc_start: 0.7913 (m-30) cc_final: 0.7527 (m-30) REVERT: A 521 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7615 (tm-30) REVERT: B 10 PHE cc_start: 0.7918 (t80) cc_final: 0.7671 (t80) REVERT: B 22 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8406 (p) REVERT: B 23 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.8009 (pt) REVERT: B 29 MET cc_start: 0.7069 (ppp) cc_final: 0.6777 (ppp) REVERT: B 121 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8179 (tttp) REVERT: B 156 GLU cc_start: 0.8087 (tt0) cc_final: 0.7824 (tt0) REVERT: B 178 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7624 (mtt180) REVERT: B 213 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7492 (pt0) REVERT: B 288 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7966 (mtm-85) REVERT: B 301 SER cc_start: 0.8677 (m) cc_final: 0.8274 (p) REVERT: B 303 LYS cc_start: 0.8615 (mtmt) cc_final: 0.8291 (mtpp) REVERT: B 308 ASP cc_start: 0.7716 (p0) cc_final: 0.7421 (p0) REVERT: B 326 TYR cc_start: 0.8578 (m-80) cc_final: 0.8099 (m-10) REVERT: B 347 ILE cc_start: 0.8485 (tp) cc_final: 0.8264 (tp) REVERT: B 370 GLN cc_start: 0.8100 (mt0) cc_final: 0.7687 (mm110) REVERT: B 380 LYS cc_start: 0.7254 (mtpt) cc_final: 0.6974 (mmtp) REVERT: B 463 ASN cc_start: 0.8619 (t0) cc_final: 0.8089 (t0) REVERT: B 466 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7791 (mm-30) REVERT: B 492 TYR cc_start: 0.8650 (t80) cc_final: 0.8061 (t80) REVERT: B 521 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8117 (tm-30) REVERT: C 16 MET cc_start: 0.7610 (ptp) cc_final: 0.7371 (ptm) REVERT: C 46 CYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7526 (t) REVERT: C 62 LYS cc_start: 0.7953 (ttpp) cc_final: 0.7616 (ttpp) REVERT: C 110 SER cc_start: 0.8348 (t) cc_final: 0.8068 (p) REVERT: C 141 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8352 (mm-40) REVERT: C 156 GLU cc_start: 0.7894 (tt0) cc_final: 0.7687 (pm20) REVERT: C 203 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7621 (tp30) REVERT: C 236 ILE cc_start: 0.8903 (mm) cc_final: 0.8655 (mp) REVERT: C 288 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7828 (mtm-85) REVERT: C 323 MET cc_start: 0.8295 (mtm) cc_final: 0.8085 (mtm) REVERT: C 346 ASN cc_start: 0.8035 (m-40) cc_final: 0.7731 (m-40) REVERT: C 363 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.7899 (p) REVERT: C 370 GLN cc_start: 0.8147 (mt0) cc_final: 0.7654 (mm-40) REVERT: C 440 ASN cc_start: 0.7775 (m-40) cc_final: 0.7489 (m-40) REVERT: C 462 SER cc_start: 0.8751 (m) cc_final: 0.8382 (t) REVERT: C 463 ASN cc_start: 0.8696 (t0) cc_final: 0.8073 (t0) REVERT: C 466 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7900 (mm-30) REVERT: C 521 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7791 (tm-30) outliers start: 35 outliers final: 21 residues processed: 369 average time/residue: 0.7166 time to fit residues: 282.9876 Evaluate side-chains 382 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 353 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 529 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 19 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 57 PHE 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 492 TYR Chi-restraints excluded: chain C residue 501 ILE 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 121 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS C 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110969 restraints weight = 17510.882| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.95 r_work: 0.3280 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13269 Z= 0.142 Angle : 0.659 12.342 18003 Z= 0.329 Chirality : 0.044 0.255 1950 Planarity : 0.005 0.060 2307 Dihedral : 4.545 32.055 2040 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.00 % Allowed : 21.48 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.21), residues: 1563 helix: 1.64 (0.20), residues: 687 sheet: 1.18 (0.30), residues: 270 loop : 0.35 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 178 TYR 0.014 0.001 TYR A 118 PHE 0.019 0.001 PHE A 33 TRP 0.022 0.002 TRP A 219 HIS 0.003 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00330 (13227) covalent geometry : angle 0.63377 (17910) SS BOND : bond 0.00424 ( 24) SS BOND : angle 3.20569 ( 48) hydrogen bonds : bond 0.03771 ( 670) hydrogen bonds : angle 4.40540 ( 1893) Misc. bond : bond 0.00027 ( 3) link_NAG-ASN : bond 0.00522 ( 15) link_NAG-ASN : angle 1.68187 ( 45) ********************** 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 384 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 356 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7631 (ttt) cc_final: 0.7323 (ttt) REVERT: A 49 MET cc_start: 0.7319 (ttt) cc_final: 0.6836 (tmm) REVERT: A 102 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7930 (mtm180) REVERT: A 178 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7843 (mtm-85) REVERT: A 288 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7957 (mtp180) REVERT: A 289 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7686 (ttt90) REVERT: A 302 ASP cc_start: 0.7756 (p0) cc_final: 0.7496 (p0) REVERT: A 370 GLN cc_start: 0.7761 (mm110) cc_final: 0.7412 (mp10) REVERT: A 373 MET cc_start: 0.8057 (mmp) cc_final: 0.7833 (mmm) REVERT: A 462 SER cc_start: 0.8739 (m) cc_final: 0.8323 (p) REVERT: A 470 ASP cc_start: 0.7903 (m-30) cc_final: 0.7549 (m-30) REVERT: A 521 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 10 PHE cc_start: 0.7955 (t80) cc_final: 0.7674 (t80) REVERT: B 22 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8495 (p) REVERT: B 29 MET cc_start: 0.7092 (ppp) cc_final: 0.6815 (ppp) REVERT: B 121 LYS cc_start: 0.8542 (ttpp) cc_final: 0.8169 (tttp) REVERT: B 156 GLU cc_start: 0.8060 (tt0) cc_final: 0.7805 (tt0) REVERT: B 178 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7648 (mtt180) REVERT: B 213 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7565 (pt0) REVERT: B 288 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7963 (mtm-85) REVERT: B 301 SER cc_start: 0.8686 (m) cc_final: 0.8271 (p) REVERT: B 303 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8287 (mtpp) REVERT: B 308 ASP cc_start: 0.7724 (p0) cc_final: 0.7424 (p0) REVERT: B 326 TYR cc_start: 0.8585 (m-80) cc_final: 0.8104 (m-10) REVERT: B 347 ILE cc_start: 0.8473 (tp) cc_final: 0.8244 (tp) REVERT: B 370 GLN cc_start: 0.8136 (mt0) cc_final: 0.7628 (mm110) REVERT: B 380 LYS cc_start: 0.7243 (mtpt) cc_final: 0.6982 (mmtp) REVERT: B 463 ASN cc_start: 0.8628 (t0) cc_final: 0.8108 (t0) REVERT: B 466 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7813 (mm-30) REVERT: B 492 TYR cc_start: 0.8650 (t80) cc_final: 0.8045 (t80) REVERT: B 521 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8035 (tm-30) REVERT: C 46 CYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7488 (t) REVERT: C 62 LYS cc_start: 0.7940 (ttpp) cc_final: 0.7612 (ttpp) REVERT: C 110 SER cc_start: 0.8353 (t) cc_final: 0.8082 (p) REVERT: C 141 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8367 (mm-40) REVERT: C 203 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7646 (mp0) REVERT: C 236 ILE cc_start: 0.8909 (mm) cc_final: 0.8673 (mp) REVERT: C 253 GLU cc_start: 0.7820 (pt0) cc_final: 0.7540 (pt0) REVERT: C 288 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7827 (mtm-85) REVERT: C 323 MET cc_start: 0.8313 (mtm) cc_final: 0.8103 (mtm) REVERT: C 346 ASN cc_start: 0.8023 (m-40) cc_final: 0.7724 (m-40) REVERT: C 352 ASP cc_start: 0.7825 (t0) cc_final: 0.7583 (t0) REVERT: C 370 GLN cc_start: 0.8147 (mt0) cc_final: 0.7847 (mm110) REVERT: C 440 ASN cc_start: 0.7802 (m-40) cc_final: 0.7540 (m-40) REVERT: C 462 SER cc_start: 0.8744 (m) cc_final: 0.8375 (t) REVERT: C 463 ASN cc_start: 0.8679 (t0) cc_final: 0.8033 (t0) REVERT: C 466 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7874 (mm-30) REVERT: C 521 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7786 (tm-30) outliers start: 28 outliers final: 20 residues processed: 367 average time/residue: 0.7034 time to fit residues: 276.9363 Evaluate side-chains 378 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 352 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 529 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 19 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 57 PHE 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 492 TYR Chi-restraints excluded: chain C residue 501 ILE 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 44 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 101 optimal weight: 0.0770 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 ASN C 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.121911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109182 restraints weight = 17569.317| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.90 r_work: 0.3306 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13269 Z= 0.135 Angle : 0.649 12.093 18003 Z= 0.324 Chirality : 0.044 0.254 1950 Planarity : 0.005 0.057 2307 Dihedral : 4.486 30.309 2040 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.14 % Allowed : 21.91 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.21), residues: 1563 helix: 1.68 (0.20), residues: 687 sheet: 1.18 (0.29), residues: 276 loop : 0.33 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 611 TYR 0.016 0.001 TYR A 118 PHE 0.025 0.001 PHE B 33 TRP 0.022 0.002 TRP A 219 HIS 0.003 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00314 (13227) covalent geometry : angle 0.62478 (17910) SS BOND : bond 0.00378 ( 24) SS BOND : angle 3.10139 ( 48) hydrogen bonds : bond 0.03689 ( 670) hydrogen bonds : angle 4.39293 ( 1893) Misc. bond : bond 0.00023 ( 3) link_NAG-ASN : bond 0.00515 ( 15) link_NAG-ASN : angle 1.64700 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5826.47 seconds wall clock time: 99 minutes 46.51 seconds (5986.51 seconds total)